From 07fe09278051f632dc94206735fa43c98363c178 Mon Sep 17 00:00:00 2001 From: Daniel Danis Date: Fri, 14 Apr 2023 12:27:06 -0400 Subject: [PATCH 01/39] Next development iteration `v0.1.5dev0`. --- recipe/meta.yaml | 2 +- src/hpotk/__init__.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/recipe/meta.yaml b/recipe/meta.yaml index 022a181..715f87c 100644 --- a/recipe/meta.yaml +++ b/recipe/meta.yaml @@ -1,5 +1,5 @@ {% set name = "hpo-toolkit" %} -{% set version = "0.1.4" %} +{% set version = "0.1.5dev0" %} package: name: {{ name|lower }} diff --git a/src/hpotk/__init__.py b/src/hpotk/__init__.py index 0330441..37d32c4 100644 --- a/src/hpotk/__init__.py +++ b/src/hpotk/__init__.py @@ -1,4 +1,4 @@ -__version__ = "0.1.4" +__version__ = "0.1.5dev0" from . import model from . import constants From 13a331f03af60ba7994ead58bd3f3a3b7227aced Mon Sep 17 00:00:00 2001 From: Daniel Danis Date: Tue, 25 Apr 2023 15:53:29 -0400 Subject: [PATCH 02/39] The rule validators can work with a sequence of `Identified` or `TermId`s. --- src/hpotk/validate/_hpo.py | 31 ++++++++++++++++++------------- src/hpotk/validate/_model.py | 24 +++++++++++++++++++----- 2 files changed, 37 insertions(+), 18 deletions(-) diff --git a/src/hpotk/validate/_hpo.py b/src/hpotk/validate/_hpo.py index f15b55f..28fc7bc 100644 --- a/src/hpotk/validate/_hpo.py +++ b/src/hpotk/validate/_hpo.py @@ -12,6 +12,9 @@ class BaseOntologyRuleValidator(RuleValidator, metaclass=abc.ABCMeta): def __init__(self, ontology: MinimalOntology): + if not isinstance(ontology, MinimalOntology): + raise ValueError(f'ontology must be an instance of hpotk.ontology.MinimalOntology ' + f'but it was an instance of {type(ontology)}') self._ontology = ontology def _primary_term_id(self, identifier: TermId) -> typing.Optional[TermId]: @@ -32,8 +35,8 @@ class AnnotationPropagationValidator(BaseOntologyRuleValidator): def __init__(self, ontology: MinimalOntology): super().__init__(ontology) - def validate(self, items: typing.Sequence[Identified]) -> ValidationResults: - term_ids = {self._primary_term_id(term.identifier) for term in items} + def validate(self, items: typing.Sequence[typing.Union[Identified, TermId]]) -> ValidationResults: + term_ids = {self._primary_term_id(self.extract_term_id(item)) for item in items} results = [] for term_id in term_ids: for ancestor in get_ancestors(self._ontology, source=term_id, include_source=False): @@ -62,18 +65,19 @@ class PhenotypicAbnormalityValidator(BaseOntologyRuleValidator): def __init__(self, ontology: MinimalOntology): super().__init__(ontology) - def validate(self, items: typing.Sequence[Identified]) -> ValidationResults: + def validate(self, items: typing.Sequence[typing.Union[Identified, TermId]]) -> ValidationResults: results = [] - for term in items: - term_id = self._primary_term_id(term.identifier) + for item in items: + term_id = self.extract_term_id(item) + term_id = self._primary_term_id(term_id) ancestors = get_ancestors(self._ontology, source=term_id, include_source=False) if PHENOTYPIC_ABNORMALITY not in ancestors: - term = self._ontology.get_term(term_id) + item = self._ontology.get_term(term_id) results.append( ValidationResult( level=ValidationLevel.ERROR, category='phenotypic_abnormality_descendant', - message=f'{term.name} [{term.identifier.value}] ' + message=f'{item.name} [{item.identifier.value}] ' f'is not a descendant of Phenotypic abnormality [{PHENOTYPIC_ABNORMALITY.value}]' ) ) @@ -86,17 +90,18 @@ class ObsoleteTermIdsValidator(BaseOntologyRuleValidator): def __init__(self, ontology: MinimalOntology): super().__init__(ontology) - def validate(self, items: typing.Sequence[Identified]) -> ValidationResults: + def validate(self, items: typing.Sequence[typing.Union[Identified, TermId]]) -> ValidationResults: results = [] - for term in items: - current_id = self._primary_term_id(term.identifier) - if current_id != term.identifier: - current_term = self._ontology.get_term(term.identifier) + for item in items: + term_id = self.extract_term_id(item) + current_id = self._primary_term_id(term_id) + if current_id != item.identifier: + current_term = self._ontology.get_term(item.identifier) results.append( ValidationResult( level=ValidationLevel.WARNING, category='obsolete_term_id_is_used', - message=f'Using the obsolete {term.identifier.value} instead of {current_id.value} ' + message=f'Using the obsolete {item.identifier.value} instead of {current_id.value} ' f'for {current_term.name}' ) ) diff --git a/src/hpotk/validate/_model.py b/src/hpotk/validate/_model.py index 7643384..504a01d 100644 --- a/src/hpotk/validate/_model.py +++ b/src/hpotk/validate/_model.py @@ -4,7 +4,7 @@ from collections import namedtuple -from hpotk.model import Identified +from hpotk.model import Identified, TermId class ValidationLevel(enum.Enum): @@ -39,14 +39,28 @@ def __repr__(self) -> str: class RuleValidator(metaclass=abc.ABCMeta): """ - `RuleValidator` checks if a sequence of `Identified` items meet the validation requirements. - The issues are returned as `ValidationResults`. + `RuleValidator` checks if a sequence of :class:`Identified` or :class:`TermId` instances meet + the validation requirements. + + The validators can check each item individually or as a collection, for instance, + to discover violation of the annotation propagation rule, etc. + + The issues are returned as :class:`ValidationResults`. """ @abc.abstractmethod - def validate(self, items: typing.Sequence[Identified]) -> ValidationResults: + def validate(self, items: typing.Sequence[typing.Union[Identified, TermId]]) -> ValidationResults: pass + @staticmethod + def extract_term_id(item: typing.Union[Identified, TermId]) -> TermId: + if isinstance(item, Identified): + return item.identifier + elif isinstance(item, TermId): + return item + else: + raise ValueError(f'Item {item} of type {type(item)} is not a TermId nor extends Identified') + class ValidationRunner: """ @@ -56,7 +70,7 @@ class ValidationRunner: def __init__(self, validators: typing.Sequence[RuleValidator]): self._validators = validators - def validate_all(self, items: typing.Sequence[Identified]) -> ValidationResults: + def validate_all(self, items: typing.Sequence[typing.Union[Identified, TermId]]) -> ValidationResults: overall = [] for validator in self._validators: results = validator.validate(items) From 740782a3d1494a2753d7e5627d5d9c013b72ca53 Mon Sep 17 00:00:00 2001 From: Daniel Danis Date: Thu, 27 Apr 2023 18:47:50 -0400 Subject: [PATCH 03/39] Introduce annotated items concept. --- src/hpotk/annotations/__init__.py | 1 + src/hpotk/annotations/_api.py | 96 +++++++++++++++++++++++++++++ src/hpotk/annotations/_base.py | 56 +++-------------- src/hpotk/annotations/_simple.py | 13 +++- tests/annotations/load/test_hpoa.py | 8 +-- 5 files changed, 121 insertions(+), 53 deletions(-) create mode 100644 src/hpotk/annotations/_api.py diff --git a/src/hpotk/annotations/__init__.py b/src/hpotk/annotations/__init__.py index 3e551e6..894819c 100644 --- a/src/hpotk/annotations/__init__.py +++ b/src/hpotk/annotations/__init__.py @@ -1,3 +1,4 @@ +from ._api import AnnotatedItem, AnnotatedItemContainer, ANNOTATED_ITEM, ANNOTATION from ._base import Ratio, EvidenceCode, Sex, AnnotationReference from ._base import HpoDiseaseAnnotation, HpoDisease, HpoDiseases from ._base import SimpleRatio diff --git a/src/hpotk/annotations/_api.py b/src/hpotk/annotations/_api.py new file mode 100644 index 0000000..5f1859f --- /dev/null +++ b/src/hpotk/annotations/_api.py @@ -0,0 +1,96 @@ +import abc +import typing + +from hpotk.model import TermId, Identified + +# ##################################################################################################################### +# The file describes generic schema for annotations, annotated items, and annotated item containers. +# An example application includes phenotypic features (annotations), diseases or samples (annotated items), +# and OMIM corpus (annotated item containers). +# ##################################################################################################################### + + +class ObservableAnnotation(Identified, metaclass=abc.ABCMeta): + """ + An identified item with present or absent state. + """ + + @property + @abc.abstractmethod + def is_present(self) -> bool: + """ + :return: `True` if the annotation has been *observed* in the annotated object. + """ + pass + + @property + def is_absent(self) -> bool: + """ + :return: `True` if the annotation has been *excluded* in the annotated object. + """ + return not self.is_present + + +ANNOTATION = typing.TypeVar('ANNOTATION', bound=ObservableAnnotation) +""" +A world item annotation with present or absent state. +""" + + +class AnnotatedItem(typing.Generic[ANNOTATION], metaclass=abc.ABCMeta): + """ + A world item with annotations. For instance, a disease annotated by phenotypic features. + """ + + @property + @abc.abstractmethod + def annotations(self) -> typing.Collection[ANNOTATION]: + """ + :return: a collection of :class:`ANNOTATION` objects for the annotated item. + """ + pass + + def present_annotations(self) -> typing.Iterable[ANNOTATION]: + """ + :return: an iterable over *present* annotations. + """ + return filter(lambda a: a.is_present, self.annotations) + + def absent_annotations(self) -> typing.Iterable[ANNOTATION]: + """ + :return: an iterable over *absent* annotations. + """ + return filter(lambda a: a.is_absent, self.annotations) + + +ANNOTATED_ITEM = typing.TypeVar('ANNOTATED_ITEM', bound=AnnotatedItem) +""" +World item that is annotated with an :class:`ANNOTATION`. +""" + + +class AnnotatedItemContainer(typing.Generic[ANNOTATED_ITEM], typing.Sized, metaclass=abc.ABCMeta): + """ + Container for annotated items. + + For instance, if OMIM disease is an item type and phenotypic feature is the annotation type, + then a corpus of OMIM diseases corresponds to a container of annotated items. + """ + + @property + @abc.abstractmethod + def items(self) -> typing.Collection[ANNOTATED_ITEM]: + """ + :return: an iterable over container items. + """ + pass + + def item_ids(self) -> typing.Iterable[TermId]: + """ + :return: an iterable over all item identifiers. + """ + return map(lambda item: item.identifier, self.items) + + def __len__(self) -> int: + return len(self.items) + diff --git a/src/hpotk/annotations/_base.py b/src/hpotk/annotations/_base.py index 0b83d37..7d0b451 100644 --- a/src/hpotk/annotations/_base.py +++ b/src/hpotk/annotations/_base.py @@ -4,6 +4,7 @@ from hpotk.model import Identified, Named, Versioned, TermId from hpotk.model import CURIE_OR_TERM_ID +from ._api import ObservableAnnotation, AnnotatedItem, AnnotatedItemContainer class Ratio(metaclass=abc.ABCMeta): @@ -127,7 +128,7 @@ class Sex(enum.Enum): @staticmethod def parse(value: str): """ - Parse :class:`Sex` from `str` value. + Parse :class:`Sex` from :class:`str` value. :param value: a `str` with the sex code. :return: the parsed enum member or `None` if `value` is not valid :class:`Sex` value. @@ -181,17 +182,21 @@ def __repr__(self): f"evidence_code={repr(self._evidence_code)})" -class HpoDiseaseAnnotation(Identified, metaclass=abc.ABCMeta): +class HpoDiseaseAnnotation(ObservableAnnotation, metaclass=abc.ABCMeta): @property @abc.abstractmethod def ratio(self) -> Ratio: """ :return: ratio representing a total number of the cohort members who displayed presence - of the phenotypic feature represented by `HpoDiseaseAnnotation` at some point in their life. + of the phenotypic feature represented by :class:`HpoDiseaseAnnotation` at some point in their life. """ pass + @property + def is_present(self) -> bool: + return not self.ratio.is_zero() + @property @abc.abstractmethod def references(self) -> typing.List[AnnotationReference]: @@ -208,12 +213,6 @@ def modifiers(self) -> typing.List[TermId]: """ pass - def is_absent(self) -> bool: - return self.ratio.is_zero() - - def is_present(self) -> bool: - return not self.is_absent() - def __str__(self): return f"HpoDiseaseAnnotation(" \ f"identifier={self.identifier}, " \ @@ -222,15 +221,7 @@ def __str__(self): f"modifiers={self.modifiers})" -class HpoDisease(Identified, Named, metaclass=abc.ABCMeta): - - @property - @abc.abstractmethod - def annotations(self) -> typing.Collection[HpoDiseaseAnnotation]: - """ - :return a collection of all (present and absent) disease annotations. - """ - pass +class HpoDisease(AnnotatedItem[HpoDiseaseAnnotation], Identified, Named, metaclass=abc.ABCMeta): @property @abc.abstractmethod @@ -240,18 +231,6 @@ def modes_of_inheritance(self) -> typing.Collection[TermId]: """ pass - def present_annotations(self) -> typing.Iterable[HpoDiseaseAnnotation]: - """ - :return: an iterable over present disease features. - """ - return filter(lambda a: a.is_present(), self.annotations) - - def absent_annotations(self) -> typing.Iterable[HpoDiseaseAnnotation]: - """ - :return: an iterable over absent/excluded disease features. - """ - return filter(lambda a: a.is_absent(), self.annotations) - def __str__(self): return f"HpoDisease(" \ f"identifier={self.identifier}, " \ @@ -259,20 +238,12 @@ def __str__(self): f"n_annotations={len(self.annotations)})" -class HpoDiseases(Versioned, typing.Sized, metaclass=abc.ABCMeta): +class HpoDiseases(AnnotatedItemContainer[HpoDiseaseAnnotation], Versioned, metaclass=abc.ABCMeta): """ A container for a set of :class:`HpoDisease`s that allows iteration over all diseases, knows about the number of diseases in the container, and supports retrieval of the disease by its identifier. """ - @property - @abc.abstractmethod - def diseases(self) -> typing.Iterable[HpoDisease]: - """ - :return: an iterable over :class:`HpoDisease`s of the container. - """ - pass - @abc.abstractmethod def __getitem__(self, disease_id: CURIE_OR_TERM_ID) -> typing.Optional[HpoDisease]: """ @@ -284,13 +255,6 @@ def __getitem__(self, disease_id: CURIE_OR_TERM_ID) -> typing.Optional[HpoDiseas """ pass - @property - def disease_ids(self) -> typing.Iterable[TermId]: - """ - :return: an iterable over all disease IDs. - """ - return map(lambda d: d.identifier, self.diseases) - def __str__(self): return f"HpoDiseases(n_diseases={len(self)}, " \ f"version={self.version})" diff --git a/src/hpotk/annotations/_simple.py b/src/hpotk/annotations/_simple.py index d231293..9ba8edf 100644 --- a/src/hpotk/annotations/_simple.py +++ b/src/hpotk/annotations/_simple.py @@ -1,6 +1,8 @@ import typing +import warnings from hpotk.model import TermId, CURIE_OR_TERM_ID +from ._api import ANNOTATED_ITEM from ._base import AnnotationReference, Ratio from ._base import HpoDisease, HpoDiseaseAnnotation, HpoDiseases @@ -67,8 +69,16 @@ def __init__(self, diseases: typing.Iterable[HpoDisease], version: str = None): self._diseases = {d.identifier: d for d in diseases} self._version = version + @property + def items(self) -> typing.Collection[ANNOTATED_ITEM]: + return self._diseases.values() + @property def diseases(self) -> typing.Collection[HpoDisease]: + # REMOVE(v1.0.0) + warnings.warn('The `diseases` property has been deprecated and will be removed in `v1.0.0`. ' + 'Use `items()` instead', + category=DeprecationWarning, stacklevel=2) return self._diseases.values() def __getitem__(self, item: CURIE_OR_TERM_ID) -> typing.Optional[HpoDisease]: @@ -83,9 +93,6 @@ def __getitem__(self, item: CURIE_OR_TERM_ID) -> typing.Optional[HpoDisease]: except KeyError: return None - def __len__(self) -> int: - return len(self._diseases) - @property def version(self) -> typing.Optional[str]: return self._version diff --git a/tests/annotations/load/test_hpoa.py b/tests/annotations/load/test_hpoa.py index ad92d46..6f02869 100644 --- a/tests/annotations/load/test_hpoa.py +++ b/tests/annotations/load/test_hpoa.py @@ -32,7 +32,7 @@ def test_load_hpo_annotations(self): self.assertIsInstance(diseases, hpotk.annotations.HpoDiseases) self.assertEqual(2, len(diseases)) - self.assertSetEqual({'ORPHA:123456', 'OMIM:987654'}, set(map(lambda d: d.value, diseases.disease_ids))) + self.assertSetEqual({'ORPHA:123456', 'OMIM:987654'}, set(map(lambda di: di.value, diseases.item_ids()))) self.assertEqual(diseases.version, '2021-08-02') def test_load_older_hpo_annotations(self): @@ -40,7 +40,7 @@ def test_load_older_hpo_annotations(self): self.assertIsInstance(diseases, hpotk.annotations.HpoDiseases) self.assertEqual(2, len(diseases)) - self.assertSetEqual({'ORPHA:123456', 'OMIM:987654'}, set(map(lambda d: d.value, diseases.disease_ids))) + self.assertSetEqual({'ORPHA:123456', 'OMIM:987654'}, set(map(lambda di: di.value, diseases.item_ids()))) class TestHpoaDiseaseProperties(TestHpoaLoaderBase): @@ -62,7 +62,7 @@ def test_hpoa_disease_properties(self): sorted(omim.annotations, key=lambda a: a.identifier.value)) first = omim_annotations[0] self.assertEqual(first.identifier.value, 'HP:0001167') - self.assertEqual(first.is_present(), True) + self.assertEqual(first.is_present, True) self.assertEqual(first.ratio.numerator, 5) self.assertEqual(first.ratio.denominator, 13) self.assertEqual(len(first.references), 2) @@ -70,7 +70,7 @@ def test_hpoa_disease_properties(self): second = omim_annotations[1] self.assertEqual(second.identifier.value, 'HP:0001238') - self.assertEqual(second.is_absent(), True) + self.assertEqual(second.is_absent, True) self.assertEqual(second.ratio.numerator, 0) self.assertEqual(second.ratio.denominator, TestHpoaDiseaseProperties.LOADER.cohort_size) self.assertEqual(len(second.references), 1) From 678aaf9918004f925d63a37fe0b78f955170556a Mon Sep 17 00:00:00 2001 From: Daniel Danis Date: Thu, 27 Apr 2023 18:48:28 -0400 Subject: [PATCH 04/39] Use auto enum numbering for hpotk.annotation enums. --- src/hpotk/annotations/_base.py | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/src/hpotk/annotations/_base.py b/src/hpotk/annotations/_base.py index 7d0b451..7742062 100644 --- a/src/hpotk/annotations/_base.py +++ b/src/hpotk/annotations/_base.py @@ -95,11 +95,11 @@ def __repr__(self): class EvidenceCode(enum.Enum): """Inferred from electronic evidence.""" - IEA = 0 + IEA = enum.auto() """Traceable author statement.""" - TAS = 1 + TAS = enum.auto() """Published clinical study.""" - PCS = 2 + PCS = enum.auto() @staticmethod def parse(value: str): @@ -121,9 +121,9 @@ def parse(value: str): class Sex(enum.Enum): - UNKNOWN = 0 - MALE = 1 - FEMALE = 2 + UNKNOWN = enum.auto() + MALE = enum.auto() + FEMALE = enum.auto() @staticmethod def parse(value: str): From efd5eb9f1364567b3e8ad17c793d5105dcbca25d Mon Sep 17 00:00:00 2001 From: Daniel Danis Date: Thu, 27 Apr 2023 18:55:46 -0400 Subject: [PATCH 05/39] Make annotated item container iterable. --- src/hpotk/annotations/_api.py | 16 +++++++++------- src/hpotk/annotations/_simple.py | 6 ++++++ 2 files changed, 15 insertions(+), 7 deletions(-) diff --git a/src/hpotk/annotations/_api.py b/src/hpotk/annotations/_api.py index 5f1859f..65c7ea9 100644 --- a/src/hpotk/annotations/_api.py +++ b/src/hpotk/annotations/_api.py @@ -1,5 +1,6 @@ import abc import typing +import warnings from hpotk.model import TermId, Identified @@ -69,7 +70,8 @@ def absent_annotations(self) -> typing.Iterable[ANNOTATION]: """ -class AnnotatedItemContainer(typing.Generic[ANNOTATED_ITEM], typing.Sized, metaclass=abc.ABCMeta): +class AnnotatedItemContainer(typing.Generic[ANNOTATED_ITEM], typing.Iterable[ANNOTATED_ITEM], typing.Sized, + metaclass=abc.ABCMeta): """ Container for annotated items. @@ -78,19 +80,19 @@ class AnnotatedItemContainer(typing.Generic[ANNOTATED_ITEM], typing.Sized, metac """ @property - @abc.abstractmethod def items(self) -> typing.Collection[ANNOTATED_ITEM]: """ :return: an iterable over container items. """ - pass + # REMOVE(v1.0.0) + warnings.warn(f'`items` property has been deprecated and will be removed in v1.0.0. ' + f'Iterate directly over the container.', + DeprecationWarning, stacklevel=2) + return list(self) def item_ids(self) -> typing.Iterable[TermId]: """ :return: an iterable over all item identifiers. """ - return map(lambda item: item.identifier, self.items) - - def __len__(self) -> int: - return len(self.items) + return map(lambda item: item.identifier, self) diff --git a/src/hpotk/annotations/_simple.py b/src/hpotk/annotations/_simple.py index 9ba8edf..df241fc 100644 --- a/src/hpotk/annotations/_simple.py +++ b/src/hpotk/annotations/_simple.py @@ -65,6 +65,9 @@ def modes_of_inheritance(self) -> typing.Collection[TermId]: class SimpleHpoDiseases(HpoDiseases): + def __iter__(self) -> typing.Iterator[HpoDiseaseAnnotation]: + return iter(self._diseases.values()) + def __init__(self, diseases: typing.Iterable[HpoDisease], version: str = None): self._diseases = {d.identifier: d for d in diseases} self._version = version @@ -93,6 +96,9 @@ def __getitem__(self, item: CURIE_OR_TERM_ID) -> typing.Optional[HpoDisease]: except KeyError: return None + def __len__(self) -> int: + return len(self._diseases) + @property def version(self) -> typing.Optional[str]: return self._version From eefd5cd107ceb1fa7990ff9abadb82ef2d87c20f Mon Sep 17 00:00:00 2001 From: Daniel Danis Date: Fri, 28 Apr 2023 12:14:45 -0400 Subject: [PATCH 06/39] Update docs. --- src/hpotk/algorithm/_traversal.py | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/src/hpotk/algorithm/_traversal.py b/src/hpotk/algorithm/_traversal.py index 797d003..0249e22 100644 --- a/src/hpotk/algorithm/_traversal.py +++ b/src/hpotk/algorithm/_traversal.py @@ -10,14 +10,14 @@ def get_ancestors(g: typing.Union[GraphAware, OntologyGraph], source: CURIE_OR_TERM_ID, include_source: bool = False) -> typing.FrozenSet[TermId]: """ - Get all ancestor `TermId`s of the `source` term (parents, grandparents, great-grandparents etc.).. + Get all ancestor :class:`TermId`\\ (s). of the `source` term (parents, grandparents, great-grandparents etc.).. - The method raises a `ValueError` if inputs do not meet the requirement described below. + The method raises a :class:`ValueError` if inputs do not meet the requirement described below. :param g: the ontology graph or a graph-aware entity - :param source: `TermId` or a term ID curie as a `str (e.g. `HP:1234567`) + :param source: `:class:`TermId` or a term ID curie as a `str (e.g. `HP:1234567`) :param include_source: whether to include the `source` term in the resulting set - :return: a `frozenset` with ancestor `TermId`s + :return: a `frozenset` with ancestor :class:`TermId`\\ (s). """ # Check g = _check_ontology_graph_is_available(g) @@ -45,14 +45,14 @@ def get_parents(g: typing.Union[GraphAware, OntologyGraph], source: CURIE_OR_TERM_ID, include_source: bool = False) -> typing.FrozenSet[TermId]: """ - Get `TermId`s of the direct parents of the `source` term. + Get :class:`TermId`\\ (s). of the direct parents of the `source` term. - The method raises a `ValueError` if inputs do not meet the requirement described below. + The method raises a :class:`ValueError` if inputs do not meet the requirement described below. :param g: the ontology graph or a graph-aware entity - :param source: `TermId` or a term ID curie as a `str (e.g. `HP:1234567`) - :param include_source: whether to include the `source` term in the resulting set - :return: a `frozenset` with parent `TermId`s + :param source: :class:`TermId` or a term ID curie as a :class:`str (e.g. `HP:1234567`) + :param include_source: whether to include the `source` term ID(s) in the results + :return: a :class:`frozenset` with parent `TermId`s """ # Check g = _check_ontology_graph_is_available(g) @@ -79,8 +79,8 @@ def get_descendants(g: typing.Union[GraphAware, OntologyGraph], :param g: the ontology graph or a graph-aware entity :param source: `TermId` or a term ID curie as a `str (e.g. `HP:1234567`) - :param include_source: whether to include the `source` term in the resulting set - :return: a `frozenset` with descendants `TermId`s + :param include_source: whether to include the `source` term ID(s) in the results + :return: a :class:`frozenset` with descendants `TermId`s """ # Check g = _check_ontology_graph_is_available(g) From efb61f5cf09e6df77b889567c13c7cc4f7f9a70a Mon Sep 17 00:00:00 2001 From: Daniel Danis Date: Fri, 28 Apr 2023 12:15:36 -0400 Subject: [PATCH 07/39] Move algorithm.traversal tests into a dedicated folder. --- .../test_traversal.py} | 30 +++++++++++-------- 1 file changed, 17 insertions(+), 13 deletions(-) rename tests/{test_algorithm.py => algorithm/test_traversal.py} (68%) diff --git a/tests/test_algorithm.py b/tests/algorithm/test_traversal.py similarity index 68% rename from tests/test_algorithm.py rename to tests/algorithm/test_traversal.py index a90a33b..c232b67 100644 --- a/tests/test_algorithm.py +++ b/tests/algorithm/test_traversal.py @@ -9,23 +9,27 @@ from hpotk.ontology import MinimalOntology from hpotk.ontology.load.obographs import load_minimal_ontology -TOY_HPO = resource_filename(__name__, os.path.join('data', 'hp.toy.json')) +TOY_HPO = resource_filename(__name__, os.path.join('../data', 'hp.toy.json')) hp.util.setup_logging() -HPO: MinimalOntology = load_minimal_ontology(TOY_HPO) - @ddt.ddt class TestTraversal(unittest.TestCase): + HPO: MinimalOntology + + @classmethod + def setUpClass(cls) -> None: + cls.HPO = load_minimal_ontology(TOY_HPO) + @ddt.data( ("HP:0001166", False, {"HP:0001238", "HP:0100807"}), ("HP:0001166", True, {"HP:0001166", "HP:0001238", "HP:0100807"}) ) @ddt.unpack def test_get_parents(self, source: str, include_source, expected): - parents = hp.algorithm.get_parents(HPO, source, include_source) + parents = hp.algorithm.get_parents(self.HPO, source, include_source) self.assertIsInstance(parents, frozenset) self.assertSetEqual(parents, {TermId.from_curie(val) for val in expected}) @@ -43,7 +47,7 @@ def test_get_parents(self, source: str, include_source, expected): ) @ddt.unpack def test_get_ancestors(self, source: str, include_source, expected): - ancestors = hp.algorithm.get_ancestors(HPO, source, include_source) + ancestors = hp.algorithm.get_ancestors(self.HPO, source, include_source) self.assertIsInstance(ancestors, frozenset) self.assertSetEqual(ancestors, {TermId.from_curie(val) for val in expected}) @@ -53,7 +57,7 @@ def test_get_ancestors(self, source: str, include_source, expected): ) @ddt.unpack def test_get_children(self, source: str, include_source, expected): - children = hp.algorithm.get_children(HPO, source, include_source) + children = hp.algorithm.get_children(self.HPO, source, include_source) self.assertIsInstance(children, frozenset) self.assertSetEqual(children, {TermId.from_curie(val) for val in expected}) @@ -62,12 +66,12 @@ def test_get_children(self, source: str, include_source, expected): ("HP:0001167", True, {"HP:0001167", "HP:0001166", "HP:0001238", "HP:0100807"}) ) @ddt.unpack - def test_get_descendents(self, source: str, include_source, expected): - descendents = hp.algorithm.get_descendents(HPO, source, include_source) - self.assertIsInstance(descendents, frozenset) - self.assertSetEqual(descendents, {TermId.from_curie(val) for val in expected}) + def test_get_descendants(self, source: str, include_source, expected): + descendants = hp.algorithm.get_descendants(self.HPO, source, include_source) + self.assertIsInstance(descendants, frozenset) + self.assertSetEqual(descendants, {TermId.from_curie(val) for val in expected}) - def test_we_get_correct_number_of_descendents(self): + def test_we_get_correct_number_of_descendants(self): all_term_id = "HP:0000001" - self.assertEqual(len(HPO) - 1, len(hp.algorithm.get_descendents(HPO, all_term_id))) - self.assertEqual(len(HPO), len(hp.algorithm.get_descendents(HPO, all_term_id, include_source=True))) + self.assertEqual(len(self.HPO) - 1, len(hp.algorithm.get_descendants(self.HPO, all_term_id))) + self.assertEqual(len(self.HPO), len(hp.algorithm.get_descendants(self.HPO, all_term_id, include_source=True))) From b6d21c6913750bfa9692687d96f2605b690528bc Mon Sep 17 00:00:00 2001 From: Daniel Danis Date: Fri, 28 Apr 2023 12:16:41 -0400 Subject: [PATCH 08/39] Add new test files - an example HPOA for Marfan syndrome + Hyperekplexia 2 and a corresponding HPO module. --- tests/data/README.md | 15 + tests/data/hp.small.json | 22352 +++++++++++++++++++++ tests/data/hp.small.term_ids.txt | 80 + tests/data/phenotype.real-shortlist.hpoa | 91 + 4 files changed, 22538 insertions(+) create mode 100644 tests/data/hp.small.json create mode 100644 tests/data/hp.small.term_ids.txt create mode 100644 tests/data/phenotype.real-shortlist.hpoa diff --git a/tests/data/README.md b/tests/data/README.md index d578bd2..0b3b94e 100644 --- a/tests/data/README.md +++ b/tests/data/README.md @@ -115,3 +115,18 @@ robot merge --input arachnodactyly.hp.obo \ rm *.obo ``` + +# Small HPO annotations file + +`phenotype.real-shortlist.hpoa` contains 2 diseases from the HPO annotation file. + +# Small HPO ontology + +The ontology that contains the terms used in `phenotype.real-shortlist.hpoa` annotation file. + +```shell +robot extract --input-iri https://github.com/obophenotype/human-phenotype-ontology/releases/download/v2023-04-05/hp-base.owl \ + -T hp.small.term_ids.txt -o hp.small.owl --method BOT --copy-ontology-annotations true +obographs convert -f json hp.small.owl +rm hp.small.owl +``` diff --git a/tests/data/hp.small.json b/tests/data/hp.small.json new file mode 100644 index 0000000..d3ac3b5 --- /dev/null +++ b/tests/data/hp.small.json @@ -0,0 +1,22352 @@ +{ + "graphs" : [ { + "id" : "http://purl.obolibrary.org/obo/hp/hp-base.owl", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000700", + "val" : "http://purl.obolibrary.org/obo/HP_0000001" + }, { + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "Human Phenotype Ontology Consortium" + }, { + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "Monarch Initiative" + }, { + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "Peter Robinson" + }, { + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "Sebastian Köhler" + }, { + "pred" : "http://purl.org/dc/elements/1.1/description", + "val" : "The Human Phenotype Ontology (HPO) provides a standardized vocabulary of phenotypic abnormalities and clinical features encountered in human disease." + }, { + "pred" : "http://purl.org/dc/elements/1.1/rights", + "val" : "Peter Robinson, Sebastian Koehler, The Human Phenotype Ontology Consortium, and The Monarch Initiative" + }, { + "pred" : "http://purl.org/dc/elements/1.1/subject", + "val" : "Phenotypic abnormalities encountered in human disease" + }, { + "pred" : "http://purl.org/dc/elements/1.1/title", + "val" : "Human Phenotype Ontology" + }, { + "pred" : "http://purl.org/dc/elements/1.1/type", + "val" : "http://purl.obolibrary.org/obo/IAO_8000001" + }, { + "pred" : "http://purl.org/dc/terms/license", + "val" : "https://hpo.jax.org/app/license" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#default-namespace", + "val" : "human_phenotype" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#logical-definition-view-relation", + "val" : "has_part" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Please see license of HPO at http://www.human-phenotype-ontology.org" + }, { + "pred" : "http://www.w3.org/2002/07/owl#versionInfo", + "val" : "2023-04-05" + } ] + }, + "nodes" : [ { + "id" : "http://purl.obolibrary.org/obo/BFO_0000050", + "lbl" : "part of", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "BFO:0000050" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "part_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000051", + "lbl" : "has part", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "BFO:0000051" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_part" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000066", + "lbl" : "occurs in", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "BFO:0000066" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "occurs_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000001", + "lbl" : "All", + "type" : "CLASS", + "meta" : { + "comments" : [ "Root of all terms in the Human Phenotype Ontology." ], + "xrefs" : [ { + "val" : "UMLS:C0444868" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000002", + "lbl" : "Abnormality of body height", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Deviation from the norm of height with respect to that which is expected according to age and gender norms.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormality of body height" + } ], + "xrefs" : [ { + "val" : "UMLS:C4025901" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2008-02-27T02:20:00Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000098", + "lbl" : "Tall stature", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A height above that which is expected according to age and gender norms.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Accelerated linear growth" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Increased body height" + }, { + "pred" : "hasExactSynonym", + "val" : "Increased linear growth" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Tall stature" + } ], + "xrefs" : [ { + "val" : "SNOMEDCT_US:248328003" + }, { + "val" : "UMLS:C0241240" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2008-02-27T02:21:00Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0001527" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0003515" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0003516" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000118", + "lbl" : "Phenotypic abnormality", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A phenotypic abnormality.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "comments" : [ "This is the root of the phenotypic abnormality subontology of the HPO." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Organ abnormality" + } ], + "xrefs" : [ { + "val" : "UMLS:C4021819" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000152", + "lbl" : "Abnormality of head or neck", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An abnormality of head and neck.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormality of head or neck" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Head and neck abnormality" + } ], + "xrefs" : [ { + "val" : "UMLS:C4021817" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000153", + "lbl" : "Abnormality of the mouth", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An abnormality of the mouth.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormal mouth", + "xrefs" : [ "https://orcid.org/0000-0002-5316-1399" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormality of the mouth" + } ], + "xrefs" : [ { + "val" : "MSH:D009056" + }, { + "val" : "SNOMEDCT_US:128334002" + }, { + "val" : "UMLS:C0026633" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000160", + "lbl" : "Narrow mouth", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Distance between the commissures of the mouth more than 2 SD below the mean. Alternatively, an apparently decreased width of the oral aperture (subjective).", + "xrefs" : [ "PMID:19125428" ] + }, + "comments" : [ "The width of the mouth varies with facial movement and must be assessed when the subject has a relaxed (neutral) face. This term replaces microstomia, small oral aperture, and small mouth because the reduced opening of the mouth is secondary to reduced width." ], + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Microstomia" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Narrow mouth" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Small mouth" + }, { + "pred" : "hasExactSynonym", + "val" : "Small oral aperture" + } ], + "xrefs" : [ { + "val" : "MSH:D008865" + }, { + "val" : "SNOMEDCT_US:14582003" + }, { + "val" : "UMLS:C0026034" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0002261" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0009095" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0009096" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000163", + "lbl" : "Abnormal oral cavity morphology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Abnormality of the oral cavity, i.e., the opening or hollow part of the mouth.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormality of the oral cavity" + } ], + "xrefs" : [ { + "val" : "UMLS:C4025887" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000164", + "lbl" : "Abnormality of the dentition", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any abnormality of the teeth.", + "xrefs" : [ "https://orcid.org/0000-0002-9338-3017" ] + }, + "comments" : [ "Any abnormality of the primary (deciduous) or permanent teeth." ], + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormal dentition" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormal teeth" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#plural_form", + "pred" : "hasExactSynonym", + "val" : "Dental abnormalities" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Dental abnormality" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#plural_form", + "pred" : "hasExactSynonym", + "val" : "Dental anomalies" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasRelatedSynonym", + "val" : "Abnormality of the teeth" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasRelatedSynonym", + "val" : "Dental problem" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#plural_form", + "pred" : "hasRelatedSynonym", + "val" : "Dental problems" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasRelatedSynonym", + "val" : "Tooth abnormalities" + } ], + "xrefs" : [ { + "val" : "MSH:D014071" + }, { + "val" : "SNOMEDCT_US:422775003" + }, { + "val" : "UMLS:C0040427" + }, { + "val" : "UMLS:C0262444" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0001567" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0006296" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0006348" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000174", + "lbl" : "Abnormal palate morphology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any abnormality of the palate, i.e., of roof of the mouth.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormality of the palate" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormality of the roof of the mouth", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Palatal anomaly", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Palate abnormality" + } ], + "xrefs" : [ { + "val" : "UMLS:C4021815" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000175", + "lbl" : "Cleft palate", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Cleft palate is a developmental defect of the palate resulting from a failure of fusion of the palatine processes and manifesting as a separation of the roof of the mouth (soft and hard palate).", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "comments" : [ "Cleft palate is a developmental defect that occurs between the 7th and 12th week of pregnancy. Normally, the palatine processes fuse during this time to form the soft and hard palate. A failure of fusion results in a cleft palate. The clinical spectrum ranges from bifid uvula, to (incomplete or complete) cleft of the soft palate, up to (complete or incomplete) cleft of both the soft and hard palate." ], + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "Cleft secondary palate" + }, { + "pred" : "hasExactSynonym", + "val" : "Cleft hard and soft palate", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432", "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Cleft of hard and soft palate", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432", "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Cleft of palate" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Cleft palate" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Cleft roof of mouth", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Palatoschisis", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Uranostaphyloschisis", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + } ], + "xrefs" : [ { + "val" : "Fyler:4876" + }, { + "val" : "MSH:D002972" + }, { + "val" : "SNOMEDCT_US:63567004" + }, { + "val" : "SNOMEDCT_US:87979003" + }, { + "val" : "UMLS:C0008925" + }, { + "val" : "UMLS:C2981150" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0410004" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000189", + "lbl" : "Narrow palate", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Width of the palate more than 2 SD below the mean (objective) or apparently decreased palatal width (subjective).", + "xrefs" : [ "PMID:19125428" ] + }, + "comments" : [ "Palatal width is measured as the distance between the maxillary first permanent molar on the right and left sides, at the lingual cervical line, using a specific device. Palate width is typically assessed subjectively in routine clinical practice. Narrowing is often associated with a High palate, but this should be assessed and coded separately. Gingival overgrowth can give the impression of a narrow palate but should be distinguished and coded separately. The term gothic palate is used to indicate that the roof of the palate is not round but rather has an inverted V-shape, and therefore, only the upper part of the palate is narrow." ], + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Decreased palatal width", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Decreased transverse dimension of palate", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Narrow palate" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Narrow roof of mouth", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + } ], + "xrefs" : [ { + "val" : "UMLS:C1398312" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000202", + "lbl" : "Orofacial cleft", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The presence of a cleft in the oral cavity, the two main types of which are cleft lip and cleft palate. In cleft lip, there is the congenital failure of the maxillary and median nasal processes to fuse, forming a groove or fissure in the lip. In cleft palate, there is a congenital failure of the palate to fuse properly, forming a grooved depression or fissure in the roof of the mouth. Clefts of the lip and palate can occur individually or together. It is preferable to code each defect separately.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199", "PMID:21331089" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Cleft of the mouth", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Oral cleft" + }, { + "pred" : "hasExactSynonym", + "val" : "Oral clefting" + }, { + "pred" : "hasNarrowSynonym", + "val" : "Cleft lip, cleft palate" + }, { + "pred" : "hasRelatedSynonym", + "val" : "Cleft lip/palate" + } ], + "xrefs" : [ { + "val" : "SNOMEDCT_US:253983005" + }, { + "val" : "SNOMEDCT_US:66948001" + }, { + "val" : "UMLS:C0158646" + }, { + "val" : "UMLS:C4021813" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000218", + "lbl" : "High palate", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Height of the palate more than 2 SD above the mean (objective) or palatal height at the level of the first permanent molar more than twice the height of the teeth (subjective).", + "xrefs" : [ "PMID:19125428" ] + }, + "comments" : [ "The measuring device for this assessment is described in (Hall JG, Froster-Iskenius UG, Allanson JE, Gripp K, Slavotinek A. 2006. Handbook of Normal Physical Measurements. 2nd edition. Oxford Medical, publishers). A high palate is often associated with a narrow palate. However, a narrow palate can easily give a false appearance of a high palate. Height and width of the palate should be assessed and coded separately. We do not recommend the subjective determination because this term can be overused and\napplied inaccurately." ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Elevated palate", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "High arched palate" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "High palate" + }, { + "pred" : "hasExactSynonym", + "val" : "High, arched palate" + }, { + "pred" : "hasExactSynonym", + "val" : "High-arched palate" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Increased palatal height", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Palate high-arched" + }, { + "pred" : "hasExactSynonym", + "val" : "Palate, high-arched" + }, { + "pred" : "hasRelatedSynonym", + "val" : "Ogival palate" + } ], + "xrefs" : [ { + "val" : "SNOMEDCT_US:27272007" + }, { + "val" : "UMLS:C0240635" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0000156" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0009080" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0009082" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0009097" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000234", + "lbl" : "Abnormality of the head", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An abnormality of the head.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormal head", + "xrefs" : [ "https://orcid.org/0000-0002-5316-1399" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormality of the head" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Head abnormality" + } ], + "xrefs" : [ { + "val" : "UMLS:C4021812" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000240", + "lbl" : "Abnormality of skull size", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any abnormality of the size of the skull.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasBroadSynonym", + "val" : "Abnormality of head size", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Abnormality of cranium size", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormality of skull size" + } ], + "xrefs" : [ { + "val" : "UMLS:C4025874" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000250", + "lbl" : "Dense calvaria", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An abnormal increase of density of the bones making up the calvaria.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Dense skull cap", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + } ], + "xrefs" : [ { + "val" : "UMLS:C1854834" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000252", + "lbl" : "Microcephaly", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Head circumference below 2 standard deviations below the mean for age and gender.", + "xrefs" : [ "PMID:15806441", "PMID:19125436", "PMID:25465325", "PMID:9683597" ] + }, + "comments" : [ "Head circumference is measured from just above the glabella (the most prominent point on the frontal bone above the root of the nose) to the most posterior prominent point of the occipital bone using a tape measure. Some standard charts are organized by centiles, others by standard deviations. It is important to add an indication of how far below the normal standard the head circumference is if an accurate assessment of this can be made. Microcephaly is an absolute term. The term relative microcephaly can be used when the head size centile is less than the centile for height, for example, head size at the 3rd centile with height at the 75% for age and sex. On prenatal ultrasound, microcephaly is diagnosed if the head circumference or the biparietal diameter is more than three standard deviations below the mean. Microcephaly is divided into primary microcephaly, which is present at birth, and secondary microcephaly, which develops postnatally. The crucial difference between these groupings is that primary microcephaly is usually a static developmental anomaly, whereas secondary microcephaly indicates a progressive neurodegenerative condition" ], + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasBroadSynonym", + "val" : "Abnormally small head", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasBroadSynonym", + "val" : "Decreased size of head", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasBroadSynonym", + "val" : "Small head", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasBroadSynonym", + "val" : "Small skull", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Abnormally small cranium", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormally small skull", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Decreased circumference of cranium", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Decreased size of cranium", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Decreased size of skull", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Reduced head circumference" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Small head circumference" + }, { + "pred" : "hasExactSynonym", + "val" : "small calvarium", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "small cranium", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + } ], + "xrefs" : [ { + "val" : "Fyler:4310" + }, { + "val" : "SNOMEDCT_US:271611007" + }, { + "val" : "UMLS:C4551563" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0001366" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0005485" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0005489" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0005497" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000253", + "lbl" : "Progressive microcephaly", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Progressive microcephaly is diagnosed when the head circumference falls progressively behind age- and gender-dependent norms.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Microcephaly, postnatal, progressive" + }, { + "pred" : "hasExactSynonym", + "val" : "Microcephaly, progressive", + "xrefs" : [ "https://orcid.org/0000-0002-5316-1399" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Progressively abnormally small cranium", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Progressively abnormally small skull", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + } ], + "xrefs" : [ { + "val" : "UMLS:C1850456" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000256", + "lbl" : "Macrocephaly", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Occipitofrontal (head) circumference greater than 97th centile compared to appropriate, age matched, sex-matched normal standards. Alternatively, a apparently increased size of the cranium.", + "xrefs" : [ "PMID:19125436" ] + }, + "comments" : [ "Macrocephaly can be due to hydrocephalus (increased CFSF), megalencephaly (increased brain volume) or thickening of the skull. Head circumference is measured from just above the glabella (the most prominent point on the frontal bone above the root of the nose) to the most posterior prominent point of the occipital bone using a tape measure. Some standard charts are organized by centiles [Hall et al. [2007]], others by standard deviations [Farkas, [1981]]. It is important to add an indication of how far above the normal standard the head circumference is if an accurate assessment of this can be made. Macrocephaly is an absolute term. The term relative macrocephaly can be used when the head size centile exceeds the centile for height, for example, head size at the 75th centile with height at the 5th centile for age and sex." ], + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasBroadSynonym", + "val" : "Big calvaria", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasBroadSynonym", + "val" : "Big cranium", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasBroadSynonym", + "val" : "Big head", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasBroadSynonym", + "val" : "Big skull", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasBroadSynonym", + "val" : "Increased size of head", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasBroadSynonym", + "val" : "Large calvaria", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasBroadSynonym", + "val" : "Large cranium", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasBroadSynonym", + "val" : "Large skull", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Increased size of cranium", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Increased size of skull", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Large head" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Large head circumference" + }, { + "pred" : "hasExactSynonym", + "val" : "Macrocephalus" + }, { + "pred" : "hasExactSynonym", + "val" : "Macrocrania" + }, { + "pred" : "hasExactSynonym", + "val" : "Megacephaly", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + } ], + "xrefs" : [ { + "val" : "Fyler:4335" + }, { + "val" : "UMLS:C4083076" + }, { + "val" : "UMLS:C4255213" + }, { + "val" : "UMLS:C4280663" + }, { + "val" : "UMLS:C4280664" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0005491" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0005496" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0200135" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000268", + "lbl" : "Dolichocephaly", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An abnormality of skull shape characterized by a increased anterior-posterior diameter, i.e., an increased antero-posterior dimension of the skull. Cephalic index less than 76%. Alternatively, an apparently increased antero-posterior length of the head compared to width. Often due to premature closure of the sagittal suture.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199", "PMID:19125436" ] + }, + "comments" : [ "Cephalic index is the ratio of head width expressed as a percentage of head length. The normal range is 76-80.9%. Head length is measured between the glabella (the most prominent point on the frontal bone above the root of the nose) and the most prominent part of the occiput in the midline, using spreading calipers. Head width is measured between the most lateral points of the parietal bones on each side of the head, using spreading calipers. Cephalic index standards are derived from Caucasians and have limited relevance for other races and ethnicities. Current norms have limited validity because of changes in infant sleeping position and consequent changes in head shape. New data should be developed. Dolichocephaly is distinct from Prominent occiput, but both can be present in the same individual and should be coded separately. Scaphocephaly is a subtype of dolichocephaly where the anterior and posterior aspects of the cranial vault are pointed (boat-shaped)." ], + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "Narrow cranium shape", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasBroadSynonym", + "val" : "Narrow head shape", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasBroadSynonym", + "val" : "Narrow skull shape", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasBroadSynonym", + "val" : "Turridolichocephaly" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Long, narrow head", + "xrefs" : [ "https://orcid.org/0000-0002-6548-5200" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Tall and narrow skull", + "xrefs" : [ "https://orcid.org/0000-0002-6548-5200" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "Large dolichocephalic skull" + } ], + "xrefs" : [ { + "val" : "SNOMEDCT_US:72239002" + }, { + "val" : "UMLS:C0221358" + }, { + "val" : "UMLS:C4280653" + }, { + "val" : "UMLS:C4280654" + }, { + "val" : "UMLS:C4280655" + }, { + "val" : "UMLS:C4280656" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0000258" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0005440" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000271", + "lbl" : "Abnormality of the face", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An abnormality of the face.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "Abnormality of the countenance", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasBroadSynonym", + "val" : "Abnormality of the physiognomy", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasBroadSynonym", + "val" : "Abnormality of the visage", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasBroadSynonym", + "val" : "Disorder of face", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormal face", + "xrefs" : [ "https://orcid.org/0000-0002-5316-1399" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormality of the face" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Facial abnormality", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasNarrowSynonym", + "val" : "Disorder of the face", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "Anomaly of face", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "Anomaly of the face", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "Facial anomaly", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + } ], + "xrefs" : [ { + "val" : "SNOMEDCT_US:118930001" + }, { + "val" : "SNOMEDCT_US:32003007" + }, { + "val" : "SNOMEDCT_US:398206004" + }, { + "val" : "SNOMEDCT_US:398302004" + }, { + "val" : "UMLS:C0266617" + }, { + "val" : "UMLS:C1290857" + }, { + "val" : "UMLS:C4025871" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000272", + "lbl" : "Malar flattening", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Underdevelopment of the malar prominence of the jugal bone (zygomatic bone in mammals), appreciated in profile, frontal view, and/or by palpation.", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463", "https://orcid.org/0000-0002-0736-9199", "PMID:19125436" ] + }, + "comments" : [ "The malar process is the most medial and superior portion of the bony midface, articulating with the maxilla and temporal and sphenoid bones, contiguous with the lateral boundary of the nasal bridge. The term malar hypoplasia is no longer preferred because surface examination cannot distinguish hypoplasia from hypotrophy." ], + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Decreased size of malar bone", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Depressed malar region" + }, { + "pred" : "hasExactSynonym", + "val" : "Flat cheekbone", + "xrefs" : [ "https://orcid.org/0000-0002-9353-5498" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Malar hypoplasia" + }, { + "pred" : "hasExactSynonym", + "val" : "Underdevelopment of malar bone", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Zygomatic flattening", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "Hypotrophic malar bone", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + } ], + "xrefs" : [ { + "val" : "UMLS:C1858085" + }, { + "val" : "UMLS:C4280651" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0000312" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0000332" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0004642" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0004658" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0004671" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0005319" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0005443" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0005455" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0100846" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000274", + "lbl" : "Small face", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A face that is short and narrow.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "comments" : [ "This term represents a combination of two terms, short face and narrow face." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Facial hypoplasia", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Hypoplasia of face", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Microface", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Microfacies", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Short and narrow face", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Small face" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Small facies", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + } ], + "xrefs" : [ { + "val" : "UMLS:C1855538" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000275", + "lbl" : "Narrow face", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Bizygomatic (upper face) and bigonial (lower face) width are both more than 2 standard deviations below the mean (objective); or, an apparent reduction in the width of the upper and lower face (subjective).", + "xrefs" : [ "PMID:19125436" ] + }, + "comments" : [ "Objective measurement of the upper facial width is made with spreading calipers. The tips of the calipers are passed over the zygomatic arches until the maximum width is determined. Objective measurement of the lower faces is made with spreading calipers, with the tips firmly pressed against the inferomedial surface of the angle of the mandible." ], + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Decreased breadth of face", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Decreased horizontal dimension of face", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Decreased transverse dimension of face", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Decreased width of face", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Horizontal deficiency of face", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Horizontal hypoplasia of face", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Horizontal insufficiency of face", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Narrow face" + }, { + "pred" : "hasExactSynonym", + "val" : "Narrow facies" + }, { + "pred" : "hasExactSynonym", + "val" : "Thin facies", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Transverse deficiency of face", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Transverse hypoplasia of face", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Transverse insufficiency of face", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasRelatedSynonym", + "val" : "Thin face" + } ], + "xrefs" : [ { + "val" : "UMLS:C1837463" + }, { + "val" : "UMLS:C1849121" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0000318" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000276", + "lbl" : "Long face", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Facial height (length) is more than 2 standard deviations above the mean (objective); or, an apparent increase in the height (length) of the face (subjective).", + "xrefs" : [ "PMID:19125436" ] + }, + "comments" : [ "Objective measurement of the face height is made with sliding calipers from the nasion, just above the depth of the nasal root, to the gnathion, the inferior border of the mandible, both in the midline. Note that long face is distinct from narrow face." ], + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Elongation of face", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Increased height of face", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Increased length of face", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Increased vertical dimension of face", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Long face" + }, { + "pred" : "hasExactSynonym", + "val" : "Long facies", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Vertical Facial Excess", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Vertical elongation of face", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Vertical enlargement of face", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Vertical excess of face", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Vertical hyperplasia of face", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Vertical overgrowth of face", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + } ], + "xrefs" : [ { + "val" : "UMLS:C1836047" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0000334" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000277", + "lbl" : "Abnormal mandible morphology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any abnormality of the mandible, the bone of the lower jaw.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormality of the lower jaw bone", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormality of the mandible" + }, { + "pred" : "hasNarrowSynonym", + "val" : "Anomaly of the mandible", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasNarrowSynonym", + "val" : "Deformity of the lower jaw bone", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "Deformity of the mandible", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasNarrowSynonym", + "val" : "Malformation of the lower jaw bone", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "Malformation of the mandible", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + } ], + "xrefs" : [ { + "val" : "UMLS:C4025870" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0000209" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000278", + "lbl" : "Retrognathia", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An abnormality in which the mandible is mislocalised posteriorly.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Lower jaw retrognathia" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Receding chin" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Receding lower jaw", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Receding mandible" + }, { + "pred" : "hasExactSynonym", + "val" : "Retrognathia of lower jaw", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Weak chin", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Weak jaw", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "Retrogenia", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + } ], + "xrefs" : [ { + "val" : "MSH:D063173" + }, { + "val" : "UMLS:C3494422" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0002053" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0002954" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000291", + "lbl" : "Abnormality of facial adipose tissue", + "type" : "CLASS", + "meta" : { + "synonyms" : [ { + "synonymType" : 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Most commonly the cornea is affected such that the refractive power in one meridian is less than that of the perpendicular axis. Astigmatism of significant degree causes blurry vision." ], + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormal curving of the cornea or lens of the eye", + "xrefs" : [ "https://orcid.org/0000-0002-6548-5200" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Astigmatism" + } ], + "xrefs" : [ { + "val" : "MSH:D001251" + }, { + "val" : "SNOMEDCT_US:82649003" + }, { + "val" : "UMLS:C0004106" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000485", + "lbl" : "Megalocornea", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An enlargement of the cornea with normal clarity and function. Megalocornea is diagnosed with a horizontal corneal diameter of 12 mm or more at birth or 13 mm or more after two years of age.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Anterior megalophthalmos" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Enlarged cornea", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Increased corneal diameter" + }, { + "pred" : "hasExactSynonym", + "val" : "Macrocornea" + } ], + "xrefs" : [ { + "val" : "MSH:C562829" + }, { + "val" : "SNOMEDCT_US:204118005" + }, { + "val" : "SNOMEDCT_US:268158009" + }, { + "val" : "UMLS:C0344530" + }, { + "val" : "UMLS:C1167712" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0007660" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000486", + "lbl" : "Strabismus", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A misalignment of the eyes so that the visual axes deviate from bifoveal fixation. The classification of strabismus may be based on a number of features including the relative position of the eyes, whether the deviation is latent or manifest, intermittent or constant, concomitant or otherwise and according to the age of onset and the relevance of any associated refractive error.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199", "https://orcid.org/0000-0003-0986-4123", "PMID:26319345" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Cross-eyed" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Squint" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Squint eyes", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432", "https://orcid.org/0000-0001-5889-4463" ] + } ], + "xrefs" : [ { + "val" : "MSH:D013285" + }, { + "val" : "SNOMEDCT_US:128602000" + }, { + "val" : "SNOMEDCT_US:22066006" + }, { + "val" : "UMLS:C0038379" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0000487" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000490", + "lbl" : "Deeply set eye", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An eye that is more deeply recessed into the plane of the face than is typical.", + "xrefs" : [ "PMID:19125427" ] + }, + "comments" : [ "This finding should be distinguished from a prominent supraorbital ridge or inferior orbital margin. In Deeply set eyes, the globe is recessed in comparison to the overall prominence of the face. There is no known objective measurement, and diagnosing this feature depends heavily on the experience of the observer." ], + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Deep set eye" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Deep-set eyes" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Deeply set eye" + }, { + "pred" : "hasExactSynonym", + "val" : "Enophthalmos" + }, { + "pred" : "hasExactSynonym", + "val" : "Ocular depression" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Sunken eye" + }, { + "pred" : "hasExactSynonym", + "val" : "Sunken eyes" + } ], + "xrefs" : [ { + "val" : "MSH:D015841" + }, { + "val" : "SNOMEDCT_US:246923005" + }, { + "val" : "SNOMEDCT_US:80093006" + }, { + "val" : "UMLS:C0014306" + }, { + "val" : "UMLS:C0423224" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0000663" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000492", + "lbl" : "Abnormal eyelid morphology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An abnormality of the eyelids.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormality of the eyelid" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormality of the eyelids" + } ], + "xrefs" : [ { + "val" : "UMLS:C4021803" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0000285" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000494", + "lbl" : "Downslanted palpebral fissures", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The palpebral fissure inclination is more than two standard deviations below the mean.", + "xrefs" : [ "PMID:19125427" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Antimongoloid eye slant" + }, { + "pred" : "hasExactSynonym", + "val" : "Antimongoloid slant of palpebral fissures" + }, { + "pred" : "hasExactSynonym", + "val" : "Antimongoloid slanted palpebral fissures" + }, { + "pred" : "hasExactSynonym", + "val" : "Down slanting palpebral fissures" + }, { + "pred" : "hasExactSynonym", + "val" : "Down-slanted palpebral fissures" + }, { + "pred" : "hasExactSynonym", + "val" : "Down-slanting palpebral fissure" + }, { + "pred" : "hasExactSynonym", + "val" : "Down-slanting palpebral fissures" + }, { + "pred" : "hasExactSynonym", + "val" : "Downslanting palpebral fissure" + }, { + "pred" : "hasExactSynonym", + "val" : "Downslanting palpebral fissures", + "xrefs" : [ "https://orcid.org/0000-0002-5316-1399" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Downward slanted palpebral fissures" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Downward slanting of the opening between the eyelids", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Downward slanting palpebral fissures", + "xrefs" : [ "https://orcid.org/0000-0002-5316-1399" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Downward-slanting palpebral fissures" + }, { + "pred" : "hasExactSynonym", + "val" : "Palpebral fissures down-slanted" + } ], + "xrefs" : [ { + "val" : "SNOMEDCT_US:246800008" + }, { + "val" : "UMLS:C0423110" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0007714" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0007908" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000496", + "lbl" : "Abnormality of eye movement", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An abnormality in voluntary or involuntary eye movements or their control.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Abnormal extraocular movement" + }, { + "pred" : "hasExactSynonym", + "val" : "Abnormal extraocular movements" + }, { + "pred" : "hasExactSynonym", + "val" : "Abnormal eye motility" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormal eye movement" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormal eye movements" + }, { + "pred" : "hasExactSynonym", + "val" : "Abnormal motility of the globe of the eye", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432", "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Abnormal movement of the globe of the eye", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432", "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Abnormal ocular movements" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormality of eye movement" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Eye movement abnormalities" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Eye movement issue" + }, { + "pred" : "hasExactSynonym", + "val" : "Ocular movement abnormalities" + }, { + "pred" : "hasExactSynonym", + "val" : "Oculomotor abnormalities" + } ], + "xrefs" : [ { + "val" : "SNOMEDCT_US:103252009" + }, { + "val" : "UMLS:C0497202" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0006860" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000498", + "lbl" : "Blepharitis", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Inflammation of the eyelids.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Cellulitis of eyelids", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Inflammation of eyelids", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + } ], + "xrefs" : [ { + "val" : "MSH:D001762" + }, { + "val" : "SNOMEDCT_US:231796003" + }, { + "val" : "SNOMEDCT_US:41446000" + }, { + "val" : "UMLS:C0005741" + }, { + "val" : "UMLS:C0339063" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000501", + "lbl" : "Glaucoma", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Glaucoma refers loss of retinal ganglion cells in a characteristic pattern of optic neuropathy usually associated with increased intraocular pressure.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199", "PMID:11815354" ] + }, + "comments" : [ "The feature that differentiates glaucoma from other causes of visual morbidity is a characteristic pattern of damage to the optic nerve head. This is most easily recognised at the superior and inferior poles of the optic disc. The vertical cup:disc ratio (VCDR) has proved to be a simple, relatively robust index of glaucomatous loss of the neuroretinal rim. As with intraocular pressure, VCDR is a continuous variable within the population." ], + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "xrefs" : [ { + "val" : "MSH:D005901" + }, { + "val" : "SNOMEDCT_US:23986001" + }, { + "val" : "UMLS:C0017601" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000510", + "lbl" : "Rod-cone dystrophy", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An inherited retinal disease subtype in which the rod photoreceptors appear to be more severely affected than the cone photoreceptors. Typical presentation is with nyctalopia (due to rod dysfunction) followed by loss of mid-peripheral field of vision, which gradually extends and leaves many patients with a small central island of vision due to the preservation of macular cones.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199", "PMID:20212494" ] + }, + "comments" : [ "Retinitis pigmentosa is a group of hereditary diseases of the eye. However, the term retinitis pigmentosa has also been used to describe the retinal findings characteristic of these diseases but also seen on other diseases such as Usher syndrome. It is preferable to describe the findings precisely if possible, but this term is kept for convenience." ], + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Retinitis pigmentosa" + }, { + "pred" : "hasExactSynonym", + "val" : "Rod cone dystrophy" + } ], + "xrefs" : [ { + "val" : "MSH:D012174" + }, { + "val" : "SNOMEDCT_US:28835009" + }, { + "val" : "UMLS:C0035334" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0000547" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0001127" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0007635" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0007645" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0007742" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0007816" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0007826" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0007927" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0008036" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000517", + "lbl" : "Abnormal lens morphology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An abnormality of the lens.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormality of the lens" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Lens issue" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasRelatedSynonym", + "val" : "Lens disease" + } ], + "xrefs" : [ { + "val" : "MSH:D007905" + }, { + "val" : "SNOMEDCT_US:10810001" + }, { + "val" : "UMLS:C0023308" + }, { + "val" : "UMLS:C0549651" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000518", + "lbl" : "Cataract", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A cataract is an opacity or clouding that develops in the crystalline lens of the eye or in its capsule.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "comments" : [ "Note that some ophthalmologists call any opacity in the lens a cataract, while others restrict the term to lens opacities that impair vision. We use the term to refer to the first meaning (any lens opacity)." ], + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Cataracts" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Clouding of the lens of the eye", + "xrefs" : [ "https://orcid.org/0000-0002-6548-5200" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Cloudy lens", + "xrefs" : [ "https://orcid.org/0000-0001-6908-9849" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Lens opacities" + }, { + "pred" : "hasExactSynonym", + "val" : "Lens opacity" + } ], + "xrefs" : [ { + "val" : "Fyler:4865" + }, { + "val" : "MSH:D002386" + }, { + "val" : "SNOMEDCT_US:128306009" + }, { + "val" : "SNOMEDCT_US:193570009" + }, { + "val" : "SNOMEDCT_US:247053007" + }, { + "val" : "UMLS:C0086543" + }, { + "val" : "UMLS:C1510497" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0001113" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0007825" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0010700" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000520", + "lbl" : "Proptosis", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An eye that is protruding anterior to the plane of the face to a greater extent than is typical.", + "xrefs" : [ "https://orcid.org/0009-0006-4530-3154", "PMID:19125427" ] + }, + "comments" : [ "Some sources define \"exophthalmos\" as a protrusion of the globe greater than 18 mm and \"proptosis\" as a protusion equal to or less than 18 mm. Others define \"exophthalmos\" as protusion secondary to endocrine dysfunction and \"proptosis\" as any non-endocrine-mediated protusion (Source: Wikipedia). This finding should be distinguished frm underdevelopment of the supraorbital ridge or maxilla/zygoma. In proptosis, the globe is anteriorly protuberant to the overall plane of the face." ], + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Anterior bulging of the globe" + }, { + "pred" : "hasExactSynonym", + "val" : "Anterior bulging of the globe of eye" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Bulging eye", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Exophthalmos" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Eyeballs bulging out", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Ocular proptosis" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Prominent eyes" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Prominent globes" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Protruding eyes" + }, { + "pred" : "hasExactSynonym", + "val" : "Protrusio bulbi" + } ], + "xrefs" : [ { + "val" : "MSH:D005094" + }, { + "val" : "SNOMEDCT_US:18265008" + }, { + "val" : "UMLS:C0015300" + }, { + "val" : "UMLS:C1837760" + }, { + "val" : "UMLS:C1848490" + }, { + "val" : "UMLS:C1862425" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0000536" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0000644" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0000645" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0007711" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0007870" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000525", + "lbl" : "Abnormality iris morphology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An abnormality of the iris, which is the pigmented muscular tissue between the cornea and the lens, that is perforated by an opening called the pupil.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormality of the iris" + } ], + "xrefs" : [ { + "val" : "UMLS:C4025845" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000526", + "lbl" : "Aniridia", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Abnormality of the iris characterized by, typically bilateral, complete or partial iris hypoplasia. The phenotype ranges from mild defects of anterior iris stroma only to almost complete absence of the iris.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199", "https://orcid.org/0000-0003-0986-4123", "PMID:24138039", "PMID:25313118", "PMID:29850208" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Absent iris", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + } ], + "xrefs" : [ { + "val" : "MSH:D015783" + }, { + "val" : "SNOMEDCT_US:69278003" + }, { + "val" : "UMLS:C0003076" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0011498" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000528", + "lbl" : "Anophthalmia", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Absence of the globe or eyeball.", + "xrefs" : [ "HPO_CONTRIBUTOR:DDD_ncarter" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Absence of eyeballs", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Absence of globes of eyes", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Anophthalmia, clinical" + }, { + "pred" : "hasExactSynonym", + "val" : "Clinical anophthalmia, unilateral/bilateral" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Failure of development of eyeball", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Missing eyeball", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432", "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Missing globe of eye", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432", "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "No eyeball", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432", "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "No globe of eye", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432", "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Ocular absence", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432", "https://orcid.org/0000-0001-5889-4463" ] + } ], + "xrefs" : [ { + "val" : "Fyler:4864" + }, { + "val" : "MSH:D000853" + }, { + "val" : "SNOMEDCT_US:204099004" + }, { + "val" : "SNOMEDCT_US:7183006" + }, { + "val" : "UMLS:C0003119" + } ], + "basicPropertyValues" : [ { + "pred" : 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"synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Detached retina" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Retinal detachment" + } ], + "xrefs" : [ { + "val" : "MSH:D012163" + }, { + "val" : "SNOMEDCT_US:42059000" + }, { + "val" : "UMLS:C0035305" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0007864" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0008021" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000545", + "lbl" : "Myopia", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An abnormality of refraction characterized by the ability to see objects nearby clearly, while objects in the distance appear blurry.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "subsets" : [ 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Retinal dystrophies are defined by their predominantly monogenic inheritance and they are frequently associated with loss or dysfunction of photoreceptor cells as a primary or secondary event.", + "xrefs" : [ "https://orcid.org/0000-0003-0986-4123" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Breakdown of light-sensitive cells in back of eye", + "xrefs" : [ "https://orcid.org/0000-0002-6548-5200" ] + } ], + "xrefs" : [ { + "val" : "MSH:D058499" + }, { + "val" : "SNOMEDCT_US:314407005" + }, { + "val" : "UMLS:C0854723" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0007736" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0007910" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0007974" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0007982" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000565", + "lbl" : "Esotropia", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A form of strabismus with one or both eyes turned inward ('crossed') to a relatively severe degree, usually defined as 10 diopters or more.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "comments" : [ "Esotropia is analogous to but more severe thatn esophoria. 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}, { + "id" : "http://purl.obolibrary.org/obo/HP_0000593", + "lbl" : "Abnormal anterior chamber morphology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Abnormality of the anterior chamber, which is the space in the eye that is behind the cornea and in front of the iris.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Abnormality of the anterior chamber" + }, { + "pred" : "hasExactSynonym", + "val" : "Anterior chamber anomalies" + }, { + "pred" : "hasExactSynonym", + "val" : "Ocular anterior chamber abnormality" + } ], + "xrefs" : [ { + "val" : "SNOMEDCT_US:204142009" + }, { + "val" : "UMLS:C3152182" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000601", + "lbl" : "Hypotelorism", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Interpupillary distance less than 2 SD below the mean (alternatively, the appearance of an decreased interpupillary distance or closely spaced eyes).", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199", "PMID:19125427" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormally close eyes", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Closely spaced eyes" + }, { + "pred" : "hasExactSynonym", + "val" : "Decreased distance between eye sockets", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Decreased distance between eyes", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Decreased interpupillary distance", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Decreased orbital separation", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Ocular hypotelorism" + } ], + "xrefs" : [ { + "val" : "SNOMEDCT_US:44593008" + }, { + "val" : "UMLS:C0424711" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0007877" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000612", + "lbl" : "Iris coloboma", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A coloboma of the iris.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199", "PMID:19369671" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Cat eye", + "xrefs" : [ "https://orcid.org/0000-0001-6908-9849" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Coloboma of iris" + }, { + "pred" : "hasExactSynonym", + "val" : "Coloboma of the iris" + }, { + "pred" : "hasExactSynonym", + "val" : "Keyhole iris" + } ], + "xrefs" : [ { + "val" : "UMLS:C0240063" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0007744" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0007748" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000625", + "lbl" : "Eyelid coloboma", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A short discontinuity of the margin of the lower or upper eyelid.", + "xrefs" : [ "PMID:19125427" ] + }, + "comments" : [ "The lateral segment of the lower eyelid is most commonly involved. As the milder forms of this finding are clearly subjective and no boundary of subjective and objective is defined, the term is considered subjective. The term eyelid coloboma has been replaced because the word coloboma should be used only for defects at the site of fusion of embryologic structures, which is not the case here. Modifiers to designate the location of the cleft may be added, such as lower and lateral." ], + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Cleft eyelid" + }, { + "pred" : "hasExactSynonym", + "val" : "Full thickness defect of the eyelid", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Notched eyelid" + } ], + "xrefs" : [ { + "val" : "SNOMEDCT_US:95202004" + }, { + "val" : "UMLS:C0521573" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000630", + "lbl" : "Abnormal retinal artery morphology", + "type" : "CLASS", + "meta" : { + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormality of retinal arteries" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Retinal arterial abnormality" + } ], + "xrefs" : [ { + "val" : "UMLS:C4021802" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000637", + "lbl" : "Long palpebral fissure", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Distance between medial and lateral canthi is more than two standard deviations above the mean for age (objective); or, apparently increased length of the palpebral fissures.", + "xrefs" : [ "PMID:19125427" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Broad opening between the eyelids", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Broad palpebral fissure", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Long opening between the eyelids", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Long palpebral fissures", + "xrefs" : [ "https://orcid.org/0000-0002-5316-1399" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Wide opening between the eyelids", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Wide palpebral fissure", + "xrefs" : [ "https://orcid.org/0000-0002-5316-1399" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Wide palpebral fissures" + } ], + "xrefs" : [ { + "val" : "UMLS:C1849340" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0007904" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000667", + "lbl" : "Phthisis bulbi", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Atrophy of the eyeball with blindness and decreased intraocular pressure due to end-stage intraocular disease.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "comments" : [ "Phthisis bulbi refers to atrophy and degeneration of a blind eye." ], + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "xrefs" : [ { + "val" : "SNOMEDCT_US:4229009" + }, { + "val" : "UMLS:C0271007" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000674", + "lbl" : "Anodontia", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The absence of all teeth from the normal series by a failure to develop.", + "xrefs" : [ "https://orcid.org/0000-0002-9338-3017", "PMID:31468724" ] + }, + "comments" : [ "Anodontia can affect both primary and permanent teeth. Alternatively, there can be anodontia of just the permanent teeth. Anodontia must be distinguished from non-erupted teeth." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Anodontia vera", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Complete agenesis of all teeth", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Complete dental agenesis" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Failure of development of all teeth", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "Complete anodontia", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "Total anodontia", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasRelatedSynonym", + "val" : "Missing all teeth", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasRelatedSynonym", + "val" : "Total absence of all teeth", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + } ], + "xrefs" : [ { + "val" : "MSH:D000848" + }, { + "val" : "SNOMEDCT_US:16958000" + }, { + "val" : "SNOMEDCT_US:26624006" + }, { + "val" : "UMLS:C0399352" + }, { + "val" : "UMLS:C4280622" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0006484" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000678", + "lbl" : "Dental crowding", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Changes in alignment of teeth in the dental arch", + "xrefs" : [ "PMID:19125428", "PMID:31468724" ] + }, + "comments" : [ "Overlapping teeth within an alveolar ridge." ], + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "Inadequate arch length for tooth size", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasBroadSynonym", + "val" : "Tooth mass arch size discrepancy", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasBroadSynonym", + "val" : "Tooth size discrepancy", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Crowded teeth" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Dental crowding" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Dental overcrowding" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Overcrowding of teeth", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + } ], + "xrefs" : [ { + "val" : "MSH:D008310" + }, { + "val" : "SNOMEDCT_US:12351004" + }, { + "val" : "SNOMEDCT_US:699222000" + }, { + "val" : "UMLS:C0040433" + }, { + "val" : "UMLS:C1317785" + }, { + "val" : "UMLS:C4280617" + }, { + "val" : "UMLS:C4280618" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000685", + "lbl" : "Hypoplasia of teeth", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Developmental hypoplasia of teeth.", + "xrefs" : [ "https://orcid.org/0000-0002-9338-3017" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasBroadSynonym", + "val" : "Decreased size of teeth", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasBroadSynonym", + "val" : "Underdevelopment of teeth", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Hypoplastic teeth" + } ], + "xrefs" : [ { + "val" : "UMLS:C0235357" + }, { + "val" : "UMLS:C4280611" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0000688" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0006281" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0006307" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000691", + "lbl" : "Microdontia", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Decreased size of the teeth, which can be defined as a mesiodistal tooth diameter (width) more than 2 SD below mean. Alternatively, an apparently decreased maximum width of tooth.", + "xrefs" : [ "https://orcid.org/0000-0002-9338-3017", "PMID:19125428" ] + }, + "comments" : [ "Standard reference has means and standard deviations by gender [Moyers et al, 1976]. It is easy to measure the width of teeth, for which reason the definition of microdontia can be made with reference to the width of the tooth. However, microdontia means that the overall size of the tooth is decreased. In microdontia, the gaps between the teeth, particularly the anterior upper and lower teeth, are increased, creating diastemata. This should be assessed and coded separately." ], + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "Hypotrophic tooth", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Decreased size of tooth", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Decreased width of tooth", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Small teeth" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Small tooth", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Tooth hypoplasia" + }, { + "pred" : "hasExactSynonym", + "val" : "Tooth hypotrophy" + }, { + "pred" : "hasExactSynonym", + "val" : "Underdeveloped tooth" + } ], + "xrefs" : [ { + "val" : "SNOMEDCT_US:32337007" + }, { + "val" : "UMLS:C0240340" + }, { + "val" : "UMLS:C4280611" + }, { + "val" : "UMLS:C4280612" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000692", + "lbl" : "Tooth malposition", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Abnormal alignment, positioning, or spacing of the teeth, i.e., misaligned teeth.", + "xrefs" : [ "https://orcid.org/0000-0002-9338-3017" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasBroadSynonym", + "val" : "Abnormality of position of teeth", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormal dental position" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormal teeth spacing" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormality of alignment of teeth", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormality of teeth spacing" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Crooked teeth", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Malaligned teeth" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Malposition of teeth" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Malpositioned teeth" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Misalignment of teeth" + }, { + "pred" : "hasExactSynonym", + "val" : "Teeth, malposition" + } ], + "xrefs" : [ { + "val" : "UMLS:C1852504" + }, { + "val" : "UMLS:C4280610" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0000693" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0001569" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0006303" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0006478" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000707", + "lbl" : "Abnormality of the nervous system", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An abnormality of the nervous system.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "comments" : [ "The nervous system comprises the neuraxis (brain, spinal cord, and ventricles), the autonomic nervous system, the enteric nervous system, and the peripheral nervous system." ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasBroadSynonym", + "val" : "Brain and/or spinal cord issue" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormality of the nervous system" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Neurologic abnormalities" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Neurological abnormality" + } ], + "xrefs" : [ { + "val" : "MSH:D009421" + }, { + "val" : "SNOMEDCT_US:88425004" + }, { + "val" : "UMLS:C0497552" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0001333" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0006987" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000765", + "lbl" : "Abnormal thorax morphology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any abnormality of the thorax (the region of the body formed by the sternum, the thoracic vertebrae and the ribs).", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormality of the chest" + }, { + "pred" : "hasExactSynonym", + "val" : "Abnormality of the thorax" + }, { + "pred" : "hasExactSynonym", + "val" : "Structural abnormality of the chest wall" + } ], + "xrefs" : [ { + "val" : "UMLS:C4021797" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0100655" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000766", + "lbl" : "Abnormal sternum morphology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An anomaly of the sternum, also known as the breastbone.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormality of the sternum" + }, { + "pred" : "hasExactSynonym", + "val" : "Pectus carinatum or pectus excavatum" + }, { + "pred" : "hasExactSynonym", + "val" : "Pectus deformities" + }, { + "pred" : "hasExactSynonym", + "val" : "Pectus deformity" + }, { + "pred" : "hasExactSynonym", + "val" : "Pectus excavatum or carinatum" + }, { + "pred" : "hasExactSynonym", + "val" : "Pectus excavatum or pectus carinatum" + }, { + "pred" : "hasExactSynonym", + "val" : "Pectus excavatum/carinatum" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Sternal anomalies" + } ], + "xrefs" : [ { + "val" : "UMLS:C1860493" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0000780" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0006586" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0006594" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0006605" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0006630" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0006708" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000767", + "lbl" : "Pectus excavatum", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A defect of the chest wall characterized by a depression of the sternum, giving the chest (\"pectus\") a caved-in (\"excavatum\") appearance.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Funnel chest" + } ], + "xrefs" : [ { + "val" : "SNOMEDCT_US:391987005" + }, { + "val" : "UMLS:C2051831" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0006613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0006617" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000768", + "lbl" : "Pectus carinatum", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A 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"val" : "Skeletal abnormalities" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Skeletal anomalies" + } ], + "xrefs" : [ { + "val" : "UMLS:C4021790" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000925", + "lbl" : "Abnormality of the vertebral column", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any abnormality of the vertebral column.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormal spine", + "xrefs" : [ "https://orcid.org/0000-0002-5316-1399" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormal vertebral column" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : 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By definition from the World Health Organization osteopenia is defined by bone densitometry as a T score -1 to -2.5.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199", "PMID:21234807" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#uk_spelling", + "pred" : "hasExactSynonym", + "val" : "Generalised osteopenia" + }, { + "pred" : "hasExactSynonym", + "val" : "Generalized osteopenia" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#uk_spelling", + "pred" : "hasExactSynonym", + "val" : "Osteopaenia" + } ], + "xrefs" : [ { + "val" : "MSH:D001851" + }, { + "val" : "SNOMEDCT_US:312894000" + }, { + "val" : "SNOMEDCT_US:78441005" + }, { + "val" : "UMLS:C0029453" + }, { + "val" : "UMLS:C0747078" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0002768" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0002799" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0002800" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000939", + "lbl" : "Osteoporosis", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Osteoporosis is a systemic skeletal disease characterized by low bone density and microarchitectural deterioration of bone tissue with a consequent increase in bone fragility. According to the WHO criteria, osteoporosis is defined as a BMD that lies 2.5 standard deviations or more below the average value for young healthy adults (a T-score below -2.5 SD).", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199", "PMID:28293453" ] + }, + "comments" : [ "Osteoporosis is a disease that is characterized by low bone mass, deterioration of bone tissue, and disruption of bone microarchitecture: it can lead to compromised bone strength and an increase in the risk of fractures." ], + "xrefs" : [ { + "val" : "MSH:D010024" + }, { + "val" : "SNOMEDCT_US:64859006" + }, { + "val" : "UMLS:C0029456" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0002774" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000951", + "lbl" : "Abnormality of the skin", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An abnormality of the skin.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormality of the skin" + }, { + "pred" : "hasExactSynonym", + "val" : "Dermatopathy", + "xrefs" : [ "https://orcid.org/0000-0002-5316-1399" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Dermopathy", + "xrefs" : [ "https://orcid.org/0000-0002-5316-1399" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "Skin abnormality" + } ], + "xrefs" : [ { + "val" : "MSH:D012868" + }, { + "val" : "MSH:D012871" + }, { + "val" : "SNOMEDCT_US:199879009" + }, { + "val" : "SNOMEDCT_US:95320005" + }, { + "val" : "UMLS:C0037268" + }, { + "val" : "UMLS:C0037274" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0001478" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0001479" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0005591" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0006736" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0007415" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0007580" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000963", + "lbl" : "Thin skin", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Reduction in thickness of the skin, generally associated with a loss of suppleness and elasticity of the skin.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Thin skin" + } ], + "xrefs" : [ { + "val" : "SNOMEDCT_US:277797007" + }, { + "val" : "UMLS:C0423757" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0001020" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001001", + "lbl" : "Abnormality of subcutaneous fat tissue", + "type" : "CLASS", + "meta" : { + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormality of fatty tissue below the skin", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + } ], + "xrefs" : [ { + "val" : "UMLS:C4025813" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001065", + "lbl" : "Striae distensae", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Thinned, erythematous, depressed bands of atrophic skin. Initially, striae appear as flattened and thinned, pinkish linear regions of the skin. Striae tend to enlarge in length and become reddish or purplish. Later, striae tend to appear as white, depressed bands that are parallel to the lines of skin tension. Striae distensae occur most often in areas that have been subject to distension such as the lower back, buttocks, thighs, breast, abdomen, and shoulders.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Purplish striae" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Stretch marks" + }, { + "pred" : "hasExactSynonym", + "val" : "Striae" + }, { + "pred" : "hasExactSynonym", + "val" : "Striae atrophicae" + }, { + "pred" : "hasExactSynonym", + "val" : "Striae cutis distensae" + } ], + "xrefs" : [ { + "val" : "MEDDRA:10040925" + }, { + "val" : "MSH:D057896" + }, { + "val" : "SNOMEDCT_US:201066002" + }, { + "val" : "SNOMEDCT_US:201067006" + }, { + "val" : "SNOMEDCT_US:47212006" + }, { + "val" : "UMLS:C0152459" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0001023" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0001066" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0100680" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001083", + "lbl" : "Ectopia lentis", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Dislocation or malposition of the crystalline lens of the eye. A partial displacement (or dislocation) of the lens is described as a subluxation of the lens, while a complete displacement is termed luxation of the lens. A complete displacement occurs if the lens is completely outside the patellar fossa of the lens, either in the anterior chamber, in the vitreous, or directly on the retina. If the lens is partially displaced but still contained within the lens space, then it is termed subluxation.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Abnormality of lens position" + }, { + "pred" : "hasExactSynonym", + "val" : "Lens dislocation" + } ], + "xrefs" : [ { + "val" : "MSH:D004479" + }, { + "val" : "MSH:D007906" + }, { + "val" : "SNOMEDCT_US:74969002" + }, { + "val" : "UMLS:C0013581" + }, { + "val" : "UMLS:C0023309" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0000665" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0007637" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0007882" + }, { + "pred" : 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synonym of this term." ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Increased size of eyes", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Large eyes" + }, { + "pred" : "hasExactSynonym", + "val" : "Megalophthalmos" + }, { + "pred" : "hasRelatedSynonym", + "val" : "Increased size of palpebral fissures", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasRelatedSynonym", + "val" : "Large eyeballs", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "Large of palpebral fissures", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + } ], + "xrefs" : [ { + "val" : "SNOMEDCT_US:246920008" + }, { + "val" : "UMLS:C0423221" + }, { + "val" : "UMLS:C1855852" + }, { + "val" : "UMLS:C4280603" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0200093" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001098", + "lbl" : "Abnormal fundus morphology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any structural abnormality of the fundus of the eye." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Abnormality of the fundus" + } ], + "xrefs" : [ { + "val" : "UMLS:C4025804" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001099", + "lbl" : "Fundus atrophy", + "type" : "CLASS", + "meta" : { + "xrefs" : [ { + "val" : "UMLS:C2673929" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001101", + "lbl" : "Iritis", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Inflammation of the iris.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Inflammation of iris", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + } ], + "xrefs" : [ { + "val" : "MSH:D007500" + }, { + "val" : "SNOMEDCT_US:65074000" + }, { + "val" : "UMLS:C0022081" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001105", + "lbl" : "Retinal atrophy", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Well-demarcated area(s) of partial or complete depigmentation in the fundus, reflecting atrophy of the retinal pigment epithelium with associated retinal photoreceptor loss.", + "xrefs" : [ "https://orcid.org/0000-0003-0986-4123" ] + }, + "xrefs" : [ { + "val" : "MSH:D012162" + }, { + "val" : "SNOMEDCT_US:405722004" + }, { + "val" : "SNOMEDCT_US:95695004" + }, { + "val" : "UMLS:C0035304" + }, { + "val" : "UMLS:C0521694" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001120", + "lbl" : "Abnormality of corneal 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"HP:0008005" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001155", + "lbl" : "Abnormality of the hand", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An abnormality affecting one or both hands.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormal hands", + "xrefs" : [ "https://orcid.org/0000-0002-5316-1399" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormality of the hand" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Hand anomalies" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Hand deformities" + } ], + "xrefs" : [ { + "val" : "MSH:D006226" + }, { + "val" : "SNOMEDCT_US:299033004" + }, { + "val" : "UMLS:C0018564" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0005858" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001161", + "lbl" : "Hand polydactyly", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A kind of polydactyly characterized by the presence of a supernumerary finger or fingers.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Extra finger", + "xrefs" : [ "https://orcid.org/0000-0001-6908-9849" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Finger polydactyly" + }, { + "pred" : "hasExactSynonym", + "val" : "Polydactyly of the hand" + }, { + "pred" : "hasExactSynonym", + "val" : "Supernumerary finger", + "xrefs" : [ "https://orcid.org/0000-0001-6908-9849" ] + } ], + "xrefs" : [ { + "val" : "MEDDRA:10036064" + }, { + "val" : "SNOMEDCT_US:81793007" + }, { + "val" : "UMLS:C0158733" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001166", + "lbl" : "Arachnodactyly", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Abnormally long and slender fingers (\"spider fingers\").", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Long slender fingers" + }, { + "pred" : "hasExactSynonym", + "val" : "Long, slender fingers" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Spider fingers" + } ], + "xrefs" : [ { + "val" : "MSH:D054119" + }, { + "val" : "SNOMEDCT_US:62250003" + }, { + "val" : "UMLS:C0003706" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0001505" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001167", + "lbl" : "Abnormal finger morphology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An anomaly of a finger.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormalities of the fingers" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormality of finger" + } ], + "xrefs" : [ { + "val" : "UMLS:C2674737" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0003035" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001176", + "lbl" : "Large hands", + "type" : "CLASS", + "meta" : { + "synonyms" : [ { + "pred" : 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fingers.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Hand has less than 5 fingers", + "xrefs" : [ "https://orcid.org/0000-0002-6548-5200" ] + } ], + "xrefs" : [ { + "val" : "SNOMEDCT_US:71358006" + }, { + "val" : "UMLS:C0728895" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001197", + "lbl" : "Abnormality of prenatal development or birth", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An abnormality of the fetus or the birth of the fetus, excluding structural abnormalities.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "comments" : [ "Because of the close link between prenatal developmental abnormalities and abnormalities of the birth process, a single term is chosen to subsume both classes of abnormality." ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", 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For younger children, consider the term Global developmental delay (HP:0001263)." ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Intellectual disability" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Mental deficiency" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Mental retardation" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Mental retardation, nonspecific" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Mental-retardation" + }, { + "pred" : "hasExactSynonym", + "val" : "Nonprogressive intellectual disability" + }, { + "pred" : "hasExactSynonym", + "val" : "Nonprogressive mental retardation" + }, { + "pred" : "hasRelatedSynonym", + "val" : 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in which there is increased muscle tone so that arms or legs, for example, are stiff and difficult to move.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "comments" : [ "Spasticity is a term that is often used interchangeably with hypertonia. Spasticity, however, is a particular type of hypertonia in which the muscles' spasms are increased by movement. In this type, patients usually have exaggerated reflex responses." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Hypertonicity" + }, { + "pred" : "hasExactSynonym", + "val" : "Increased muscle tone" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasNarrowSynonym", + "val" : "Spasticity and rigidity of muscles", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432", "https://orcid.org/0000-0002-6548-5200" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "Muscle hypertonia" + } ], + "xrefs" : [ { + "val" : "MSH:D009122" + }, { + "val" : "SNOMEDCT_US:41581000" + }, { + "val" : "SNOMEDCT_US:56731001" + }, { + "val" : "UMLS:C0026826" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0002388" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001284", + "lbl" : "Areflexia", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Absence of neurologic reflexes such as the knee-jerk reaction.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "comments" : [ "The strectch reflexes (also called deep tendon relfexes) include the knee-jerk reflex (patellar reflex, the biceps reflex, the triceps reflex, and the ankle jerk reflex or Achilles tendon reflex)." ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasBroadSynonym", + "val" : "Absent reflexes" + }, { + "pred" : "hasExactSynonym", + "val" : "Absent deep tendon reflexes" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Absent tendon reflexes" + }, { + "pred" : "hasExactSynonym", + "val" : "Deep tendon reflexes absent" + }, { + "pred" : "hasExactSynonym", + "val" : "Loss of deep tendon reflexes" + } ], + "xrefs" : [ { + "val" : "MSH:D012021" + }, { + "val" : "SNOMEDCT_US:349006" + }, { + "val" : "SNOMEDCT_US:37280007" + }, { + "val" : "UMLS:C0234146" + }, { + "val" : "UMLS:C0241772" + }, { + "val" : "UMLS:C0278124" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0001314" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001315", + "lbl" : "Reduced tendon reflexes", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Diminution of tendon reflexes, which is an invariable sign of peripheral nerve disease.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199", "PMID:20941667" ] + }, + "comments" : [ "The deep tendon reflex is a monosynaptic reflex arc with sensory and motor nerve components, but the arc is much more vulnerable to sensory nerve damage. Ankle plantar flexion is retained in all but the most severe peripheral neuropathies, and thus loss of the Achilles tendon reflex in an objective indication of a substantial sensory nerve defect." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Absent or decreased deep tendon reflexes" + }, { + "pred" : "hasExactSynonym", + "val" : "Decreased deep tendon reflexes" + }, { + "pred" : "hasExactSynonym", + "val" : "Decreased tendon reflexes" + }, { + "pred" : "hasExactSynonym", + "val" : "Decreased to absent deep tendon reflexes" + }, { + "pred" : "hasExactSynonym", + "val" : "Decreased/absent deep tendon reflexes" + }, { + "pred" : "hasExactSynonym", + "val" : "Depressed tendon reflexes" + }, { + "pred" : "hasExactSynonym", + "val" : "Diminished deep tendon reflexes" + }, { + "pred" : "hasExactSynonym", + "val" : "Diminished or absent deep tendon reflexes" + }, { + "pred" : "hasExactSynonym", + "val" : "Diminished or absent tendon reflexes" + }, { + "pred" : "hasExactSynonym", + "val" : "Hypoactive to absent deep tendon reflexes" + }, { + "pred" : "hasExactSynonym", + "val" : "Impaired tendon reflexes" + }, { + "pred" : "hasExactSynonym", + "val" : "Reduced/absent deep tendon reflexes" + }, { + "pred" : "hasExactSynonym", + "val" : "Weak or absent deep tendon reflexes" + } ], + "xrefs" : [ { + "val" : "UMLS:C1866934" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0001316" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001336", + "lbl" : "Myoclonus", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Very brief, involuntary random muscular contractions occurring at rest, in response to sensory stimuli, or accompanying voluntary movements.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199", "PMID:20589866" ] + }, + "comments" : [ "Myoclonus may be synchronous (several muscle contracting simultaneously), spreading (several muscles contracting in sequence), or asynchronous (several muscles contracting with varying and unpredictable relative timing). Myoclonus is characterized by sudden unidirectional movement due to muscle contraction (positive myoclonus) or due to sudden brief muscle relaxation (negative myoclonus). Electrophysiological tests are very helpful in determining whether myoclonus is cortical, subcortical or spinal." ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasBroadSynonym", + "val" : "Jerking" + }, { + "pred" : "hasExactSynonym", + "val" : "Myoclonic jerks" + }, { + "pred" : "hasRelatedSynonym", + "val" : "Involuntary jerking movements" + } ], + "xrefs" : [ { + "val" : "MSH:D009207" + }, { + "val" : "SNOMEDCT_US:127324008" + }, { + "val" : "SNOMEDCT_US:17450006" + }, { + "val" : "UMLS:C0027066" + }, { + "val" : "UMLS:C1854302" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0002535" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0007087" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001347", + "lbl" : "Hyperreflexia", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Hyperreflexia is the presence of hyperactive stretch reflexes of the muscles.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "comments" : [ "Reflexes are graded according to the following scale: 0=absent; 1=present but diminished; 2=normoactive; 3=exaggerated; and 4=clonus. Clonus is always abnormal, and a grade 3 reflex may be abnormal if it is asymmetric or if it was previously grade 2 or less." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Increased deep tendon reflexes" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Increased reflexes" + } ], + "xrefs" : [ { + "val" : "MSH:D012021" + }, { + "val" : "SNOMEDCT_US:86854008" + }, { + "val" : "UMLS:C0151889" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0001282" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0006820" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0007184" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0007318" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001362", + "lbl" : "Calvarial skull defect", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A localized defect in the bone of the skull resulting from abnormal embryological development. The defect is covered by normal skin. In some cases, skull x-rays have shown underlying lytic bone lesions which have closed before the age of one year.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Cranial defect", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Skull defect" + }, { + "pred" : "hasNarrowSynonym", + "val" : "Calvarial defect", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + } ], + "xrefs" : [ { + "val" : "UMLS:C4025787" + }, { + "val" : "UMLS:C4280595" + }, { + "val" : "UMLS:C4280596" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001367", + "lbl" : "Abnormal joint morphology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An abnormal structure or form of the joints, i.e., one or more of the articulations where two bones join.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormal shape of joints", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormality of the joints" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Anomaly of the joints" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasRelatedSynonym", + "val" : "Joint disease" + } ], + "xrefs" : [ { + "val" : "MSH:D007592" + }, { + "val" : "SNOMEDCT_US:399269003" + }, { + "val" : "UMLS:C0022408" + }, { + "val" : "UMLS:C0240083" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001369", + "lbl" : "Arthritis", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Inflammation of a joint.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Arthritis" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Joint inflammation", + "xrefs" : [ "https://orcid.org/0000-0002-6548-5200" ] + } ], + "xrefs" : [ { + "val" : "MSH:D001168" + }, { + "val" : "SNOMEDCT_US:3723001" + }, { + "val" : "UMLS:C0003864" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001371", + "lbl" : "Flexion contracture", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A flexion contracture is a bent (flexed) joint that cannot be straightened actively or passively. It is thus a chronic loss of joint motion due to structural changes in muscle, tendons, ligaments, or skin that prevents normal movement of joints.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Flexed joint that cannot be straightened" + }, { + "pred" : "hasExactSynonym", + "val" : "Flexion contractures" + }, { + "pred" : "hasExactSynonym", + "val" : "Flexion contractures of joints" + } ], + "xrefs" : [ { + "val" : "MSH:D003286" + }, { + "val" : "SNOMEDCT_US:203598005" + }, { + "val" : "SNOMEDCT_US:385522000" + }, { + "val" : "SNOMEDCT_US:55033002" + }, { + "val" : "SNOMEDCT_US:57048009" + }, { + "val" : "SNOMEDCT_US:7890003" + }, { + "val" : "SNOMEDCT_US:88565003" + }, { + "val" : "UMLS:C0009917" + }, { + "val" : "UMLS:C0009918" + }, { + "val" : "UMLS:C0333068" + }, { + "val" : "UMLS:C1850530" + } ], + "basicPropertyValues" : [ { + "pred" : 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"http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Restricted elbow extension" + } ], + "xrefs" : [ { + "val" : "UMLS:C1867103" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0005073" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001382", + "lbl" : "Joint hypermobility", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The ability of a joint to move beyond its normal range of motion.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Double-Jointed" + }, { + "pred" : "hasExactSynonym", + "val" : "Extensible joints" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Flexible joints" + }, { + "pred" : "hasExactSynonym", + "val" : "Hyperextensible 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"http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasBroadSynonym", + "val" : "Undergrowth" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Faltering weight", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Postnatal failure to thrive" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Weight faltering", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasRelatedSynonym", + "val" : "Poor weight gain" + } ], + "xrefs" : [ { + "val" : "SNOMEDCT_US:36440009" + }, { + "val" : "SNOMEDCT_US:432788009" + }, { + "val" : "UMLS:C0231246" + }, { + "val" : "UMLS:C2315100" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0001535" + }, { + 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"http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Growth delay" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Growth failure" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Growth retardation" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Poor growth" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Retarded growth" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasRelatedSynonym", + "val" : "Very poor growth", + "xrefs" : [ "https://orcid.org/0000-0002-5316-1399" ] + } ], + "xrefs" : [ { + "val" : "SNOMEDCT_US:276617005" + }, { + "val" : "SNOMEDCT_US:444896005" + }, { + "val" : "SNOMEDCT_US:59576002" + }, { + "val" : "UMLS:C0151686" + }, { + "val" : "UMLS:C0456070" + }, { + "val" : "UMLS:C0878787" + }, { + "val" : "UMLS:C1837385" + }, { + "val" : "UMLS:C3552463" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0001434" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0001512" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0001514" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0001517" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0001532" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0008847" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0008870" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0008886" + }, { 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The extremities as well as the hands and feet are unusually slim.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199", "https://orcid.org/0000-0002-6410-0882" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Dolichostenomelia" + }, { + "pred" : "hasExactSynonym", + "val" : "Marfanoid body habitus" + }, { + "pred" : "hasExactSynonym", + "val" : "Marfanoid habitus" + }, { + "pred" : "hasExactSynonym", + "val" : "Reduced upper-lower segment ratio" + } ], + "xrefs" : [ { + "val" : "MSH:D054119" + }, { + "val" : "SNOMEDCT_US:62250003" + }, { + "val" : "UMLS:C0003706" + }, { + "val" : "UMLS:C1836996" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0003511" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0008864" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001547", + "lbl" : "Abnormal rib cage morphology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A morphological anomaly of the rib cage.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormality of the rib cage" + } ], + "xrefs" : [ { + "val" : "UMLS:C4025763" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001548", + "lbl" : "Overgrowth", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Excessive postnatal growth which may comprise increased weight, increased length, and/or increased head circumference.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "General overgrowth" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#uk_spelling", + "pred" : "hasRelatedSynonym", + "val" : "Generalised overgrowth" + }, { + "pred" : "hasRelatedSynonym", + "val" : "Generalized overgrowth", + "xrefs" : [ "https://orcid.org/0000-0002-5316-1399" ] + } ], + "xrefs" : [ { + "val" : "UMLS:C1849265" + }, { + "val" : "UMLS:C1851731" + }, { + "val" : "UMLS:C3150281" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001557", + "lbl" : "Prenatal movement abnormality", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An abnormality of fetal movement.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "comments" : [ "Fetal movements generally become apparent during the second trimester of pregnancy around the 20th week but occasionally up to the 25th week. The initiation of perceptible fetal movements is referred to as 'quickening'." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Abnormal intrauterine movements" + } ], + "xrefs" : [ { + "val" : "UMLS:C1849510" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0007629" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001572", + "lbl" : "Macrodontia", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Increased size of the teeth, which can be defined as a mesiodistal tooth diameter (width) more than 2 SD above mean for age. Alternatively, an apparently increased maximum width of the tooth.", + "xrefs" : [ "https://orcid.org/0000-0002-9338-3017", "PMID:19125428" ] + }, + "comments" : [ "The standard reference has means and standard deviations by gender [Moyers et al, 1976]. Although it is easy to measure the width of teeth, and the definition is made with reference to the width of teeth, macrodontia actually means that the overall size of the tooth is increased." ], + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "Hyperplasia of tooth", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasBroadSynonym", + "val" : "Hypertrophy of tooth", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Increased size of tooth", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Increased width of tooth", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Large tooth" + }, { + "pred" : "hasExactSynonym", + "val" : "Megalodontia" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasRelatedSynonym", + "val" : "Tooth mass excess", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + } ], + "xrefs" : [ { + "val" : "SNOMEDCT_US:71485000" + }, { + "val" : "UMLS:C0266036" + }, { + "val" : "UMLS:C4280590" + }, { + "val" : "UMLS:C4280591" + }, { + "val" : "UMLS:C4280592" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001574", + "lbl" : "Abnormality of the integument", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An abnormality of the integument, which consists of the skin and the superficial fascia.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "comments" : [ "Abnormality of skin, hair, or nails." ], + "xrefs" : [ { + "val" : "UMLS:C4025761" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001626", + 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{ + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0003116" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001627", + "lbl" : "Abnormal heart morphology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any structural anomaly of the heart.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Abnormality of cardiac morphology" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormality of the heart" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormally shaped heart", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Cardiac abnormality" + }, { + "pred" : "hasExactSynonym", + "val" : "Cardiac anomalies" + }, { + "pred" : "hasExactSynonym", + "val" : "Cardiac 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responsible for the failure of the heart to pump blood at a rate that is commensurate with the needs of the tissues or a state in which abnormally elevated filling pressures are required for the heart to do so. Heart failure is frequently related to a defect in myocardial contraction.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#abbreviation", + "pred" : "hasExactSynonym", + "val" : "CHF" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Cardiac failure" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Cardiac failures", + "xrefs" : [ "https://orcid.org/0000-0002-5316-1399" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Cardiac insufficiency" + }, { + "pred" : "hasExactSynonym", + "val" : "Chronic heart failure" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Heart failure" + } ], + "xrefs" : [ { + "val" : "MSH:D006333" + }, { + "val" : "SNOMEDCT_US:42343007" + }, { + "val" : "SNOMEDCT_US:84114007" + }, { + "val" : "UMLS:C0018801" + }, { + "val" : "UMLS:C0018802" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0006686" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001640", + "lbl" : "Cardiomegaly", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Increased size of the heart, clinically defined as an increased transverse diameter of the cardiac silhouette that is greater than or equal to 50% of the transverse diameter of the chest (increased cardiothoracic ratio) on a posterior-anterior projection of a chest radiograph or a computed tomography.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199", "PMID:31194436" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Enlarged heart" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Increased heart size", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + } ], + "xrefs" : [ { + "val" : "MSH:D006332" + }, { + "val" : "SNOMEDCT_US:8186001" + }, { + "val" : "UMLS:C0018800" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001646", + "lbl" : "Abnormal aortic valve morphology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any abnormality of the aortic valve.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Abnormality of the aortic valve" + } ], + "xrefs" : [ { + "val" : "Fyler:1400" + }, { + "val" : "Fyler:1408" + }, { + "val" : "SNOMEDCT_US:448743001" + }, { + "val" : "UMLS:C3164445" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001647", + "lbl" : "Bicuspid aortic valve", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The presence of an aortic valve with two instead of the normal three cusps (flaps). Bicuspid aortic valvue is a malformation of a commissure (small space between the attachment of each cusp to the aortic wall) and the adjacent parts of the two corresponding cusps forming a raphe (the fused area of the two underdeveloped cusps turning into a malformed commissure between both cusps; the raphe is a fibrous ridge that extends from the commissure to the free edge of the two underdeveloped, conjoint cusps).", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199", "PMID:17467434", "PMID:24827036" ] + }, + "comments" : [ "A normal aortic valve is composed of three aortic-valve cusps, each semilunar in appearance. The leaflets are housed within a small dilatation of the proximal aorta associated with each cusp, called the sinuses of Valsalva or aortic sinuses, and their association with the respective coronary ostia identifies them: left, right, and non-coronary sinuses. Each cusp is attached to the wall of the aorta by the outward edges of its semicircular border, and the attachment point between each leaflet is called a commissure [PMID:24827036]." ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Aortic valve has two leaflets rather than three", + "xrefs" : [ "https://orcid.org/0000-0002-6548-5200" ] + } ], + "xrefs" : [ { + "val" : "MSH:C562388" + }, { + "val" : "SNOMEDCT_US:72352009" + }, { + "val" : "UMLS:C0149630" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001653", + "lbl" : "Mitral regurgitation", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An abnormality of the mitral valve characterized by insufficiency or incompetence of the mitral valve resulting in retrograde leaking of blood through the mitral valve upon ventricular contraction.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Mitral incompetence" + }, { + "pred" : "hasExactSynonym", + "val" : "Mitral insufficiency" + }, { + "pred" : "hasExactSynonym", + "val" : "Mitral valve insufficiency" + }, { + "pred" : "hasExactSynonym", + "val" : "Mitral valve regurgitation" + }, { + "pred" : "hasRelatedSynonym", + "val" : "Mitral regurgitation, mild" + } ], + "xrefs" : [ { + "val" : "Fyler:1151" + }, { + "val" : "MSH:D008944" + }, { + "val" : "SNOMEDCT_US:48724000" + }, { + "val" : "UMLS:C0026266" + }, { + "val" : "UMLS:C3551535" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001654", + "lbl" : "Abnormal heart valve morphology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any structural abnormality of a cardiac valve.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Abnormality of the heart valves" + }, { + "pred" : "hasExactSynonym", + "val" : "Valvular abnormality" + }, { + "pred" : "hasRelatedSynonym", + "val" : "Valvular heart disease" + } ], + "xrefs" : [ { + "val" : "MSH:D006349" + }, { + "val" : "SNOMEDCT_US:368009" + }, { + "val" : "UMLS:C0018824" + }, { + "val" : "UMLS:C0241654" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0001703" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001659", + "lbl" : "Aortic regurgitation", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An insufficiency of the aortic valve, leading to regurgitation (backward flow) of blood from the aorta into the left ventricle.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Aortic insufficiency" + }, { + "pred" : "hasExactSynonym", + "val" : "Aortic valve regurgitation" + } ], + "xrefs" : [ { + "val" : "MSH:D001022" + }, { + "val" : "SNOMEDCT_US:60234000" + }, { + "val" : "UMLS:C0003504" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001679", + "lbl" : "Abnormal aortic morphology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An abnormality of the aorta.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199", "PMID:24910511" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Abnormal aorta morphology", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Abnormality of the aorta" + } ], + "xrefs" : [ { + "val" : "Fyler:1453" + }, { + "val" : "UMLS:C4025756" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0030963" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001702", + "lbl" : "Abnormal tricuspid valve morphology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any structural anomaly of the tricuspid valve.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Abnormality of the tricuspid valve" + } ], + "xrefs" : [ { + "val" : "EPCC:06.01.00" + }, { + "val" : "UMLS:C4025753" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0031440" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001704", + "lbl" : "Tricuspid valve prolapse", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "One or more of the leaflets (cusps) of the tricuspid valve bulges back into the right atrium upon contraction of the right ventricle.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "xrefs" : [ { + "val" : "Fyler:1733" + }, { + "val" : "MSH:D014263" + }, { + "val" : "SNOMEDCT_US:253383003" + }, { + "val" : "UMLS:C0040962" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001760", + "lbl" : "Abnormal foot morphology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An abnormality of the skeleton of foot.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "comments" : [ "A disorder of the foot that can either be congenital or acquired. Such deformities can include hammer toe, club foot deformity, flat feet, pes cavus, congenital vertical talus (rocker bottom foot), and many others." ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormal feet structure" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormality of the feet" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormality of the foot" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Foot deformities" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Foot deformity" + } ], + "xrefs" : [ { + "val" : "MSH:D005530" + }, { + "val" : "SNOMEDCT_US:229844004" + }, { + "val" : "UMLS:C0016506" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0010216" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0010611" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001761", + "lbl" : "Pes cavus", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An increase in height of the medial longitudinal arch of the foot that does not flatten on weight bearing (i.e., a distinctly hollow form of the sole of the foot when it is bearing weight).", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199", "PMID:19125433" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Cavus foot" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "High-arched foot", + "xrefs" : [ "https://orcid.org/0000-0002-6548-5200" ] + } ], + "xrefs" : [ { + "val" : "MEDDRA:10034743" + }, { + "val" : "SNOMEDCT_US:205091006" + }, { + "val" : "UMLS:C0728829" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001763", + "lbl" : "Pes planus", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A foot where the longitudinal arch of the foot is in contact with the ground or floor when the individual is standing; or, in a patient lying supine, a foot where the arch is in contact with the surface of a flat board pressed against the sole of the foot by the examiner with a pressure similar to that expected from weight bearing; or, the height of the arch is reduced.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199", "PMID:19125433" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Flat feet" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Flat foot" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasRelatedSynonym", + "val" : "Dropped arches" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasRelatedSynonym", + "val" : "Fallen arches" + } ], + "xrefs" : [ { + "val" : "MSH:D005413" + }, { + "val" : "SNOMEDCT_US:203534009" + }, { + "val" : "SNOMEDCT_US:53226007" + }, { + "val" : "UMLS:C0016202" + }, { + "val" : "UMLS:C0264133" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001765", + "lbl" : "Hammertoe", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Hyperextension of the metatarsal-phalangeal joint with hyperflexion of the proximal interphalangeal (PIP) joint.", + "xrefs" : [ "PMID:19125433" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Hammer toe" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Hammertoe" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Hammertoes" + } ], + "xrefs" : [ { + "val" : "MSH:D037801" + }, { + "val" : "SNOMEDCT_US:122481008" + }, { + "val" : "UMLS:C1136179" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001773", + "lbl" : "Short foot", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A measured foot length that is more than 2 SD below the mean for a newborn of 27 - 41 weeks gestation, or foot that is less than the 3rd centile for individuals from birth to 16 years of age (objective). Alternatively, a foot that appears disproportionately short (subjective).", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199", "PMID:19125433" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Hypoplastic feet" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Short feet" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Short foot" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Small feet" + } ], + "xrefs" : [ { + "val" : "UMLS:C1848673" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0001764" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0001766" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0001778" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0008135" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001780", + "lbl" : "Abnormal toe morphology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An anomaly of a toe.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormalities of the toes" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormality of toe" + } ], + "xrefs" : [ { + "val" : "UMLS:C2674738" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001786", + "lbl" : "Narrow foot", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A foot for which the measured width is below the 5th centile for age; or, a foot that appears disproportionately narrow for its length.", + "xrefs" : [ "PMID:19125433" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Narrow foot" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Slender feet" + } ], + "xrefs" : [ { + "val" : "SNOMEDCT_US:299464006" + }, { + "val" : "UMLS:C0576227" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001824", + "lbl" : "Weight loss", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Reduction of total body weight.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Loss of weight" + } ], + "xrefs" : [ { + "val" : "MSH:D015431" + }, { + "val" : "SNOMEDCT_US:161832001" + }, { + "val" : "SNOMEDCT_US:262285001" + }, { + "val" : "SNOMEDCT_US:89362005" + }, { + "val" : "UMLS:C1262477" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001829", + "lbl" : "Foot polydactyly", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A kind of polydactyly characterized by the presence of a supernumerary toe or toes.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Duplication of bones of the toes" + }, { + "pred" : "hasExactSynonym", + "val" : "Polydactyly of feet" + }, { + "pred" : "hasExactSynonym", + "val" : "Polydactyly of the foot" + } ], + "xrefs" : [ { + "val" : "SNOMEDCT_US:62218008" + }, { + "val" : "UMLS:C0158734" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0009135" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001831", + "lbl" : "Short toe", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A toe that appears disproportionately short compared to the foot.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "comments" : [ "This finding must be distinguished from digits that are of increased girth but of normal length and that of a long mid- and hind foot with normal digit lengths. The affected digits should be specified as described in the introductory comments. Note that we designate brachydactyly as a synonym, but this use of the term is distinct from the use of the same word in Bell's classification of brachdactyly." ], + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Brachydactyly of the foot" + }, { + "pred" : "hasExactSynonym", + "val" : "Hypoplasia of the toe" + }, { + "pred" : "hasExactSynonym", + "val" : "Hypoplastic toes" + }, { + "pred" : "hasExactSynonym", + "val" : "Short foot phalanges" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Short toe" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Short toes" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Stubby toes", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + } ], + "xrefs" : [ { + "val" : "UMLS:C1836195" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0001767" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0001781" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0001855" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0004701" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0005889" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0008099" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001832", + "lbl" : "Abnormal metatarsal morphology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Abnormalities of the metatarsal bones (i.e. of five tubular bones located between the tarsal bones of the hind- and mid-foot and the phalanges of the toes).", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormality of the long bone of foot", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + } ], + "xrefs" : [ { + "val" : "UMLS:C4025745" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001833", + "lbl" : "Long foot", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Increased back to front length of the foot.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Disproportionately large feet" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Long foot" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "large feet" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "long feet" + } ], + "xrefs" : [ { + "val" : "SNOMEDCT_US:299462005" + }, { + "val" : "UMLS:C0576225" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0008136" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0008143" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001840", + "lbl" : "Metatarsus adductus", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The metatarsals are deviated medially (tibially), that is, the bones in the front half of the foot bend or turn in toward the body.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199", "PMID:19125433" ] + }, + "comments" : [ "Metatarsus varus (adductus) is one of the most common foot deformities, that is defined as a transverse plane deformity in Lisfranc's (tarsometatarsal) joints in which the metatarsals are deviated medially. The relationship between talus and calcaneus is normal. On inspection the toes angle abruptly towards the midline, creating a C-shaped lateral foot border with a prominent styloid process of the 5th metatarsal. The result is that the forefoot is twisted inwards relative to the heel, so that the sole faces the midline." ], + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Forefoot varus" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Front half of foot turns inward", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432", "https://orcid.org/0000-0002-6548-5200" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Metatarsus adductovarsus" + }, { + "pred" : "hasExactSynonym", + "val" : "Metatarsus varus" + }, { + "pred" : "hasRelatedSynonym", + "val" : "Intoe" + } ], + "xrefs" : [ { + "val" : "MSH:D000070592" + }, { + "val" : "SNOMEDCT_US:77599005" + }, { + "val" : "UMLS:C0231791" + }, { + "val" : "UMLS:C4082169" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0001768" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0010217" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001849", + "lbl" : "Foot oligodactyly", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A developmental defect resulting in the presence of fewer than the normal number of toes.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Missing toes" + }, { + "pred" : "hasExactSynonym", + "val" : "Oligodactyly of feet" + } ], + "xrefs" : [ { + "val" : "SNOMEDCT_US:249820005" + }, { + "val" : "UMLS:C0426934" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0001777" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001850", + "lbl" : "Abnormality of the tarsal bones", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An abnormality of the tarsus are the cluster of seven bones in the foot between the tibia and fibula and the metatarsus, including the calcaneus (heel) bone and the talus (ankle) bone.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormal ankle bones", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Abnormal tarsals" + } ], + "xrefs" : [ { + "val" : "UMLS:C1862136" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001883", + "lbl" : "Talipes", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A deformity of foot and ankle that has different subtypes that are talipes equinovarus, talipes equinovalgus, talipes calcaneovarus and talipes calcaneovalgus.", + "xrefs" : [ "https://orcid.org/0009-0006-4530-3154" ] + }, + "comments" : [ "Talipes means (a deformity of) foot and ankle. There are four types of talipes.\n1) Talipes equinovarus - the foot is pointing inwards and down (the most common form)\n2) Talipes equinovalgus - where the foot points outwards and down\n3) Talipes calcaneovarus - where the foot points inwards and up\n4) Talipes calcaneovalgus - where the foot points inwards and down." ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "Talipes foot deformities", + "xrefs" : [ "https://orcid.org/0000-0002-5316-1399" ] + } ], + "xrefs" : [ { + "val" : "MSH:D000070558" + }, { + "val" : "SNOMEDCT_US:398309008" + }, { + "val" : "UMLS:C1301937" + }, { + "val" : "UMLS:C3552713" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001961", + "lbl" : "Hypoplastic heart", + "type" : "CLASS", + "meta" : { + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Small heart", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Underdeveloped heart", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + } ], + "xrefs" : [ { + "val" : "UMLS:C3151525" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001964", + "lbl" : "Aplasia/Hypoplasia of metatarsal bones", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Absence or underdevelopment of the metatarsal bones.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Absent or hypoplastic metatarsal" + }, { + "pred" : "hasExactSynonym", + "val" : "Absent/hypoplastic metacarpals" + }, { + "pred" : "hasExactSynonym", + "val" : "Absent/hypoplastic metatarsals" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Absent/small long bone of foot", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Absent/underdeveloped long bone of foot", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Aplastic/hypoplastic metatarsals" + } ], + "xrefs" : [ { + "val" : "UMLS:C1860182" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001991", + "lbl" : "Aplasia/Hypoplasia of toe", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Absence or hypoplasia of toes.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Absent/small toe", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Absent/underdeveloped toe", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Aplastic/hypoplastic toe phalanges" + }, { + "pred" : "hasRelatedSynonym", + "val" : "Absent/hypoplastic toes", + "xrefs" : [ "https://orcid.org/0000-0002-5316-1399" ] + } ], + "xrefs" : [ { + "val" : "UMLS:C3551148" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001999", + "lbl" : "Abnormal facial shape", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An abnormal morphology (form) of the face or its components.", + "xrefs" : [ "https://orcid.org/0000-0002-9602-2321" ] + }, + "comments" : [ "This term now covers many of the historical inexact descriptions such as Bird-like facies that probably should be avoided in modern genetics. This portion of the Ontology should be revised." ], + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasBroadSynonym", + "val" : "Deformity of face", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasBroadSynonym", + "val" : "Malformation of face", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormal facial shape" + }, { + "pred" : "hasExactSynonym", + "val" : "Abnormal morphology of the face", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Distinctive facies" + }, { + "pred" : "hasExactSynonym", + "val" : "Dysmorphic facial features" + }, { + "pred" : "hasExactSynonym", + "val" : "Dysmorphic facies", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Facial dysmorphism", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Unusual facial appearance", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Unusual facies" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasRelatedSynonym", + "val" : "Distortion of face", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasRelatedSynonym", + "val" : "Funny looking face", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + } ], + "xrefs" : [ { + "val" : "SNOMEDCT_US:248200007" + }, { + "val" : "SNOMEDCT_US:32003007" + }, { + "val" : "SNOMEDCT_US:398206004" + }, { + "val" : "SNOMEDCT_US:398302004" + }, { + "val" : "UMLS:C0266617" + }, { + "val" : "UMLS:C0424503" + }, { + "val" : "UMLS:C1385263" + }, { + "val" : "UMLS:C4072832" + }, { + "val" : "UMLS:C4072833" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0002004" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0002260" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0004643" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0004649" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0004652" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0004655" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0004675" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0005124" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0002011", + "lbl" : "Morphological central nervous system abnormality", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A structural abnormality of the central nervous system.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Abnormality of the central nervous system" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#abbreviation", + "pred" : "hasExactSynonym", + "val" : "Morphological abnormality of the CNS" + }, { + "pred" : "hasExactSynonym", + "val" : "Morphological abnormality of the central nervous system" + }, { + "pred" : "hasRelatedSynonym", + "val" : "Central nervous system disease" + } ], + "xrefs" : [ { + "val" : "MSH:D002493" + }, { + "val" : "SNOMEDCT_US:23853001" + }, { + "val" : "UMLS:C0007682" + }, { + "val" : "UMLS:C4021765" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0002405" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0002413" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0002481" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0007319" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0002020", + "lbl" : "Gastroesophageal reflux", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A condition in which the stomach contents leak backwards from the stomach into the esophagus through the lower esophageal sphincter.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Acid reflux" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Acid reflux disease" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#abbreviation", + "pred" : "hasExactSynonym", + "val" : "GERD", + "xrefs" : [ "https://orcid.org/0000-0002-5316-1399" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Gastro-esophageal reflux" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#uk_spelling", + "pred" : "hasExactSynonym", + "val" : "Gastro-oesophageal reflux" + }, { + "pred" : "hasExactSynonym", + "val" : "Gastroesophageal reflux disease" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Heartburn", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + } ], + "xrefs" : [ { + "val" : "MSH:D005764" + }, { + "val" : "MSH:D006356" + }, { + "val" : "SNOMEDCT_US:16331000" + }, { + "val" : "SNOMEDCT_US:235595009" + }, { 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In this subhierarchy, we therefore use aneurysm as the primary label and list dilatation as a broad synonym." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Aortic dilatation" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Bulge in wall of large artery that carries blood away from heart", + "xrefs" : [ "https://orcid.org/0000-0002-6548-5200" ] + } ], + "xrefs" : [ { + "val" : "Fyler:2301" + }, { + "val" : "Fyler:2708" + }, { + "val" : "MSH:D001014" + }, { + "val" : "SNOMEDCT_US:67362008" + }, { + "val" : "UMLS:C0003486" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0001724" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0004960", + "lbl" : "Absent pulmonary artery", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A congenital defect with aplasia (absence) of one of the right or left pulmonary artery.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199", "PMID:17192541" ] + }, + "comments" : [ "This is a rare feature that has been observed in recessive lethal osteogenesis imperfecta with mutation in CRTAP." ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Absent lung artery", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Missing pulmonary artery", + "xrefs" : [ "https://orcid.org/0000-0001-6908-9849" ] + } ], + "xrefs" : [ { + "val" : "SNOMEDCT_US:86252004" + }, { + "val" : "UMLS:C0265905" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0004962", + "lbl" : "Thoracic aorta calcification", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An accumulation of calcium and phosphate in arteries with mineral deposits in the intimal or medial layer of the vessel wall in the thoracic aorta.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "xrefs" : [ { + "val" : "UMLS:C1969292" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0004963", + "lbl" : "Calcification of the aorta", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Calcification, that is, pathological deposition of calcium salts in the aorta.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "comments" : [ "Note that the phrase \"aortic calcification\" is mainly used to describe calcification of the aortic valve rather than of the aorta itself." ], + "xrefs" : [ { + "val" : "UMLS:C1096249" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0004970", + "lbl" : "Ascending tubular aorta aneurysm", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An abnormal localized widening (dilatation) of the tubular part of the ascending aorta." + }, + "comments" : [ "Aneurysm is considered a severe form of dilatation." ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "Ascending aorta dilation" + }, { + "pred" : "hasExactSynonym", + "val" : "Aneurysm of the ascending tubular aorta" + }, { + "pred" : "hasExactSynonym", + "val" : "Ascending aortic aneurysm" + }, { + "pred" : "hasExactSynonym", + "val" : "Ascending aortic dilation" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Bulging of wall of large artery located above heart", + "xrefs" : [ "https://orcid.org/0000-0002-6548-5200" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Dilatation of ascending aorta" + } ], + "xrefs" : [ { + "val" : "Fyler:2310" + }, { + "val" : "Fyler:2701" + }, { + "val" : "SNOMEDCT_US:253645007" + }, { + "val" : "UMLS:C0345049" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0005111" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0005128" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0004971", + "lbl" : "Pulmonary artery hypoplasia", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Underdevelopment of the pulmonary artery.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Underdeveloped lung artery", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Underdeveloped pulmonary artery", + "xrefs" : [ "https://orcid.org/0000-0001-6908-9849" ] + } ], + "xrefs" : [ { + "val" : "Fyler:2966" + }, { + "val" : "SNOMEDCT_US:54682008" + }, { + "val" : "UMLS:C0265910" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0005086", + "lbl" : "Knee osteoarthritis", + "type" : "CLASS", + "meta" : { + "xrefs" : [ { + "val" : "MSH:D020370" + }, { + "val" : "SNOMEDCT_US:239873007" + }, { + "val" : "UMLS:C0409959" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0005136", + "lbl" : "Mitral annular calcification", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Mitral annular calcification (MAC) results from progressive calcium deposition along and beneath the mitral valve annulus.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199", "PMID:23587525" ] + }, + "comments" : [ "MAC is a common degenerative process involving the fibrous annulus of the mitral valve, and is generally an incidental finding associated with aging. This term applies if MAC occurs at a substantially younger age than usual." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Premature calcification of mitral annulus" + } ], + "xrefs" : [ { + "val" : "UMLS:C1835130" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0005146", + "lbl" : "Cardiac valve calcification", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Abnormal calcification of a cardiac valve.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Calcifications of the cardiac valves" + } ], + "xrefs" : [ { + "val" : "UMLS:C1856483" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0005180", + "lbl" : "Tricuspid regurgitation", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Failure of the tricuspid valve to close sufficiently upon contraction of the right ventricle, causing blood to regurgitate (flow backward) into the right atrium.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "comments" : [ "This term should not be applied to Ebstein's anomaly of the tricuspid valve (see HP:0010316)." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Tricuspid insufficiency" + }, { + "pred" : "hasExactSynonym", + "val" : "Tricuspid valve regurgitation", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + } ], + "xrefs" : [ { + "val" : "Fyler:1161" + }, { + "val" : "MSH:D014262" + }, { + "val" : "SNOMEDCT_US:111287006" + }, { + "val" : "UMLS:C0040961" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0004753" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0005199", + "lbl" : "Aplasia of the abdominal wall musculature", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Absence of the abdominal musculature.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Absent abdominal musculature" + } ], + "xrefs" : [ { + "val" : "UMLS:C3149223" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0005257", + "lbl" : "Thoracic hypoplasia", + "type" : "CLASS", + "meta" : { + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Small chest" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Small thorax" + } ], + "xrefs" : [ { + "val" : "UMLS:C1837482" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0001590" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0005262", + "lbl" : "Abnormality of the synovia", + "type" : "CLASS", + "meta" : { + "xrefs" : [ { + "val" : "UMLS:C4025225" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2008-03-26T04:27:00Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0005263", + "lbl" : "Gastritis", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The presence of inflammation of the gastric mucous membrane.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Stomach inflammation", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + } ], + "xrefs" : [ { + "val" : "MEDDRA:10017853" + }, { + "val" : "MSH:D005756" + }, { + "val" : "SNOMEDCT_US:4556007" + }, { + "val" : "UMLS:C0017152" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2008-03-26T04:32:00Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0005311", + "lbl" : "Agenesis of pulmonary vessels", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A developmental defect characterized by the lack of formation of the pulmonary blood vessels." + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Absent lung vessels", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + } ], + "xrefs" : [ { + "val" : "UMLS:C1970630" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0005320", + "lbl" : "Lack of facial subcutaneous fat", + "type" : "CLASS", + "meta" : { + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Lack of facial fat below the skin", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + } ], + "xrefs" : [ { + "val" : "UMLS:C3277426" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0005450", + "lbl" : "Calvarial osteosclerosis", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An increase in bone density affecting the calvaria (roof of the skull).", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "xrefs" : [ { + "val" : "UMLS:C1855657" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0005464", + "lbl" : "Craniofacial osteosclerosis", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Abnormally increased density of craniofacial bone tissue.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "Cranial sclerosis" + } ], + "xrefs" : [ { + "val" : "UMLS:C1845805" + }, { + "val" : "UMLS:C4025193" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0005474", + "lbl" : "Decreased calvarial ossification", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Abnormal reduction in ossification of the calvaria (roof of the skull consisting of the frontal bone, parietal bones, temporal bones, and occipital bone).", + "xrefs" : [ "https://orcid.org/0000-0001-8612-1062", "https://orcid.org/0000-0002-0736-9199", "https://orcid.org/0000-0002-2972-5481", "PMID:31173381" ] + }, + "comments" : [ "A hypomineralised skull castes little or no acoustic shadow on prenatal ultrasound. This makes visualisation of the intracranial anatomy clearer than normal. In conditions associated with profound hypomineralisation, the skull shape can be distorted by pressure from the ultrasound transducer later in pregnancy." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Poorly ossified calvaria" + }, { + "pred" : "hasExactSynonym", + "val" : "Poorly ossified calvarium" + }, { + "pred" : "hasExactSynonym", + "val" : "Soft calvaria" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Soft skullcap", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Undermineralized calvarium" + }, { + "pred" : "hasRelatedSynonym", + "val" : "Skull soft on palpation" + } ], + "xrefs" : [ { + "val" : "UMLS:C1833762" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0002701" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0002702" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0005454" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0005471" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0005484", + "lbl" : "Secondary microcephaly", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Head circumference which falls below 2 standard deviations below the mean for age and gender because of insufficient head growth after birth.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasBroadSynonym", + "val" : "Development of small head that was not present at birth", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Acquired microcephaly", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Deceleration of head growth" + }, { + "pred" : "hasExactSynonym", + "val" : "Microcephaly, acquired" + }, { + "pred" : "hasExactSynonym", + "val" : "Microcephaly, postnatal" + }, { + "pred" : "hasExactSynonym", + "val" : "Postnatal deceleration of head circumference" + }, { + "pred" : "hasExactSynonym", + "val" : "Postnatal microcephaly" + } ], + "xrefs" : [ { + "val" : "UMLS:C1847514" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0000241" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0000259" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0005499" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0005557", + "lbl" : "Abnormal zygomatic arch morphology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An abnormality of the zygomatic arch, also known as the cheek bone.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "comments" : [ "The zygomatic arch is formed by the zygomatic process of temporal bone and the temporal process of the zygomatic bone." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Abnormality of the malar arch", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Abnormality of the zygomatic arch" + }, { + "pred" : "hasNarrowSynonym", + "val" : "Anomaly of the malar arch", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "Anomaly of the zygomatic arch", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "Deformity of the malar arch", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "Deformity of the zygomatic arch", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "Malformation of the malar arch", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "Malformation of the zygomatic arch", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + } ], + "xrefs" : [ { + "val" : "UMLS:C4025179" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2008-03-27T10:20:00Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0005623", + "lbl" : "Absent ossification of calvaria", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Absent ossification of the calvaria (vault of the skull).", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : 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"val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2008-04-04T11:44:00Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0100492" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0008369", + "lbl" : "Abnormal tarsal ossification", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An abnormality of the formation and mineralization of any of the tarsal bones, seven bones of the foot comprising the calcaneus, talus, cuboid, navicular, and the cuneiform bones.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Abnormal ossification of tarsal bones" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Hardening of ankle bones", + "xrefs" : [ "https://orcid.org/0000-0001-6908-9849" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasRelatedSynonym", + "val" : "Abnormal maturation of ankle bones", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + } ], + "xrefs" : [ { + "val" : "UMLS:C4021544" + }, { + "val" : "UMLS:C4025075" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2008-04-04T11:53:00Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0008371", + "lbl" : "Abnormal metatarsal ossification", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any abnormal process of ossification of the metatarsal bones, which normally are each ossified from two centers: one for the body, and one for the head (metatarsal II,III,IV, and V) and one for the body and one for the base (metatarsal I). The ossification process begins in the center of the body about the ninth week, and extends toward either extremity. The center for the base of the first metatarsal appears about the third year, and the centers for the heads of the other bones between the fifth and eighth years. They join the bodies between the eighteenth and twentieth years.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Abnormal ossification involving metatarsal bones" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasRelatedSynonym", + "val" : "Abnormal maturation of long bone of foot", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + } ], + "xrefs" : [ { + "val" : "UMLS:C4021543" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2008-04-04T11:59:00Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0008518", + "lbl" : "Aplasia/Hypoplasia involving the vertebral column", + "type" : "CLASS", + "meta" : { + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Absent/small backbone", + "xrefs" : [ "https://orcid.org/0000-0001-6908-9849" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Absent/small spine", + "xrefs" : [ "https://orcid.org/0000-0001-6908-9849" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Absent/small vertebral column", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Absent/underdeveloped backbone", + "xrefs" : [ "https://orcid.org/0000-0001-6908-9849" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Absent/underdeveloped spine", + "xrefs" : [ "https://orcid.org/0000-0001-6908-9849" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Absent/underdeveloped vertebral column", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + } ], + "xrefs" : [ { + "val" : "UMLS:C4024659" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2008-04-04T02:33:00Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0008873", + "lbl" : "Disproportionate short-limb short stature", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A type of disproportionate short stature characterized by a short limbs but an average-sized trunk.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "comments" : [ "A type of dwarfism (marked short stature with adult height below 147 cm) in which the limbs are disproportionatley affected. Note that brachymelia is a general term refering to shortening of the limbs. Micromelia refers to the shortening of entire limbs (in contrast to rhizomelia, mesomelia, and acromelia, which refer to shortening of the proximal, middle, or distal portions of the limbs)." ], + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Brachymelic dwarfism" + }, { + "pred" : "hasExactSynonym", + "val" : "Disproportionate short limb dwarfism" + }, { + "pred" : "hasExactSynonym", + "val" : "Dwarfism, short-limbed" + }, { + "pred" : "hasExactSynonym", + "val" : "Micromelic dwarfism" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Short limb dwarfism, disproportionate" + }, { + "pred" : "hasExactSynonym", + "val" : "Short stature, disproportionate short limb" + }, { + "pred" : "hasExactSynonym", + "val" : "Short stature, disproportionate short-limb" + }, { + "pred" : "hasExactSynonym", + "val" : "Short-limb dwarfism" + }, { + "synonymType" 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extremities.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Hypoplasia involving bones of the extremities" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Limb undergrowth" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Short limb" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Short limbs", + "xrefs" : [ "https://orcid.org/0000-0002-5316-1399" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "limb shortening" + } ], + "xrefs" : [ { + "val" : "UMLS:C0239399" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0009-0006-4530-3154" + }, { + "pred" : 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bones" + } ], + "xrefs" : [ { + "val" : "UMLS:C4021349" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0009-0006-4530-3154" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2009-05-26T02:28:25Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0009143" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0009998", + "lbl" : "Complete duplication of phalanx of hand", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A complete duplication affecting one or more of the phalanges of the hand. As opposed to a partial duplication were there is still a variable degree of fusion between the duplicated bones, a complete duplication leads to two separate bones appearing side to side (radio-ulnar axis) as seen on x-rays. A duplication leading to an accesory bone appearing in the proximo-distal axis on x-rays, is a different entity called a Pseudoepiphyses (see according terms) sometimes also referred to as Hyperphalangism.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Complete duplication of hand bones", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + } ], + "xrefs" : [ { + "val" : "UMLS:C4024121" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0009-0006-4530-3154" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2009-05-26T02:30:16Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0009999", + "lbl" : "Partial duplication of the phalanx of hand", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A partial duplication, depending on severity leading to a broad or bifid appearance, affecting one or more of the phalanges of the hand. As opposed to a complete duplication there is still a variable degree of fusion between the duplicated bones.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Partial duplication of hand bones", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + } ], + "xrefs" : [ { + "val" : "UMLS:C4024120" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0009-0006-4530-3154" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2009-05-26T02:30:35Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0010303", + "lbl" : "Abnormal spinal meningeal morphology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any abnormality of the spinal meninges, the system of membranes (dura mater, the arachnoid mater, and the pia mater) which envelops the spinal cord.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Abnormality of the spinal meninges" + } ], + "xrefs" : [ { + "val" : "UMLS:C4023914" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2009-07-12T01:10:09Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0010306", + "lbl" : "Short thorax", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Reduced inferior to superior extent of the thorax.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Shorter than typical length between neck and abdomen", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432", "https://orcid.org/0000-0002-6548-5200" ] + } ], + "xrefs" : [ { + "val" : "SNOMEDCT_US:249670005" + }, { + "val" : "UMLS:C0426789" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2009-07-12T02:13:42Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0010308", + "lbl" : "Asternia", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The congenital absence of the sternum.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199", "PMID:3424262" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Aplasia of the sternum" + }, { + "pred" : "hasExactSynonym", + "val" : "Breast bone aplasia" + } ], + "xrefs" : [ { + "val" : "UMLS:C4023912" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2009-07-12T02:21:46Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0010318", + "lbl" : "Aplasia/Hypoplasia of the abdominal wall musculature", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Absence or underdevelopment of the abdominal musculature.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Absent/small abdominal wall muscles", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Absent/underdeveloped abdominal wall muscles", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + } ], + "xrefs" : [ { + "val" : "UMLS:C4023909" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2009-07-14T11:51:46Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0010442", + "lbl" : "Polydactyly", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A congenital anomaly characterized by the presence of supernumerary fingers or toes.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "More than five fingers or toes on hands or feet", + "xrefs" : [ "https://orcid.org/0000-0002-6548-5200" ] + } ], + "xrefs" : [ { + "val" : "Fyler:4103" + }, { + "val" : "MSH:D017689" + }, { + "val" : "SNOMEDCT_US:367506006" + }, { + "val" : "UMLS:C0152427" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0009-0006-4530-3154" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2009-07-29T01:39:27Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0006034" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0006046" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0006123" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0009605" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0010500", + "lbl" : "Hyperextensibility of the knee", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The ability of the knee joint to extend beyond its normal range of motion (the lower leg is moved beyond a straight position with respect to the thigh).", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "xrefs" : [ { + "val" : "UMLS:C4023802" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2009-09-19T09:44:04Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0010510", + "lbl" : "Hypermobility of toe joints", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An ability of the toe joints to move beyond their normal range of motion.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "xrefs" : [ { + "val" : "UMLS:C4023798" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2009-09-19T10:15:12Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0010511", + "lbl" : "Long toe", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Toes that appear disproportionately long compared to the foot.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199", "PMID:19125433" ] + }, + "comments" : [ "This finding must be distinguished from digits that are thin but of normal length and that of a short mid and hind foot with normal digit lengths. The affected digits should be specified. If only a subset of the digits of a limb is lengthened, the affected digits should be specified." ], + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Increased length of toes" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Long toe" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Long toes" + } ], + "xrefs" : [ { + "val" : "UMLS:C3150613" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2009-09-19T10:40:43Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0010519", + "lbl" : "Increased fetal movement", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An abnormal increase in quantity or strength of fetal movements.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Fetal hyperkinesia" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#uk_spelling", + "pred" : "hasExactSynonym", + "val" : "Foetal hyperkinesia" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#uk_spelling", + "pred" : "hasExactSynonym", + "val" : "Increased foetal movement" + } ], + "xrefs" : [ { + "val" : "UMLS:C4021256" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2009-09-20T10:44:15Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0010539", + "lbl" : "Thin calvarium", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The presence of an abnormally thin calvarium.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasBroadSynonym", + "val" : "Thin skull bone", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Thin cranial bone", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + } ], + "xrefs" : [ { + "val" : "UMLS:C1856231" + }, { + "val" : "UMLS:C4280379" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2009-09-21T10:21:29Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0010647", + "lbl" : "Abnormal elasticity of skin", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any abnormal increase or reduction in skin elasticity.", + "xrefs" : [ "https://orcid.org/0000-0003-1773-4011" ] + }, + "xrefs" : [ { + "val" : "UMLS:C4023760" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0009-0006-4530-3154" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2010-02-23T11:42:34Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0010651", + "lbl" : "Abnormal meningeal morphology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An abnormality of the Meninges, including any abnormality of the Dura mater, the Arachnoid mater, and the Pia mater.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Abnormality of the meninges" + } ], + "xrefs" : [ { + "val" : "UMLS:C4023758" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2010-02-25T10:19:40Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0010660", + "lbl" : "Abnormal hand bone ossification", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An abnormality of the formation and mineralization of any bone of the skeleton of hand.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Abnormal ossification of hand bones" + }, { + "pred" : "hasExactSynonym", + "val" : "Abnormality of the mineralisation and ossification of bones of the hand" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasRelatedSynonym", + "val" : "Abnormal maturation of the hand bones", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + } ], + "xrefs" : [ { + "val" : "UMLS:C4021244" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0009-0006-4530-3154" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2010-02-25T05:18:19Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0005921" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0010668", + "lbl" : "Abnormal zygomatic bone morphology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An abnormality of the zygomatic bone.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Abnormal malar bone morphology" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormality of the cheekbone", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Abnormality of the zygomatic bone" + }, { + "pred" : "hasNarrowSynonym", + "val" : "Anomaly of the zygomatic bone", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasNarrowSynonym", + "val" : "Deformity of the cheekbone", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "Deformity of the zygomatic bone", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "Malformation of the zygomatic bone", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + } ], + "xrefs" : [ { + "val" : "UMLS:C4023749" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2010-02-26T08:13:11Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0012369" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0010669", + "lbl" : "Hypoplasia of the zygomatic bone", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Underdevelopment of the zygomatic bone. That is, a reduction in size of the zygomatic bone, including the zygomatic process of the temporal bone of the skull, which forms part of the zygomatic arch.", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463", "https://orcid.org/0000-0002-0736-9199", "PMID:19125436" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasBroadSynonym", + "val" : "Depressed cheekbone", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasBroadSynonym", + "val" : "Depressed zygomatic bone", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasBroadSynonym", + "val" : "Flattening of the zygomatic bone", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasBroadSynonym", + "val" : "Small cheekbone", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasBroadSynonym", + "val" : "Small malar bone", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasBroadSynonym", + "val" : "Small zygomatic bone", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Cheekbone underdevelopment", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Decreased size of cheekbone", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Decreased size of zygomatic bone", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Hypoplasia of cheekbone", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Underdevelopment of cheekbone", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Underdevelopment of zygomatic bone", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "Hypotrophic cheekbone", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "Hypotrophic zygomatic bone", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "Hypotrophy of the cheekbone", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "Hypotrophy of the zygomatic bone", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + } ], + "xrefs" : [ { + "val" : "UMLS:C4021242" + }, { + "val" : "UMLS:C4072879" + }, { + "val" : "UMLS:C4280368" + }, { + "val" : "UMLS:C4280369" + }, { + "val" : "UMLS:C4280370" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2010-02-26T08:14:04Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0010674", + "lbl" : "Abnormality of the curvature of the vertebral column", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The presence of an abnormal curvature of the vertebral column.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormal curve of the backbone", + "xrefs" : [ "https://orcid.org/0000-0001-6908-9849" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormal curve of the spine", + "xrefs" : [ "https://orcid.org/0000-0001-6908-9849" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Abnormal curving of the spine" + }, { + "pred" : "hasExactSynonym", + "val" : "Curvature of spine" + }, { + "pred" : "hasExactSynonym", + "val" : "Curved spine" + } ], + "xrefs" : [ { + "val" : "UMLS:C4023747" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "sandra1" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2010-02-27T06:28:19Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0010675", + "lbl" : "Abnormal foot bone ossification", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An abnormality of the formation and mineralization of any bone of the skeleton of foot.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Abnormality of the mineralisation and ossification of bones of the feet" + }, { + "pred" : "hasRelatedSynonym", + "val" : "Abnormal maturation of foot bones", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "Abnormal ossification involving bones of the feet" + } ], + "xrefs" : [ { + "val" : "UMLS:C4020768" + }, { + "val" : "UMLS:C4021241" + }, { + "val" : "UMLS:C4280367" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "sandra1" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2010-02-28T05:27:47Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0008370" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0009133" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0010743", + "lbl" : "Short metatarsal", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Diminished length of a metatarsal bone, with resultant proximal displacement of the associated toe.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199", "PMID:19125433" ] + }, + "comments" : [ "This is a subjective assessment and one generally compares the position of the MTP joint to that of the contralateral digit or the putatively shortened ray in proportion to the other rays. The affected digits should be specified." ], + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Hypoplasia of the metatarsal bones" + }, { + "pred" : "hasExactSynonym", + "val" : "Hypoplastic metatarsals" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Short long bone of foot", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Short metatarsal bone" + }, { + "pred" : "hasExactSynonym", + "val" : "Short metatarsals" + }, { + "pred" : "hasExactSynonym", + "val" : "Shortened metatarsals" + }, { + "pred" : "hasRelatedSynonym", + "val" : "Short metatarsal bones", + "xrefs" : [ "https://orcid.org/0000-0002-5316-1399" ] + } ], + "xrefs" : [ { + "val" : "UMLS:C1849020" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0009-0006-4530-3154" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2010-04-22T04:30:18Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0001779" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0001865" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0003092" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0004706" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0005754" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0010760", + "lbl" : "Absent toe", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Aplasia of a toe. That is, absence of all phalanges of a non-hallux digit of the foot and the associated soft tissues.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "comments" : [ "This descriptor does NOT require absence of the metatarsal. 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Osteosclerosis can be detected on radiological examination as an increased whiteness (density) of affected bones.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "comments" : [ "This term may be merged with Increased bone density in the future or made obsolete." ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Increased bone density" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Increased bone mineral density" + }, { + "pred" : "hasExactSynonym", + "val" : "Osteosclerosis" + }, { + "pred" : "hasExactSynonym", + "val" : "Osteosclerosis of bones" + } ], + "xrefs" : [ { + "val" : "MSH:D010026" + }, { + "val" : "SNOMEDCT_US:49347007" + }, { + "val" : "UMLS:C0029464" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0009-0006-4530-3154" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2011-02-13T11:57:32Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0002796" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0004350" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0005711" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0005741" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0010738" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0011002", + "lbl" : "Osteopetrosis", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Abnormally increased formation of dense trabecular bone tissue. Despite the increased density of bone tissue, osteopetrotic bones tend to be more fracture-prone than normal.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Harder, denser, fracture-prone bones", + "xrefs" : [ "https://orcid.org/0000-0002-6548-5200" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "Albers-Schoenberg disease" + }, { + "pred" : "hasRelatedSynonym", + "val" : "Albers-Schonberg disease" + }, { + "pred" : "hasRelatedSynonym", + "val" : "Albers-Schönberg disease" + }, { + "pred" : "hasRelatedSynonym", + "val" : "Marble bone disease" + } ], + "xrefs" : [ { + "val" : "MSH:D010022" + }, { + "val" : "SNOMEDCT_US:1926006" + }, { + "val" : "SNOMEDCT_US:367489004" + }, { + "val" : "UMLS:C0029454" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0009-0006-4530-3154" + }, { + 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gastrointestinal tract" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasRelatedSynonym", + "val" : "Digestive system disease" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasRelatedSynonym", + "val" : "Gastrointestinal disease" + } ], + "xrefs" : [ { + "val" : "MSH:D004066" + }, { + "val" : "MSH:D005767" + }, { + "val" : "SNOMEDCT_US:119292006" + }, { + "val" : "SNOMEDCT_US:25374005" + }, { + "val" : "SNOMEDCT_US:53619000" + }, { + "val" : "UMLS:C0012242" + }, { + "val" : "UMLS:C0017178" + }, { + "val" : "UMLS:C4023588" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2011-03-01T07:52:06Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0011025", + "lbl" : "Abnormal cardiovascular system physiology", + "type" : "CLASS", + 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"Abnormality of tooth part", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormality of tooth structure", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + } ], + "xrefs" : [ { + "val" : "UMLS:C4023557" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2011-03-10T01:44:04Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0011069", + "lbl" : "Supernumerary tooth", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The presence of one or more teeth additional to the normal number.", + "xrefs" : [ "https://orcid.org/0000-0002-9338-3017", "PMID:31468724" ] + }, + "comments" : [ "Age-related physiological sequential eruption should be taken into account during evaluation. The type and the location of the additional tooth/teeth should be added to the description. Supernumerary teeth are uncommon (in 0.21% of deciduous dentitions and in 0.9% of permanent dentitions), and often abnormal positioning of a normal number of teeth is wrongly classified as supernumerary teeth. Supernumerary teeth are most frequent in the upper maxilla, and typically, a single additional tooth is present. We discourage the use of distodens, distomolars (an extra fourth molar posterior to the third molar), paramolars (supernumerary tooth in the molar region) but rather to mention the presence of the supernumerary tooth mesial to or distal to a tooth from the normal series. Diagnosing a supernumerary tooth may require radiographic examination. 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That is, an abnormality of the skin resulting from the local accumulation of fluid, plasma proteins, and leukocytes.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Abnormal tendency to infections of the skin" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Inflammatory abnormality of the skin" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Skin inflammation" + }, { + "pred" : "hasRelatedSynonym", + "val" : "Dermatitis" + }, { + "pred" : "hasRelatedSynonym", + "val" : "Inflammatory skin disease" + } ], + "xrefs" : [ { + "val" : "MP:0004947" + }, { + "val" : "MSH:D003872" + }, { + "val" : "SNOMEDCT_US:703938007" + }, { + "val" : "UMLS:C0011603" + }, { + "val" : "UMLS:C3875321" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2011-06-12T10:06:04Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0002727" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0007423" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0011139", + "lbl" : "Gastric duplication", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Gastric duplication is a usually cystic malformation of gastrointestinal tract, usually attached to the greater curvature of the stomach and has no communication with the stomach.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "comments" : [ "Gastric duplication usually presents as gastric outlet obstruction. They are usually spherical in form, do not communicate with the stomach, and are generally localized at the greater curvature. In some cases they may exhibit adhesion to the pancreas and even communicate with aberrant pancreatic ducts. Gastric duplication is more frequent in females. It is generally either diagnosed in infancy because of symptoms of gastric outlet obstruction or is an incidental finding in adulthood." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Gastric duplication cyst" + } ], + "xrefs" : [ { + "val" : "UMLS:C4021201" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2011-06-25T08:57:09Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0011140", + "lbl" : "Gastrointestinal duplication", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A spherical hollow structure with a smooth muscle coat, lined by a mucous membrane, and attached to any part of the gastrointestinal tract, from the base of the tongue to the anus.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199", "PMID:21218094" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#abbreviation", + "pred" : "hasExactSynonym", + "val" : "GI duplication" + } ], + "xrefs" : [ { + "val" : "SNOMEDCT_US:33257003" + }, { + "val" : "UMLS:C0266019" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2011-06-25T09:02:50Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0011219", + "lbl" : "Short face", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Facial height (length) is more than two standard deviations below the mean (objective); or an apparent decrease in the height (length) of the face (subjective).", + "xrefs" : [ "PMID:19125436" ] + }, + "comments" : [ "Objective measurement of face height is made with sliding calipers from the nasion, just above the depth of the nasal root to the gnathion, the inferior border of the mandible, both in the midline. Note that short face is distinct from wide face." ], + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Decreased height of face", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Decreased length of face", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Decreased vertical dimension of face", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Short face" + }, { + "pred" : "hasExactSynonym", + "val" : "Short facies", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Vertical Facial Deficiency", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Vertical deficiency of face", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Vertical facial insufficiency", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Vertical hypoplasia of face", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Vertical insufficiency of face", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Vertical shortening of face", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + } ], + "xrefs" : [ { + "val" : "UMLS:C4023457" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : 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"2011-12-13T08:38:23Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0011297", + "lbl" : "Abnormal digit morphology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A morphological abnormality of a digit, i.e., of a finger or toe.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Abnormality of digit" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormality of fingers or toes" + }, { + "pred" : "hasExactSynonym", + "val" : "Digital anomalies" + } ], + "xrefs" : [ { + "val" : "UMLS:C3550704" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2012-02-11T07:16:22Z" + } ] + } + }, { 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ossification", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any anomaly in the formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199", "PMID:18157903" ] + }, + "comments" : [ "All bones are formed by the replacement by osteocytes of mesenchyme-derived connective tissue. Intramembranous ossification refers to the direct replacement of primitive mesenchyme with bone, and is responsible for bones such as the calvarium (e.g., frontals, parietals, interparietal) and the clavicula. In endochondral ossification, the mesenchyme differentiates into a cartilaginous intermediate, which serves as a template (anlange) that is subsequently removed and replaced by bone. Most bones are formed via endochondral ossification, including those at the base of the skull, the vertebral column, pectoral and pelvic regions and long bones of the extremities. A reduction in the amount of mineralized bone compared with that expected for a given developmental age. In clinicakl parlance, reduced ossification and delayed ossification are often used synonymously, but in principle a bone delayed ossification in a child can display normal ossification at a later developmental stage. The HPO will therefore treat poor, reduced, and decreased officiation as synonymous, and delayed ossification as a specific kind of reduced ossification." ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasRelatedSynonym", + "val" : "Abnormal bone maturation", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + } ], + "xrefs" : [ { + "val" : "MP:0008271" + }, { + "val" : "UMLS:C4023161" + }, { + "val" : "UMLS:C4280317" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2012-05-15T07:39:58Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0011863", + "lbl" : "Abnormal sternal ossification", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any anomaly in the formation of the bony substance of the sternum.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "comments" : [ "The sternum develops from two cartilaginous bars, situated one on either side of the median plane and connected with the cartilages of the upper nine ribs of its own side. During development, the two cartilaginous bars fuse with each other to form the cartilaginous sternum. This in turn is ossified from six centers: one in the manubrium, four in the body of the sternum, and one in the xiphoid process." ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormal maturation of breastbone", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Sternal ossification center abnormalities" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#uk_spelling", + "pred" : "hasExactSynonym", + "val" : "Sternal ossification centre abnormalities" + } ], + "xrefs" : [ { + "val" : "UMLS:C1860243" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2012-05-27T04:08:55Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0006624" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0011915", + "lbl" : "Cardiovascular calcification", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Abnormal calcification in the cardiovascular system.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "xrefs" : [ { + "val" : "UMLS:C4023128" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2012-06-05T10:35:58Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0011927", + "lbl" : "Short digit", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "One or more digit that appears disproportionately short compared to the hand/foot, whereby either the entire digit or a specific phalanx is shortened.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "comments" : [ "Note that the term brachydactyly is reserved for specific patterns of short digits, see HP:0001156." ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Short digit" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasRelatedSynonym", + "val" : "Very short digits", + "xrefs" : [ "https://orcid.org/0000-0002-5316-1399" ] + } ], + "xrefs" : [ { + "val" : "UMLS:C1860176" + }, { + "val" : "UMLS:C4023124" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2012-06-10T09:18:42Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0011947", + "lbl" : "Respiratory tract infection", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An infection of the upper or lower respiratory tract.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Respiratory infection" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Respiratory tract infection" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasRelatedSynonym", + "val" : "Respiratory infections", + "xrefs" : [ "https://orcid.org/0000-0002-5316-1399" ] + } ], + "xrefs" : [ { + "val" : "MSH:D012141" + }, { + "val" : "SNOMEDCT_US:275498002" + }, { + "val" : "UMLS:C0035243" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2012-06-21T08:26:36Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0012046", + "lbl" : "Areflexia of upper limbs", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Inability to elicit tendon reflexes in the upper limbs.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "xrefs" : [ { + "val" : "UMLS:C2674177" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2012-08-01T12:24:31Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0012165", + "lbl" : "Oligodactyly", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A developmental defect resulting in the presence of fewer than the normal number of digits.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "xrefs" : [ { + "val" : "UMLS:C3887496" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2013-02-16T10:44:40Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0012252", + "lbl" : "Abnormal respiratory system morphology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A structural anomaly of the respiratory system.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "xrefs" : [ { + "val" : "Fyler:4235" + }, { + "val" : "UMLS:C4022992" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2013-04-07T09:11:09Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0012368", + "lbl" : "Flat face", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Absence of concavity or convexity of the face when viewed in profile.", + "xrefs" : [ "PMID:19125436" ] + }, + "comments" : [ "A useful guide is to imagine that a line connecting the glabella to the anterior most part of the mandible touches the top of the philtrum where it meets the base of the columella. The glabella is the most prominent point on the frontal bone above the root of the nose. If the superior philtrum is anterior to this line the face is convex, if the superior philtrum is posterior to this line the face is concave." ], + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Flat face" + }, { + "pred" : "hasExactSynonym", + "val" : "Flat facial profile", + "xrefs" : [ "https://orcid.org/0000-0002-5316-1399" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Flat facial shape", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Flat facies", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + } ], + "xrefs" : [ { + "val" : "UMLS:C1853241" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2013-10-13T01:49:13Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0012372", + "lbl" : "Abnormal eye morphology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A structural anomaly of the globe of the eye, or bulbus oculi.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "comments" : [ "previously: Abnormal globe morphology" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormal eye structure" + }, { + "pred" : "hasExactSynonym", + "val" : "Abnormality of the globe" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormally shaped eye", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + } ], + "xrefs" : [ { + "val" : "Fyler:4863" + }, { + "val" : "UMLS:C4022925" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2013-10-13T03:44:43Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0000489" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0012374" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0012373", + "lbl" : "Abnormal eye physiology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A functional anomaly of the eye.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormal eye physiology" + } ], + "xrefs" : [ { + "val" : "UMLS:C4022924" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2013-10-13T03:45:37Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0012385", + "lbl" : "Camptodactyly", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The distal interphalangeal joint and/or the proximal interphalangeal joint of the fingers or toes cannot be extended to 180 degrees by either active or passive extension.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Permanent flexion of the finger or toe", + "xrefs" : [ "https://orcid.org/0000-0002-6548-5200" ] + } ], + "xrefs" : [ { + "val" : "SNOMEDCT_US:29271008" + }, { + "val" : "UMLS:C0685409" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6996-5279" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2013-10-20T08:08:19Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0012391", + "lbl" : "Hyporeflexia of upper limbs", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Reduced intensity of muscle tendon reflexes in the upper limbs. Reflexes are elicited by stretching the tendon of a muscle, e.g., by tapping.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "xrefs" : [ { + "val" : "UMLS:C1836835" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2013-11-07T07:42:49Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0012443", + "lbl" : "Abnormality of brain morphology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A structural abnormality of the brain, which has as its parts the forebrain, midbrain, and hindbrain.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormal shape of brain", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormality of the brain" + } ], + "xrefs" : [ { + "val" : "UMLS:C4021085" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2013-11-23T02:38:00Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0012444", + "lbl" : "Brain atrophy", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Partial or complete wasting (loss) of brain tissue that was once present.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Brain degeneration", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Brain wasting", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + } ], + "xrefs" : [ { + "val" : "SNOMEDCT_US:278849000" + }, { + "val" : "SNOMEDCT_US:418143002" + }, { + "val" : "SNOMEDCT_US:52522001" + }, { + "val" : "UMLS:C0154671" + }, { + "val" : "UMLS:C0235946" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2013-11-23T02:46:15Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0012486", + "lbl" : "Myelitis", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Inflammation of the spinal cord.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Inflammation of spinal cord", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + } ], + "xrefs" : [ { + "val" : "MSH:D009187" + }, { + "val" : "SNOMEDCT_US:41370002" + }, { + "val" : "UMLS:C0026975" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2013-11-29T08:10:12Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0012490", + "lbl" : "Panniculitis", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Inflammation of adipose tissue.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "comments" : [ "Panniculitis most commonly affects the skin and characterized by reddened subcutaneous nodules." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Inflammation of adipose tissue", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Inflammation of fat tissue", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + } ], + "xrefs" : [ { + "val" : "MSH:D015434" + }, { + "val" : "SNOMEDCT_US:22125009" + }, { + "val" : "UMLS:C0030326" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2013-11-29T09:28:11Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0012638", + "lbl" : "Abnormal nervous system physiology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A functional anomaly of the nervous system.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Abnormality of nervous system physiology" + } ], + "xrefs" : [ { + "val" : "UMLS:C4022811" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2014-01-19T08:02:46Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0012639", + "lbl" : "Abnormal nervous system morphology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A structural anomaly of the nervous system.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormal shape of nervous system", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Abnormality of nervous system morphology" + } ], + "xrefs" : [ { + "val" : "Fyler:4135" + }, { + "val" : "Fyler:4300" + }, { + "val" : "UMLS:C4022810" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2014-01-19T08:03:08Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0012647", + "lbl" : "Abnormal inflammatory response", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any anomaly of the inflammatory response, a response to injury or infection characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.", + "xrefs" : [ "https://orcid.org/0000-0001-9114-8737" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormal inflammatory response" + } ], + "xrefs" : [ { + "val" : "UMLS:C4022805" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2014-02-01T01:25:42Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0012648", + "lbl" : "Decreased inflammatory response", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An abnormal reduction in the inflammatory response to injury or infection.", + "xrefs" : [ "https://orcid.org/0000-0001-9114-8737" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Decreased inflammatory response" + } ], + "xrefs" : [ { + "val" : "UMLS:C4022804" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2014-02-01T01:29:24Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0012649", + "lbl" : "Increased inflammatory response", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A abnormal increase in the inflammatory response to injury or infection.", + "xrefs" : [ "https://orcid.org/0000-0001-9114-8737" ] + }, + "xrefs" : [ { + "val" : "UMLS:C4022803" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2014-02-01T01:29:58Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0012718", + "lbl" : "Morphological abnormality of the gastrointestinal tract", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Abnormal structure of the gastrointestinal tract.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormal shape of the digestive system", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#abbreviation", + "pred" : "hasExactSynonym", + "val" : "Morphological abnormality of the GI tract" + }, { + "pred" : "hasExactSynonym", + "val" : "Morphological anomaly of the digestive system" + } ], + "xrefs" : [ { + "val" : "UMLS:C4021073" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2014-03-23T01:09:02Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0012719", + "lbl" : "Functional abnormality of the gastrointestinal tract", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Abnormal functionality of the gastrointestinal tract.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#abbreviation", + "pred" : "hasExactSynonym", + "val" : "Functional abnormality of the GI tract" + }, { + "pred" : "hasExactSynonym", + "val" : "GI dysfunction", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + } ], + "xrefs" : [ { + "val" : "UMLS:C4022755" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2014-03-23T01:10:47Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0012727", + "lbl" : "Thoracic aortic aneurysm", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An abnormal localized widening (dilatation) of the thoracic aorta.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "comments" : [ "Aneurysm is considered a severe form of dilatation." ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "Dilatation of the thoracic aorta" + } ], + "xrefs" : [ { + "val" : "MSH:D017545" + }, { + "val" : "SNOMEDCT_US:433068007" + }, { + "val" : "UMLS:C0162872" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2014-03-23T02:22:20Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0012745", + "lbl" : "Short palpebral fissure", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Distance between the medial and lateral canthi is more than 2 SD below the mean for age (objective); or, apparently reduced length of the palpebral fissures.", + "xrefs" : [ "PMID:19125427" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Decreased height of palpebral fissure", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Short opening between the eyelids", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Short palpebral fissures", + "xrefs" : [ "https://orcid.org/0000-0002-5316-1399" ] + } ], + "xrefs" : [ { + "val" : "SNOMEDCT_US:246802000" + }, { + "val" : "UMLS:C0423112" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2014-03-23T05:27:40Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0012758", + "lbl" : "Neurodevelopmental delay", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Neurodevelopmental delay (NDD) refers to delays in the maturation of the brain and central nervous system; infants and young children with NDD may experience delays in the development of one or more skills including gross motor abilities, fine-motor coordination, language abilities and ability to solve increasingly complex problems.", + "xrefs" : [ "https://orcid.org/0000-0002-6670-9157", "PMID:31783983" ] + }, + "comments" : [ "Though the definitions of NDD vary broadly in the literature, all are used to signify a delay in one or more developmental domains compared to typical development." ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#abbreviation", + "pred" : "hasExactSynonym", + "val" : "NDD" + } ], + "xrefs" : [ { + "val" : "UMLS:C4022738" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2014-04-03T12:16:19Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0012759", + "lbl" : "Neurodevelopmental abnormality", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A deviation from normal of the neurological development of a child, which may include any or all of the aspects of the development of personal, social, gross or fine motor, and cognitive abilities.", + "xrefs" : [ "HPO_CONTRIBUTOR:KI_phemming" ] + }, + "comments" : [ "This term should be used to describe abnormalities with onset in the developmental period." ], + "xrefs" : [ { + "val" : "UMLS:C4022737" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2014-04-03T12:20:28Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0012772", + "lbl" : "Abnormal upper to lower segment ratio", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A deviation from normal of the relation between the upper and the lower segment of the body, where the lower segment is defined as the length between the top of pubic symphysis to floor, and the upper segment is defined as the top of head to top of pubic symphysis.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "xrefs" : [ { + "val" : "UMLS:C4022728" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2014-04-07T03:12:56Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0012773", + "lbl" : "Reduced upper to lower segment ratio", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Decreased ratio between the upper and the lower segment of the body, where the lower segment is defined as the length between the top of pubic symphysis to floor, and the upper segment is defined as the top of head to top of pubic symphysis. Consider the term Disproportionate tall stature (HP:0001519) if tall stature is also present.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "comments" : [ "A ratio of less than 0.86 (or according to other sources 0.89) is considered abnormally reduced." ], + "xrefs" : [ { + "val" : "UMLS:C1836996" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2014-04-07T03:14:28Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0012785", + "lbl" : "Flexion contracture of finger", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Chronic loss of joint motion in a finger due to structural changes in non-bony tissue.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "comments" : [ "Note that the term camptodactyly refers to a painless flexion contracture of the proximal interphalangeal (PIP) joint and not to a finger joint contracture in general." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Flexion deformity of finger" + } ], + "xrefs" : [ { + "val" : "UMLS:C1857304" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2014-04-20T04:09:34Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0012789", + "lbl" : "Hypoplasia of the calcaneus", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Underdevelopment of the heel bone.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Hypoplastic calcaneus" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Small heel bone", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Underdeveloped heel bone", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + } ], + "xrefs" : [ { + "val" : "UMLS:C3550873" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2014-04-22T09:58:48Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0012801", + "lbl" : "Narrow jaw", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Bigonial distance (lower facial width) more than 2 standard deviations below the mean (objective); or an apparently decreased width of the lower jaw (mandible) when viewed from the front (subjective).", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199", "PMID:19125436" ] + }, + "comments" : [ "The width of the jaw is measured from the right gonion to the left gonion using spreading calipers. The gonion is the point at the angle of the bony mandible where the ramus changes direction to become the body of the mandible. It faces inferiorly and medially and is best found by placing a finger over the outward facing angle and rolling the finger downwards and inwards." ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Narrow jaw" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Narrow lower face" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Narrow lower jaw" + }, { + "pred" : "hasExactSynonym", + "val" : "Narrow mandible" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasRelatedSynonym", + "val" : "Thin lower face", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasRelatedSynonym", + "val" : "Thin lower jaw", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + } ], + "xrefs" : [ { + "val" : "UMLS:C4021066" + }, { + "val" : "UMLS:C4280310" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6996-5279" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2014-05-25T02:37:13Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0020045", + "lbl" : "Esodeviation", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A manifest or latent ocular deviation in which one or both eyes tends to deviate nasally.", + "xrefs" : [ "https://orcid.org/0000-0003-0986-4123" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Convergent squint" + }, { + "pred" : "hasExactSynonym", + "val" : "Convergent strabismus" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/date", + "val" : "2017-12-20T17:20:06Z" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0020049", + "lbl" : "Exodeviation", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A manifest or latent ocular deviation in which one or both eyes tends to deviate temporally.", + "xrefs" : [ "https://orcid.org/0000-0003-0986-4123" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Divergent strabismus" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/date", + "val" : "2017-12-22T15:01:01Z" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025015", + "lbl" : "Abnormal vascular morphology", + "type" : "CLASS", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/date", + "val" : "2016-08-12T11:24:56Z" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025031", + "lbl" : "Abnormality of the digestive system", + "type" : "CLASS", + "meta" : { + "comments" : [ "Any anomaly of the digestive system, a collection of organs that is made up of the gastrointestinal tract and the liver, pancreas, and gallbladder. The gastrointestinal tract is a series of hollow organs joined in a long, twisting tube from the mouth to the anus, including the mouth, esophagus, stomach, small intestine, large intestine and anus." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/date", + "val" : "2016-08-27T13:44:32Z" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025032", + "lbl" : "Abnormality of digestive system physiology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A functional anomaly of the digestive system." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/date", + "val" : "2016-08-27T13:58:05Z" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025033", + "lbl" : "Abnormality of digestive system morphology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A structural anomaly of the digestive system." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/date", + "val" : "2016-08-27T13:58:23Z" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025270", + "lbl" : "Abnormal esophagus physiology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any physiological abnormality of the esophagus." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Abnormality of esophagus physiology" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#uk_spelling", + "pred" : "hasExactSynonym", + "val" : "Abnormality of oesophagus physiology" + }, { + "pred" : "hasExactSynonym", + "val" : "Functional abnormality of the esophagus" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#uk_spelling", + "pred" : "hasExactSynonym", + "val" : "Functional abnormality of the oesophagus" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/date", + "val" : "2016-12-18T13:39:06Z" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025323", + "lbl" : "Abnormal arterial physiology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An anomaly of arterial function." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/date", + "val" : "2017-02-03T12:08:38Z" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025586", + "lbl" : "Hypertropia", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A type of strabismus characterized by permanent upward deviation of the visual axis of one eye.", + "xrefs" : [ "https://orcid.org/0000-0003-0986-4123" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/date", + "val" : "2018-01-13T19:44:01Z" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025587", + "lbl" : "Hyperdeviation", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A type of strabismus in which the visual axis of one eye is higher than that of the other.", + "xrefs" : [ "https://orcid.org/0000-0003-0986-4123" ] + }, + "comments" : [ "Hyperphoria is a latent deviation where the eyes remain aligned under normal binocular vision. 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In primary inferior oblique muscle overaction, an upshoot of the adducting eye occurs when gaze is directed into the field of action of the inferior oblique muscle, producing a greater upward excursion of the adducted eye than of the abducted eye.", + "xrefs" : [ "https://orcid.org/0000-0003-0986-4123", "PMID:11545636" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/date", + "val" : "2018-01-13T21:25:58Z" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0030044", + "lbl" : "Flexion contracture of digit", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A bent (flexed) finger or toe joint that cannot be straightened actively or passively. It is thus a chronic loss of joint motion due to structural changes in muscle, tendons, ligaments, or skin that prevents normal movement of joints." + }, + "xrefs" : [ { + "val" : "UMLS:C1839864" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0030163", + "lbl" : "Abnormal vascular physiology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Abnormality of vascular function.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "xrefs" : [ { + "val" : "UMLS:C4022603" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0030236", + "lbl" : "Abnormality of muscle size", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Abnormalities of the overall muscle bulk based on clinical observation.", + "xrefs" : [ "https://orcid.org/0000-0001-9046-3540" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormality of muscle size" + } ], + "xrefs" : [ { + "val" : "UMLS:C4022563" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0030506", + "lbl" : "Yellow/white lesions of the retina", + "type" : "CLASS", + "meta" : { + "xrefs" : [ { + "val" : "UMLS:C4072991" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0030669", + "lbl" : "Abnormal ocular adnexa morphology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A structural anomaly of the adjacent structures (i.e., adnexa) of the eye, defined as the lacrimal apparatus, the extraocular muscles and the eyelids, eyelashes, eyebrows and the conjunctiva." + }, + "xrefs" : [ { + "val" : "UMLS:C4073120" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0030680", + "lbl" : "Abnormality of cardiovascular system morphology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any structural anomaly of the heart and great vessels." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Cardiovascular malformations" + } ], + "xrefs" : [ { + "val" : "UMLS:C4049796" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0001632" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0002564" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0002565" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0030791", + "lbl" : "Abnormal jaw morphology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A structural anomaly of the jaw, the bony structure of the mouth that consists of the mandible and the maxilla.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "xrefs" : [ { + "val" : "UMLS:C4280767" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0030904", + "lbl" : "Glabellar reflex", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A type of primitive reflex that is elicited by repetitive tapping on the forehead. Normal subjects usually blink in response to the first several taps, but if blinking persists, the response is abnormal and considered to be a sign of frontal release. Persistent blinking is also known as Myerson's sign.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "Myerson's sign" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0030961", + "lbl" : "Microspherophakia", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Lens of the eye is smaller than normal and spherically shaped." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/date", + "val" : "2017-04-18T12:55:01Z" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0030962", + "lbl" : "Abnormal morphology of the great vessels", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A structural anomaly affecting a blood vessel involved in the circulation of the heart, i.e., the superior or inferior vena cava, the pulmonary arteries, the pulmonary veins, and the aorta." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/date", + "val" : "2017-04-18T13:00:44Z" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0030964", + "lbl" : "Abnormal aortic physiology", + "type" : "CLASS", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/date", + "val" : "2017-04-18T13:14:14Z" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0030966", + "lbl" : "Abnormal pulmonary artery morphology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An abnormality of the structure of the pulmonary artery." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/date", + "val" : "2017-04-18T13:29:12Z" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0031051", + "lbl" : "Tarsal sclerosis", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An elevation in bone density in one or more tarsal bones of the foot. 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The musculoskeletal system supports the weight of the body, maintains body position and produces movements of the body or of parts of the body." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/date", + "val" : "2020-09-05T13:35:03Z" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0033353", + "lbl" : "Abnormal blood vessel morphology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any structural anomaly of a blood vessel (artery, arteriole, capillary, venule, or vein)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/date", + "val" : "2020-12-01T11:42:14Z" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0033429", + "lbl" : "Neuroinflammation", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Activation of the brain's innate immune system in response to an inflammatory challenge and is characterized by a host of cellular and molecular changes within the brain." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/date", + "val" : "2021-01-09T17:51:49Z" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0034057", + "lbl" : "Fetal anomaly", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Structural or functional abnormalities of the fetus. 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The normal response to to blink (shut the eyelids) immediately. To evaluate the corneal reflex, the examiner uses a cotton-tipped applicator, the tip of which has been pulled into a thin strand. The examiner stabilizes the patient's head by placing a hand on the patient's eyebrow and head. 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The lens zonules are developmentally hypoplastic and abnormally weak and due to non-attachment of the posterior zonules to the equatorial zone of the lens, the lens changes its normal shape to spherical." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/date", + "val" : "2022-09-05T11:42:37Z" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0034376", + "lbl" : "Atrioventricular valve regurgitation", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Regurgitation of a heart valve that controls blood flow from a an atrium to a ventricle, including mitral, tricuspid, or, rarely, single atrioventicular valve." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/date", + "val" : "2022-09-05T11:50:30Z" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0034391", + "lbl" : "Elbow contracture", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A limitation in the passive range of motion of the elbow resulting from loss of elasticity in the periarticular tissues owing to structural changes of non-bony tissues, such as muscles, tendons, ligaments, joint capsules or skin." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/date", + "val" : "2022-09-30T12:50:12Z" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0034392", + "lbl" : "Joint contracture", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A limitation in the passive range of motion of the elbow resulting from loss of elasticity in the periarticular tissues owing to structural changes of non-bony tissues, such as muscles, tendons, ligaments, joint capsules or skin. A contracture prevents movement of the associated body part.", + "xrefs" : [ "PMID:22938881", "PMID:26247029", "PMID:30928194" ] + }, + "comments" : [ "To assess a joint contracture, the passive or active range of motion (ROM) of a joint with a contracture is assessed by moving the joint through its natural range with no active effort from the individual. The angular distance of the joint motion and the loss of ROM in a contracture is recorded through comparison with the contralateral joint or normative values. Conventionally, a joint contracture is named according to the joint involved and the direction opposite the lack of range. For example, inability to fully extend the knee is referred to as a knee flexion contracture, compared to inability to bend (flex) the knee, which is referred to as a knee extension contracture. Contractures in neuromuscular diseases develop due to intrinsic myotendinous structural changes and extrinsic factors. Known contributing extrinsic factors include decreased ability to actively move a limb through its full range of motion, immobility or static positioning for prolonged periods of time, and agonist antagonist muscle imbalance. Intrinsic muscle tissue alterations in dystrophic myopathies contribute to contracture formation. The most significant histologic changes are those of muscle fiber loss, abnormal residual dystrophic muscle fibers, segmental necrosis of muscle fibers, and increased amounts of adipose tissue, connective tissue, and fibrosis." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Contracture" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/date", + "val" : "2022-09-30T12:53:13Z" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0034398", + "lbl" : "Toe deformity", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Abnormal positioning of toe phalanges. Deformities of the lesser toes often occur gradually, though they can be brought on by trauma. The main adult sagittal plane deformities consist of claw toes, hammer toes and mallet toes. Axial plane deformities include crossover toes.", + "xrefs" : [ "PMID:28461920" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/date", + "val" : "2022-11-05T13:26:14Z" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0034430", + "lbl" : "Abnormal joint physiology", + "type" : "CLASS", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/date", + "val" : "2022-11-24T00:18:11Z" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0034669", + "lbl" : "Abnormal knee morphology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A structural abnormality of the knee joint or surrounding structures." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/date", + 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It is also a documented side effect of the lipid-lowering drugs such as statins and fibrates. Elevation of creatine kinase in blood is indicative of myositis." ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Muscle inflammation", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + } ], + "xrefs" : [ { + "val" : "MSH:D009220" + }, { + "val" : "SNOMEDCT_US:128496001" + }, { + "val" : "SNOMEDCT_US:26889001" + }, { + "val" : "UMLS:C0027121" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0009-0006-4530-3154" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2010-12-28T11:14:59Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0100625", + "lbl" : "Enlarged thorax", + "type" : "CLASS", + "meta" : { + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Wide rib cage" + }, { + "pred" : "hasExactSynonym", + "val" : "Wide thorax" + } ], + "xrefs" : [ { + "val" : "UMLS:C4020962" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0009-0006-4530-3154" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2010-12-28T04:14:55Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0100659", + "lbl" : "Abnormal cerebral vascular morphology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An anomaly of the cerebral blood vessels.", + "xrefs" : [ "PMID:30335330" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormality of the cerebral blood vessels", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Abnormality of the cerebral vasculature" + } ], + "xrefs" : [ { + "val" : "UMLS:C4022001" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0009-0006-4530-3154" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2010-12-30T11:39:15Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0100679", + "lbl" : "Lack of skin elasticity", + "type" : "CLASS", + "meta" : { + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasRelatedSynonym", + "val" : "Tight skin" + } ], + "xrefs" : [ { + "val" : "SNOMEDCT_US:297957009" + }, { + "val" : "UMLS:C0558242" + }, { + "val" : "UMLS:C4021998" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0009-0006-4530-3154" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2010-12-30T01:48:15Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0100681", + "lbl" : "Esophageal duplication", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A developmental disorder in which there is a duplication of a portion of the muscle and submucosa of the esophagus without epithelial duplication.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199", "PMID:10464795" ] + }, + "comments" : [ "Esophageal duplication is a rare cause of mediastinal mass. An esophageal duplication may be a simple epithelial cyst or duplication that contains muscle and submucosa but not epithelium. In most cases, the duplication is located in the lower thrid of the esophagus, and the most common associated symptom is difficulty in swallowing. Esophageal duplication occurs because of maldevelopment of the posterior division of embryonic foregut." ], + "xrefs" : [ { + "val" : "SNOMEDCT_US:66865009" + }, { + "val" : "UMLS:C0266135" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0009-0006-4530-3154" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2010-12-30T02:08:38Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0100689", + "lbl" : "Decreased corneal thickness", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A decreased anteroposterior thickness of the cornea.", + "xrefs" : [ "https://orcid.org/0000-0001-8727-6592" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Thin cornea" + } ], + "xrefs" : [ { + "val" : "SNOMEDCT_US:423459005" + }, { + "val" : "UMLS:C1096274" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0009-0006-4530-3154" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2011-02-18T04:40:41Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0100691", + "lbl" : "Abnormality of the curvature of the cornea", + "type" : "CLASS", + "meta" : { + "xrefs" : [ { + "val" : "UMLS:C4021995" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0009-0006-4530-3154" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2011-02-18T04:58:48Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0100711", + "lbl" : "Abnormal thoracic spine morphology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An abnormality of the thoracic vertebral column.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Abnormality of the thoracic spine" + } ], + "xrefs" : [ { + "val" : "UMLS:C4021989" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0009-0006-4530-3154" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2011-05-05T09:37:17Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0100719", + "lbl" : "Lens coloboma", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A sectoral indentation of the crystalline lens, usually due to zonular weakness or absence.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "xrefs" : [ { + "val" : "SNOMEDCT_US:204134008" + }, { + "val" : "UMLS:C0344516" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0009-0006-4530-3154" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2011-06-06T02:16:53Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0100729", + "lbl" : "Large face", + "type" : "CLASS", + "meta" : { + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Big face", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Large face" + }, { + "pred" : "hasExactSynonym", + "val" : "Large facies", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + } ], + "xrefs" : [ { + "val" : "UMLS:C2748652" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0009-0006-4530-3154" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2011-06-06T04:50:47Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0100775", + "lbl" : "Dural ectasia", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A widening or ballooning of the dural sac surrounding the spinal cord usually at the lumbosacral level.", + "xrefs" : [ "https://orcid.org/0009-0006-4530-3154" ] + }, + "comments" : [ "Dural ectasia is one of the major manifestations of Marfan syndrome. It may cause low back pain, headaches and neurological signs such as weakness and loss of bowel and bladder function, but in many patients it is asymptomatic. It is also a cause of posterior vertebral scalloping present in radiographs in patients who are diagnosed with Neurofibromatosis. Dural ectasia may also manifest in Ehlers-Danlos Syndrome, cauda equina syndrome and in ankylosing spondylitis." ], + "xrefs" : [ { + "val" : "UMLS:C1851712" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0009-0006-4530-3154" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2011-06-07T05:22:13Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0100790", + "lbl" : "Hernia", + "type" : "CLASS", + "meta" : { + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "Hernias", + "xrefs" : [ "https://orcid.org/0000-0002-5316-1399" ] + } ], + "xrefs" : [ { + "val" : "MSH:D006547" + }, { + "val" : "SNOMEDCT_US:414403008" + }, { + "val" : "SNOMEDCT_US:52515009" + }, { + "val" : "UMLS:C0019270" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0009-0006-4530-3154" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2011-06-08T02:33:37Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0100807", + "lbl" : "Long fingers", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The middle finger is more than 2 SD above the mean for newborns 27 to 41 weeks EGA or above the 97th centile for children from birth to 16 years of age AND the five digits retain their normal length proportions relative to each other (i.e., it is not the case that the middle finger is the only lengthened digit), or, Fingers that appear disproportionately long compared to the palm of the hand.", + "xrefs" : [ "PMID:19125433" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Long fingers" + } ], + "xrefs" : [ { + "val" : "UMLS:C1858091" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0009-0006-4530-3154" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2011-06-09T01:13:15Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0006010" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0100886", + "lbl" : "Abnormality of globe location", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An abnormality in the placement of the ocular globe (eyeball).", + "xrefs" : [ "https://orcid.org/0009-0006-4530-3154" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormality of eyeball location", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormality of eyeball position", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Abnormality of globe position", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + } ], + "xrefs" : [ { + "val" : "UMLS:C4021946" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0009-0006-4530-3154" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2011-12-13T04:25:29Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0100887", + "lbl" : "Abnormality of globe size", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An abnormality in the size of the ocular globe (eyeball).", + "xrefs" : [ "https://orcid.org/0009-0006-4530-3154" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormality of eyeball size", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Eye size difference" + } ], + "xrefs" : [ { + "val" : "UMLS:C4021945" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0009-0006-4530-3154" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2011-12-13T04:25:29Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0010725" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0100899", + "lbl" : "Sclerosis of finger phalanx", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An elevation in bone density in one or more phalanges of the fingers. Sclerosis is normally detected on a radiograph as an area of increased opacity.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Increased bone density in the finger bone", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Sclerosis of the phalanges of the hand" + } ], + "xrefs" : [ { + "val" : "UMLS:C4020941" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0009-0006-4530-3154" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2011-12-02T09:34:05Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0100925", + "lbl" : "Sclerosis of foot bone", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An elevation in bone density in one or more foot bones. Sclerosis is normally detected on a radiograph as an area of increased opacity.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Increased bone density in foot bone", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Sclerosis of bones of the feet" + } ], + "xrefs" : [ { + "val" : "UMLS:C4020931" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0009-0006-4530-3154" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2011-12-02T11:12:32Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0200005", + "lbl" : "Abnormal shape of the palpebral fissure", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The presence of an abnormal shape of the palpebral fissure.", + "xrefs" : [ 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new file mode 100644 index 0000000..93fa44c --- /dev/null +++ b/tests/data/phenotype.real-shortlist.hpoa @@ -0,0 +1,91 @@ +#description: "HPO annotations for rare diseases [2: OMIM; 0: DECIPHER; 0 ORPHANET]" +#version: 2023-04-05-short +#tracker: https://github.com/obophenotype/human-phenotype-ontology/issues +#hpo-version: http://purl.obolibrary.org/obo/hp/releases/2023-04-05/hp.json +database_id disease_name qualifier hpo_id reference evidence onset frequency sex modifier aspect biocuration +OMIM:154700 Marfan syndrome HP:0001377 PMID:28050285;PMID:33436942 PCS 29/199 P HPO:probinson[2021-05-27];HPO:probinson[2021-04-01] +OMIM:154700 Marfan syndrome HP:0000486 PMID:8172269 PCS 110/573 P HPO:skoehler[2015-07-26];HPO:probinson[2020-08-03] +OMIM:154700 Marfan syndrome HP:0005136 OMIM:154700 IEA P HPO:probinson[2012-04-24] +OMIM:154700 Marfan syndrome HP:0001371 OMIM:154700 IEA P HPO:probinson[2012-04-24] +OMIM:154700 Marfan syndrome HP:0003199 OMIM:154700 IEA P HPO:probinson[2012-04-24] +OMIM:154700 Marfan syndrome HP:0025586 PMID:8172269 PCS 8/573 P HPO:skoehler[2018-10-08];HPO:probinson[2021-05-27] +OMIM:154700 Marfan syndrome HP:0000518 PMID:33436942;PMID:26903188 PCS 118/199 P HPO:probinson[2012-04-24];HP:probinson[2018-09-03];HPO:probinson[2021-04-01] +OMIM:154700 Marfan syndrome HP:0008132 OMIM:154700 IEA P HPO:probinson[2012-04-24] +OMIM:154700 Marfan syndrome HP:0002816 OMIM:154700 IEA P HPO:probinson[2012-04-24] +OMIM:154700 Marfan syndrome HP:0002616 PMID:33436942 PCS 45/58 P HPO:probinson[2012-04-24];HPO:probinson[2021-04-01] +OMIM:154700 Marfan syndrome HP:0001647 PMID:33436942 PCS 1/58 P HPO:probinson[2021-04-01] +OMIM:154700 Marfan syndrome HP:0000678 PMID:33436942 PCS 8/53 P HPO:probinson[2012-04-24];HPO:probinson[2021-04-01] +OMIM:154700 Marfan syndrome HP:0008138 PMID:28050285 PCS 31/146 P HPO:probinson[2021-05-27] +OMIM:154700 Marfan syndrome HP:0001840 PMID:33436942 PCS 7/53 P HPO:probinson[2021-04-01] +OMIM:154700 Marfan syndrome HP:0001763 PMID:33436942 PCS 27/53 P HPO:probinson[2012-04-24];HPO:probinson[2021-04-01] +OMIM:154700 Marfan syndrome HP:0000278 OMIM:154700 IEA P HPO:probinson[2012-04-24] +OMIM:154700 Marfan syndrome HP:0007800 OMIM:154700 IEA P HPO:probinson[2012-04-24] +OMIM:154700 Marfan syndrome HP:0001765 OMIM:154700 IEA P HPO:probinson[2012-04-24] +OMIM:154700 Marfan syndrome HP:0002751 PMID:28050285 PCS 37/146 P HPO:probinson[2012-04-24];HPO:probinson[2021-05-27] +OMIM:154700 Marfan syndrome HP:0000494 PMID:33436942 PCS 19/53 P HPO:probinson[2012-04-24];HPO:probinson[2021-04-01] +OMIM:154700 Marfan syndrome HP:0000098 OMIM:154700 TAS P HPO:probinson[2012-04-24] +OMIM:154700 Marfan syndrome HP:0004970 OMIM:154700 IEA P HPO:probinson[2012-04-24] +OMIM:154700 Marfan syndrome HP:0001382 PMID:33436942 PCS 11/53 P HPO:probinson[2012-04-24];HPO:probinson[2021-04-01] +OMIM:154700 Marfan syndrome HP:0003088 OMIM:154700 IEA P HPO:probinson[2012-04-24] +OMIM:154700 Marfan syndrome HP:0000490 PMID:33436942;OMIM:154700 PCS 25/63 P HPO:probinson[2021-04-01];HPO:probinson[2012-04-24] +OMIM:154700 Marfan syndrome HP:0001065 PMID:33436942 PCS 11/53 P HPO:probinson[2012-04-24];HPO:probinson[2021-04-01] +OMIM:154700 Marfan syndrome HP:0005180 PMID:33436942 PCS 26/58 P HPO:probinson[2021-04-01] +OMIM:154700 Marfan syndrome HP:0012385 PMID:33436942 PCS 19/53 P HPO:probinson[2021-04-01] +OMIM:154700 Marfan syndrome HP:0100775 PMID:10489951;PMID:3189335 PCS 112/140 P HPO:probinson[2020-08-03];HPO:skoehler[2013-01-22];HPO:probinson[2020-08-03] +OMIM:154700 Marfan syndrome HP:0000767 PMID:28050285 PCS 44/146 P HPO:probinson[2012-04-24];HPO:probinson[2021-05-27] +OMIM:154700 Marfan syndrome HP:0004927 OMIM:154700 IEA P HPO:probinson[2012-04-24] +OMIM:154700 Marfan syndrome HP:0003758 OMIM:154700 IEA P HPO:probinson[2012-04-24] +OMIM:154700 Marfan syndrome HP:0001659 PMID:33436942 PCS 14/58 P HPO:probinson[2012-04-24];HPO:probinson[2021-04-01] +OMIM:154700 Marfan syndrome HP:0007676 OMIM:154700 IEA P HPO:probinson[2012-04-24] +OMIM:154700 Marfan syndrome HP:0000768 PMID:28050285 PCS 58/146 P HPO:probinson[2012-04-24];HPO:probinson[2021-05-27] +OMIM:154700 Marfan syndrome HP:0000565 PMID:8172269 PCS 12/573 P HPO:skoehler[2015-07-26];HPO:probinson[2020-08-03] +OMIM:154700 Marfan syndrome HP:0001653 PMID:33436942 PCS 33/58 P HPO:probinson[2012-04-24];HPO:probinson[2021-04-01] +OMIM:154700 Marfan syndrome HP:0002107 PMID:33436942 PCS 6/53 P HPO:probinson[2012-04-24];HPO:probinson[2021-04-01] +OMIM:154700 Marfan syndrome HP:0000006 PMID:17502658 PCS I HPO:probinson[2012-04-24] +OMIM:154700 Marfan syndrome HP:0032934 PMID:8530937 PCS HP:0011462 HP:0040284 P HPO:probinson[2020-08-03] +OMIM:154700 Marfan syndrome HP:0000189 OMIM:154700 TAS P HPO:skoehler[2013-08-18] +OMIM:154700 Marfan syndrome HP:0000541 OMIM:154700 IEA P HPO:probinson[2012-04-24] +OMIM:154700 Marfan syndrome HP:0003179 PMID:28050285;PMID:26339165 PCS 140/292 P HPO:probinson[2012-04-24];HP:probinson[2018-09-03];HPO:probinson[2021-05-27] +OMIM:154700 Marfan syndrome HP:0012773 PMID:28050285 PCS 54/146 P HPO:probinson[2021-05-27] +OMIM:154700 Marfan syndrome HP:0001704 PMID:33436942 PCS 31/58 P HPO:probinson[2012-04-24];HPO:probinson[2021-04-01] +OMIM:154700 Marfan syndrome HP:0000218 PMID:33436942 PCS 34/53 P HPO:probinson[2012-04-24];HPO:probinson[2021-04-01] +OMIM:154700 Marfan syndrome HP:0001786 PMID:33436942 PCS 33/53 P HPO:probinson[2021-04-01] +OMIM:154700 Marfan syndrome HP:0000577 PMID:8172269;PMID:33436942 PCS 72/626 P HPO:skoehler[2015-07-26];HPO:probinson[2020-08-03];HPO:probinson[2021-04-01] +OMIM:154700 Marfan syndrome HP:0001166 PMID:28050285;PMID:33436942 PCS 124/197 P HPO:probinson[2012-04-24];HPO:probinson[2021-04-01];HPO:probinson[2021-05-27] +OMIM:154700 Marfan syndrome HP:0000275 OMIM:154700 TAS P HPO:probinson[2012-05-01] +OMIM:154700 Marfan syndrome HP:0003302 OMIM:154700 IEA P HPO:probinson[2012-04-24] +OMIM:154700 Marfan syndrome HP:0002650 PMID:33436942 PCS 16/53 P HPO:probinson[2021-04-01] +OMIM:154700 Marfan syndrome HP:0001883 PMID:33436942 PCS 13/53 P HPO:probinson[2021-04-01] +OMIM:154700 Marfan syndrome HP:0004872 OMIM:154700 IEA P HPO:probinson[2012-04-24] +OMIM:154700 Marfan syndrome HP:0000276 OMIM:154700 TAS P HPO:probinson[2012-05-01] +OMIM:154700 Marfan syndrome HP:0030961 PMID:33436942 PCS 2/53 P HPO:probinson[2021-04-01] +OMIM:154700 Marfan syndrome HP:0001761 PMID:28050285 PCS 49/146 P HPO:probinson[2012-04-24];HPO:probinson[2021-05-27] +OMIM:154700 Marfan syndrome HP:0025599 PMID:8172269 PCS 3/573 P HPO:probinson[2021-05-27] +OMIM:154700 Marfan syndrome HP:0002097 OMIM:154700 TAS HP:0040283 P HPO:probinson[2012-04-24] +OMIM:154700 Marfan syndrome HP:0000272 PMID:33436942 PCS 31/53 P HPO:probinson[2012-04-24];HPO:probinson[2021-04-01] +OMIM:154700 Marfan syndrome HP:0001083 PMID:28050285;PMID:29587526;PMID:33436942 PCS 119/251 P HPO:probinson[2012-04-24];HPO:probinson[2021-04-01];HPO:probinson[2021-05-27] +OMIM:154700 Marfan syndrome HP:0001519 PMID:33436942 PCS 38/53 P HPO:probinson[2021-04-01] +OMIM:154700 Marfan syndrome HP:0001635 OMIM:154700 IEA P HPO:probinson[2012-04-24] +OMIM:154700 Marfan syndrome HP:0002647 PMID:33436942 PCS 1/58 P HPO:probinson[2012-04-24];HPO:probinson[2021-04-01] +OMIM:154700 Marfan syndrome HP:0000268 PMID:33436942 PCS 36/53 P HPO:probinson[2012-04-24];HPO:probinson[2021-04-01] +OMIM:154700 Marfan syndrome HP:0000501 PMID:1494814;PMID:29587526 PCS 29/625 P HPO:skoehler[2013-01-22];HPO:probinson[2021-05-27];HPO:probinson[2021-05-27] +OMIM:154700 Marfan syndrome HP:0000347 OMIM:154700 IEA P HPO:probinson[2012-04-24] +OMIM:154700 Marfan syndrome HP:0001634 PMID:2791251;PMID:33436942 PCS 67/111 P HPO:probinson[2012-04-24];HPO:probinson[2021-04-01];HPO:probinson[2021-05-27] +OMIM:154700 Marfan syndrome HP:0000545 PMID:28050285;PMID:29587526;PMID:33436942 PCS 93/251 P HPO:probinson[2012-04-24];HPO:probinson[2021-04-01];HPO:probinson[2021-05-27] +OMIM:614619 Hyperekplexia 2 HP:0001276 PMID:11929858 PCS 1/1 P HPO:probinson[2013-08-10];HPO:probinson[2022-08-17] +OMIM:614619 Hyperekplexia 2 HP:0002036 PMID:11929858 PCS 1/1 P HPO:probinson[2022-08-17] +OMIM:614619 Hyperekplexia 2 HP:0002267 PMID:11929858 PCS 1/1 P HPO:probinson[2013-08-10];HPO:probinson[2022-08-17] +OMIM:614619 Hyperekplexia 2 HP:0010519 PMID:21391991 PCS HP:0011461 9/9 P HPO:probinson[2022-08-17] +OMIM:614619 Hyperekplexia 2 HP:0000483 PMID:21391991 PCS P HPO:skoehler[2018-10-08];HPO:probinson[2022-08-17] +OMIM:614619 Hyperekplexia 2 HP:0003577 PMID:21391991 PCS 9/9 C HPO:probinson[2022-08-17] +OMIM:614619 Hyperekplexia 2 HP:0003552 PMID:21391991 PCS HP:0003577 9/9 P HPO:probinson[2022-08-17] +OMIM:614619 Hyperekplexia 2 HP:0002020 PMID:11929858 PCS 1/1 P HPO:probinson[2022-08-17] +OMIM:614619 Hyperekplexia 2 HP:0001270 PMID:11929858 PCS 1/1 P HPO:probinson[2022-08-17] +OMIM:614619 Hyperekplexia 2 HP:0030904 PMID:21391991 PCS 2/9 P HPO:skoehler[2018-10-08];HPO:probinson[2022-08-17] +OMIM:614619 Hyperekplexia 2 HP:0000007 PMID:11929858 PCS I HPO:probinson[2013-08-10];HPO:probinson[2022-08-17] +OMIM:614619 Hyperekplexia 2 HP:0000565 PMID:21391991 PCS 7/9 P HPO:probinson[2013-08-10];HPO:probinson[2022-08-17] +OMIM:614619 Hyperekplexia 2 HP:0000545 PMID:21391991 PCS P HPO:skoehler[2018-10-08];HPO:probinson[2022-08-17] +OMIM:614619 Hyperekplexia 2 HP:0001249 PMID:21391991 PCS 1/9 P HPO:probinson[2022-08-17] +OMIM:614619 Hyperekplexia 2 HP:0003623 PMID:11929858 PCS 1/1 C HPO:probinson[2022-08-17] +OMIM:614619 Hyperekplexia 2 HP:0001336 PMID:11929858 PCS 1/1 P HPO:skoehler[2018-10-08];HPO:probinson[2022-08-17] +OMIM:614619 Hyperekplexia 2 HP:0001347 PMID:11929858 PCS 1/1 P HPO:skoehler[2018-10-08];HPO:probinson[2022-08-17] From 011fd83e70e618023921831012ad67c671a03296 Mon Sep 17 00:00:00 2001 From: Daniel Danis Date: Fri, 28 Apr 2023 12:17:03 -0400 Subject: [PATCH 09/39] Make algorithm tests a module. --- tests/algorithm/__init__.py | 0 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 tests/algorithm/__init__.py diff --git a/tests/algorithm/__init__.py b/tests/algorithm/__init__.py new file mode 100644 index 0000000..e69de29 From 647e27e8acc38ea374ef8dd29ccceb405b3a33ef Mon Sep 17 00:00:00 2001 From: Daniel Danis Date: Fri, 28 Apr 2023 12:17:38 -0400 Subject: [PATCH 10/39] Create an `algorithm.similarity` package. --- src/hpotk/algorithm/__init__.py | 1 + src/hpotk/algorithm/similarity/__init__.py | 0 2 files changed, 1 insertion(+) create mode 100644 src/hpotk/algorithm/similarity/__init__.py diff --git a/src/hpotk/algorithm/__init__.py b/src/hpotk/algorithm/__init__.py index 2951c16..cd792e5 100644 --- a/src/hpotk/algorithm/__init__.py +++ b/src/hpotk/algorithm/__init__.py @@ -1,3 +1,4 @@ from ._traversal import get_ancestors, get_parents from ._traversal import get_children, get_descendents, get_descendants from ._traversal import exists_path +from . import similarity diff --git a/src/hpotk/algorithm/similarity/__init__.py b/src/hpotk/algorithm/similarity/__init__.py new file mode 100644 index 0000000..e69de29 From 15182466e44c96226d0585d51f003fd8dabe6e05 Mon Sep 17 00:00:00 2001 From: Daniel Danis Date: Fri, 28 Apr 2023 12:18:09 -0400 Subject: [PATCH 11/39] Add functions for augmenting a set of `TermId`s with ancestors/descendants. --- src/hpotk/algorithm/_augment.py | 54 +++++++++++++++++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 src/hpotk/algorithm/_augment.py diff --git a/src/hpotk/algorithm/_augment.py b/src/hpotk/algorithm/_augment.py new file mode 100644 index 0000000..54726ba --- /dev/null +++ b/src/hpotk/algorithm/_augment.py @@ -0,0 +1,54 @@ +import typing + +from hpotk.graph import GraphAware, OntologyGraph +from hpotk.model import TermId +from ._traversal import get_ancestors, get_descendants + + +def augment_with_ancestors(g: typing.Union[GraphAware, OntologyGraph], + source: typing.Union[TermId, typing.Collection[TermId]], + include_source: bool = False) -> frozenset[TermId]: + """ + Get a set of ancestors of the source :class:`TermId`\\ (s). + The ancestor set may or may not include the source term IDs depending on the value of `include_source` argument. + + :param g: an ontology graph or an ontology graph-aware item + :param source: source term ID or a collection of term IDs. + :param include_source: whether to include the `source` term ID(s) in the results + :return: a :class:`frozenset` with ancestor :class:`TermId`\ s + """ + return _augment_impl(g, source, include_source, get_ancestors) + + +def augment_with_descendants(g: typing.Union[GraphAware, OntologyGraph], + source: typing.Union[TermId, typing.Collection[TermId]], + include_source: bool = False) -> frozenset[TermId]: + """ + Get a set of descendants of the source :class:`TermId`\\ (s). + The descendant set may or may not include the source term IDs depending on the value of `include_source` argument. + + :param g: an ontology graph or an ontology graph-aware item + :param source: source term ID or a collection of term IDs. + :param include_source: whether to include the `source` term ID(s) in the results + :return: a :class:`frozenset` with descendant :class:`TermId`\ s + """ + return _augment_impl(g, source, include_source, get_descendants) + + +def _augment_impl(g: typing.Union[GraphAware, OntologyGraph], + source: typing.Union[TermId, typing.Collection[TermId]], + include_source: bool, + func: typing.Callable[[typing.Union[GraphAware, OntologyGraph], TermId, bool], frozenset[TermId]]) \ + -> frozenset[TermId]: + if not (isinstance(g, GraphAware) or isinstance(g, OntologyGraph)): + raise ValueError(f'hpo must be instance of GraphAware or an OntologyGraph but was {type(g)}') + if isinstance(source, TermId): + return get_ancestors(g, source, include_source) + elif isinstance(source, typing.Collection): + augmented_term_ids = set() + for term_id in source: + for augmented in func(g, term_id, include_source): + augmented_term_ids.add(augmented) + return frozenset(augmented_term_ids) + else: + raise ValueError(f'source should be a TermId or a Collection of TermIds but got a {type(source)}') From aa490b6f455a1aad690858ae5f4a29768f41fbf8 Mon Sep 17 00:00:00 2001 From: Daniel Danis Date: Fri, 28 Apr 2023 12:25:23 -0400 Subject: [PATCH 12/39] Calculate IC for `TermId`s of annotated items. --- src/hpotk/algorithm/similarity/__init__.py | 1 + src/hpotk/algorithm/similarity/_ic.py | 44 ++++++++++++++++++ tests/algorithm/test_similarity.py | 52 ++++++++++++++++++++++ 3 files changed, 97 insertions(+) create mode 100644 src/hpotk/algorithm/similarity/_ic.py create mode 100644 tests/algorithm/test_similarity.py diff --git a/src/hpotk/algorithm/similarity/__init__.py b/src/hpotk/algorithm/similarity/__init__.py index e69de29..f5228cd 100644 --- a/src/hpotk/algorithm/similarity/__init__.py +++ b/src/hpotk/algorithm/similarity/__init__.py @@ -0,0 +1 @@ +from ._ic import calculate_ic_for_annotated_items diff --git a/src/hpotk/algorithm/similarity/_ic.py b/src/hpotk/algorithm/similarity/_ic.py new file mode 100644 index 0000000..c6019eb --- /dev/null +++ b/src/hpotk/algorithm/similarity/_ic.py @@ -0,0 +1,44 @@ +import math +import typing +from collections import Counter + +from hpotk.annotations import AnnotatedItemContainer +from hpotk.graph import OntologyGraph, GraphAware +from hpotk.model import TermId +from .._augment import augment_with_ancestors + + +def calculate_ic_for_annotated_items(items: AnnotatedItemContainer, + graph: typing.Union[GraphAware, OntologyGraph], + base: typing.Optional[float] = None) -> typing.Mapping[TermId, float]: + """ + Calculate information content (IC) for each :class:`TermId` based on a collection of annotated `items`. + + :param items: a collection of :class:`hpotk.annotations.AnnotatedItem`\ s + :param graph: ontology graph or an object that has the ontology graph + :param base: information content base or `None` for *e* + (produces IC in `nats `_) + :return: a mapping from :class:`TermId` to information content in nats, bits, or else, depending on the `base` value + """ + if isinstance(graph, GraphAware): + root = graph.graph.root + elif isinstance(graph, OntologyGraph): + root = graph.root + else: + raise ValueError(f'graph must be either an instance of `OntologyGraph` or `GraphAware` ' + f'but it was {type(graph)}') + + hit_count = Counter() + + for i, item in enumerate(items): + for annotation in item.annotations: + if annotation.is_present: + for ancestor in augment_with_ancestors(graph, annotation.identifier, include_source=True): + hit_count[ancestor] += 1 + + log_func = math.log if base is None else lambda c: math.log(c, base) + + population_count = hit_count[root] + return { + term_id: -log_func(count / population_count) for term_id, count in hit_count.items() + } diff --git a/tests/algorithm/test_similarity.py b/tests/algorithm/test_similarity.py new file mode 100644 index 0000000..18fe90c --- /dev/null +++ b/tests/algorithm/test_similarity.py @@ -0,0 +1,52 @@ +import os +import unittest + +from pkg_resources import resource_filename + +from hpotk.algorithm.similarity import calculate_ic_for_annotated_items + +from hpotk.model import TermId +from hpotk.annotations import HpoDiseases, HpoDiseaseAnnotation +from hpotk.annotations.load.hpoa import SimpleHpoaDiseaseLoader +from hpotk.ontology import MinimalOntology +from hpotk.ontology.load.obographs import load_minimal_ontology + +TOY_HPO = resource_filename(__name__, os.path.join('../data', 'hp.small.json')) +TOY_HPOA = resource_filename(__name__, os.path.join('../data', 'phenotype.real-shortlist.hpoa')) + + +class TestResnik(unittest.TestCase): + HPO: MinimalOntology + DISEASES: HpoDiseases[HpoDiseaseAnnotation] + + @classmethod + def setUpClass(cls) -> None: + cls.HPO: MinimalOntology = load_minimal_ontology(TOY_HPO) + hpoa_loader = SimpleHpoaDiseaseLoader(cls.HPO) + cls.DISEASES: HpoDiseases[HpoDiseaseAnnotation] = hpoa_loader.load(TOY_HPOA) + + def test_calculate_ic_for_hpo_diseases(self): + mica = calculate_ic_for_annotated_items(self.DISEASES, self.HPO.graph) + + expected = { + # All the way down to Arachnodactyly + 'HP:0000001': 0., # All + 'HP:0000118': 0., # Phenotypic abnormality + 'HP:0040064': 1.921812597476252, # Abnormality of limbs + 'HP:0002817': 3.713572066704308, # Abnormality of the upper limb + 'HP:0001155': 4.406719247264253, # Abnormality of the hand + 'HP:0001167': 4.406719247264253, # Abnormal finger morphology + 'HP:0100807': 4.406719247264253, # Long fingers + 'HP:0001166': 4.406719247264253, # Arachnodactyly + + # Check some other terms + 'HP:0012373': 2.1041341542702074, # Abnormal eye physiology + 'HP:0033127': 1.1108823812599240, # Abnormality of the musculoskeletal system + 'HP:0000924': 1.3621968095408301, # Abnormality of the skeletal system + } + + for curie, ic in expected.items(): + term_id = TermId.from_curie(curie) + self.assertAlmostEqual(mica[term_id], ic) + + self.assertEqual(len(mica), 282) From 701df3f5e135367c93ac19ca01a3a1f25cbc2257 Mon Sep 17 00:00:00 2001 From: Daniel Danis Date: Mon, 1 May 2023 13:17:33 -0400 Subject: [PATCH 13/39] Implement calculation and persistence of Resnik similarity. --- src/hpotk/algorithm/similarity/__init__.py | 3 +- src/hpotk/algorithm/similarity/_ic.py | 47 ++++- src/hpotk/algorithm/similarity/_resnik.py | 196 +++++++++++++++++++++ src/hpotk/annotations/_api.py | 8 +- src/hpotk/annotations/_base.py | 2 +- src/hpotk/annotations/load/hpoa/_impl.py | 6 +- src/hpotk/model/__init__.py | 2 +- src/hpotk/model/_base.py | 36 ++++ src/hpotk/ontology/load/obographs/_load.py | 5 +- src/hpotk/util.py | 75 ++++++-- tests/algorithm/test_similarity.py | 28 ++- tests/data/phenotype.real-shortlist.hpoa | 2 +- 12 files changed, 378 insertions(+), 32 deletions(-) create mode 100644 src/hpotk/algorithm/similarity/_resnik.py diff --git a/src/hpotk/algorithm/similarity/__init__.py b/src/hpotk/algorithm/similarity/__init__.py index f5228cd..ba8d337 100644 --- a/src/hpotk/algorithm/similarity/__init__.py +++ b/src/hpotk/algorithm/similarity/__init__.py @@ -1 +1,2 @@ -from ._ic import calculate_ic_for_annotated_items +from ._ic import calculate_ic_for_annotated_items, AnnotationIcContainer +from ._resnik import precalculate_resnik_similarity_for_hpo, SimilarityContainer diff --git a/src/hpotk/algorithm/similarity/_ic.py b/src/hpotk/algorithm/similarity/_ic.py index c6019eb..62f055a 100644 --- a/src/hpotk/algorithm/similarity/_ic.py +++ b/src/hpotk/algorithm/similarity/_ic.py @@ -1,16 +1,49 @@ import math import typing from collections import Counter +from typing import Iterator from hpotk.annotations import AnnotatedItemContainer from hpotk.graph import OntologyGraph, GraphAware -from hpotk.model import TermId +from hpotk.model import TermId, MetadataAware from .._augment import augment_with_ancestors +class AnnotationIcContainer(typing.Mapping[TermId, float], MetadataAware): + """ + A container for information content of item annotations. + """ + + def __init__(self, data: typing.Mapping[TermId, float], + metadata: typing.Optional[typing.Mapping[str, str]] = None): + if not isinstance(data, typing.Mapping): + raise ValueError(f'data must be an instance of Mapping but it was: {type(data)}') + self._data = data + + self._meta = dict() + if metadata is not None: + if not isinstance(metadata, dict): + raise ValueError(f'meta must be a dict but was {type(metadata)}') + else: + self._meta.update(metadata) + + def __getitem__(self, key: TermId) -> float: + return self._data[key] + + def __len__(self) -> int: + return len(self._data) + + def __iter__(self) -> Iterator[TermId]: + return iter(self._data) + + @property + def metadata(self) -> typing.Mapping[str, str]: + return self._meta + + def calculate_ic_for_annotated_items(items: AnnotatedItemContainer, graph: typing.Union[GraphAware, OntologyGraph], - base: typing.Optional[float] = None) -> typing.Mapping[TermId, float]: + base: typing.Optional[float] = None) -> AnnotationIcContainer: """ Calculate information content (IC) for each :class:`TermId` based on a collection of annotated `items`. @@ -18,7 +51,8 @@ def calculate_ic_for_annotated_items(items: AnnotatedItemContainer, :param graph: ontology graph or an object that has the ontology graph :param base: information content base or `None` for *e* (produces IC in `nats `_) - :return: a mapping from :class:`TermId` to information content in nats, bits, or else, depending on the `base` value + :return: a container with mappings from :class:`TermId` to information content in nats, bits, or else, + depending on the `base` value """ if isinstance(graph, GraphAware): root = graph.graph.root @@ -39,6 +73,7 @@ def calculate_ic_for_annotated_items(items: AnnotatedItemContainer, log_func = math.log if base is None else lambda c: math.log(c, base) population_count = hit_count[root] - return { - term_id: -log_func(count / population_count) for term_id, count in hit_count.items() - } + + data = {term_id: -log_func(count / population_count) for term_id, count in hit_count.items()} + metadata = {'version': items.version} + return AnnotationIcContainer(data, metadata=metadata) diff --git a/src/hpotk/algorithm/similarity/_resnik.py b/src/hpotk/algorithm/similarity/_resnik.py new file mode 100644 index 0000000..d155c47 --- /dev/null +++ b/src/hpotk/algorithm/similarity/_resnik.py @@ -0,0 +1,196 @@ +import csv +import datetime +import functools +import logging +import re +import typing +from collections import defaultdict + +from hpotk.model import MetadataAware +from hpotk.constants.hpo.base import PHENOTYPIC_ABNORMALITY +from hpotk.model import TermId +from hpotk.ontology import MinimalOntology +from hpotk.util import open_text_io_handle_for_writing, open_text_io_handle_for_reading +from .._traversal import get_descendants, get_ancestors, get_children +from ._ic import AnnotationIcContainer + +# implement Resnik IC computation starting from a collection of world documents +# and see if we can plug in excluded into the values. + +HPO_PATTERN = re.compile(r"HP:(?P\d{7})") + +logger = logging.getLogger('hpotk.algorithm.similarity') + + +class SimilarityContainer(MetadataAware, typing.Sized): + """ + A container for pre-calculated semantic similarity results. + """ + + def __init__(self, metadata: typing.Optional[typing.Mapping[str, str]] = None): + self._meta = dict() + if metadata is not None: + if not isinstance(metadata, dict): + raise ValueError(f'meta must be a dict but was {type(metadata)}') + else: + self._meta.update(metadata) + self._data = self._prepare_datadict() + + def get_similarity(self, a: str, b: str) -> float: + """ + Get similarity of two entries `a` and `b`. + + :param a: an item, e.g. `HP:1234567` + :param b: another item, e.g. `HP:9876543` + :return: a non-negative semantic similarity + """ + o, i = (a, b) if a <= b else (b, a) + outer = self._data.get(o, None) + if outer: + return outer.get(i, 0.) + else: + return 0. + + def set_similarity(self, a: str, b: str, sim: float): + """ + Set semantic similarity for items `a` and `b`. + :param a: an item, e.g. `HP:1234567` + :param b: another item, e.g. `HP:9876543` + :param sim: a non-negative semantic similarity + """ + if sim < 0.: + raise ValueError(f'Similarity must be non-negative: {sim}') + if a <= b: + self._data[a][b] = sim + else: + self._data[b][a] = sim + + def items(self): + """ + Get a generator of semantic similarities. + + Each item is a tuple with three items: + * left item (`str`) + * right item (`str`) + * similarity (`float`) + """ + for a, vals in self._data.items(): + for b, sim in vals.items(): + yield a, b, sim + + @property + def metadata(self) -> typing.Mapping[str, str]: + return self._meta + + @staticmethod + def _prepare_datadict() -> typing.MutableMapping[str, typing.MutableMapping[str, float]]: + def inner() -> float: + return 0. + + def outer() -> defaultdict: + return defaultdict(inner) + + return defaultdict(outer) + + def to_csv(self, fh: typing.Union[str, typing.IO]): + now = datetime.datetime.now() + self._meta['created'] = now.strftime('%Y-%m-%d-%H:%M:%S') + with open_text_io_handle_for_writing(fh) as handle: + # (0) Comments + handle.write('#Information content of the most informative common ancestor for term pairs\n') + handle.write('#' + self.metadata_to_str() + '\n') + + # (1) Header + fieldnames = ['term_a', 'term_b', 'ic_mica'] + writer = csv.DictWriter(handle, fieldnames=fieldnames) + writer.writeheader() + + # (2) Entries + for left, right, sim in self.items(): + writer.writerow({'term_a': left, 'term_b': right, 'ic_mica': sim}) + + @staticmethod + def from_csv(fh: typing.Union[str, typing.IO]): + header = [] + records = [] + + def store_header(row: str) -> bool: + if row[0] == '#': + header.append(row) + return False + return True + + with open_text_io_handle_for_reading(fh) as handle: + reader = csv.DictReader(filter(store_header, handle)) + for record in reader: + records.append((record['term_a'], record['term_b'], float(record['ic_mica']))) + + meta = SimilarityContainer._parse_meta(header) + data = SimilarityContainer(meta) + for record in records: + data.set_similarity(record[0], record[1], record[2]) + + return data + + @staticmethod + def _parse_meta(header: typing.Sequence[str]) -> typing.Mapping[str, str]: + # Poor man's parsing. + if len(header) < 2 or len(header[1]) < 2: + return {} + else: + # The 2nd line is the metadata line, and we strip off the first and the last char (# and \n) + return MetadataAware.metadata_from_str(header[1][1:-1]) + + def __len__(self) -> int: + return sum([len(inner) for inner in self._data.values()]) + + +def _get_common_ancestors(hpo: MinimalOntology, + left: TermId, + right: TermId) -> frozenset[TermId]: + la = get_ancestors(hpo, left, include_source=True) + ra = get_ancestors(hpo, right, include_source=True) + return la.intersection(ra) + + +def precalculate_resnik_similarity_for_hpo(ic: AnnotationIcContainer, + hpo: MinimalOntology) -> SimilarityContainer: + """ + Precalculate Resnik semantic similarity for :class:`TermId` pairs. + + :param ic: a mapping for obtaining an information content of a :class:`TermId`. + :param hpo: HPO ontology. + :return: a mapping with Resnik similarity for :class:`TermId` pairs where the similarity :math:`s>0`. + """ + metadata = {'hpo_version': hpo.version} + metadata.update(ic.metadata) + data = SimilarityContainer(metadata=metadata) + groups = list(get_children(hpo, PHENOTYPIC_ABNORMALITY)) + count = 0 + for section_top in groups: + term = hpo.get_term(section_top) + term_ids = list(get_descendants(hpo, section_top, include_source=True)) + logger.info(f'Calculating for {term.name} with {len(term_ids) - 1} descendants') + for i in range(len(term_ids)): + left = term_ids[i] + for j in range(i, len(term_ids)): + right = term_ids[j] + + ic_mica = functools.reduce(max, + map(lambda term_id: ic.get(term_id, 0.), + _get_common_ancestors(hpo, left, right)), + 0.) + + if left.value < right.value: + a, b = left.value, right.value + else: + a, b = right.value, left.value + + if ic_mica > 0.: + previous = data.get_similarity(a, b) + data.set_similarity(a, b, max(ic_mica, previous)) + count += 1 + if count % 5_000 == 0 and count != 0: + logger.info(f'Processed {count:,d} term pairs') + + return data diff --git a/src/hpotk/annotations/_api.py b/src/hpotk/annotations/_api.py index 65c7ea9..f95d68c 100644 --- a/src/hpotk/annotations/_api.py +++ b/src/hpotk/annotations/_api.py @@ -2,7 +2,8 @@ import typing import warnings -from hpotk.model import TermId, Identified +from hpotk.model import TermId, Identified, Versioned + # ##################################################################################################################### # The file describes generic schema for annotations, annotated items, and annotated item containers. @@ -70,7 +71,10 @@ def absent_annotations(self) -> typing.Iterable[ANNOTATION]: """ -class AnnotatedItemContainer(typing.Generic[ANNOTATED_ITEM], typing.Iterable[ANNOTATED_ITEM], typing.Sized, +class AnnotatedItemContainer(typing.Generic[ANNOTATED_ITEM], + typing.Iterable[ANNOTATED_ITEM], + typing.Sized, + Versioned, metaclass=abc.ABCMeta): """ Container for annotated items. diff --git a/src/hpotk/annotations/_base.py b/src/hpotk/annotations/_base.py index 7742062..2dc2e0b 100644 --- a/src/hpotk/annotations/_base.py +++ b/src/hpotk/annotations/_base.py @@ -238,7 +238,7 @@ def __str__(self): f"n_annotations={len(self.annotations)})" -class HpoDiseases(AnnotatedItemContainer[HpoDiseaseAnnotation], Versioned, metaclass=abc.ABCMeta): +class HpoDiseases(AnnotatedItemContainer[HpoDiseaseAnnotation], metaclass=abc.ABCMeta): """ A container for a set of :class:`HpoDisease`s that allows iteration over all diseases, knows about the number of diseases in the container, and supports retrieval of the disease by its identifier. diff --git a/src/hpotk/annotations/load/hpoa/_impl.py b/src/hpotk/annotations/load/hpoa/_impl.py index 028947c..edc2e39 100644 --- a/src/hpotk/annotations/load/hpoa/_impl.py +++ b/src/hpotk/annotations/load/hpoa/_impl.py @@ -7,7 +7,7 @@ from hpotk.annotations import SimpleHpoDiseaseAnnotation, SimpleHpoDisease, SimpleHpoDiseases from hpotk.model import TermId from hpotk.ontology import MinimalOntology -from hpotk.util import open_text_io_handle +from hpotk.util import open_text_io_handle_for_reading from hpotk.constants.hpo.frequency import parse_hpo_frequency from hpotk.annotations.load._api import HpoDiseaseLoader @@ -19,7 +19,7 @@ 'sex', 'modifiers', 'aspect', 'curators'] ) -HPOA_VERSION_PATTERN = re.compile(r'^#date: (?P[\w-]+)\w?$') +HPOA_VERSION_PATTERN = re.compile(r'^#(date|version): (?P[\w-]+)\w?$') HPO_PATTERN = re.compile(r'^HP:\d{7}$') RATIO_PATTERN = re.compile(r'^(?P\d+)/(?P\d+)$') PERCENTAGE_PATTERN = re.compile(r'^(?P\d+\.?(\d+)?)%$') @@ -43,7 +43,7 @@ def load(self, file: typing.Union[typing.IO, str]) -> HpoDiseases: data = defaultdict(list) version = None expecting_to_see_header_line = True - with open_text_io_handle(file) as fh: + with open_text_io_handle_for_reading(file) as fh: for line in fh: if expecting_to_see_header_line: if line.startswith('#'): diff --git a/src/hpotk/model/__init__.py b/src/hpotk/model/__init__.py index 267ab3a..1701acf 100644 --- a/src/hpotk/model/__init__.py +++ b/src/hpotk/model/__init__.py @@ -1,7 +1,7 @@ import typing from ._term_id import TermId -from ._base import Identified, Named, Versioned +from ._base import Identified, Named, Versioned, MetadataAware from ._term import MinimalTerm, Term, Synonym, SynonymType, SynonymCategory # Types diff --git a/src/hpotk/model/_base.py b/src/hpotk/model/_base.py index 1241cea..6e6fe33 100644 --- a/src/hpotk/model/_base.py +++ b/src/hpotk/model/_base.py @@ -44,3 +44,39 @@ def version(self) -> typing.Optional[str]: :return: version `str` or `None` if the version is not available. """ pass + + +class MetadataAware(metaclass=abc.ABCMeta): + """ + Base class for entities that have metadata. + """ + + @property + @abc.abstractmethod + def metadata(self) -> typing.Mapping[str, str]: + """ + :return: a mapping with entity metadata. + """ + pass + + def metadata_to_str(self) -> str: + """ + Dump the metadata to a single string. + """ + forbidden = {';', '='} + for k, v in self.metadata.items(): + if any([token in k or token in v for token in forbidden]): + raise ValueError(f'Metadata contains forbidden characters {forbidden}') + + return ';'.join([f'{k}={v}' for k, v in self.metadata.items()]) + + @staticmethod + def metadata_from_str(value: str) -> typing.Mapping[str, str]: + """ + Load the metadata from `str` created by `metadata_to_str`. + """ + data = {} + for item in value.split(';'): + k, v = item.split('=') + data[k] = v + return data diff --git a/src/hpotk/ontology/load/obographs/_load.py b/src/hpotk/ontology/load/obographs/_load.py index 84b23f5..85753db 100644 --- a/src/hpotk/ontology/load/obographs/_load.py +++ b/src/hpotk/ontology/load/obographs/_load.py @@ -7,7 +7,7 @@ from hpotk.graph import OntologyGraph from hpotk.graph import GraphFactory, CsrGraphFactory, OWL_THING from hpotk.ontology import MinimalOntology, Ontology, create_ontology, create_minimal_ontology -from hpotk.util import open_text_io_handle +from hpotk.util import open_text_io_handle_for_reading from ._model import create_node, create_edge from ._model import Node, Edge, NodeType @@ -21,6 +21,7 @@ PURL_PATTERN = re.compile(r'http://purl\.obolibrary\.org/obo/(?P(?P\w+)_(?P\d{7}))') DATE_PATTERN = re.compile(r'.*/(?P\d{4}-\d{2}-\d{2})/.*') + def load_minimal_ontology(file: typing.Union[typing.IO, str], term_factory: ObographsTermFactory[MinimalTerm] = MinimalTermFactory(), graph_factory: GraphFactory = CsrGraphFactory()) -> MinimalOntology: @@ -53,7 +54,7 @@ def _load_impl(file: typing.Union[typing.IO, str], def get_hpo_graph(file: typing.Union[typing.IO, str]): - with open_text_io_handle(file) as fh: + with open_text_io_handle_for_reading(file) as fh: document = json.load(fh) if not isinstance(document, dict): raise ValueError(f'The JSON document should have been a dict but was {type(document)}') diff --git a/src/hpotk/util.py b/src/hpotk/util.py index a7827cf..1e23f3d 100644 --- a/src/hpotk/util.py +++ b/src/hpotk/util.py @@ -3,6 +3,7 @@ import logging import sys import typing +import warnings from urllib.request import urlopen DEFAULT_LOG_FMT = '%(asctime)s %(name)-20s %(levelname)-3s : %(message)s' @@ -37,9 +38,18 @@ def looks_gzipped(file: str) -> bool: return file.endswith('.gz') -def open_text_io_handle(fh: typing.Union[typing.IO, str], - timeout: int = 30, - encoding: str = None) -> typing.TextIO: +def _parse_encoding(encoding, logger) -> str: + if encoding is None: + encoding = sys.getdefaultencoding() + logger.debug(f'Using default encoding \'{encoding}\'') + else: + logger.debug(f'Using provided encoding \'{encoding}\'') + return encoding + + +def open_text_io_handle_for_reading(fh: typing.Union[typing.IO, str], + timeout: int = 30, + encoding: str = None) -> typing.TextIO: """ Open a `io.TextIO` file handle based on `fh`. @@ -52,13 +62,9 @@ def open_text_io_handle(fh: typing.Union[typing.IO, str], :return: the `io.TextIO` wrapper """ logger = logging.getLogger('hpotk.util') - logger.debug(f'Opening {fh}') - if encoding is None: - encoding = sys.getdefaultencoding() - logger.debug(f'Using default encoding \'{encoding}\'') - else: - logger.debug(f'Using provided encoding \'{encoding}\'') + encoding = _parse_encoding(encoding, logger) + logger.debug(f'Opening {fh}') if isinstance(fh, str): # Can be a path to local file or URL if looks_like_url(fh): @@ -72,10 +78,10 @@ def open_text_io_handle(fh: typing.Union[typing.IO, str], handle = open(fh, 'rb') if looks_gzipped(fh): - logger.debug(f'Looks like a gzipped data, uncompressing on the fly') + logger.debug(f'Looks like a gzipped data, decompressing on the fly') return gzip.open(handle, mode='rt', newline='', encoding=encoding) else: - logger.debug(f'Looks like un-compressed data') + logger.debug(f'Looks like decompressed data') return io.TextIOWrapper(handle, encoding=encoding) elif isinstance(fh, typing.IO): if isinstance(fh, typing.BinaryIO): @@ -87,3 +93,50 @@ def open_text_io_handle(fh: typing.Union[typing.IO, str], raise ValueError(f'Unexpected type {type(fh)}') else: raise ValueError(f'Unexpected type {type(fh)}') + + +def open_text_io_handle(fh: typing.Union[typing.IO, str], + timeout: int = 30, + encoding: str = None) -> typing.TextIO: + """ + Open a `io.TextIO` file handle based on `fh`. + + :param fh: a `str` or `typing.IO` to read from. If `str`, then it should be a path to a local file or a URL + of a remote resource. Either `http` or `https` protocols are supported. The content will be uncompressed on the fly + if the file name ends with `.gz`. If `fh` is an IO wrapper, the function ensures we get a text wrapper that uses + given encoding. + :param timeout: timeout in seconds used when accessing a remote resource + :param encoding: encoding used to decode the input or the system preferred encoding if unset. + :return: the `io.TextIO` wrapper + """ + # REMOVE(v1.0.0) + warnings.warn('The method has been deprecated and will be removed in v1.0.0. ' + 'Use `open_text_io_handle_for_reading` instead', DeprecationWarning, stacklevel=2) + return open_text_io_handle_for_reading(fh, timeout, encoding) + + +def open_text_io_handle_for_writing(fh: typing.Union[str, typing.IO], + encoding: str = None) -> typing.TextIO: + """ + Open a `io.TextIO` file handle based on `fpath`. + + :param fh: a `str` with a path to a local file The content will be compressed on the fly if the file name ends with `.gz`. + :param encoding: encoding used to encode the output or the system preferred encoding if unset. + :return: the `io.TextIO` wrapper + """ + logger = logging.getLogger('hpotk.util') + encoding = _parse_encoding(encoding, logger) + + if isinstance(fh, str): + if looks_gzipped(fh): + logger.debug(f'Looks like a gzipped data, compressing on the fly') + return gzip.open(fh, mode='wt', newline='', encoding=encoding) + else: + return open(fh, 'w') + elif isinstance(fh, typing.BinaryIO): + logger.debug(f'Looks like a binary IO') + return io.TextIOWrapper(fh, encoding=encoding) + elif isinstance(fh, typing.TextIO): + return fh + else: + raise ValueError(f'Unexpected type {type(fh)}') diff --git a/tests/algorithm/test_similarity.py b/tests/algorithm/test_similarity.py index 18fe90c..31e8fd1 100644 --- a/tests/algorithm/test_similarity.py +++ b/tests/algorithm/test_similarity.py @@ -3,10 +3,10 @@ from pkg_resources import resource_filename -from hpotk.algorithm.similarity import calculate_ic_for_annotated_items +from hpotk.algorithm.similarity import calculate_ic_for_annotated_items, precalculate_resnik_similarity_for_hpo from hpotk.model import TermId -from hpotk.annotations import HpoDiseases, HpoDiseaseAnnotation +from hpotk.annotations import HpoDiseases from hpotk.annotations.load.hpoa import SimpleHpoaDiseaseLoader from hpotk.ontology import MinimalOntology from hpotk.ontology.load.obographs import load_minimal_ontology @@ -17,13 +17,13 @@ class TestResnik(unittest.TestCase): HPO: MinimalOntology - DISEASES: HpoDiseases[HpoDiseaseAnnotation] + DISEASES: HpoDiseases @classmethod def setUpClass(cls) -> None: cls.HPO: MinimalOntology = load_minimal_ontology(TOY_HPO) hpoa_loader = SimpleHpoaDiseaseLoader(cls.HPO) - cls.DISEASES: HpoDiseases[HpoDiseaseAnnotation] = hpoa_loader.load(TOY_HPOA) + cls.DISEASES: HpoDiseases = hpoa_loader.load(TOY_HPOA) def test_calculate_ic_for_hpo_diseases(self): mica = calculate_ic_for_annotated_items(self.DISEASES, self.HPO.graph) @@ -50,3 +50,23 @@ def test_calculate_ic_for_hpo_diseases(self): self.assertAlmostEqual(mica[term_id], ic) self.assertEqual(len(mica), 282) + + @unittest.skip + def test_precalculate_ic_mica(self): + # Takes ~15 seconds, and it isn't run regularly. + term_id2ic = calculate_ic_for_annotated_items(self.DISEASES, self.HPO) + + sim_container = precalculate_resnik_similarity_for_hpo(term_id2ic, self.HPO) + + self.assertAlmostEqual(sim_container.get_similarity('HP:0000118', 'HP:0000118'), 0.) # Phenotypic abnormality + + # Arachnodactyly with Phenotypic abnormality + self.assertAlmostEqual(sim_container.get_similarity('HP:0001166', 'HP:0000118'), 0.) + # Arachnodactyly (self-similarity) + self.assertAlmostEqual(sim_container.get_similarity('HP:0001166', 'HP:0001166'), 4.406719247264253) + # Arachnodactyly with Abnormality of limbs + self.assertAlmostEqual(sim_container.get_similarity('HP:0001166', 'HP:0040064'), 1.921812597476252) + self.assertAlmostEqual(sim_container.get_similarity('HP:0040064', 'HP:0001166'), 1.921812597476252) + + # Total number of items + self.assertEqual(len(sim_container), 50_928) diff --git a/tests/data/phenotype.real-shortlist.hpoa b/tests/data/phenotype.real-shortlist.hpoa index 93fa44c..8e36cd4 100644 --- a/tests/data/phenotype.real-shortlist.hpoa +++ b/tests/data/phenotype.real-shortlist.hpoa @@ -1,5 +1,5 @@ #description: "HPO annotations for rare diseases [2: OMIM; 0: DECIPHER; 0 ORPHANET]" -#version: 2023-04-05-short +#version: 2023-04-05 #tracker: https://github.com/obophenotype/human-phenotype-ontology/issues #hpo-version: http://purl.obolibrary.org/obo/hp/releases/2023-04-05/hp.json database_id disease_name qualifier hpo_id reference evidence onset frequency sex modifier aspect biocuration From e8daa257fa9d0b3149c9b1203969f2529ad2f485 Mon Sep 17 00:00:00 2001 From: Daniel Danis Date: Tue, 2 May 2023 09:31:41 -0400 Subject: [PATCH 14/39] Separate data classes. --- src/hpotk/algorithm/similarity/__init__.py | 5 +- src/hpotk/algorithm/similarity/_ic.py | 39 +---- src/hpotk/algorithm/similarity/_model.py | 170 +++++++++++++++++++++ src/hpotk/algorithm/similarity/_resnik.py | 132 +--------------- 4 files changed, 178 insertions(+), 168 deletions(-) create mode 100644 src/hpotk/algorithm/similarity/_model.py diff --git a/src/hpotk/algorithm/similarity/__init__.py b/src/hpotk/algorithm/similarity/__init__.py index ba8d337..0cb0eb5 100644 --- a/src/hpotk/algorithm/similarity/__init__.py +++ b/src/hpotk/algorithm/similarity/__init__.py @@ -1,2 +1,3 @@ -from ._ic import calculate_ic_for_annotated_items, AnnotationIcContainer -from ._resnik import precalculate_resnik_similarity_for_hpo, SimilarityContainer +from ._ic import calculate_ic_for_annotated_items +from ._model import AnnotationIcContainer, SimpleAnnotationIcContainer, SimilarityContainer +from ._resnik import precalculate_resnik_similarity_for_hpo diff --git a/src/hpotk/algorithm/similarity/_ic.py b/src/hpotk/algorithm/similarity/_ic.py index 62f055a..ed02591 100644 --- a/src/hpotk/algorithm/similarity/_ic.py +++ b/src/hpotk/algorithm/similarity/_ic.py @@ -1,46 +1,13 @@ import math import typing from collections import Counter -from typing import Iterator from hpotk.annotations import AnnotatedItemContainer from hpotk.graph import OntologyGraph, GraphAware -from hpotk.model import TermId, MetadataAware +from ._model import SimpleAnnotationIcContainer, AnnotationIcContainer from .._augment import augment_with_ancestors -class AnnotationIcContainer(typing.Mapping[TermId, float], MetadataAware): - """ - A container for information content of item annotations. - """ - - def __init__(self, data: typing.Mapping[TermId, float], - metadata: typing.Optional[typing.Mapping[str, str]] = None): - if not isinstance(data, typing.Mapping): - raise ValueError(f'data must be an instance of Mapping but it was: {type(data)}') - self._data = data - - self._meta = dict() - if metadata is not None: - if not isinstance(metadata, dict): - raise ValueError(f'meta must be a dict but was {type(metadata)}') - else: - self._meta.update(metadata) - - def __getitem__(self, key: TermId) -> float: - return self._data[key] - - def __len__(self) -> int: - return len(self._data) - - def __iter__(self) -> Iterator[TermId]: - return iter(self._data) - - @property - def metadata(self) -> typing.Mapping[str, str]: - return self._meta - - def calculate_ic_for_annotated_items(items: AnnotatedItemContainer, graph: typing.Union[GraphAware, OntologyGraph], base: typing.Optional[float] = None) -> AnnotationIcContainer: @@ -64,7 +31,7 @@ def calculate_ic_for_annotated_items(items: AnnotatedItemContainer, hit_count = Counter() - for i, item in enumerate(items): + for item in items: for annotation in item.annotations: if annotation.is_present: for ancestor in augment_with_ancestors(graph, annotation.identifier, include_source=True): @@ -76,4 +43,4 @@ def calculate_ic_for_annotated_items(items: AnnotatedItemContainer, data = {term_id: -log_func(count / population_count) for term_id, count in hit_count.items()} metadata = {'version': items.version} - return AnnotationIcContainer(data, metadata=metadata) + return SimpleAnnotationIcContainer(data, metadata=metadata) diff --git a/src/hpotk/algorithm/similarity/_model.py b/src/hpotk/algorithm/similarity/_model.py new file mode 100644 index 0000000..abe851e --- /dev/null +++ b/src/hpotk/algorithm/similarity/_model.py @@ -0,0 +1,170 @@ +import abc +import csv +import typing +from collections import defaultdict +from datetime import datetime + +from hpotk.model import TermId, MetadataAware +from hpotk.util import open_text_io_handle_for_writing, open_text_io_handle_for_reading + + +class AnnotationIcContainer(typing.Mapping[TermId, float], MetadataAware, metaclass=abc.ABCMeta): + """ + A container for storing information content of item annotations. + """ + pass + + +class SimpleAnnotationIcContainer(AnnotationIcContainer): + """ + An implementation of a :class:`AnnotationIcContainer` that is backed by a :class:`dict`. + """ + + def __init__(self, data: typing.Mapping[TermId, float], + metadata: typing.Optional[typing.Mapping[str, str]] = None): + if not isinstance(data, typing.Mapping): + raise ValueError(f'data must be an instance of Mapping but it was: {type(data)}') + self._data = data + + self._meta = dict() + if metadata is not None: + if not isinstance(metadata, dict): + raise ValueError(f'meta must be a dict but was {type(metadata)}') + else: + self._meta.update(metadata) + + def __getitem__(self, key: TermId) -> float: + return self._data[key] + + def __len__(self) -> int: + return len(self._data) + + def __iter__(self) -> typing.Iterator[TermId]: + return iter(self._data) + + @property + def metadata(self) -> typing.Mapping[str, str]: + return self._meta + + +class SimilarityContainer(MetadataAware, typing.Sized): + """ + A container for pre-calculated semantic similarity results. + """ + + def __init__(self, metadata: typing.Optional[typing.Mapping[str, str]] = None): + self._meta = dict() + if metadata is not None: + if not isinstance(metadata, dict): + raise ValueError(f'meta must be a dict but was {type(metadata)}') + else: + self._meta.update(metadata) + self._data = self._prepare_datadict() + + def get_similarity(self, a: str, b: str) -> float: + """ + Get similarity of two entries `a` and `b`. + + :param a: an item, e.g. `HP:1234567` + :param b: another item, e.g. `HP:9876543` + :return: a non-negative semantic similarity + """ + o, i = (a, b) if a <= b else (b, a) + outer = self._data.get(o, None) + if outer: + return outer.get(i, 0.) + else: + return 0. + + def set_similarity(self, a: str, b: str, sim: float): + """ + Set semantic similarity for items `a` and `b`. + :param a: an item, e.g. `HP:1234567` + :param b: another item, e.g. `HP:9876543` + :param sim: a non-negative semantic similarity + """ + if sim < 0.: + raise ValueError(f'Similarity must be non-negative: {sim}') + if a <= b: + self._data[a][b] = sim + else: + self._data[b][a] = sim + + def items(self): + """ + Get a generator of semantic similarities. + + Each item is a tuple with three items: + * left item (`str`) + * right item (`str`) + * similarity (`float`) + """ + for a, vals in self._data.items(): + for b, sim in vals.items(): + yield a, b, sim + + @property + def metadata(self) -> typing.Mapping[str, str]: + return self._meta + + @staticmethod + def _prepare_datadict() -> typing.MutableMapping[str, typing.MutableMapping[str, float]]: + def inner() -> float: + return 0. + + def outer() -> defaultdict: + return defaultdict(inner) + + return defaultdict(outer) + + def to_csv(self, fh: typing.Union[str, typing.IO]): + now = datetime.datetime.now() + self._meta['created'] = now.strftime('%Y-%m-%d-%H:%M:%S') + with open_text_io_handle_for_writing(fh) as handle: + # (0) Comments + handle.write('#Information content of the most informative common ancestor for term pairs\n') + handle.write('#' + self.metadata_to_str() + '\n') + + # (1) Header + fieldnames = ['term_a', 'term_b', 'ic_mica'] + writer = csv.DictWriter(handle, fieldnames=fieldnames) + writer.writeheader() + + # (2) Entries + for left, right, sim in self.items(): + writer.writerow({'term_a': left, 'term_b': right, 'ic_mica': sim}) + + @staticmethod + def from_csv(fh: typing.Union[str, typing.IO]): + header = [] + records = [] + + def store_header(row: str) -> bool: + if row[0] == '#': + header.append(row) + return False + return True + + with open_text_io_handle_for_reading(fh) as handle: + reader = csv.DictReader(filter(store_header, handle)) + for record in reader: + records.append((record['term_a'], record['term_b'], float(record['ic_mica']))) + + meta = SimilarityContainer._parse_meta(header) + data = SimilarityContainer(meta) + for record in records: + data.set_similarity(record[0], record[1], record[2]) + + return data + + @staticmethod + def _parse_meta(header: typing.Sequence[str]) -> typing.Mapping[str, str]: + # Poor man's parsing. + if len(header) < 2 or len(header[1]) < 2: + return {} + else: + # The 2nd line is the metadata line, and we strip off the first and the last char (# and \n) + return MetadataAware.metadata_from_str(header[1][1:-1]) + + def __len__(self) -> int: + return sum([len(inner) for inner in self._data.values()]) diff --git a/src/hpotk/algorithm/similarity/_resnik.py b/src/hpotk/algorithm/similarity/_resnik.py index d155c47..5f51ee0 100644 --- a/src/hpotk/algorithm/similarity/_resnik.py +++ b/src/hpotk/algorithm/similarity/_resnik.py @@ -1,18 +1,13 @@ -import csv -import datetime import functools import logging import re -import typing -from collections import defaultdict -from hpotk.model import MetadataAware from hpotk.constants.hpo.base import PHENOTYPIC_ABNORMALITY from hpotk.model import TermId from hpotk.ontology import MinimalOntology -from hpotk.util import open_text_io_handle_for_writing, open_text_io_handle_for_reading -from .._traversal import get_descendants, get_ancestors, get_children from ._ic import AnnotationIcContainer +from ._model import SimilarityContainer +from .._traversal import get_descendants, get_ancestors, get_children # implement Resnik IC computation starting from a collection of world documents # and see if we can plug in excluded into the values. @@ -22,129 +17,6 @@ logger = logging.getLogger('hpotk.algorithm.similarity') -class SimilarityContainer(MetadataAware, typing.Sized): - """ - A container for pre-calculated semantic similarity results. - """ - - def __init__(self, metadata: typing.Optional[typing.Mapping[str, str]] = None): - self._meta = dict() - if metadata is not None: - if not isinstance(metadata, dict): - raise ValueError(f'meta must be a dict but was {type(metadata)}') - else: - self._meta.update(metadata) - self._data = self._prepare_datadict() - - def get_similarity(self, a: str, b: str) -> float: - """ - Get similarity of two entries `a` and `b`. - - :param a: an item, e.g. `HP:1234567` - :param b: another item, e.g. `HP:9876543` - :return: a non-negative semantic similarity - """ - o, i = (a, b) if a <= b else (b, a) - outer = self._data.get(o, None) - if outer: - return outer.get(i, 0.) - else: - return 0. - - def set_similarity(self, a: str, b: str, sim: float): - """ - Set semantic similarity for items `a` and `b`. - :param a: an item, e.g. `HP:1234567` - :param b: another item, e.g. `HP:9876543` - :param sim: a non-negative semantic similarity - """ - if sim < 0.: - raise ValueError(f'Similarity must be non-negative: {sim}') - if a <= b: - self._data[a][b] = sim - else: - self._data[b][a] = sim - - def items(self): - """ - Get a generator of semantic similarities. - - Each item is a tuple with three items: - * left item (`str`) - * right item (`str`) - * similarity (`float`) - """ - for a, vals in self._data.items(): - for b, sim in vals.items(): - yield a, b, sim - - @property - def metadata(self) -> typing.Mapping[str, str]: - return self._meta - - @staticmethod - def _prepare_datadict() -> typing.MutableMapping[str, typing.MutableMapping[str, float]]: - def inner() -> float: - return 0. - - def outer() -> defaultdict: - return defaultdict(inner) - - return defaultdict(outer) - - def to_csv(self, fh: typing.Union[str, typing.IO]): - now = datetime.datetime.now() - self._meta['created'] = now.strftime('%Y-%m-%d-%H:%M:%S') - with open_text_io_handle_for_writing(fh) as handle: - # (0) Comments - handle.write('#Information content of the most informative common ancestor for term pairs\n') - handle.write('#' + self.metadata_to_str() + '\n') - - # (1) Header - fieldnames = ['term_a', 'term_b', 'ic_mica'] - writer = csv.DictWriter(handle, fieldnames=fieldnames) - writer.writeheader() - - # (2) Entries - for left, right, sim in self.items(): - writer.writerow({'term_a': left, 'term_b': right, 'ic_mica': sim}) - - @staticmethod - def from_csv(fh: typing.Union[str, typing.IO]): - header = [] - records = [] - - def store_header(row: str) -> bool: - if row[0] == '#': - header.append(row) - return False - return True - - with open_text_io_handle_for_reading(fh) as handle: - reader = csv.DictReader(filter(store_header, handle)) - for record in reader: - records.append((record['term_a'], record['term_b'], float(record['ic_mica']))) - - meta = SimilarityContainer._parse_meta(header) - data = SimilarityContainer(meta) - for record in records: - data.set_similarity(record[0], record[1], record[2]) - - return data - - @staticmethod - def _parse_meta(header: typing.Sequence[str]) -> typing.Mapping[str, str]: - # Poor man's parsing. - if len(header) < 2 or len(header[1]) < 2: - return {} - else: - # The 2nd line is the metadata line, and we strip off the first and the last char (# and \n) - return MetadataAware.metadata_from_str(header[1][1:-1]) - - def __len__(self) -> int: - return sum([len(inner) for inner in self._data.values()]) - - def _get_common_ancestors(hpo: MinimalOntology, left: TermId, right: TermId) -> frozenset[TermId]: From e3962cf6395abb0ed1da48ebbee676510f97dfc4 Mon Sep 17 00:00:00 2001 From: Daniel Danis Date: Wed, 3 May 2023 17:52:25 -0400 Subject: [PATCH 15/39] Implement serialization of the TermId2IC container. --- src/hpotk/algorithm/similarity/_ic.py | 2 +- src/hpotk/algorithm/similarity/_model.py | 27 +++++++++++++++++++++--- src/hpotk/model/_base.py | 2 +- 3 files changed, 26 insertions(+), 5 deletions(-) diff --git a/src/hpotk/algorithm/similarity/_ic.py b/src/hpotk/algorithm/similarity/_ic.py index ed02591..a0f6c23 100644 --- a/src/hpotk/algorithm/similarity/_ic.py +++ b/src/hpotk/algorithm/similarity/_ic.py @@ -42,5 +42,5 @@ def calculate_ic_for_annotated_items(items: AnnotatedItemContainer, population_count = hit_count[root] data = {term_id: -log_func(count / population_count) for term_id, count in hit_count.items()} - metadata = {'version': items.version} + metadata = {'annotated_items_version': items.version} return SimpleAnnotationIcContainer(data, metadata=metadata) diff --git a/src/hpotk/algorithm/similarity/_model.py b/src/hpotk/algorithm/similarity/_model.py index abe851e..1f7e19a 100644 --- a/src/hpotk/algorithm/similarity/_model.py +++ b/src/hpotk/algorithm/similarity/_model.py @@ -12,7 +12,28 @@ class AnnotationIcContainer(typing.Mapping[TermId, float], MetadataAware, metacl """ A container for storing information content of item annotations. """ - pass + + def to_csv(self, fh: typing.Union[str, typing.IO]): + """ + Store the term ID to IC mapping with metadata into a CSV file. + :param fh: where to write the + :return: + """ + now = datetime.now() + self.metadata['created'] = now.strftime('%Y-%m-%d-%H:%M:%S') + with open_text_io_handle_for_writing(fh) as handle: + # (0) Comments + handle.write('#Information content of the term ID calculated from HPO annotations\n') + handle.write('#' + self.metadata_to_str() + '\n') + + # (1) Header + fieldnames = ['term_id', 'ic'] + writer = csv.DictWriter(handle, fieldnames=fieldnames) + writer.writeheader() + + # (2) Entries + for term_id, ic in self.items(): + writer.writerow({'term_id': term_id, 'ic': ic}) class SimpleAnnotationIcContainer(AnnotationIcContainer): @@ -43,7 +64,7 @@ def __iter__(self) -> typing.Iterator[TermId]: return iter(self._data) @property - def metadata(self) -> typing.Mapping[str, str]: + def metadata(self) -> typing.MutableMapping[str, str]: return self._meta @@ -118,7 +139,7 @@ def outer() -> defaultdict: return defaultdict(outer) def to_csv(self, fh: typing.Union[str, typing.IO]): - now = datetime.datetime.now() + now = datetime.now() self._meta['created'] = now.strftime('%Y-%m-%d-%H:%M:%S') with open_text_io_handle_for_writing(fh) as handle: # (0) Comments diff --git a/src/hpotk/model/_base.py b/src/hpotk/model/_base.py index 6e6fe33..47b3f80 100644 --- a/src/hpotk/model/_base.py +++ b/src/hpotk/model/_base.py @@ -53,7 +53,7 @@ class MetadataAware(metaclass=abc.ABCMeta): @property @abc.abstractmethod - def metadata(self) -> typing.Mapping[str, str]: + def metadata(self) -> typing.MutableMapping[str, str]: """ :return: a mapping with entity metadata. """ From 2ca04ad84633eb9bf3e6e07dd2f651d3d2b73849 Mon Sep 17 00:00:00 2001 From: Daniel Danis Date: Tue, 9 May 2023 17:15:17 -0400 Subject: [PATCH 16/39] Implement incremental building of the ontology graph. Deprecate `CsrGraphFactory`. --- src/hpotk/graph/__init__.py | 3 +- src/hpotk/graph/_csr_graph.py | 14 +- src/hpotk/graph/_factory.py | 171 +++++++++++++++++---- src/hpotk/graph/csr/__init__.py | 3 +- src/hpotk/graph/csr/_csr.py | 6 + src/hpotk/graph/test__factory.py | 146 ++++++++++++++++++ src/hpotk/ontology/load/obographs/_load.py | 6 +- tests/ontology/__init__.py | 0 tests/ontology/load/__init__.py | 0 tests/ontology/load/test_obographs.py | 166 ++++++++++++++++++++ 10 files changed, 477 insertions(+), 38 deletions(-) create mode 100644 src/hpotk/graph/test__factory.py create mode 100644 tests/ontology/__init__.py create mode 100644 tests/ontology/load/__init__.py create mode 100644 tests/ontology/load/test_obographs.py diff --git a/src/hpotk/graph/__init__.py b/src/hpotk/graph/__init__.py index 312c1e7..27b3694 100644 --- a/src/hpotk/graph/__init__.py +++ b/src/hpotk/graph/__init__.py @@ -1,3 +1,4 @@ from ._api import OntologyGraph, GraphAware, OWL_THING from ._csr_graph import SimpleCsrOntologyGraph -from ._factory import GraphFactory, CsrGraphFactory +from ._factory import CsrGraphFactory # REMOVE(v1.0.0) +from ._factory import GraphFactory, IncrementalCsrGraphFactory diff --git a/src/hpotk/graph/_csr_graph.py b/src/hpotk/graph/_csr_graph.py index 7562893..412f7ef 100644 --- a/src/hpotk/graph/_csr_graph.py +++ b/src/hpotk/graph/_csr_graph.py @@ -1,5 +1,7 @@ import typing +import numpy as np + from ._api import OntologyGraph, NODE from .csr import ImmutableCsrMatrix @@ -17,7 +19,7 @@ def __init__(self, root: NODE, nodes: typing.Sequence[NODE], connectivity_matrix: ImmutableCsrMatrix): self._root = root - self._nodes = nodes + self._nodes = np.array(nodes) self._node_to_idx = {node: idx for idx, node in enumerate(nodes)} self._connectivity_matrix = connectivity_matrix @@ -26,12 +28,14 @@ def root(self) -> NODE: return self._root def get_children(self, source: NODE) -> typing.Iterator[NODE]: - return self._get_nodes_with_relationship(source, - SimpleCsrOntologyGraph.CHILD_RELATIONSHIP_CODE) + # In other words, find a row in the CSR corresponding to the `source` + # and retrieve the columns to which the `source` is the PARENT. + return self._get_nodes_with_relationship(source, SimpleCsrOntologyGraph.PARENT_RELATIONSHIP_CODE) def get_parents(self, source: NODE) -> typing.Iterator[NODE]: - return self._get_nodes_with_relationship(source, - SimpleCsrOntologyGraph.PARENT_RELATIONSHIP_CODE) + # In other words, find a row in the CSR corresponding to the `source` + # and retrieve the columns to which the `source` is the CHILD. + return self._get_nodes_with_relationship(source, SimpleCsrOntologyGraph.CHILD_RELATIONSHIP_CODE) def _get_nodes_with_relationship(self, source, relationship): node_idx = self._node_to_idx[source] diff --git a/src/hpotk/graph/_factory.py b/src/hpotk/graph/_factory.py index 54c663a..d505c52 100644 --- a/src/hpotk/graph/_factory.py +++ b/src/hpotk/graph/_factory.py @@ -1,14 +1,15 @@ import abc +import bisect import logging import typing +import warnings +from collections import defaultdict from hpotk.model import TermId from ._api import OntologyGraph, NODE, OWL_THING from ._csr_graph import SimpleCsrOntologyGraph from .csr import CsrMatrixBuilder, ImmutableCsrMatrix -import numpy as np - # A newtype for stronger typing. We use these in `GraphFactory` below. DirectedEdge = typing.Tuple[TermId, TermId] GRAPH = typing.TypeVar('GRAPH', bound=OntologyGraph) @@ -33,53 +34,73 @@ def create_graph(self, edge_list: typing.Sequence[DirectedEdge]) -> GRAPH: pass -class CsrGraphFactory(GraphFactory[SimpleCsrOntologyGraph]): - """ - A factory for creating `OntologyGraph` that is backed by a compressed sparse row (CSR) connectivity matrix. - """ +class AbstractCsrGraphFactory(GraphFactory[SimpleCsrOntologyGraph], metaclass=abc.ABCMeta): - def create_graph(self, edge_list: typing.Sequence[DirectedEdge]) -> SimpleCsrOntologyGraph: + def create_graph(self, edge_list: typing.Sequence[DirectedEdge]) -> GRAPH: # Find root node self._logger.debug(f'Creating ontology graph from {len(edge_list)} edges') root, edge_list = _phenol_find_root(edge_list) self._logger.debug(f'Found root {root.value}') - # Prepare node list - nodes = _extract_nodes(edge_list) + # Prepare node list. We MUST sort the list, otherwise building of the IncrementalCsrMatrix won't work. + nodes = get_list_of_unique_and_sorted_nodes(edge_list) self._logger.debug(f'Extracted {len(nodes)} nodes') - # Build connectivity matrix + # Build the adjacency matrix self._logger.debug(f'Building sparse adjacency matrix') + cm = self._build_adjacency_matrix(nodes, edge_list) + # Assemble the ontology + self._logger.debug(f'Finalizing the ontology graph') + return SimpleCsrOntologyGraph(root, nodes, cm) + + @abc.abstractmethod + def _build_adjacency_matrix(self, nodes: typing.Sequence[TermId], + edges: typing.Sequence[DirectedEdge]) -> ImmutableCsrMatrix: + pass + + +class CsrGraphFactory(AbstractCsrGraphFactory): + """ + A factory for creating `OntologyGraph` that is backed by a compressed sparse row (CSR) connectivity matrix. + + The factory was deprecated. Use :class:`hpotk.graph.IncrementalCsrGraphFactory` instead. + """ + + def __init__(self): + # REMOVE(v1.0.0) + warnings.warn('CsrGraphFactory was deprecated and will be removed in v1.0.0', DeprecationWarning, stacklevel=2) + super().__init__() + + def _build_adjacency_matrix(self, nodes: typing.Sequence[TermId], + edges: typing.Sequence[DirectedEdge]): node_to_idx = {node: idx for idx, node in enumerate(nodes)} builder = CsrMatrixBuilder(shape=(len(nodes), len(nodes))) - - for edge in edge_list: + for edge in edges: src_idx = node_to_idx[edge[0]] dest_idx = node_to_idx[edge[1]] - builder[src_idx, dest_idx] = SimpleCsrOntologyGraph.PARENT_RELATIONSHIP_CODE - builder[dest_idx, src_idx] = SimpleCsrOntologyGraph.CHILD_RELATIONSHIP_CODE - - self._logger.debug(f'Assembling the adjacency matrix') - connectivity_matrix = ImmutableCsrMatrix(builder.row, - builder.col, - builder.data, - builder.shape, - dtype=int) - # Assemble the ontology - self._logger.debug(f'Finalizing the ontology graph') - return SimpleCsrOntologyGraph(root, nodes, connectivity_matrix) + builder[src_idx, dest_idx] = SimpleCsrOntologyGraph.CHILD_RELATIONSHIP_CODE + builder[dest_idx, src_idx] = SimpleCsrOntologyGraph.PARENT_RELATIONSHIP_CODE + return ImmutableCsrMatrix(builder.row, + builder.col, + builder.data, + builder.shape, + dtype=int) -def _extract_and_sort_nodes(edge_list: typing.Sequence[DirectedEdge]): - return np.sort(_extract_nodes(edge_list)) +def get_list_of_unique_and_sorted_nodes(edge_list: typing.Sequence[DirectedEdge]): + return list(sorted(get_unique_nodes(edge_list))) -def _extract_nodes(edge_list: typing.Sequence[DirectedEdge]): +def get_list_of_unique_nodes(edge_list: typing.Sequence[DirectedEdge]): + return list(get_unique_nodes(edge_list)) + + +def get_unique_nodes(edge_list: typing.Sequence[DirectedEdge]) -> typing.Collection[TermId]: nodes: typing.Set[TermId] = set() for edge in edge_list: nodes.add(edge[0]) nodes.add(edge[1]) - return np.array(list(nodes), dtype=object) + return nodes def _phenol_find_root(edge_list: typing.Sequence[DirectedEdge]) -> typing.Tuple[NODE, typing.Sequence[DirectedEdge]]: @@ -116,3 +137,97 @@ def _phenol_find_root(edge_list: typing.Sequence[DirectedEdge]) -> typing.Tuple[ edge_list_copy.append(edge) return OWL_THING, edge_list_copy + + +class IncrementalCsrGraphFactory(AbstractCsrGraphFactory): + """ + The CSR graph factory that builds the `row`, `col` and `data` in an incremental fashion. + """ + + def _build_adjacency_matrix(self, nodes: typing.Sequence[TermId], + edges: typing.Sequence[DirectedEdge]): + row, col, data = make_row_col_data(nodes, edges) + shape = (len(nodes), len(nodes)) + return ImmutableCsrMatrix(row, col, data, shape, dtype=int) + + +def make_row_col_data(nodes: typing.Sequence[TermId], + edge_list: typing.Sequence[DirectedEdge]): + row = [0] + col = [] + data = [] + partitioned_edges = _partition_edges(nodes, edge_list) + + for row_idx, node in enumerate(nodes): + relevant_edges = partitioned_edges[row_idx] + + for target, relationship_code in sorted(_preprocess_edges(node, relevant_edges), + key=lambda e: e[0]): # We sort by the TermId + idx = _index_of_using_binary_search(nodes, target) + col.append(idx) + data.append(relationship_code) + + row.append(len(data)) + + return row, col, data + + +def _partition_edges(nodes: typing.Sequence[TermId], + edge_list: typing.Sequence[DirectedEdge]) -> typing.Mapping[int, typing.Sequence[DirectedEdge]]: + """ + Prepare a mapping from a node index to all edges that reference the node. + + :param nodes: a sequence of nodes. + :param edge_list: a sequence of edges. + :return: a mapping from a node index to a sequence of edges that reference the node. + """ + data = defaultdict(list) + last_src = None + last_idx = None + for edge in edge_list: + src = edge[0] + if src == last_src: + # leverage Let's save one binary search + src_idx = last_idx + else: + last_src = src + src_idx = _index_of_using_binary_search(nodes, src) + last_idx = src_idx + dest = edge[1] + dest_idx = _index_of_using_binary_search(nodes, dest) + + if src_idx is not None: + data[src_idx].append(edge) + if dest_idx is not None: + data[dest_idx].append(edge) + + return data + + +def _preprocess_edges(source: TermId, + relevant_edges: typing.Iterable[DirectedEdge]): + """ + Get a generator for yielding tuples with a term_id and a relationship code for terms/nodes that have a relationship + with the `source`. + + :param source: a term ID for which we are generating the CSR row. + :param relevant_edges: a sequence of edges that reference the `source` term ID + :return: a tuple with the node/term ID and the relationship to store in the graph. + """ + for edge in relevant_edges: + sub, obj = edge + if source != sub and source == obj: + # `source` is the object. Since we are getting `is_a` relationships, the current edge must represent + # something `is_a` `source`, hence `source` is the parent. + yield sub, SimpleCsrOntologyGraph.PARENT_RELATIONSHIP_CODE + elif source != obj and source == sub: + yield obj, SimpleCsrOntologyGraph.CHILD_RELATIONSHIP_CODE + else: + raise ValueError(f'source {source} must either be a subject or object of the edge {edge}') + + +def _index_of_using_binary_search(a: typing.Sequence[TermId], x: TermId) -> typing.Optional[int]: + idx = bisect.bisect_left(a, x) + if idx != len(a) and a[idx] == x: + return idx + return None diff --git a/src/hpotk/graph/csr/__init__.py b/src/hpotk/graph/csr/__init__.py index 22e3fc8..a4e3924 100644 --- a/src/hpotk/graph/csr/__init__.py +++ b/src/hpotk/graph/csr/__init__.py @@ -1 +1,2 @@ -from ._csr import CsrMatrixBuilder, ImmutableCsrMatrix +from ._csr import CsrMatrixBuilder # REMOVE(v1.0.0) +from ._csr import ImmutableCsrMatrix diff --git a/src/hpotk/graph/csr/_csr.py b/src/hpotk/graph/csr/_csr.py index da4e2cf..39cf359 100644 --- a/src/hpotk/graph/csr/_csr.py +++ b/src/hpotk/graph/csr/_csr.py @@ -1,5 +1,6 @@ import abc import typing +import warnings import numpy as np from collections import deque @@ -14,6 +15,9 @@ def shape(self): class CsrMatrixBuilder(ShapedMixin): + """ + The builder has been deprecated due to poor performance and will be removed in v1.0.0. + """ def __init__(self, shape: typing.Tuple[int, int]): _check_shape(shape) @@ -21,6 +25,8 @@ def __init__(self, shape: typing.Tuple[int, int]): self._row = np.zeros(shape=(shape[0] + 1,), dtype=int) self._col = deque([]) self._data = deque([]) + warnings.warn('CsrMatrixBuilder has been deprecated and will be removed in v1.0.0', + DeprecationWarning, stacklevel=2) def __setitem__(self, key, value): if isinstance(key, tuple): diff --git a/src/hpotk/graph/test__factory.py b/src/hpotk/graph/test__factory.py new file mode 100644 index 0000000..a5407d7 --- /dev/null +++ b/src/hpotk/graph/test__factory.py @@ -0,0 +1,146 @@ +import unittest + +import ddt +import numpy as np + +from hpotk.model import TermId +from ._csr_graph import SimpleCsrOntologyGraph +from ._factory import IncrementalCsrGraphFactory +from ._factory import make_row_col_data + + +def make_nodes_and_edges(): + """Prepare nodes and edges for testing.""" + # Nodes are sorted. + nodes = [ + TermId.from_curie('HP:01'), + TermId.from_curie('HP:010'), + TermId.from_curie('HP:011'), + TermId.from_curie('HP:0110'), + TermId.from_curie('HP:02'), + TermId.from_curie('HP:020'), + TermId.from_curie('HP:021'), + TermId.from_curie('HP:022'), + TermId.from_curie('HP:03'), + TermId.from_curie('HP:1'), + ] + + # Edges for a graph with a single root node: HP:1 + edges = [ + # source -> destination + (TermId.from_curie('HP:01'), TermId.from_curie('HP:1')), + (TermId.from_curie('HP:010'), TermId.from_curie('HP:01')), + (TermId.from_curie('HP:011'), TermId.from_curie('HP:01')), + # This one is multi-parent. + (TermId.from_curie('HP:0110'), TermId.from_curie('HP:010')), + (TermId.from_curie('HP:0110'), TermId.from_curie('HP:011')), + + (TermId.from_curie('HP:02'), TermId.from_curie('HP:1')), + (TermId.from_curie('HP:020'), TermId.from_curie('HP:02')), + (TermId.from_curie('HP:021'), TermId.from_curie('HP:02')), + (TermId.from_curie('HP:022'), TermId.from_curie('HP:02')), + + (TermId.from_curie('HP:03'), TermId.from_curie('HP:1')), + ] + return nodes, edges + + +class TestFunctions(unittest.TestCase): + """ + Test the functions of the `_factory.py` file. + """ + + def test_make_row_col_data(self): + """ + We must get these `row`, `col`, and `data` values from given `nodes` and `edges`. + """ + nodes, edges = make_nodes_and_edges() + + row, col, data = make_row_col_data(nodes, edges) + + self.assertListEqual(row, [0, 3, 5, 7, 9, 13, 14, 15, 16, 17, 20]) + self.assertListEqual(col, [1, 2, 9, 0, 3, 0, 3, 1, 2, 5, 6, 7, 9, 4, 4, 4, 9, 0, 4, 8]) + self.assertListEqual(data, [-1, -1, 1, 1, -1, 1, -1, 1, 1, -1, -1, -1, 1, 1, 1, 1, 1, -1, -1, -1]) + + @unittest.skip + def test_compare_with_scipy(self): + """ + Compare that the row, col, data arrays are the same as those obtained from scipy.dense.csr_matrix when + starting from a dense matrix. + """ + # ############################## Expected values ############################## + try: + from scipy.sparse import csr_matrix + except ImportError: + raise Exception(f'We cannot run this test if scipy is not installed.') + # This is the dense array that we expect for the nodes and edges created in `make_nodes_and_edges()` + expected = np.array([[0, -1, -1, 0, 0, 0, 0, 0, 0, 1], + [1, 0, 0, -1, 0, 0, 0, 0, 0, 0], + [1, 0, 0, -1, 0, 0, 0, 0, 0, 0], + [0, 1, 1, 0, 0, 0, 0, 0, 0, 0], + [0, 0, 0, 0, 0, -1, -1, -1, 0, 1], + [0, 0, 0, 0, 1, 0, 0, 0, 0, 0], + [0, 0, 0, 0, 1, 0, 0, 0, 0, 0], + [0, 0, 0, 0, 1, 0, 0, 0, 0, 0], + [0, 0, 0, 0, 0, 0, 0, 0, 0, 1], + [1, 0, 0, 0, -1, 0, 0, 0, -1, 0]]) + csr = csr_matrix(expected) + + # ############################## Actual values ############################## + row, col, data = make_row_col_data(*make_nodes_and_edges()) + + np.array_equal(csr.indptr, row) + np.array_equal(csr.indices, col) + np.array_equal(csr.data, data) + + +class TestIncrementalCsrGraphFactory(unittest.TestCase): + + def setUp(self) -> None: + self.factory = IncrementalCsrGraphFactory() + + def test_create_graph(self): + nodes, edges = make_nodes_and_edges() + + graph = self.factory.create_graph(edges) + self.assertEqual(graph.root, TermId.from_curie('HP:1')) + + +@ddt.ddt +class TestTraversalOfIncrementalCsrGraphFactory(unittest.TestCase): + GRAPH: SimpleCsrOntologyGraph + + @classmethod + def setUpClass(cls) -> None: + nodes, edges = make_nodes_and_edges() + factory = IncrementalCsrGraphFactory() + cls.GRAPH: SimpleCsrOntologyGraph = factory.create_graph(edges) + + @ddt.data( + ("HP:1", {"HP:01", "HP:02", "HP:03"}), + ("HP:01", {"HP:010", "HP:011"}), + ("HP:010", {"HP:0110"}), + ("HP:011", {"HP:0110"}), + ("HP:0110", {}), + + ("HP:02", {"HP:020", "HP:021", "HP:022"}), + + ("HP:03", {}) + ) + @ddt.unpack + def test_get_children(self, source, expected): + children = set(self.GRAPH.get_children(TermId.from_curie(source))) + self.assertSetEqual(children, set([TermId.from_curie(curie) for curie in expected])) + + @ddt.data( + ("HP:1", {}), + ("HP:01", {"HP:1"}), + ("HP:010", {"HP:01"}), + ("HP:0110", {"HP:010", "HP:011"}), + + ("HP:03", {"HP:1"}) + ) + @ddt.unpack + def test_get_parents(self, source, expected): + children = set(self.GRAPH.get_parents(TermId.from_curie(source))) + self.assertSetEqual(children, set([TermId.from_curie(curie) for curie in expected])) diff --git a/src/hpotk/ontology/load/obographs/_load.py b/src/hpotk/ontology/load/obographs/_load.py index 85753db..e366842 100644 --- a/src/hpotk/ontology/load/obographs/_load.py +++ b/src/hpotk/ontology/load/obographs/_load.py @@ -5,7 +5,7 @@ from hpotk.model import TermId, MinimalTerm, Term from hpotk.graph import OntologyGraph -from hpotk.graph import GraphFactory, CsrGraphFactory, OWL_THING +from hpotk.graph import GraphFactory, IncrementalCsrGraphFactory, OWL_THING from hpotk.ontology import MinimalOntology, Ontology, create_ontology, create_minimal_ontology from hpotk.util import open_text_io_handle_for_reading @@ -24,13 +24,13 @@ def load_minimal_ontology(file: typing.Union[typing.IO, str], term_factory: ObographsTermFactory[MinimalTerm] = MinimalTermFactory(), - graph_factory: GraphFactory = CsrGraphFactory()) -> MinimalOntology: + graph_factory: GraphFactory = IncrementalCsrGraphFactory()) -> MinimalOntology: return _load_impl(file, term_factory, graph_factory, create_minimal_ontology) def load_ontology(file: typing.Union[typing.IO, str], term_factory: ObographsTermFactory[Term] = TermFactory(), - graph_factory: GraphFactory = CsrGraphFactory()) -> Ontology: + graph_factory: GraphFactory = IncrementalCsrGraphFactory()) -> Ontology: return _load_impl(file, term_factory, graph_factory, create_ontology) diff --git a/tests/ontology/__init__.py b/tests/ontology/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tests/ontology/load/__init__.py b/tests/ontology/load/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tests/ontology/load/test_obographs.py b/tests/ontology/load/test_obographs.py new file mode 100644 index 0000000..5562464 --- /dev/null +++ b/tests/ontology/load/test_obographs.py @@ -0,0 +1,166 @@ +import datetime +import os +import unittest + +from pkg_resources import resource_filename + +import hpotk as hp +from hpotk.graph import CsrGraphFactory, IncrementalCsrGraphFactory +from hpotk.model import TermId +from hpotk.ontology.load.obographs import * + +TOY_HPO = resource_filename(__name__, os.path.join('../../data', 'hp.toy.json')) + +hp.util.setup_logging() + + +@unittest.skip +class TestBench(unittest.TestCase): + + HPO = '/home/ielis/data/ontologies/hpo/2023-04-05/hp.2023-04-05.json' + + def test_load_old(self): + start = datetime.datetime.now() + hpo = load_minimal_ontology(self.HPO, graph_factory=CsrGraphFactory()) + end = datetime.datetime.now() + print(end - start) + + def test_load_new(self): + start = datetime.datetime.now() + hpo = load_minimal_ontology(self.HPO, graph_factory=IncrementalCsrGraphFactory()) + end = datetime.datetime.now() + print(end - start) + + +class TestLoad(unittest.TestCase): + + def test_load_minimal_ontology(self): + o: hp.ontology.MinimalOntology = load_minimal_ontology(TOY_HPO) + self.assertIsNotNone(o, "Ontology must not be None") + self.assertIsInstance(o, hp.ontology.MinimalOntology) + self.assertEqual(o.version, '2022-10-05') + self.assertEqual(393, len(o), "There must be 393 terms in the ontology") + self.assertEqual(557, len(list(o.term_ids)), "There must be 557 term IDs in the ontology") + self.assertEqual(557, len(set(o.term_ids)), "There must be 557 unique term IDs in the ontology") + self.assertTrue(all([term_id in o for term_id in o.term_ids]), "The ontology must contain all term IDs") + self.assertTrue(all([o.get_term(k) is not None for k in o.term_ids]), + "The `get_term` must get primary term for any term ID from ontology") + self.assertTrue(all([o.get_term(k.value) is not None for k in o.term_ids]), + "The `get_term` must get primary term for any term ID value from ontology") + self.assertTrue(all([o.get_term(k).identifier == k or k in o.get_term(k).alt_term_ids for k in o.term_ids]), + "Each term ID must be either primary or alternative ID") + + def test_load_ontology(self): + o: hp.ontology.Ontology = load_ontology(TOY_HPO) + self.assertIsNotNone(o, "Ontology must not be None") + self.assertIsInstance(o, hp.ontology.Ontology) + self.assertEqual(o.version, '2022-10-05') + self.assertEqual(393, len(o), "There must be 393 terms in the ontology") + self.assertEqual(557, len(list(o.term_ids)), "There must be 557 term IDs in the ontology") + self.assertEqual(557, len(set(o.term_ids)), "There must be 557 unique term IDs in the ontology") + self.assertTrue(all([term_id in o for term_id in o.term_ids]), "The ontology must contain all term IDs") + self.assertTrue(all([o.get_term(k) is not None for k in o.term_ids]), + "The `get_term` must get primary term for any term ID from ontology") + self.assertTrue(all([o.get_term(k).identifier == k or k in o.get_term(k).alt_term_ids for k in o.term_ids]), + "Each term ID must be either primary or alternative ID") + + def test_load_minimal_ontology_backed_by_csr(self): + term_factory = hp.ontology.load.obographs.MinimalTermFactory() + graph_factory = hp.graph.CsrGraphFactory() + o: hp.ontology.MinimalOntology = load_minimal_ontology(TOY_HPO, term_factory=term_factory, graph_factory=graph_factory) + self.assertIsNotNone(o, "Ontology must not be None") + + arachnodactyly = TermId.from_curie("HP:0001166") + assert all([val.value in {"HP:0001238", "HP:0100807"} for val in (o.graph.get_parents(arachnodactyly))]) + assert len(list(o.graph.get_children(arachnodactyly))) == 0 + + @unittest.skip + def test_real_life(self): + o: hp.ontology.Ontology = load_ontology('/home/ielis/data/ontologies/hpo/2023-01-27/hp.json') + self.assertIsNotNone(o, "Ontology must not be None") + + @unittest.skip + def test_print_stats(self): + import json + with open(TOY_HPO) as fh: + graphs = json.load(fh) + + graph = graphs['graphs'][0] + all_nodes = graph['nodes'] + all_edges = graph['edges'] + print(f'All nodes: {len(all_nodes)}, all edges: {len(all_edges)}') + current_nodes = self._get_current_nodes(all_nodes) + print(f'Current nodes: {len(current_nodes)}') + # Getting the number of all term IDs is too complicated to be implemented here at this moment. + # The functionality should be implemented later if necessary. + + @staticmethod + def _get_current_nodes(nodes): + result = [] + for node in nodes: + if 'meta' in node: + meta = node['meta'] + if 'deprecated' in meta: + deprecated = meta['deprecated'] + if not deprecated: + result.append(node) + else: + result.append(node) + return result + + +class TestTerms(unittest.TestCase): + """ + We only load the ontology once, and we test the properties of the loaded data. + """ + + ONTOLOGY: hp.ontology.Ontology = None + + @classmethod + def setUpClass(cls) -> None: + cls.ONTOLOGY = load_ontology(TOY_HPO) + + def test_term_properties(self): + # Test properties of a Term + term = TestTerms.ONTOLOGY.get_term('HP:0001626') + + self.assertEqual(term.identifier.value, 'HP:0001626') + self.assertEqual(term.name, 'Abnormality of the cardiovascular system') + self.assertEqual(term.definition, 'Any abnormality of the cardiovascular system.') + self.assertEqual(term.comment, 'The cardiovascular system consists of the heart, vasculature, and the ' + 'lymphatic system.') + self.assertEqual(term.is_obsolete, False) + self.assertListEqual(term.alt_term_ids, [TermId.from_curie('HP:0003116')]) + + synonyms = term.synonyms + self.assertEqual(len(synonyms), 3) + + one = synonyms[0] + self.assertEqual(one.name, 'Cardiovascular disease') + self.assertEqual(one.category, hp.model.SynonymCategory.RELATED) + self.assertEqual(one.synonym_type, hp.model.SynonymType.LAYPERSON_TERM) + self.assertIsNone(one.xrefs) + + two = synonyms[1] + self.assertEqual(two.name, 'Cardiovascular abnormality') + self.assertEqual(two.category, hp.model.SynonymCategory.EXACT) + self.assertEqual(two.synonym_type, hp.model.SynonymType.LAYPERSON_TERM) + self.assertIsNone(two.xrefs) + + three = synonyms[2] + self.assertEqual(three.name, 'Abnormality of the cardiovascular system') + self.assertEqual(three.category, hp.model.SynonymCategory.EXACT) + self.assertEqual(three.synonym_type, hp.model.SynonymType.LAYPERSON_TERM) + self.assertIsNone(three.xrefs) + + self.assertEqual(term.xrefs, [TermId.from_curie(curie) for curie in ('UMLS:C0243050', 'UMLS:C0007222', + 'MSH:D018376', 'SNOMEDCT_US:49601007', + 'MSH:D002318')]) + + def test_synonym_properties(self): + term = TestTerms.ONTOLOGY.get_term('HP:0001627') + synonym = term.synonyms[7] + self.assertEqual(synonym.name, 'Abnormally shaped heart') + self.assertEqual(synonym.category, hp.model.SynonymCategory.EXACT) + self.assertEqual(synonym.synonym_type, hp.model.SynonymType.LAYPERSON_TERM) + self.assertEqual(synonym.xrefs, [TermId.from_curie('ORCID:0000-0001-5208-3432')]) From 6cb5020cdb03caea9388585b757420e4e2d0e9a9 Mon Sep 17 00:00:00 2001 From: Daniel Danis Date: Tue, 9 May 2023 17:15:37 -0400 Subject: [PATCH 17/39] Add badges with build status and PyPi downloads. --- README.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/README.md b/README.md index 8fba702..bdd9126 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,8 @@ # hpo-toolkit +![Build status](https://img.shields.io/github/actions/workflow/status/TheJacksonLaboratory/hpo-toolkit/python_ci.yml) +![PyPi downloads](https://img.shields.io/pypi/dm/hpo-toolkit.svg?label=Pypi%20downloads) + A toolkit for working with Human Phenotype Ontology in Python ## Install From 64d07b4e65200d101110810833aed9608574cd25 Mon Sep 17 00:00:00 2001 From: Daniel Danis Date: Tue, 9 May 2023 17:17:05 -0400 Subject: [PATCH 18/39] Remove local tests. --- tests/ontology/load/test_obographs.py | 20 -------- tests/test_obographs.py | 72 --------------------------- 2 files changed, 92 deletions(-) diff --git a/tests/ontology/load/test_obographs.py b/tests/ontology/load/test_obographs.py index 5562464..3d0ed6c 100644 --- a/tests/ontology/load/test_obographs.py +++ b/tests/ontology/load/test_obographs.py @@ -1,11 +1,9 @@ -import datetime import os import unittest from pkg_resources import resource_filename import hpotk as hp -from hpotk.graph import CsrGraphFactory, IncrementalCsrGraphFactory from hpotk.model import TermId from hpotk.ontology.load.obographs import * @@ -14,24 +12,6 @@ hp.util.setup_logging() -@unittest.skip -class TestBench(unittest.TestCase): - - HPO = '/home/ielis/data/ontologies/hpo/2023-04-05/hp.2023-04-05.json' - - def test_load_old(self): - start = datetime.datetime.now() - hpo = load_minimal_ontology(self.HPO, graph_factory=CsrGraphFactory()) - end = datetime.datetime.now() - print(end - start) - - def test_load_new(self): - start = datetime.datetime.now() - hpo = load_minimal_ontology(self.HPO, graph_factory=IncrementalCsrGraphFactory()) - end = datetime.datetime.now() - print(end - start) - - class TestLoad(unittest.TestCase): def test_load_minimal_ontology(self): diff --git a/tests/test_obographs.py b/tests/test_obographs.py index 746ed75..00e823d 100644 --- a/tests/test_obographs.py +++ b/tests/test_obographs.py @@ -12,78 +12,6 @@ hp.util.setup_logging() -class TestObographs(unittest.TestCase): - - def test_load_minimal_ontology(self): - o: hp.ontology.MinimalOntology = load_minimal_ontology(TOY_HPO) - self.assertIsNotNone(o, "Ontology must not be None") - self.assertIsInstance(o, hp.ontology.MinimalOntology) - self.assertEqual(o.version, '2022-10-05') - self.assertEqual(393, len(o), "There must be 393 terms in the ontology") - self.assertEqual(557, len(list(o.term_ids)), "There must be 557 term IDs in the ontology") - self.assertEqual(557, len(set(o.term_ids)), "There must be 557 unique term IDs in the ontology") - self.assertTrue(all([term_id in o for term_id in o.term_ids]), "The ontology must contain all term IDs") - self.assertTrue(all([o.get_term(k) is not None for k in o.term_ids]), - "The `get_term` must get primary term for any term ID from ontology") - self.assertTrue(all([o.get_term(k.value) is not None for k in o.term_ids]), - "The `get_term` must get primary term for any term ID value from ontology") - self.assertTrue(all([o.get_term(k).identifier == k or k in o.get_term(k).alt_term_ids for k in o.term_ids]), - "Each term ID must be either primary or alternative ID") - - def test_load_ontology(self): - o: hp.ontology.Ontology = load_ontology(TOY_HPO) - self.assertIsNotNone(o, "Ontology must not be None") - self.assertIsInstance(o, hp.ontology.Ontology) - self.assertEqual(o.version, '2022-10-05') - self.assertEqual(393, len(o), "There must be 393 terms in the ontology") - self.assertEqual(557, len(list(o.term_ids)), "There must be 557 term IDs in the ontology") - self.assertEqual(557, len(set(o.term_ids)), "There must be 557 unique term IDs in the ontology") - self.assertTrue(all([term_id in o for term_id in o.term_ids]), "The ontology must contain all term IDs") - self.assertTrue(all([o.get_term(k) is not None for k in o.term_ids]), - "The `get_term` must get primary term for any term ID from ontology") - self.assertTrue(all([o.get_term(k).identifier == k or k in o.get_term(k).alt_term_ids for k in o.term_ids]), - "Each term ID must be either primary or alternative ID") - - def test_load_minimal_ontology_backed_by_csr(self): - term_factory = hp.ontology.load.obographs.MinimalTermFactory() - graph_factory = hp.graph.CsrGraphFactory() - o: hp.ontology.MinimalOntology = load_minimal_ontology(TOY_HPO, term_factory=term_factory, graph_factory=graph_factory) - self.assertIsNotNone(o, "Ontology must not be None") - - arachnodactyly = TermId.from_curie("HP:0001166") - assert all([val.value in {"HP:0001238", "HP:0100807"} for val in (o.graph.get_parents(arachnodactyly))]) - assert len(list(o.graph.get_children(arachnodactyly))) == 0 - - @unittest.skip - def test_print_stats(self): - import json - with open(TOY_HPO) as fh: - graphs = json.load(fh) - - graph = graphs['graphs'][0] - all_nodes = graph['nodes'] - all_edges = graph['edges'] - print(f'All nodes: {len(all_nodes)}, all edges: {len(all_edges)}') - current_nodes = self._get_current_nodes(all_nodes) - print(f'Current nodes: {len(current_nodes)}') - # Getting the number of all term IDs is too complicated to be implemented here at this moment. - # The functionality should be implemented later if necessary. - - @staticmethod - def _get_current_nodes(nodes): - result = [] - for node in nodes: - if 'meta' in node: - meta = node['meta'] - if 'deprecated' in meta: - deprecated = meta['deprecated'] - if not deprecated: - result.append(node) - else: - result.append(node) - return result - - class TestTerms(unittest.TestCase): """ We only load the ontology once, and we test the properties of the loaded data. From 8f9c70bdddf861de31bc3393b55fab03850f3a4b Mon Sep 17 00:00:00 2001 From: Daniel Danis Date: Tue, 9 May 2023 22:25:04 -0400 Subject: [PATCH 19/39] Add instance validation utilities. --- src/hpotk/util.py | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/src/hpotk/util.py b/src/hpotk/util.py index 1e23f3d..ec7dde3 100644 --- a/src/hpotk/util.py +++ b/src/hpotk/util.py @@ -140,3 +140,40 @@ def open_text_io_handle_for_writing(fh: typing.Union[str, typing.IO], return fh else: raise ValueError(f'Unexpected type {type(fh)}') + + +T = typing.TypeVar('T') + + +def validate_instance(obj: T, + clz: type, + param_name: typing.Optional[str] = None) -> T: + """ + Validate that `obj` is instance of `clz` or raise `ValueError` otherwise. + + :param obj: and instance for validation. + :param clz: the target class. + :param param_name: name of the object to include in the error message. + :return: the `obj` if the validation passes. + """ + if not isinstance(obj, clz): + if param_name is None: + raise ValueError(f'The object must be an instance of {clz} but was {type(obj)}') + else: + raise ValueError(f'{param_name} must be an instance of {clz} but was {type(obj)}') + return obj + + +def validate_optional_instance(obj: typing.Optional[T], + clz: type, + param_name: typing.Optional[str] = None) -> T: + """ + Validate that `obj` is instance of `clz` or `None`, or raise `ValueError` otherwise. + + :param obj: and instance for validation or `None`. + :param clz: the target class. + :param param_name: name of the object to include in the error message. + :return: the `obj` if the validation passes. + """ + if obj is not None: + return validate_instance(obj, clz, param_name) From 382579b9d8211e88b1020eb45879c4399de2017f Mon Sep 17 00:00:00 2001 From: Daniel Danis Date: Tue, 9 May 2023 22:30:24 -0400 Subject: [PATCH 20/39] Export the most commonly used data model classes at the top-level. --- src/hpotk/__init__.py | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/src/hpotk/__init__.py b/src/hpotk/__init__.py index 37d32c4..9f091a9 100644 --- a/src/hpotk/__init__.py +++ b/src/hpotk/__init__.py @@ -1,10 +1,14 @@ __version__ = "0.1.5dev0" -from . import model +from . import algorithm +from . import annotations from . import constants from . import graph +from . import model from . import ontology -from . import algorithm -from . import annotations -from . import validate from . import util +from . import validate + +from .graph import OntologyGraph, GraphAware +from .model import TermId, Term, MinimalTerm, Synonym, SynonymType, SynonymCategory +from .ontology import Ontology, MinimalOntology From 89ebbe71118bf5870af723740ee78a1ed53b9d2c Mon Sep 17 00:00:00 2001 From: Daniel Danis Date: Wed, 10 May 2023 10:42:30 -0400 Subject: [PATCH 21/39] Use binary search to look up node index in CSR ontology graph. Ontology graph performs lazy graph traversal and does not allocate intermediate container object. Increase test coverage. --- src/hpotk/graph/__init__.py | 2 +- src/hpotk/graph/_api.py | 10 +-- src/hpotk/graph/_csr_graph.py | 104 +++++++++++++++++++++------ src/hpotk/graph/_factory.py | 14 ++-- src/hpotk/graph/csr/_csr.py | 2 +- src/hpotk/graph/test__csr_graph.py | 110 +++++++++++++++++++++++++++++ 6 files changed, 209 insertions(+), 33 deletions(-) create mode 100644 src/hpotk/graph/test__csr_graph.py diff --git a/src/hpotk/graph/__init__.py b/src/hpotk/graph/__init__.py index 27b3694..8ff13f2 100644 --- a/src/hpotk/graph/__init__.py +++ b/src/hpotk/graph/__init__.py @@ -1,4 +1,4 @@ from ._api import OntologyGraph, GraphAware, OWL_THING -from ._csr_graph import SimpleCsrOntologyGraph +from ._csr_graph import SimpleCsrOntologyGraph # REMOVE(v1.0.0) from ._factory import CsrGraphFactory # REMOVE(v1.0.0) from ._factory import GraphFactory, IncrementalCsrGraphFactory diff --git a/src/hpotk/graph/_api.py b/src/hpotk/graph/_api.py index 1a306a1..665267f 100644 --- a/src/hpotk/graph/_api.py +++ b/src/hpotk/graph/_api.py @@ -1,9 +1,10 @@ import abc - import typing from hpotk.model import TermId +# TODO - enforce presence of the natural ordering? +# Note, the NODE must also have natural ordering. NODE = typing.TypeVar('NODE', bound=TermId) # Term ID that is added as an artificial root if >1 root candidates are found in the ontology graph. OWL_THING = TermId.from_curie("owl:Thing") @@ -13,7 +14,8 @@ class OntologyGraph(typing.Generic[NODE], metaclass=abc.ABCMeta): """ A simple graph with one node type and one edge type. - The graph is generic over a node type which must extend `hpotk.base.model.TermId`. The graph must not be empty + The graph is generic over a node type which must extend :class:`TermId`. + The graph must not be empty, it must consist of at least one node. """ @property @@ -22,11 +24,11 @@ def root(self) -> NODE: pass @abc.abstractmethod - def get_children(self, source: NODE) -> typing.Iterator[NODE]: + def get_children(self, source: NODE) -> typing.Iterable[NODE]: pass @abc.abstractmethod - def get_parents(self, source: NODE) -> typing.Iterator[NODE]: + def get_parents(self, source: NODE) -> typing.Iterable[NODE]: pass @abc.abstractmethod diff --git a/src/hpotk/graph/_csr_graph.py b/src/hpotk/graph/_csr_graph.py index 412f7ef..b88b5d1 100644 --- a/src/hpotk/graph/_csr_graph.py +++ b/src/hpotk/graph/_csr_graph.py @@ -1,49 +1,111 @@ +import abc +import bisect import typing +import warnings import numpy as np +from hpotk.model import TermId +from hpotk.util import validate_instance from ._api import OntologyGraph, NODE from .csr import ImmutableCsrMatrix -class SimpleCsrOntologyGraph(OntologyGraph): - """ - Simple CSR ontology graph uses a dict to map a NODE to connectivity matrix index. - """ - - # TODO - try replacing `self._node_to_idx` with binary search. +class BaseCsrOntologyGraph(OntologyGraph, metaclass=abc.ABCMeta): CHILD_RELATIONSHIP_CODE = 1 PARENT_RELATIONSHIP_CODE = -1 def __init__(self, root: NODE, - nodes: typing.Sequence[NODE], - connectivity_matrix: ImmutableCsrMatrix): - self._root = root - self._nodes = np.array(nodes) - self._node_to_idx = {node: idx for idx, node in enumerate(nodes)} - self._connectivity_matrix = connectivity_matrix + nodes: np.ndarray[NODE], + adjacency_matrix: ImmutableCsrMatrix): + self._root = validate_instance(root, TermId, 'root') + self._nodes = validate_instance(nodes, np.ndarray, 'nodes') + self._adjacency_matrix = validate_instance(adjacency_matrix, ImmutableCsrMatrix, 'adjacency_matrix') @property def root(self) -> NODE: return self._root - def get_children(self, source: NODE) -> typing.Iterator[NODE]: + def get_children(self, source: NODE) -> typing.Iterable[NODE]: # In other words, find a row in the CSR corresponding to the `source` # and retrieve the columns to which the `source` is the PARENT. - return self._get_nodes_with_relationship(source, SimpleCsrOntologyGraph.PARENT_RELATIONSHIP_CODE) + return map(self._get_node_for_idx, + self._get_nodes_with_relationship(source, SimpleCsrOntologyGraph.PARENT_RELATIONSHIP_CODE)) - def get_parents(self, source: NODE) -> typing.Iterator[NODE]: + def get_parents(self, source: NODE) -> typing.Iterable[NODE]: # In other words, find a row in the CSR corresponding to the `source` # and retrieve the columns to which the `source` is the CHILD. - return self._get_nodes_with_relationship(source, SimpleCsrOntologyGraph.CHILD_RELATIONSHIP_CODE) + return map(self._get_node_for_idx, + self._get_nodes_with_relationship(source, SimpleCsrOntologyGraph.CHILD_RELATIONSHIP_CODE)) - def _get_nodes_with_relationship(self, source, relationship): - node_idx = self._node_to_idx[source] - child_idxs = self._connectivity_matrix.col_indices_of_val(node_idx, relationship) - return self._nodes[child_idxs] + def _get_nodes_with_relationship(self, source: NODE, relationship) -> typing.Generator[int, None, None]: + row_idx = self._get_idx_for_node(source) + if row_idx is None: + return + col_indices = self._adjacency_matrix.col_indices_of_val(row_idx, relationship) + for col_idx in col_indices: + yield col_idx def __contains__(self, item: NODE) -> bool: - return item in self._node_to_idx + return self._get_idx_for_node(item) is not None def __iter__(self) -> typing.Iterator[NODE]: return iter(self._nodes) + + @abc.abstractmethod + def _get_idx_for_node(self, node: NODE) -> typing.Optional[int]: + pass + + def _get_node_for_idx(self, idx: int) -> NODE: + return self._nodes[idx] + + +class SimpleCsrOntologyGraph(BaseCsrOntologyGraph): + """ + An implementation of :class:`OntologyGraph` that uses a :class:`dict` to map a NODE to adjacency matrix index. + """ + + def __init__(self, root: NODE, + nodes: np.ndarray[NODE], + adjacency_matrix: ImmutableCsrMatrix): + super().__init__(root, nodes, adjacency_matrix) + self._node_to_idx = {node: idx for idx, node in enumerate(nodes)} + warnings.warn('SimpleCsrOntologyGraph will be removed from the public API in v1.0.0', DeprecationWarning, stacklevel=2) + + def _get_idx_for_node(self, node: NODE) -> typing.Optional[int]: + return self._node_to_idx[node] + + +class BisectPoweredCsrOntologyGraph(BaseCsrOntologyGraph): + """ + An implementation of :class:`OntologyGraph` that uses binary search to look up NODE index. + """ + + def __init__(self, root: NODE, + nodes: np.ndarray[NODE], + adjacency_matrix: ImmutableCsrMatrix, + skip_validation: bool = False): + super().__init__(root, nodes, adjacency_matrix) + if not skip_validation: + # NOTE - the `nodes` array ABSOLUTELY MUST be a sorted. + # Otherwise, the traversal functionality will not work! + check_items_are_sorted(nodes) + + def _get_idx_for_node(self, node: NODE) -> typing.Optional[int]: + idx = bisect.bisect_left(self._nodes, node) + if idx != len(self._nodes) and self._nodes[idx] == node: + return idx + return None + + +def check_items_are_sorted(items: typing.Iterable[NODE]): + """ + Check that items are sorted in ascending order according to their natural ordering. + :param items: an iterable of items. + :return: `None` if the items are sorted or raise :class:`ValueError` if the items is unsorted. + """ + previous = None + for i, node in enumerate(items): + if previous and node < previous: + raise ValueError(f'Unsorted sequence. Item #{i} ({node}) was less than #{i - 1} ({previous})') + previous = node diff --git a/src/hpotk/graph/_factory.py b/src/hpotk/graph/_factory.py index d505c52..3f44cd6 100644 --- a/src/hpotk/graph/_factory.py +++ b/src/hpotk/graph/_factory.py @@ -5,9 +5,11 @@ import warnings from collections import defaultdict +import numpy as np + from hpotk.model import TermId from ._api import OntologyGraph, NODE, OWL_THING -from ._csr_graph import SimpleCsrOntologyGraph +from ._csr_graph import SimpleCsrOntologyGraph, BisectPoweredCsrOntologyGraph from .csr import CsrMatrixBuilder, ImmutableCsrMatrix # A newtype for stronger typing. We use these in `GraphFactory` below. @@ -34,7 +36,7 @@ def create_graph(self, edge_list: typing.Sequence[DirectedEdge]) -> GRAPH: pass -class AbstractCsrGraphFactory(GraphFactory[SimpleCsrOntologyGraph], metaclass=abc.ABCMeta): +class AbstractCsrGraphFactory(GraphFactory[OntologyGraph], metaclass=abc.ABCMeta): def create_graph(self, edge_list: typing.Sequence[DirectedEdge]) -> GRAPH: # Find root node @@ -43,7 +45,7 @@ def create_graph(self, edge_list: typing.Sequence[DirectedEdge]) -> GRAPH: self._logger.debug(f'Found root {root.value}') # Prepare node list. We MUST sort the list, otherwise building of the IncrementalCsrMatrix won't work. - nodes = get_list_of_unique_and_sorted_nodes(edge_list) + nodes = get_array_of_unique_and_sorted_nodes(edge_list) self._logger.debug(f'Extracted {len(nodes)} nodes') # Build the adjacency matrix @@ -51,7 +53,7 @@ def create_graph(self, edge_list: typing.Sequence[DirectedEdge]) -> GRAPH: cm = self._build_adjacency_matrix(nodes, edge_list) # Assemble the ontology self._logger.debug(f'Finalizing the ontology graph') - return SimpleCsrOntologyGraph(root, nodes, cm) + return BisectPoweredCsrOntologyGraph(root, nodes, cm) @abc.abstractmethod def _build_adjacency_matrix(self, nodes: typing.Sequence[TermId], @@ -87,8 +89,8 @@ def _build_adjacency_matrix(self, nodes: typing.Sequence[TermId], dtype=int) -def get_list_of_unique_and_sorted_nodes(edge_list: typing.Sequence[DirectedEdge]): - return list(sorted(get_unique_nodes(edge_list))) +def get_array_of_unique_and_sorted_nodes(edge_list: typing.Sequence[DirectedEdge]) -> np.ndarray: + return np.fromiter(sorted(get_unique_nodes(edge_list)), dtype=object) def get_list_of_unique_nodes(edge_list: typing.Sequence[DirectedEdge]): diff --git a/src/hpotk/graph/csr/_csr.py b/src/hpotk/graph/csr/_csr.py index 39cf359..4fbdf9f 100644 --- a/src/hpotk/graph/csr/_csr.py +++ b/src/hpotk/graph/csr/_csr.py @@ -159,7 +159,7 @@ def __getitem__(self, item): def col_indices_of_val(self, row: int, query): """ - Return indices of colums with matching query value in a given row. + Return indices of columns with matching query value in a given row. Raises IndexError if `row` is out of bounds. """ diff --git a/src/hpotk/graph/test__csr_graph.py b/src/hpotk/graph/test__csr_graph.py new file mode 100644 index 0000000..b1c88eb --- /dev/null +++ b/src/hpotk/graph/test__csr_graph.py @@ -0,0 +1,110 @@ +import unittest + +import ddt +import numpy as np + +from hpotk.model import TermId + +from .csr import ImmutableCsrMatrix +from ._csr_graph import check_items_are_sorted +from ._csr_graph import BisectPoweredCsrOntologyGraph + + +@ddt.ddt +class TestFunctions(unittest.TestCase): + + @ddt.data( + ([],), + ([1],), + ([1, 2],), + (['a', 'b', 'c'],), + ) + @ddt.unpack + def test_check_items_are_sorted(self, items): + self.assertIsNone(check_items_are_sorted(items)) + + @ddt.data( + ([2, 1], 'Unsorted sequence. Item #1 (1) was less than #0 (2)'), + ([2, 1, 3, 4, 5, 6], 'Unsorted sequence. Item #1 (1) was less than #0 (2)'), + ([1, 2, 30, 4, 5, 6], 'Unsorted sequence. Item #3 (4) was less than #2 (30)'), + ([1, 2, 3, 4, 6, 5], 'Unsorted sequence. Item #5 (5) was less than #4 (6)'), + ) + @ddt.unpack + def test_check_items_are_sorted__unsorted_cases(self, items, message): + with self.assertRaises(ValueError) as ctx: + check_items_are_sorted(items) + self.assertEqual(message, ctx.exception.args[0]) + + +@ddt.ddt +class TestBisectPoweredCsrOntologyGraph(unittest.TestCase): + + NODES: np.ndarray + GRAPH: BisectPoweredCsrOntologyGraph + + @classmethod + def setUpClass(cls) -> None: + root = TermId.from_curie('HP:1') + curies = [ + 'HP:01', 'HP:010', 'HP:011', 'HP:0110', + 'HP:02', 'HP:020', 'HP:021', 'HP:022', + 'HP:03', 'HP:1' + ] + nodes = np.fromiter(map(TermId.from_curie, curies), dtype=object) + row = [0, 3, 5, 7, 9, 13, 14, 15, 16, 17, 20] + col = [1, 2, 9, 0, 3, 0, 3, 1, 2, 5, 6, 7, 9, 4, 4, 4, 9, 0, 4, 8] + data = [-1, -1, 1, 1, -1, 1, -1, 1, 1, -1, -1, -1, 1, 1, 1, 1, 1, -1, -1, -1] + am = ImmutableCsrMatrix(row, col, data, shape=(len(nodes), len(nodes)), dtype=int) + + cls.NODES = nodes + cls.GRAPH = BisectPoweredCsrOntologyGraph(root, nodes, am) + + def test_root(self): + self.assertEqual(TermId.from_curie('HP:1'), self.GRAPH.root) + + @ddt.data( + ('HP:1', ['HP:01', 'HP:02', 'HP:03']), + ('HP:1', ['HP:01', 'HP:02', 'HP:03']), + ('HP:02', ['HP:020', 'HP:021', 'HP:022']), + ('HP:03', []), + ) + @ddt.unpack + def test_get_children(self, source, expected): + src = TermId.from_curie(source) + expected = set(map(TermId.from_curie, expected)) + + actual = set(self.GRAPH.get_children(src)) + self.assertSetEqual(expected, actual) + + def test_get_children__unknown_node(self): + unknown = TermId.from_curie('HP:999') + expected = set(self.GRAPH.get_children(unknown)) + self.assertTrue(len(expected) == 0) + + @ddt.data( + ('HP:1', []), + ('HP:01', ['HP:1']), + ('HP:03', ['HP:1']), + ('HP:0110', ['HP:010', 'HP:011']), + ) + @ddt.unpack + def test_get_parents(self, source, expected): + src = TermId.from_curie(source) + expected = set(map(TermId.from_curie, expected)) + + actual = set(self.GRAPH.get_parents(src)) + self.assertSetEqual(expected, actual) + + def test_get_parents__unknown_node(self): + unknown = TermId.from_curie('HP:999') + expected = set(self.GRAPH.get_parents(unknown)) + self.assertTrue(len(expected) == 0) + + def test_contains(self): + for node in self.NODES: + self.assertTrue(node in self.GRAPH) + + def test_iter(self): + expected = set(self.NODES) + actual = set(iter(self.GRAPH)) + self.assertSetEqual(expected, actual) From 84fc8acea2636f49745ccf9d6f38ac945b7005ba Mon Sep 17 00:00:00 2001 From: Daniel Danis Date: Wed, 10 May 2023 14:08:59 -0400 Subject: [PATCH 22/39] Implement getting ancestors and descendants of an ontology graph node. Improve python docs. --- src/hpotk/graph/_api.py | 23 +++++++++++++ src/hpotk/graph/_csr_graph.py | 54 ++++++++++++++++++++++++------ src/hpotk/graph/test__csr_graph.py | 38 +++++++++++++++++++++ 3 files changed, 105 insertions(+), 10 deletions(-) diff --git a/src/hpotk/graph/_api.py b/src/hpotk/graph/_api.py index 665267f..1bc970a 100644 --- a/src/hpotk/graph/_api.py +++ b/src/hpotk/graph/_api.py @@ -21,14 +21,37 @@ class OntologyGraph(typing.Generic[NODE], metaclass=abc.ABCMeta): @property @abc.abstractmethod def root(self) -> NODE: + """ + Get the root node of the ontology graph. + """ pass @abc.abstractmethod def get_children(self, source: NODE) -> typing.Iterable[NODE]: + """ + Get an iterable with the children of the `source` node. + """ + pass + + @abc.abstractmethod + def get_descendants(self, source: NODE) -> typing.Iterable[NODE]: + """ + Get an iterable with the descendants of the `source` node. + """ pass @abc.abstractmethod def get_parents(self, source: NODE) -> typing.Iterable[NODE]: + """ + Get an iterable with the parents of the `source` node. + """ + pass + + @abc.abstractmethod + def get_ancestors(self, source: NODE) -> typing.Iterable[NODE]: + """ + Get an iterable with the ancestors of the `source` node. + """ pass @abc.abstractmethod diff --git a/src/hpotk/graph/_csr_graph.py b/src/hpotk/graph/_csr_graph.py index b88b5d1..0a4cd91 100644 --- a/src/hpotk/graph/_csr_graph.py +++ b/src/hpotk/graph/_csr_graph.py @@ -2,6 +2,7 @@ import bisect import typing import warnings +from collections import deque import numpy as np @@ -30,21 +31,23 @@ def get_children(self, source: NODE) -> typing.Iterable[NODE]: # In other words, find a row in the CSR corresponding to the `source` # and retrieve the columns to which the `source` is the PARENT. return map(self._get_node_for_idx, - self._get_nodes_with_relationship(source, SimpleCsrOntologyGraph.PARENT_RELATIONSHIP_CODE)) + self._get_node_indices_with_relationship(source, BaseCsrOntologyGraph.PARENT_RELATIONSHIP_CODE)) + + def get_descendants(self, source: NODE) -> typing.Iterable[NODE]: + # See `self.get_children()` for explanation of `BaseCsrOntologyGraph.PARENT_RELATIONSHIP_CODE`. + return map(self._get_node_for_idx, + self._traverse_graph(source, BaseCsrOntologyGraph.PARENT_RELATIONSHIP_CODE)) def get_parents(self, source: NODE) -> typing.Iterable[NODE]: # In other words, find a row in the CSR corresponding to the `source` # and retrieve the columns to which the `source` is the CHILD. return map(self._get_node_for_idx, - self._get_nodes_with_relationship(source, SimpleCsrOntologyGraph.CHILD_RELATIONSHIP_CODE)) + self._get_node_indices_with_relationship(source, BaseCsrOntologyGraph.CHILD_RELATIONSHIP_CODE)) - def _get_nodes_with_relationship(self, source: NODE, relationship) -> typing.Generator[int, None, None]: - row_idx = self._get_idx_for_node(source) - if row_idx is None: - return - col_indices = self._adjacency_matrix.col_indices_of_val(row_idx, relationship) - for col_idx in col_indices: - yield col_idx + def get_ancestors(self, source: NODE) -> typing.Iterable[NODE]: + # See `self.get_parents()` for explanation of `BaseCsrOntologyGraph.CHILD_RELATIONSHIP_CODE`. + return map(self._get_node_for_idx, + self._traverse_graph(source, BaseCsrOntologyGraph.CHILD_RELATIONSHIP_CODE)) def __contains__(self, item: NODE) -> bool: return self._get_idx_for_node(item) is not None @@ -52,6 +55,36 @@ def __contains__(self, item: NODE) -> bool: def __iter__(self) -> typing.Iterator[NODE]: return iter(self._nodes) + def _traverse_graph(self, source: NODE, relationship) -> typing.Generator[int, None, None]: + seen: set[int] = set() + buffer: typing.Deque[int] = deque() + + # Init + for idx in self._get_node_indices_with_relationship(source, relationship): + seen.add(idx) + buffer.append(idx) + + # Loop + while buffer: + current = buffer.popleft() + for idx in self._get_cols_with_relationship(current, relationship): + if idx not in seen: + seen.add(idx) + buffer.append(idx) + + yield current + + def _get_node_indices_with_relationship(self, source: NODE, relationship) -> typing.Generator[int, None, None]: + row_idx = self._get_idx_for_node(source) + return self._get_cols_with_relationship(row_idx, relationship) + + def _get_cols_with_relationship(self, idx: typing.Optional[int], relationship) -> typing.Generator[int, None, None]: + if idx is None: + return + col_indices = self._adjacency_matrix.col_indices_of_val(idx, relationship) + for col_idx in col_indices: + yield int(col_idx) # Numpy returns np.i64 but we need int + @abc.abstractmethod def _get_idx_for_node(self, node: NODE) -> typing.Optional[int]: pass @@ -70,7 +103,8 @@ def __init__(self, root: NODE, adjacency_matrix: ImmutableCsrMatrix): super().__init__(root, nodes, adjacency_matrix) self._node_to_idx = {node: idx for idx, node in enumerate(nodes)} - warnings.warn('SimpleCsrOntologyGraph will be removed from the public API in v1.0.0', DeprecationWarning, stacklevel=2) + warnings.warn('SimpleCsrOntologyGraph will be removed from the public API in v1.0.0', + DeprecationWarning, stacklevel=2) def _get_idx_for_node(self, node: NODE) -> typing.Optional[int]: return self._node_to_idx[node] diff --git a/src/hpotk/graph/test__csr_graph.py b/src/hpotk/graph/test__csr_graph.py index b1c88eb..28ab0e9 100644 --- a/src/hpotk/graph/test__csr_graph.py +++ b/src/hpotk/graph/test__csr_graph.py @@ -81,6 +81,29 @@ def test_get_children__unknown_node(self): expected = set(self.GRAPH.get_children(unknown)) self.assertTrue(len(expected) == 0) + @ddt.data( + ('HP:1', ['HP:01', 'HP:010', 'HP:011', 'HP:0110', + 'HP:02', 'HP:020', 'HP:021', 'HP:022', + 'HP:03']), + ('HP:01', ['HP:010', 'HP:011', 'HP:0110']), + ('HP:010', ['HP:0110']), + ('HP:011', ['HP:0110']), + ('HP:0110', []), + + ('HP:02', ['HP:020', 'HP:021', 'HP:022']), + ('HP:020', []), + ('HP:021', []), + ('HP:022', []), + ('HP:03', []), + ) + @ddt.unpack + def test_get_descendants(self, source, expected): + src = TermId.from_curie(source) + expected = list(sorted(map(TermId.from_curie, expected))) + + actual = list(sorted(self.GRAPH.get_descendants(src))) + self.assertListEqual(expected, actual) + @ddt.data( ('HP:1', []), ('HP:01', ['HP:1']), @@ -100,6 +123,21 @@ def test_get_parents__unknown_node(self): expected = set(self.GRAPH.get_parents(unknown)) self.assertTrue(len(expected) == 0) + @ddt.data( + ('HP:1', []), + ('HP:01', ['HP:1']), + ('HP:0110', ['HP:010', 'HP:011', 'HP:01', 'HP:1']), + ('HP:022', ['HP:02', 'HP:1']), + ('HP:03', ['HP:1']), + ) + @ddt.unpack + def test_get_ancestors(self, source, expected): + src = TermId.from_curie(source) + expected = list(sorted(map(TermId.from_curie, expected))) + + actual = list(sorted(self.GRAPH.get_ancestors(src))) + self.assertListEqual(expected, actual) + def test_contains(self): for node in self.NODES: self.assertTrue(node in self.GRAPH) From c6b8679fb1dfc4d3e3d3013832da68a77b0a3db8 Mon Sep 17 00:00:00 2001 From: Daniel Danis Date: Wed, 10 May 2023 14:50:15 -0400 Subject: [PATCH 23/39] Use graph methods for traversal algorithms. --- src/hpotk/algorithm/_traversal.py | 54 ++++++++++--------------------- 1 file changed, 17 insertions(+), 37 deletions(-) diff --git a/src/hpotk/algorithm/_traversal.py b/src/hpotk/algorithm/_traversal.py index 0249e22..f328422 100644 --- a/src/hpotk/algorithm/_traversal.py +++ b/src/hpotk/algorithm/_traversal.py @@ -1,6 +1,5 @@ import typing from warnings import warn -from collections import deque from hpotk.model import TermId, CURIE_OR_TERM_ID from hpotk.graph import OntologyGraph, GraphAware @@ -24,20 +23,12 @@ def get_ancestors(g: typing.Union[GraphAware, OntologyGraph], source = _check_curie_or_term_id(source) # Init - buffer: typing.Deque[TermId] = deque() + builder: set[TermId] = set() if include_source: - buffer.append(source) - else: - for parent in g.get_parents(source): - buffer.append(parent) + builder.add(source) + + builder.update(g.get_ancestors(source)) - # Loop - builder: typing.Set[TermId] = set() - while buffer: - current = buffer.popleft() - for parent in g.get_parents(current): - buffer.append(parent) - builder.add(current) return frozenset(builder) @@ -63,9 +54,8 @@ def get_parents(g: typing.Union[GraphAware, OntologyGraph], if include_source: builder.add(source) - # Loop - for parent in g.get_parents(source): - builder.add(parent) + builder.update(g.get_parents(source)) + return frozenset(builder) @@ -87,20 +77,12 @@ def get_descendants(g: typing.Union[GraphAware, OntologyGraph], source = _check_curie_or_term_id(source) # Init - buffer: typing.Deque[TermId] = deque() + builder: set[TermId] = set() if include_source: - buffer.append(source) - else: - for child in g.get_children(source): - buffer.append(child) + builder.add(source) + + builder.update(g.get_descendants(source)) - # Loop - builder: typing.Set[TermId] = set() - while buffer: - current = buffer.popleft() - for child in g.get_children(current): - buffer.append(child) - builder.add(current) return frozenset(builder) @@ -114,8 +96,8 @@ def get_descendents(g: typing.Union[GraphAware, OntologyGraph], :param g: the ontology graph or a graph-aware entity :param source: `TermId` or a term ID curie as a `str (e.g. `HP:1234567`) - :param include_source: whether to include the `source` term in the resulting set - :return: a `frozenset` with descendants `TermId`s + :param include_source: whether to include the `source` term in the results + :return: a :class:`frozenset` with descendants `TermId`s """ # TODO[v0.3.0] - remove the deprecated method warn('The method is deprecated due to typo and will be removed in v0.3.0. Use get_descendants() instead', @@ -133,21 +115,19 @@ def get_children(g: typing.Union[GraphAware, OntologyGraph], :param g: the ontology graph or a graph-aware entity :param source: `TermId` or a CURIE `str` (e.g. `HP:1234567`) - :param include_source: whether to include the `source` term in the resulting set - :return: a `frozenset` with children `TermId`s + :param include_source: whether to include the `source` term in the results + :return: an iterable with child `TermId`s """ # Check g = _check_ontology_graph_is_available(g) source = _check_curie_or_term_id(source) - # Init - builder: typing.Set[TermId] = set() + builder: set[TermId] = set() if include_source: builder.add(source) - # Loop - for child in g.get_children(source): - builder.add(child) + builder.update(g.get_children(source)) + return frozenset(builder) From 192ede5eca87f658ea53c4962d06730f2fb21b1d Mon Sep 17 00:00:00 2001 From: Daniel Danis Date: Wed, 10 May 2023 22:42:48 -0400 Subject: [PATCH 24/39] Use `set.update` instead of iterative addition in `hpotk.algorithm._augment` --- src/hpotk/algorithm/_augment.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/src/hpotk/algorithm/_augment.py b/src/hpotk/algorithm/_augment.py index 54726ba..0966942 100644 --- a/src/hpotk/algorithm/_augment.py +++ b/src/hpotk/algorithm/_augment.py @@ -47,8 +47,7 @@ def _augment_impl(g: typing.Union[GraphAware, OntologyGraph], elif isinstance(source, typing.Collection): augmented_term_ids = set() for term_id in source: - for augmented in func(g, term_id, include_source): - augmented_term_ids.add(augmented) + augmented_term_ids.update(func(g, term_id, include_source)) return frozenset(augmented_term_ids) else: raise ValueError(f'source should be a TermId or a Collection of TermIds but got a {type(source)}') From f36421f622357463fff25df88bed94c07bc1a74b Mon Sep 17 00:00:00 2001 From: Daniel Danis Date: Wed, 10 May 2023 23:03:51 -0400 Subject: [PATCH 25/39] Remove type subscription on `np.ndarray` --- src/hpotk/graph/_csr_graph.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/hpotk/graph/_csr_graph.py b/src/hpotk/graph/_csr_graph.py index 0a4cd91..77d49c2 100644 --- a/src/hpotk/graph/_csr_graph.py +++ b/src/hpotk/graph/_csr_graph.py @@ -17,7 +17,7 @@ class BaseCsrOntologyGraph(OntologyGraph, metaclass=abc.ABCMeta): PARENT_RELATIONSHIP_CODE = -1 def __init__(self, root: NODE, - nodes: np.ndarray[NODE], + nodes: np.ndarray, adjacency_matrix: ImmutableCsrMatrix): self._root = validate_instance(root, TermId, 'root') self._nodes = validate_instance(nodes, np.ndarray, 'nodes') From d978c20d81c8abfbb8eb27cb619232e5a1931f02 Mon Sep 17 00:00:00 2001 From: Daniel Danis Date: Wed, 10 May 2023 23:05:47 -0400 Subject: [PATCH 26/39] Remove type subscription on `np.ndarray` on the remaining instances. --- src/hpotk/graph/_csr_graph.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/hpotk/graph/_csr_graph.py b/src/hpotk/graph/_csr_graph.py index 77d49c2..038df6e 100644 --- a/src/hpotk/graph/_csr_graph.py +++ b/src/hpotk/graph/_csr_graph.py @@ -99,7 +99,7 @@ class SimpleCsrOntologyGraph(BaseCsrOntologyGraph): """ def __init__(self, root: NODE, - nodes: np.ndarray[NODE], + nodes: np.ndarray, adjacency_matrix: ImmutableCsrMatrix): super().__init__(root, nodes, adjacency_matrix) self._node_to_idx = {node: idx for idx, node in enumerate(nodes)} @@ -116,7 +116,7 @@ class BisectPoweredCsrOntologyGraph(BaseCsrOntologyGraph): """ def __init__(self, root: NODE, - nodes: np.ndarray[NODE], + nodes: np.ndarray, adjacency_matrix: ImmutableCsrMatrix, skip_validation: bool = False): super().__init__(root, nodes, adjacency_matrix) From 93ebe5d3caad30cd4d72b206ce2b48287d5ea24f Mon Sep 17 00:00:00 2001 From: Daniel Danis Date: Wed, 10 May 2023 23:10:10 -0400 Subject: [PATCH 27/39] Use `typing.FrozenSet[TermId]` instead of `frozenset[TermId]`. --- src/hpotk/algorithm/_augment.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/hpotk/algorithm/_augment.py b/src/hpotk/algorithm/_augment.py index 0966942..1aee352 100644 --- a/src/hpotk/algorithm/_augment.py +++ b/src/hpotk/algorithm/_augment.py @@ -7,7 +7,7 @@ def augment_with_ancestors(g: typing.Union[GraphAware, OntologyGraph], source: typing.Union[TermId, typing.Collection[TermId]], - include_source: bool = False) -> frozenset[TermId]: + include_source: bool = False) -> typing.FrozenSet[TermId]: """ Get a set of ancestors of the source :class:`TermId`\\ (s). The ancestor set may or may not include the source term IDs depending on the value of `include_source` argument. @@ -22,7 +22,7 @@ def augment_with_ancestors(g: typing.Union[GraphAware, OntologyGraph], def augment_with_descendants(g: typing.Union[GraphAware, OntologyGraph], source: typing.Union[TermId, typing.Collection[TermId]], - include_source: bool = False) -> frozenset[TermId]: + include_source: bool = False) -> typing.FrozenSet[TermId]: """ Get a set of descendants of the source :class:`TermId`\\ (s). The descendant set may or may not include the source term IDs depending on the value of `include_source` argument. @@ -38,8 +38,8 @@ def augment_with_descendants(g: typing.Union[GraphAware, OntologyGraph], def _augment_impl(g: typing.Union[GraphAware, OntologyGraph], source: typing.Union[TermId, typing.Collection[TermId]], include_source: bool, - func: typing.Callable[[typing.Union[GraphAware, OntologyGraph], TermId, bool], frozenset[TermId]]) \ - -> frozenset[TermId]: + func: typing.Callable[[typing.Union[GraphAware, OntologyGraph], TermId, bool], typing.FrozenSet[TermId]]) \ + -> typing.FrozenSet[TermId]: if not (isinstance(g, GraphAware) or isinstance(g, OntologyGraph)): raise ValueError(f'hpo must be instance of GraphAware or an OntologyGraph but was {type(g)}') if isinstance(source, TermId): From fc193e2b6a4fd3eae5572660e1e142cf406b9ef1 Mon Sep 17 00:00:00 2001 From: Daniel Danis Date: Wed, 10 May 2023 23:13:00 -0400 Subject: [PATCH 28/39] Use `typing.FrozenSet[TermId]` instead of `frozenset[TermId]` in Resnik sim code. --- src/hpotk/algorithm/similarity/_resnik.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/hpotk/algorithm/similarity/_resnik.py b/src/hpotk/algorithm/similarity/_resnik.py index 5f51ee0..ff01487 100644 --- a/src/hpotk/algorithm/similarity/_resnik.py +++ b/src/hpotk/algorithm/similarity/_resnik.py @@ -1,6 +1,7 @@ import functools import logging import re +import typing from hpotk.constants.hpo.base import PHENOTYPIC_ABNORMALITY from hpotk.model import TermId @@ -19,7 +20,7 @@ def _get_common_ancestors(hpo: MinimalOntology, left: TermId, - right: TermId) -> frozenset[TermId]: + right: TermId) -> typing.FrozenSet[TermId]: la = get_ancestors(hpo, left, include_source=True) ra = get_ancestors(hpo, right, include_source=True) return la.intersection(ra) From dddee30ee9e9f88a2e5818a98c8b286975887d73 Mon Sep 17 00:00:00 2001 From: Daniel Danis Date: Fri, 12 May 2023 10:18:20 -0400 Subject: [PATCH 29/39] Put `disease_ids()` back to `SimpleHpoDiseases` to maintain backward compatibility. --- src/hpotk/annotations/_simple.py | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/src/hpotk/annotations/_simple.py b/src/hpotk/annotations/_simple.py index df241fc..ca11bc8 100644 --- a/src/hpotk/annotations/_simple.py +++ b/src/hpotk/annotations/_simple.py @@ -84,6 +84,14 @@ def diseases(self) -> typing.Collection[HpoDisease]: category=DeprecationWarning, stacklevel=2) return self._diseases.values() + @property + def disease_ids(self): + # REMOVE(v1.0.0) + warnings.warn(f'`disease_ids` property has been deprecated and will be removed in v1.0.0. ' + f'Iterate over `item_ids()` instead.', + DeprecationWarning, stacklevel=2) + return list(self.item_ids()) + def __getitem__(self, item: CURIE_OR_TERM_ID) -> typing.Optional[HpoDisease]: if isinstance(item, TermId): pass From 44492bf1634f046bb4d681be479f3241f916b0eb Mon Sep 17 00:00:00 2001 From: Daniel Danis Date: Fri, 12 May 2023 10:36:25 -0400 Subject: [PATCH 30/39] Update the documentation tutorial. --- notebooks/Tutorial.ipynb | 56 ++++++++++++++++++++++++++++++++-------- 1 file changed, 45 insertions(+), 11 deletions(-) diff --git a/notebooks/Tutorial.ipynb b/notebooks/Tutorial.ipynb index 18bf723..967d8e7 100644 --- a/notebooks/Tutorial.ipynb +++ b/notebooks/Tutorial.ipynb @@ -24,6 +24,30 @@ "!pip install hpo-toolkit" ] }, + { + "cell_type": "markdown", + "id": "67f52cee-6b59-4284-a8b3-5bb004bde19b", + "metadata": {}, + "source": [ + "# API update\n", + "\n", + "As of `v0.1.5`, we re-export most commonly used classes from the top-level package to save some typing:\n", + "\n", + "| Class | Previous | New API (top-level reexport) |\n", + "|:-----------------|:-----------------------------------|:--------------------------------|\n", + "| TermId | `hpotk.model.TermId` | `hpotk.TermId` |\n", + "| Term | `hpotk.model.Term` | `hpotk.Term` |\n", + "| MinimalTerm | `hpotk.model.MinimalTerm` | `hpotk.MinimalTerm` |\n", + "| Synonym | `hpotk.model.Synonym` | `hpotk.Synonym` |\n", + "| SynonymType | `hpotk.model.SynonymType` | `hpotk.SynonymType` |\n", + "| SynonymCategory | `hpotk.model.SynonymCategory` | `hpotk.SynonymCategory` |\n", + "| OntologyGraph | `hpotk.graph.OntologyGraph` | `hpotk.OntologyGraph` |\n", + "| GraphAware | `hpotk.graph.GraphAware` | `hpotk.GraphAware` |\n", + "| Ontology | `hpotk.ontology.Ontology` | `hpotk.Ontology` |\n", + "| Ontology | `hpotk.ontology.Ontology` | `hpotk.Ontology` |\n", + "| MinimalOntology | `hpotk.ontology.MinimalOntology` | `hpotk.MinimalOntology` |\n" + ] + }, { "cell_type": "markdown", "id": "6e41fb89-d16e-427f-8e53-ec92710af8c8", @@ -48,7 +72,7 @@ }, "outputs": [], "source": [ - "from hpotk.ontology import Ontology\n", + "from hpotk import Ontology\n", "from hpotk.ontology.load.obographs import load_ontology\n", "\n", "o: Ontology = load_ontology('http://purl.obolibrary.org/obo/hp.json')" @@ -75,20 +99,20 @@ "\n", "HPO toolkit includes several classes that serve as building blocks in the data model. This section provides basic information, starting from the bottom of the class hierarchy.\n", "\n", - "- `hpotk.model.TermId` - an identifier of an ontology concept.\n", - "- `hpotk.model.MinimalTerm` - represents minimal useful information of the ontology concept. `MinimalTerm` has the following attributes:\n", + "- `hpotk.TermId` - an identifier of an ontology concept.\n", + "- `hpotk.MinimalTerm` - represents minimal useful information of the ontology concept. `MinimalTerm` has the following attributes:\n", " - `identifier`, `TermId` (e.g. `HP:0001166`)\n", " - `name`, `str` (e.g. `Arachnodactyly`)\n", " - `is_current`/`is_obsolete`, whether or not the concept has been obsoleted\n", " - `alt_term_ids`, a sequence of obsolete `TermId`s that represented the term previously\n", - "- `hpotk.model.Term` - the complete info regarding the ontology concept. The `Term` has all attributes of the `MinimalTerm` plus the following:\n", + "- `hpotk.Term` - the complete info regarding the ontology concept. The `Term` has all attributes of the `MinimalTerm` plus the following:\n", " - `definition` - an optional description of the term in slightly more verbiage\n", " - `comment` - additional comment (optional)\n", " - `synonyms` - alternative designations of the `Term` (optional)\n", " - `xrefs` - a sequence of cross-references between the `Term` and concepts from different databases\n", - "- `hpotk.ontology.MinimalOntology` - the container for ontology data that uses `MinimalTerm`s\n", - "- `hpotk.ontology.Ontology` - the ontology data container that contains `Term`s\n", - "- `hpotk.graph.OntologyGraph` - a specification of graph for storing the ontology concept hierarchy and the required graph functionality. As long as the graph implements the methods, it can work with the rest of the toolkit framework\n", + "- `hpotk.MinimalOntology` - the container for ontology data that uses `MinimalTerm`s\n", + "- `hpotk.Ontology` - the ontology data container that contains `Term`s\n", + "- `hpotk.OntologyGraph` - a specification of graph for storing the ontology concept hierarchy and the required graph functionality. As long as the graph implements the methods, it can work with the rest of the toolkit framework\n", "\n", "Now, let's go over some examples to explore the provided functionality." ] @@ -235,7 +259,7 @@ "metadata": {}, "outputs": [], "source": [ - "from hpotk.model import TermId\n", + "from hpotk import TermId\n", "assert current_arachnodactyly_id in o and TermId.from_curie(current_arachnodactyly_id) in o" ] }, @@ -415,7 +439,7 @@ "metadata": {}, "outputs": [], "source": [ - "from hpotk.model import MinimalTerm\n", + "from hpotk import MinimalTerm\n", "\n", "from hpotk.validate import ValidationLevel\n", "from hpotk.validate import ObsoleteTermIdsValidator\n", @@ -891,7 +915,7 @@ } ], "source": [ - "print(next(iter(diseases.diseases)))" + "print(next(iter(diseases.items)))" ] }, { @@ -920,7 +944,7 @@ ], "source": [ "# Iterate over disease identifiers\n", - "print(next(iter(diseases.disease_ids)))" + "print(next(iter(diseases.item_ids())))" ] }, { @@ -1003,6 +1027,16 @@ "The HPO annotations API is still evolving. Stay tuned for more features to come!" ] }, + { + "cell_type": "markdown", + "id": "2c94a367-e7a7-4b24-8aa8-3cdd9449bb12", + "metadata": {}, + "source": [ + "# Semantic similarity\n", + "\n", + "TODO - describe `hpotk.algorithm.similarity`." + ] + }, { "cell_type": "markdown", "id": "a3634603-e270-4b7b-a8c1-bc4813b3066a", From d15affa793634213e369d7a97ad73482e11ed1c0 Mon Sep 17 00:00:00 2001 From: Daniel Danis Date: Fri, 12 May 2023 11:18:46 -0400 Subject: [PATCH 31/39] Store ontology version in `AnnotationIcContainer`. Reword HPO IC MICA function. --- src/hpotk/algorithm/similarity/__init__.py | 2 +- src/hpotk/algorithm/similarity/_ic.py | 20 +++++++++----------- src/hpotk/algorithm/similarity/_resnik.py | 6 +++--- tests/algorithm/test_similarity.py | 8 ++++---- 4 files changed, 17 insertions(+), 19 deletions(-) diff --git a/src/hpotk/algorithm/similarity/__init__.py b/src/hpotk/algorithm/similarity/__init__.py index 0cb0eb5..b3365fe 100644 --- a/src/hpotk/algorithm/similarity/__init__.py +++ b/src/hpotk/algorithm/similarity/__init__.py @@ -1,3 +1,3 @@ from ._ic import calculate_ic_for_annotated_items from ._model import AnnotationIcContainer, SimpleAnnotationIcContainer, SimilarityContainer -from ._resnik import precalculate_resnik_similarity_for_hpo +from ._resnik import precalculate_ic_mica_for_hpo_concept_pairs diff --git a/src/hpotk/algorithm/similarity/_ic.py b/src/hpotk/algorithm/similarity/_ic.py index a0f6c23..4b38c00 100644 --- a/src/hpotk/algorithm/similarity/_ic.py +++ b/src/hpotk/algorithm/similarity/_ic.py @@ -3,31 +3,29 @@ from collections import Counter from hpotk.annotations import AnnotatedItemContainer -from hpotk.graph import OntologyGraph, GraphAware +from hpotk.ontology import MinimalOntology +from hpotk.util import validate_instance from ._model import SimpleAnnotationIcContainer, AnnotationIcContainer from .._augment import augment_with_ancestors def calculate_ic_for_annotated_items(items: AnnotatedItemContainer, - graph: typing.Union[GraphAware, OntologyGraph], + ontology: MinimalOntology, base: typing.Optional[float] = None) -> AnnotationIcContainer: """ Calculate information content (IC) for each :class:`TermId` based on a collection of annotated `items`. :param items: a collection of :class:`hpotk.annotations.AnnotatedItem`\ s - :param graph: ontology graph or an object that has the ontology graph + :param ontology: ontology with concepts used to annotate the `items` :param base: information content base or `None` for *e* (produces IC in `nats `_) :return: a container with mappings from :class:`TermId` to information content in nats, bits, or else, depending on the `base` value """ - if isinstance(graph, GraphAware): - root = graph.graph.root - elif isinstance(graph, OntologyGraph): - root = graph.root - else: - raise ValueError(f'graph must be either an instance of `OntologyGraph` or `GraphAware` ' - f'but it was {type(graph)}') + ontology = validate_instance(ontology, MinimalOntology, 'ontology') + + graph = ontology.graph + root = graph.root hit_count = Counter() @@ -42,5 +40,5 @@ def calculate_ic_for_annotated_items(items: AnnotatedItemContainer, population_count = hit_count[root] data = {term_id: -log_func(count / population_count) for term_id, count in hit_count.items()} - metadata = {'annotated_items_version': items.version} + metadata = {'annotated_items_version': items.version, 'ontology_version': ontology.version} return SimpleAnnotationIcContainer(data, metadata=metadata) diff --git a/src/hpotk/algorithm/similarity/_resnik.py b/src/hpotk/algorithm/similarity/_resnik.py index ff01487..2b93bdf 100644 --- a/src/hpotk/algorithm/similarity/_resnik.py +++ b/src/hpotk/algorithm/similarity/_resnik.py @@ -26,10 +26,10 @@ def _get_common_ancestors(hpo: MinimalOntology, return la.intersection(ra) -def precalculate_resnik_similarity_for_hpo(ic: AnnotationIcContainer, - hpo: MinimalOntology) -> SimilarityContainer: +def precalculate_ic_mica_for_hpo_concept_pairs(ic: AnnotationIcContainer, + hpo: MinimalOntology) -> SimilarityContainer: """ - Precalculate Resnik semantic similarity for :class:`TermId` pairs. + Precalculate Resnik semantic similarity for HPO :class:`TermId` pairs. :param ic: a mapping for obtaining an information content of a :class:`TermId`. :param hpo: HPO ontology. diff --git a/tests/algorithm/test_similarity.py b/tests/algorithm/test_similarity.py index 31e8fd1..197535a 100644 --- a/tests/algorithm/test_similarity.py +++ b/tests/algorithm/test_similarity.py @@ -3,7 +3,7 @@ from pkg_resources import resource_filename -from hpotk.algorithm.similarity import calculate_ic_for_annotated_items, precalculate_resnik_similarity_for_hpo +from hpotk.algorithm.similarity import calculate_ic_for_annotated_items, precalculate_ic_mica_for_hpo_concept_pairs from hpotk.model import TermId from hpotk.annotations import HpoDiseases @@ -26,7 +26,7 @@ def setUpClass(cls) -> None: cls.DISEASES: HpoDiseases = hpoa_loader.load(TOY_HPOA) def test_calculate_ic_for_hpo_diseases(self): - mica = calculate_ic_for_annotated_items(self.DISEASES, self.HPO.graph) + mica = calculate_ic_for_annotated_items(self.DISEASES, self.HPO) expected = { # All the way down to Arachnodactyly @@ -52,11 +52,11 @@ def test_calculate_ic_for_hpo_diseases(self): self.assertEqual(len(mica), 282) @unittest.skip - def test_precalculate_ic_mica(self): + def test_precalculate_mica_for_hpo_concept_pairs(self): # Takes ~15 seconds, and it isn't run regularly. term_id2ic = calculate_ic_for_annotated_items(self.DISEASES, self.HPO) - sim_container = precalculate_resnik_similarity_for_hpo(term_id2ic, self.HPO) + sim_container = precalculate_ic_mica_for_hpo_concept_pairs(term_id2ic, self.HPO) self.assertAlmostEqual(sim_container.get_similarity('HP:0000118', 'HP:0000118'), 0.) # Phenotypic abnormality From de44c9863b3a77fc49526beabdeea44160a8dd5e Mon Sep 17 00:00:00 2001 From: Daniel Danis Date: Fri, 12 May 2023 11:50:45 -0400 Subject: [PATCH 32/39] Describe `hpotk.algorithm.similarity` in the doc notebook. --- notebooks/Tutorial.ipynb | 156 ++++++++++++++++++++++++++++++++++++++- 1 file changed, 155 insertions(+), 1 deletion(-) diff --git a/notebooks/Tutorial.ipynb b/notebooks/Tutorial.ipynb index 967d8e7..30ad283 100644 --- a/notebooks/Tutorial.ipynb +++ b/notebooks/Tutorial.ipynb @@ -1034,7 +1034,161 @@ "source": [ "# Semantic similarity\n", "\n", - "TODO - describe `hpotk.algorithm.similarity`." + "## Information content of ontology terms\n", + "\n", + "We can calculate information content (IC) for all ontology terms and obtain `AnnotationIcContainer`:" + ] + }, + { + "cell_type": "code", + "execution_count": 29, + "id": "fe09955e-9a7d-49dc-9cd7-e7db4b876af5", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "from hpotk.algorithm.similarity import calculate_ic_for_annotated_items, AnnotationIcContainer\n", + "\n", + "term_id2ic: AnnotationIcContainer = calculate_ic_for_annotated_items(diseases, o)" + ] + }, + { + "cell_type": "markdown", + "id": "000836e9-98da-4fdc-8c76-eab5c163d779", + "metadata": {}, + "source": [ + "`AnnotationIcContainer` is a mapping from `TermId` to IC (`float`):" + ] + }, + { + "cell_type": "code", + "execution_count": 30, + "id": "7ad52558-e398-413f-8d65-0e67d6099d42", + "metadata": { + "tags": [] + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "IC of Arachnodactyly: 7.259769077238713 nats\n" + ] + } + ], + "source": [ + "ic_arachnodactyly = term_id2ic[arachnodactyly.identifier]\n", + "print(f'IC of {arachnodactyly.name}: {ic_arachnodactyly} nats')" + ] + }, + { + "cell_type": "markdown", + "id": "341f7123-3606-4a6f-be77-2944af843412", + "metadata": {}, + "source": [ + "By default, the `base` parameter of the `calculate_ic_for_annotated_items` is set to $e$ (Euler's number), returning the IC values in [nats](https://en.wikipedia.org/wiki/Nat_(unit)). Set `base=2` to get the IC in bits." + ] + }, + { + "cell_type": "markdown", + "id": "255a4fbf-f1e9-40e8-8efa-6b91724968a5", + "metadata": {}, + "source": [ + "The versions of the items and ontology used to calculate the ICs are preserved in the `metadata` attribute of the `AnnotationIcContainer`:" + ] + }, + { + "cell_type": "code", + "execution_count": 31, + "id": "deb939b7-847f-4b9f-a823-61ea8e9cbb1a", + "metadata": { + "tags": [] + }, + "outputs": [ + { + "data": { + "text/plain": [ + "{'annotated_items_version': '2023-04-05', 'ontology_version': '2023-04-06'}" + ] + }, + "execution_count": 31, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "term_id2ic.metadata" + ] + }, + { + "cell_type": "markdown", + "id": "cb372d93-34c1-48b1-a097-9b174dca54c8", + "metadata": {}, + "source": [ + "## Resnik similarity\n", + "\n", + "We can use the term IC to calculate semantic similarity of items (e.g. diseases, patients) annotated with ontology concepts.\n", + "\n", + "Resnik similarity uses the information content of the *most informative common ancestor* ($IC_{MICA}$ to calculate semantic similarity. `hpo-toolkit` offers a function for calculating $IC_{MICA}$ for all ontology concept pairs:" + ] + }, + { + "cell_type": "code", + "execution_count": 32, + "id": "4e4afd86-1c26-454e-a627-07b29eb00f01", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "from hpotk.algorithm.similarity import precalculate_ic_mica_for_hpo_concept_pairs, SimilarityContainer\n", + "\n", + "#sc: SimilarityContainer = precalculate_ic_mica_for_hpo_concept_pairs(term_id2ic, o)" + ] + }, + { + "cell_type": "markdown", + "id": "b0b9de40-efa5-4b28-bc95-f86e933faf1e", + "metadata": {}, + "source": [ + "The function is commented out/not run in the notebook because it is a bit slow..\n", + "\n", + "However, for the purpose of the demonstration, let's assume we have the `SimilarityContainer` on hand." + ] + }, + { + "cell_type": "code", + "execution_count": 33, + "id": "bea2ed63-59bc-4081-a9e8-d81ec6d06d80", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "sc = SimilarityContainer()" + ] + }, + { + "cell_type": "markdown", + "id": "d6c99e9a-37e7-4fdd-96b8-dec09e6f5004", + "metadata": {}, + "source": [ + "We can query the $IC_{MICA}$ of two HPO terms by:" + ] + }, + { + "cell_type": "code", + "execution_count": 34, + "id": "0ade7bf4-7d4c-4f5d-b612-dd3f8d9e2c57", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "a = 'HP:0001166' # Arachnodactyly\n", + "b = 'HP:0001182' # Tapered finger\n", + "ic_mica = sc.get_similarity(a, b)" ] }, { From ba86b651e6bc5f9de2b9c8fa415b8a2ceb91ece1 Mon Sep 17 00:00:00 2001 From: Daniel Danis Date: Fri, 12 May 2023 12:20:40 -0400 Subject: [PATCH 33/39] Update classifiers to indicate the supported Python versions. Run tests for py3[8-11]. --- README.md | 1 + pyproject.toml | 8 ++++++-- tox.ini | 1 + 3 files changed, 8 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index bdd9126..084c5c7 100644 --- a/README.md +++ b/README.md @@ -2,6 +2,7 @@ ![Build status](https://img.shields.io/github/actions/workflow/status/TheJacksonLaboratory/hpo-toolkit/python_ci.yml) ![PyPi downloads](https://img.shields.io/pypi/dm/hpo-toolkit.svg?label=Pypi%20downloads) +![PyPI - Python Version](https://img.shields.io/pypi/pyversions/hpo-toolkit) A toolkit for working with Human Phenotype Ontology in Python diff --git a/pyproject.toml b/pyproject.toml index 7cb85da..dc9512d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -10,12 +10,16 @@ authors = [ ] readme = "README.md" -requires-python = ">=3.6" +requires-python = ">=3.8" keywords = ["human phenotype ontology", "HPO", "library"] license = { file = "LICENSE" } classifiers = [ - "Programming Language :: Python :: 3", + "Development Status :: 3 - Alpha", "Operating System :: OS Independent", + "Programming Language :: Python :: 3.8", + "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", ] dependencies = [ diff --git a/tox.ini b/tox.ini index 189d3bd..f818fb7 100644 --- a/tox.ini +++ b/tox.ini @@ -1,6 +1,7 @@ [tox] env_list = py38 + py39 py310 py311 minversion = 4.0.16 From 68162d9fbe20dd62cc68b48708f1853e62007b40 Mon Sep 17 00:00:00 2001 From: Daniel Danis Date: Fri, 12 May 2023 12:28:05 -0400 Subject: [PATCH 34/39] Run documentation on Ubuntu only. --- .github/workflows/notebooks.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/notebooks.yml b/.github/workflows/notebooks.yml index e98d65b..3aff0e3 100644 --- a/.github/workflows/notebooks.yml +++ b/.github/workflows/notebooks.yml @@ -13,8 +13,8 @@ jobs: strategy: fail-fast: false matrix: - os: [ windows-latest, macOS-latest, ubuntu-latest ] - python: [ "3.11" ] + os: ubuntu-latest + python: 3.11 steps: - uses: actions/checkout@v2 From afb0ce0e8659c23bf11f4398efd53ef0d179c598 Mon Sep 17 00:00:00 2001 From: Daniel Danis Date: Fri, 12 May 2023 12:32:05 -0400 Subject: [PATCH 35/39] Run CI on all supported Python versions. --- .github/workflows/python_ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/python_ci.yml b/.github/workflows/python_ci.yml index 39a2db4..c08f7a1 100644 --- a/.github/workflows/python_ci.yml +++ b/.github/workflows/python_ci.yml @@ -17,7 +17,7 @@ jobs: fail-fast: false matrix: os: [ windows-latest, macOS-latest, ubuntu-latest ] - python: [ "3.8", "3.10", "3.11" ] + python: [ "3.8", "3.9", "3.10", "3.11" ] steps: - uses: actions/checkout@v2 From 997910a354fd349b10f153af42a6eeee30dd630c Mon Sep 17 00:00:00 2001 From: Daniel Danis Date: Fri, 12 May 2023 12:40:31 -0400 Subject: [PATCH 36/39] Run notebooks on one OS only. --- .github/workflows/notebooks.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/notebooks.yml b/.github/workflows/notebooks.yml index 3aff0e3..2baa8d0 100644 --- a/.github/workflows/notebooks.yml +++ b/.github/workflows/notebooks.yml @@ -13,8 +13,8 @@ jobs: strategy: fail-fast: false matrix: - os: ubuntu-latest - python: 3.11 + os: [ ubuntu-latest ] + python: [ "3.11" ] steps: - uses: actions/checkout@v2 From 9838e4dc7c86878c2a7bc90613a82c17003c1bd3 Mon Sep 17 00:00:00 2001 From: Daniel Danis Date: Fri, 12 May 2023 12:59:01 -0400 Subject: [PATCH 37/39] Fix bug in obsolete term usage validator, update doc notebook. --- notebooks/Tutorial.ipynb | 4 +++- src/hpotk/validate/_hpo.py | 6 +++--- tests/algorithm/test_similarity.py | 7 +++++++ 3 files changed, 13 insertions(+), 4 deletions(-) diff --git a/notebooks/Tutorial.ipynb b/notebooks/Tutorial.ipynb index 30ad283..1a1ad3f 100644 --- a/notebooks/Tutorial.ipynb +++ b/notebooks/Tutorial.ipynb @@ -424,6 +424,8 @@ "\n", "The toolkit provides functions for performing multiple useful sanity checks.\n", "\n", + "The validators validate a sequence of `Identified` (a thing that has a `TermId` identifier) or `TermId`s.\n", + "\n", "## Obsolete term IDs\n", "\n", "We should always use the primary term IDs instead of the obsolete terms.\n", @@ -448,7 +450,7 @@ "\n", "# The term uses an obsolete term ID `HP:0006010` instead of the current `HP:0100807`.\n", "inputs = [\n", - " MinimalTerm.create_minimal_term(TermId.from_curie('HP:0006010'), name='Long fingers', alt_term_ids=[], is_obsolete=False)\n", + " TermId.from_curie('HP:0006010')\n", "]\n", "results = obso_validator.validate(inputs)\n", "\n", diff --git a/src/hpotk/validate/_hpo.py b/src/hpotk/validate/_hpo.py index 28fc7bc..fa9379b 100644 --- a/src/hpotk/validate/_hpo.py +++ b/src/hpotk/validate/_hpo.py @@ -95,13 +95,13 @@ def validate(self, items: typing.Sequence[typing.Union[Identified, TermId]]) -> for item in items: term_id = self.extract_term_id(item) current_id = self._primary_term_id(term_id) - if current_id != item.identifier: - current_term = self._ontology.get_term(item.identifier) + if current_id != term_id: + current_term = self._ontology.get_term(current_id) results.append( ValidationResult( level=ValidationLevel.WARNING, category='obsolete_term_id_is_used', - message=f'Using the obsolete {item.identifier.value} instead of {current_id.value} ' + message=f'Using the obsolete {term_id} instead of {current_id.value} ' f'for {current_term.name}' ) ) diff --git a/tests/algorithm/test_similarity.py b/tests/algorithm/test_similarity.py index 197535a..c4a7dc8 100644 --- a/tests/algorithm/test_similarity.py +++ b/tests/algorithm/test_similarity.py @@ -12,7 +12,9 @@ from hpotk.ontology.load.obographs import load_minimal_ontology TOY_HPO = resource_filename(__name__, os.path.join('../data', 'hp.small.json')) +# TOY_HPO = '/home/ielis/data/ontologies/hpo/2023-04-05/hp.2023-04-05.json' TOY_HPOA = resource_filename(__name__, os.path.join('../data', 'phenotype.real-shortlist.hpoa')) +# TOY_HPOA = '/home/ielis/data/hpoa/phenotype.2023-04-05.hpoa' class TestResnik(unittest.TestCase): @@ -25,6 +27,11 @@ def setUpClass(cls) -> None: hpoa_loader = SimpleHpoaDiseaseLoader(cls.HPO) cls.DISEASES: HpoDiseases = hpoa_loader.load(TOY_HPOA) + @unittest.skip + def test_precalculate_and_store(self): + mica = calculate_ic_for_annotated_items(self.DISEASES, self.HPO) + mica.to_csv('ic.csv.gz') + def test_calculate_ic_for_hpo_diseases(self): mica = calculate_ic_for_annotated_items(self.DISEASES, self.HPO) From 659483b8b342db158b4321b96c49de0c0201232f Mon Sep 17 00:00:00 2001 From: Daniel Danis Date: Fri, 12 May 2023 13:17:48 -0400 Subject: [PATCH 38/39] Set version to `v0.1.5`. --- src/hpotk/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/hpotk/__init__.py b/src/hpotk/__init__.py index 9f091a9..4f5e382 100644 --- a/src/hpotk/__init__.py +++ b/src/hpotk/__init__.py @@ -1,4 +1,4 @@ -__version__ = "0.1.5dev0" +__version__ = "0.1.5" from . import algorithm from . import annotations From ed56cd8862570b5040e581404494cece2a766f9b Mon Sep 17 00:00:00 2001 From: Daniel Danis Date: Fri, 12 May 2023 13:19:26 -0400 Subject: [PATCH 39/39] Update the version in the conda recipe. --- recipe/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipe/meta.yaml b/recipe/meta.yaml index 715f87c..04700e6 100644 --- a/recipe/meta.yaml +++ b/recipe/meta.yaml @@ -1,5 +1,5 @@ {% set name = "hpo-toolkit" %} -{% set version = "0.1.5dev0" %} +{% set version = "0.1.5" %} package: name: {{ name|lower }}