diff --git a/.github/workflows/notebooks.yml b/.github/workflows/notebooks.yml index e98d65b..2baa8d0 100644 --- a/.github/workflows/notebooks.yml +++ b/.github/workflows/notebooks.yml @@ -13,7 +13,7 @@ jobs: strategy: fail-fast: false matrix: - os: [ windows-latest, macOS-latest, ubuntu-latest ] + os: [ ubuntu-latest ] python: [ "3.11" ] steps: 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 diff --git a/README.md b/README.md index 8fba702..084c5c7 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,9 @@ # 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) +![PyPI - Python Version](https://img.shields.io/pypi/pyversions/hpo-toolkit) + A toolkit for working with Human Phenotype Ontology in Python ## Install diff --git a/notebooks/Tutorial.ipynb b/notebooks/Tutorial.ipynb index 18bf723..1a1ad3f 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" ] }, @@ -400,6 +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", @@ -415,7 +441,7 @@ "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", @@ -424,7 +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", @@ -891,7 +917,7 @@ } ], "source": [ - "print(next(iter(diseases.diseases)))" + "print(next(iter(diseases.items)))" ] }, { @@ -920,7 +946,7 @@ ], "source": [ "# Iterate over disease identifiers\n", - "print(next(iter(diseases.disease_ids)))" + "print(next(iter(diseases.item_ids())))" ] }, { @@ -1003,6 +1029,170 @@ "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", + "## 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)" + ] + }, { "cell_type": "markdown", "id": "a3634603-e270-4b7b-a8c1-bc4813b3066a", 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/recipe/meta.yaml b/recipe/meta.yaml index 022a181..04700e6 100644 --- a/recipe/meta.yaml +++ b/recipe/meta.yaml @@ -1,5 +1,5 @@ {% set name = "hpo-toolkit" %} -{% set version = "0.1.4" %} +{% set version = "0.1.5" %} package: name: {{ name|lower }} diff --git a/src/hpotk/__init__.py b/src/hpotk/__init__.py index 0330441..4f5e382 100644 --- a/src/hpotk/__init__.py +++ b/src/hpotk/__init__.py @@ -1,10 +1,14 @@ -__version__ = "0.1.4" +__version__ = "0.1.5" -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 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/_augment.py b/src/hpotk/algorithm/_augment.py new file mode 100644 index 0000000..1aee352 --- /dev/null +++ b/src/hpotk/algorithm/_augment.py @@ -0,0 +1,53 @@ +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) -> 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. + + :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) -> 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. + + :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], 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): + return get_ancestors(g, source, include_source) + elif isinstance(source, typing.Collection): + augmented_term_ids = set() + for term_id in source: + 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)}') diff --git a/src/hpotk/algorithm/_traversal.py b/src/hpotk/algorithm/_traversal.py index 797d003..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 @@ -10,34 +9,26 @@ 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) 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) @@ -45,14 +36,14 @@ 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) @@ -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) @@ -79,28 +69,20 @@ 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) 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) diff --git a/src/hpotk/algorithm/similarity/__init__.py b/src/hpotk/algorithm/similarity/__init__.py new file mode 100644 index 0000000..b3365fe --- /dev/null +++ b/src/hpotk/algorithm/similarity/__init__.py @@ -0,0 +1,3 @@ +from ._ic import calculate_ic_for_annotated_items +from ._model import AnnotationIcContainer, SimpleAnnotationIcContainer, SimilarityContainer +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 new file mode 100644 index 0000000..4b38c00 --- /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.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, + 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 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 + """ + ontology = validate_instance(ontology, MinimalOntology, 'ontology') + + graph = ontology.graph + root = graph.root + + hit_count = Counter() + + 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): + hit_count[ancestor] += 1 + + log_func = math.log if base is None else lambda c: math.log(c, base) + + 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, 'ontology_version': ontology.version} + 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..1f7e19a --- /dev/null +++ b/src/hpotk/algorithm/similarity/_model.py @@ -0,0 +1,191 @@ +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. + """ + + 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): + """ + 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.MutableMapping[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.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 new file mode 100644 index 0000000..2b93bdf --- /dev/null +++ b/src/hpotk/algorithm/similarity/_resnik.py @@ -0,0 +1,69 @@ +import functools +import logging +import re +import typing + +from hpotk.constants.hpo.base import PHENOTYPIC_ABNORMALITY +from hpotk.model import TermId +from hpotk.ontology import MinimalOntology +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. + +HPO_PATTERN = re.compile(r"HP:(?P\d{7})") + +logger = logging.getLogger('hpotk.algorithm.similarity') + + +def _get_common_ancestors(hpo: MinimalOntology, + left: 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) + + +def precalculate_ic_mica_for_hpo_concept_pairs(ic: AnnotationIcContainer, + hpo: MinimalOntology) -> SimilarityContainer: + """ + 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. + :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/__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..f95d68c --- /dev/null +++ b/src/hpotk/annotations/_api.py @@ -0,0 +1,102 @@ +import abc +import typing +import warnings + +from hpotk.model import TermId, Identified, Versioned + + +# ##################################################################################################################### +# 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.Iterable[ANNOTATED_ITEM], + typing.Sized, + Versioned, + 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 + def items(self) -> typing.Collection[ANNOTATED_ITEM]: + """ + :return: an iterable over container items. + """ + # 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) + diff --git a/src/hpotk/annotations/_base.py b/src/hpotk/annotations/_base.py index 0b83d37..2dc2e0b 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): @@ -94,11 +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): @@ -120,14 +121,14 @@ 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): """ - 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], 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..ca11bc8 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 @@ -63,14 +65,33 @@ 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 + @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() + @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 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/graph/__init__.py b/src/hpotk/graph/__init__.py index 312c1e7..8ff13f2 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 ._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..1bc970a 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") @@ -13,20 +14,44 @@ 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 @abc.abstractmethod def root(self) -> NODE: + """ + Get the root node of the ontology graph. + """ pass @abc.abstractmethod - def get_children(self, source: NODE) -> typing.Iterator[NODE]: + def get_children(self, source: NODE) -> typing.Iterable[NODE]: + """ + Get an iterable with the children of the `source` node. + """ pass @abc.abstractmethod - def get_parents(self, source: NODE) -> typing.Iterator[NODE]: + 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 7562893..038df6e 100644 --- a/src/hpotk/graph/_csr_graph.py +++ b/src/hpotk/graph/_csr_graph.py @@ -1,45 +1,145 @@ +import abc +import bisect import typing +import warnings +from collections import deque +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 = nodes - self._node_to_idx = {node: idx for idx, node in enumerate(nodes)} - self._connectivity_matrix = connectivity_matrix + nodes: np.ndarray, + 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]: - return self._get_nodes_with_relationship(source, - SimpleCsrOntologyGraph.CHILD_RELATIONSHIP_CODE) + 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_node_indices_with_relationship(source, BaseCsrOntologyGraph.PARENT_RELATIONSHIP_CODE)) - def get_parents(self, source: NODE) -> typing.Iterator[NODE]: - return self._get_nodes_with_relationship(source, - SimpleCsrOntologyGraph.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_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_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_node_indices_with_relationship(source, BaseCsrOntologyGraph.CHILD_RELATIONSHIP_CODE)) + + 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 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) + + 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 + + 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, + 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, + 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 54c663a..3f44cd6 100644 --- a/src/hpotk/graph/_factory.py +++ b/src/hpotk/graph/_factory.py @@ -1,14 +1,17 @@ import abc +import bisect import logging import typing +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 -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 +36,73 @@ 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[OntologyGraph], 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_array_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 BisectPoweredCsrOntologyGraph(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 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 _extract_and_sort_nodes(edge_list: typing.Sequence[DirectedEdge]): - return np.sort(_extract_nodes(edge_list)) +def get_list_of_unique_nodes(edge_list: typing.Sequence[DirectedEdge]): + return list(get_unique_nodes(edge_list)) -def _extract_nodes(edge_list: typing.Sequence[DirectedEdge]): +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 +139,97 @@ 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..4fbdf9f 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): @@ -153,7 +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..28ab0e9 --- /dev/null +++ b/src/hpotk/graph/test__csr_graph.py @@ -0,0 +1,148 @@ +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: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']), + ('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) + + @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) + + def test_iter(self): + expected = set(self.NODES) + actual = set(iter(self.GRAPH)) + self.assertSetEqual(expected, actual) 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/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..47b3f80 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.MutableMapping[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..e366842 100644 --- a/src/hpotk/ontology/load/obographs/_load.py +++ b/src/hpotk/ontology/load/obographs/_load.py @@ -5,9 +5,9 @@ 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 +from hpotk.util import open_text_io_handle_for_reading from ._model import create_node, create_edge from ._model import Node, Edge, NodeType @@ -21,15 +21,16 @@ 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: + 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) @@ -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..ec7dde3 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 +93,87 @@ 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)}') + + +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) diff --git a/src/hpotk/validate/_hpo.py b/src/hpotk/validate/_hpo.py index f15b55f..fa9379b 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 != 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 {term.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/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) diff --git a/tests/algorithm/__init__.py b/tests/algorithm/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tests/algorithm/test_similarity.py b/tests/algorithm/test_similarity.py new file mode 100644 index 0000000..c4a7dc8 --- /dev/null +++ b/tests/algorithm/test_similarity.py @@ -0,0 +1,79 @@ +import os +import unittest + +from pkg_resources import resource_filename + +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 +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_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): + HPO: MinimalOntology + DISEASES: HpoDiseases + + @classmethod + def setUpClass(cls) -> None: + cls.HPO: MinimalOntology = load_minimal_ontology(TOY_HPO) + 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) + + 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) + + @unittest.skip + 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_ic_mica_for_hpo_concept_pairs(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/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))) 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) 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. 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abnormalities.", + "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 eye", + "xrefs" : [ "https://orcid.org/0000-0002-5316-1399" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormality of the eye" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasRelatedSynonym", + "val" : "Eye disease" + } ], + "xrefs" : [ { + "val" : "MSH:D005124" + }, { + "val" : "MSH:D005128" + }, { + "val" : "SNOMEDCT_US:19416009" + }, { + "val" : "SNOMEDCT_US:371405004" + }, { + "val" : "SNOMEDCT_US:371409005" + }, { + "val" : "UMLS:C0015393" + }, { + "val" : "UMLS:C0015397" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000479", + "lbl" : "Abnormal retinal morphology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A structural abnormality of the retina.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Abnormal retina", + "xrefs" : [ "https://orcid.org/0000-0002-5316-1399" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Abnormality of the retina" + }, { + "pred" : "hasExactSynonym", + "val" : "Anomaly of the retina" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Retina issue" + }, { + "pred" : "hasRelatedSynonym", + "val" : "Retinal disease" + } ], + "xrefs" : [ { + "val" : "MSH:D012164" + }, { + "val" : "SNOMEDCT_US:29555009" + }, { + "val" : "UMLS:C0035300" + }, { + "val" : "UMLS:C0035309" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0007938" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000480", + "lbl" : "Retinal coloboma", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A notch or cleft of the retina.", + "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" : "Hole in the back of the eye", + "xrefs" : [ "https://orcid.org/0000-0002-6548-5200" ] + } ], + "xrefs" : [ { + "val" : "UMLS:C3540764" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0007808" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000481", + "lbl" : "Abnormal cornea morphology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any abnormality of the cornea, which is the transparent tissue at the front of the eye that covers the iris, pupil, and anterior chamber.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Abnormality of the cornea" + }, { + "pred" : "hasExactSynonym", + "val" : "Corneal abnormalities" + }, { + "pred" : "hasExactSynonym", + "val" : "Corneal abnormality" + }, { + "pred" : "hasRelatedSynonym", + "val" : "Cornela disease" + } ], + "xrefs" : [ { + "val" : "UMLS:C1855670" + }, { + "val" : "UMLS:C4020889" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0007771" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0007972" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000482", + "lbl" : "Microcornea", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A congenital abnormality of the cornea in which the cornea and the anterior segment of the eye are smaller than normal. The horizontal diameter of the cornea does not reach 10 mm even in adulthood.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "comments" : [ "Note that the cornea's diameter is normally about 9.5-10.0 mm at birth and reaches 10.0-12-5 mm in adulthood." ], + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Cornea of eye less than 10mm in diameter", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432", "https://orcid.org/0000-0002-6548-5200" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Decreased corneal diameter" + } ], + "xrefs" : [ { + "val" : "SNOMEDCT_US:26098002" + }, { + "val" : "UMLS:C0266544" + }, { + "val" : "UMLS:C1167713" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0100688" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000483", + "lbl" : "Astigmatism", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A type of astigmatism associated with abnormal curvatures on the anterior and/or posterior surface of the cornea.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199", "https://orcid.org/0000-0003-0986-4123", "HPO_CONTRIBUTOR:DDD_ncarter" ] + }, + "comments" : [ "The irregular curvature associated with astigmatism means that the optical system is not symmetric about the optical axis. 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" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0001485" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0007664" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000539", + "lbl" : "Abnormality of refraction", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An abnormality in the process of focusing of light by the eye in order to produce a sharp image on the retina.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "xrefs" : [ { + "val" : "UMLS:C4025843" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000541", + "lbl" : "Retinal detachment", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Separation of the inner layers of the retina (neural retina) from the pigment epithelium.", + "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" : "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" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Close sighted", + "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" : "Near sighted", + "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" : "Near sightedness", + "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" : "Nearsightedness" + } ], + "xrefs" : [ { + "val" : "MSH:D009216" + }, { + "val" : "SNOMEDCT_US:57190000" + }, { + "val" : "UMLS:C0027092" + } ], 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], + "xrefs" : [ { + "val" : "MSH:D012162" + }, { + "val" : "SNOMEDCT_US:95695004" + }, { + "val" : "UMLS:C0035304" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0007632" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0007790" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0007863" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0007893" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000549", + "lbl" : "Abnormal conjugate eye movement", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any deviation from the normal motor coordination of the eyes that allows for bilateral fixation on a single object.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Disconjugate eye movements" + } ], + "xrefs" : [ { + "val" : "UMLS:C1845274" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000553", + "lbl" : "Abnormal uvea morphology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An abnormality of the uvea, the vascular layer of the eyeball.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Abnormality of the uvea" + } ], + "xrefs" : [ { + "val" : "UMLS:C4025842" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000554", + "lbl" : "Uveitis", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Inflammation of one or all portions of the uveal tract.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "comments" : [ "The uvea is the pigmented middle layer of the eye consisting of the iris and ciliary body together with the choroid." ], + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "xrefs" : [ { + "val" : "MSH:D014605" + }, { + "val" : "SNOMEDCT_US:128473001" + }, { + "val" : "UMLS:C0042164" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000556", + "lbl" : "Retinal dystrophy", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Retinal dystrophy is an abnormality of the retina associated with a hereditary process. 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. Affected children are more likely to have amblyopia or require corrective eye muscle surgery than children with esophoria." ], + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Inward turning cross eyed", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + } ], + "xrefs" : [ { + "val" : "MSH:D004948" + }, { + "val" : "SNOMEDCT_US:16596007" + }, { + "val" : "UMLS:C0014877" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000568", + "lbl" : "Microphthalmia", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A developmental anomaly characterized by abnormal smallness of one or both eyes.", + "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" : "Decreased size of eyeball", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasBroadSynonym", + "val" : "Decreased size of globe of eye", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormally small eyeball", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Abnormally small globe of eye", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Microphthalmos" + }, { + "pred" : "hasRelatedSynonym", + "val" : "Nanophthalmos" + } ], + "xrefs" : [ { + "val" : "Fyler:4877" + }, { + "val" : "MSH:D008850" + }, { + "val" : "SNOMEDCT_US:204108000" + }, { + "val" : "SNOMEDCT_US:61142002" + }, { + "val" : "UMLS:C0026010" + }, { + "val" : "UMLS:C4280625" + }, { + "val" : "UMLS:C4280808" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0007996" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000577", + "lbl" : "Exotropia", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A form of strabismus with one or both eyes deviated outward.", + "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" : "Outward facing eye ball", + "xrefs" : [ "https://orcid.org/0000-0001-6908-9849" ] + } ], + "xrefs" : [ { + "val" : "MSH:D005099" + }, { + "val" : "SNOMEDCT_US:399054005" + }, { + "val" : "SNOMEDCT_US:399252000" + }, { + "val" : "UMLS:C0015310" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0008033" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000589", + "lbl" : "Coloboma", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A developmental defect characterized by a cleft of some portion of the eye or ocular adnexa.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Notched pupil" + }, { + "pred" : "hasExactSynonym", + "val" : "Ocular coloboma" + }, { + "pred" : "hasExactSynonym", + "val" : "Ocular colobomas" + } ], + "xrefs" : [ { + "val" : "Fyler:4311" + }, { + "val" : "MSH:D003103" + }, { + "val" : "SNOMEDCT_US:92828000" + }, { + "val" : "SNOMEDCT_US:93390002" + }, { + "val" : "UMLS:C0009363" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0007767" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0007995" + } ] + } + }, { + "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" : [ 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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" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0008016" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001089", + "lbl" : "Iris atrophy", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Loss of iris tissue (atrophy)", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Iris degeneration", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + } ], + "xrefs" : [ { + "val" : "SNOMEDCT_US:95709007" + }, { + "val" : "UMLS:C0423319" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001090", + "lbl" : "Abnormally large globe", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Diffusely large eye (with megalocornea) without glaucoma.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "comments" : [ "Note that Increased size of palpebral fissues is not a 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 size", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any abnormality of the size or morphology of the cornea.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "xrefs" : [ { + "val" : "UMLS:C4025802" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001131", + "lbl" : "Corneal dystrophy", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The term corneal dystrophy embraces a heterogenous group of bilateral genetically determined non-inflammatory corneal diseases that are restricted to the cornea.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "xrefs" : [ { + "val" : "SNOMEDCT_US:5587004" + }, { + "val" : "UMLS:C0010036" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0007775" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "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" : "hasExactSynonym", + "val" : "Disproportionately large hands" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Large hands" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "large hand" + } ], + "xrefs" : [ { + "val" : "SNOMEDCT_US:249752003" + }, { + "val" : "UMLS:C0426870" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0002820" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0006044" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0006219" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001180", + "lbl" : "Hand oligodactyly", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A developmental defect resulting in the presence of fewer than the normal number of 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", + "pred" : "hasExactSynonym", + "val" : "Abnormality of prenatal development or birth" + } ], + "xrefs" : [ { + "val" : "UMLS:C4025797" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001238", + "lbl" : "Slender finger", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Fingers that are disproportionately narrow (reduced girth) for the hand/foot size or build of the individual.", + "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 fingers" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Slender finger" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Slender fingers", + "xrefs" : [ "https://orcid.org/0000-0002-5316-1399" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "thin fingers" + } ], + "xrefs" : [ { + "val" : "UMLS:C1857482" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0001249", + "lbl" : "Intellectual disability", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Subnormal intellectual functioning which originates during the developmental period. Intellectual disability, previously referred to as mental retardation, has been defined as an IQ score below 70.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "comments" : [ "This term should be used for children at least five years old. 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" : "Dull intelligence" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasRelatedSynonym", + "val" : "Low intelligence" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasRelatedSynonym", + "val" : "Poor school performance" + } ], + "xrefs" : [ { + "val" : "MSH:D008607" + }, { + "val" : "SNOMEDCT_US:228156007" + }, { + "val" : "SNOMEDCT_US:247578003" + }, { + "val" : "SNOMEDCT_US:91138005" + }, { + "val" : "UMLS:C0025362" + }, { + "val" : "UMLS:C0423903" + }, { + "val" : "UMLS:C0917816" + }, { + "val" : "UMLS:C1843367" + }, { + "val" : "UMLS:C3714756" + }, { + "val" : "UMLS:C4020876" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0000730" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0001267" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0001286" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0002122" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0002192" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0002316" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0002382" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0002386" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0002402" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0002458" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0002482" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0002499" + }, { + "pred" : 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"hasExactSynonym", + "val" : "Delay in motor development" + }, { + "pred" : "hasExactSynonym", + "val" : "Delayed early motor milestones" + }, { + "pred" : "hasExactSynonym", + "val" : "Delayed motor development" + }, { + "pred" : "hasExactSynonym", + "val" : "Delayed motor milestones" + }, { + "pred" : "hasExactSynonym", + "val" : "Locomotor delay" + }, { + "pred" : "hasExactSynonym", + "val" : "Motor developmental delay" + }, { + "pred" : "hasExactSynonym", + "val" : "Motor developmental milestones not achieved" + }, { + "pred" : "hasExactSynonym", + "val" : "Motor retardation" + }, { + "pred" : "hasExactSynonym", + "val" : "Retarded motor development" + }, { + "pred" : "hasRelatedSynonym", + "val" : "No development of motor milestones" + } ], + "xrefs" : [ { + "val" : "UMLS:C1854301" + }, { + "val" : "UMLS:C4020874" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0001307" + }, { + "pred" : 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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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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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"hasExactSynonym", + "val" : "Anomaly of the esophagus" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#uk_spelling", + "pred" : "hasExactSynonym", + "val" : "Anomaly of the oesophagus" + } ], + "xrefs" : [ { + "val" : "SNOMEDCT_US:69771008" + }, { + "val" : "UMLS:C0266126" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0002036", + "lbl" : "Hiatus hernia", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The presence of a hernia in which the upper part of the stomach, i.e., mainly the gastric cardia protrudes through the diaphragmatic esophageal hiatus.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "comments" : [ "A tendency for the upper part of the stomach to herniate into the thorax because of a weakness of the esophageal hiatus, which is the hole in the diaphragm through which the esophagus passes. Hiatus hernia can be asymptomatic or can lead to acid reflux symptoms (heartburn)." ], + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Hiatal hernia" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Stomach hernia", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + } ], + "xrefs" : [ { + "val" : "MEDDRA:10020028" + }, { + "val" : "MSH:D006551" + }, { + "val" : "SNOMEDCT_US:84089009" + }, { + "val" : "UMLS:C3489393" + } ], + "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" : "2008-02-20T11:28:00Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0002059", + "lbl" : "Cerebral atrophy", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Atrophy (wasting, decrease in size of cells or tissue) affecting the cerebrum.", + "xrefs" : [ "https://orcid.org/0009-0006-4530-3154" ] + }, + "comments" : [ "Atrophy may be progressive over time." ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Degeneration of cerebrum", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "Supratentorial atrophy" + } ], + "xrefs" : [ { + "val" : "SNOMEDCT_US:278849000" + }, { + "val" : "SNOMEDCT_US:418143002" + }, { + "val" : "SNOMEDCT_US:52522001" + }, { + "val" : "UMLS:C0154671" + }, { + "val" : "UMLS:C0235946" + }, { + "val" : "UMLS:C4020860" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0002422" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0006890" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0002060", + "lbl" : "Abnormal cerebral morphology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any structural abnormality of the telencephalon, which is also known as the cerebrum.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Abnormality of the cerebrum" + }, { + "pred" : "hasExactSynonym", + "val" : "Abnormality of the telencephalon" + }, { + "pred" : "hasExactSynonym", + "val" : "Cerebral lesion" + } ], + "xrefs" : [ { + "val" : "UMLS:C4021762" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0002071", + "lbl" : "Abnormality of extrapyramidal motor function", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A neurological condition related to lesions of the basal ganglia leading to typical abnormalities including akinesia (inability to initiate changes in activity and perform volitional movements rapidly and easily), muscular rigidity (continuous contraction of muscles with constant resistance to passive movement), chorea (widespread arrhythmic movements of a forcible, rapid, jerky, and restless nature), athetosis (inability to sustain the muscles of the fingers, toes, or other group of muscles in a fixed position), and akathisia (inability to remain motionless).", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "comments" : [ "The basal ganglia, paired subcortical masses of grey matter that form distinct nuclei, subserve motor functions that are distinct from those of the pyramidal (i.e., corticospinal) tract. 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This vascular calcification reduces aortic and arterial elastance, which impairs cardiovascular hemodynamics, resulting in substantial morbidity and mortality in the form of hypertension, aortic stenosis, cardiac hypertrophy, myocardial and lower-limb ischemia, congestive heart failure, and compromised structural integrity.The severity and extent of mineralization reflect atherosclerotic plaque burden and strongly and independently predict cardiovascular morbidity and mortality. (From PMID:18519861)." ], + "xrefs" : [ { + "val" : "UMLS:C1168153" + } ], + "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" : "2008-03-26T04:05:00Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0012455" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0003272", + "lbl" : "Abnormal hip bone morphology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An abnormality of the hip bone.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "comments" : [ "The hip region comprises the vasculature of hip, skin of hip, superficial fascia of hip, the hip bone, hip joint, and musculature of hip. 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}, { + "id" : "http://purl.obolibrary.org/obo/HP_0004326", + "lbl" : "Cachexia", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Severe weight loss, wasting of muscle, loss of appetite, and general debility related to a chronic disease.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Wasting syndrome", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + } ], + "xrefs" : [ { + "val" : "MSH:D002100" + }, { + "val" : "SNOMEDCT_US:238108007" + }, { + "val" : "SNOMEDCT_US:285384003" + }, { + "val" : "UMLS:C0006625" + } ], + "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" : "2008-02-27T03:23:00Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0004328", + 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{ + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0003780" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0004334", + "lbl" : "Dermal atrophy", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Partial or complete wasting (atrophy) of the skin.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Atrophic skin" + }, { + "pred" : "hasExactSynonym", + "val" : "Skin atrophy" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Skin degeneration", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + } ], + "xrefs" : [ { + "val" : "MEDDRA:10040799" + }, { + "val" : "SNOMEDCT_US:399979006" + }, { + "val" : "SNOMEDCT_US:400190005" + }, { + "val" : "UMLS:C0151514" + } ], + "basicPropertyValues" : [ { + "pred" : 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Changes may affect all bones of the organism, just certain bones or only parts of bones and include decreased mineralisation as may be seen in osteoporosis or increased mineralisation and or ossification as in osteopetrosis, exostoses or any kind of atopic calicfications of different origin and distribution. The overall amount of mineralization of the bone-organ can be measured as the amount of matter per cubic centimeter of bones, usually measured by densitometry of the lumbar spine or hip. The measurements are usually reported as g/cm3 or as a Z-score (the number of standard deviations above or below the mean for the patient's age and sex). Note that measurement with this method does not reflect local changes in other bones, and as such might not be correct with regard the hole bone-organ.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Abnormality of bone mineralisation and ossification" + } ], + "xrefs" : [ { + "val" : "UMLS:C4021657" + } ], + "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" : "2008-03-11T08:10:00Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0004349", + "lbl" : "Reduced bone mineral density", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A reduction of bone mineral density, that is, of the amount of matter per cubic centimeter of bones.", + "xrefs" : [ "https://orcid.org/0009-0006-4530-3154" ] + }, + "synonyms" : [ { + "pred" : 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In contrast, an aneurysm is defined as a localized dilation of the aorta that is more than 150 percent of predicted (ratio of observed to expected diameter 1.5 or more). Aneurysm should be distinguished from ectasia, which represents a diffuse dilation of the aorta less than 50 percent of normal aorta diameter." + }, + "comments" : [ "Aneurysm is considered a severe (pathological) form of dilatation of a segment of a blood vessel. In clinical practice, dilatation and aneurysm are occasionally used interchangably. 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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. 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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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Teeth agenesis encompasses hypodontia, oligodontia, and anodontia. The total number and the type of teeth missing should be added to the description. The clinical absence of a tooth due to a disturbed eruption should not be termed teeth agenesis but a missing tooth." ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Decreased tooth count", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Dental agenesis" + }, { + "pred" : "hasExactSynonym", + "val" : "Failure of development of some teeth", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Reduced number of teeth" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#plural_form", + "pred" : "hasExactSynonym", + "val" : "Teeth, agenesis" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasRelatedSynonym", + "val" : "Decreased number of teeth", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasRelatedSynonym", + "val" : "Fewer teeth than normal", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasRelatedSynonym", + "val" : "Missing some teeth", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + } ], + "xrefs" : [ { + "val" : "UMLS:C4024202" + }, { + "val" : "UMLS:C4083050" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2009-02-14T06:20:53Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0009810", + "lbl" : "Abnormality of upper limb joint", + "type" : "CLASS", + "meta" : { + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormality of the joints of the upper limbs" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormality of upper limb joint" + } ], + "xrefs" : [ { + "val" : "UMLS:C4021387" + } ], + "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" : "2009-02-23T04:57:56Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0009811", + "lbl" : "Abnormality of the elbow", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An anomaly of the joint that connects the upper and the lower arm.", + "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 elbow" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormality of the elbows" + } ], + "xrefs" : [ { + "val" : "UMLS:C4021386" + } ], + "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" : "2009-02-23T04:59:43Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0002966" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0009815", + "lbl" : "Aplasia/hypoplasia of the extremities", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Absence (due to failure to form) or underdevelopment of the extremities.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Absent/small extremities", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Absent/underdeveloped extremities", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Short or absent limbs" + }, { + "pred" : "hasExactSynonym", + "val" : "Shortened limbs" + } ], + "xrefs" : [ { + "val" : "UMLS:C0239399" + } ], + "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" : "2009-02-23T05:06:40Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0002969" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0006497" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0009816", + "lbl" : "Lower limb undergrowth", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Leg shortening because of underdevelopment of one or more bones of the lower extremity.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Hypoplasia involving bones of the lower limbs" + }, { + "pred" : "hasExactSynonym", + "val" : "Hypoplasia of the lower limbs" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Lower limb undergrowth" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Underdeveloped lower limb bones", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + } ], + "xrefs" : [ { + "val" : "SNOMEDCT_US:253959002" + }, { + "val" : "UMLS:C0345371" + } ], + "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" : "2009-02-23T05:09:32Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0003087" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0005884" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0006399" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0009824", + "lbl" : "Upper limb undergrowth", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Arm shortening because of underdevelopment of one or more bones of the upper extremity.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Hypoplasia involving bones of the upper limbs" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Short arms" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Shortening of the arms" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Upper limb undergrowth" + } ], + "xrefs" : [ { + "val" : "UMLS:C1837406" + } ], + "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" : "2009-02-23T05:13:20Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0003056" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0006364" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0009826", + "lbl" : "Limb undergrowth", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Limb shortening because of underdevelopment of one or more bones of the 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" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2009-02-23T05:16:44Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0003058" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0005049" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0005057" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0009997", + "lbl" : "Duplication of phalanx of hand", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "This term applies if one or more of the phalanges of the hand are either partially duplicated, depending on severity leading to a broad or bifid appearance of the phalanges, or completely duplicated.", + "xrefs" : [ "https://orcid.org/0009-0006-4530-3154" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Duplication of finger 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. The definition excludes partial absent hallux." ], + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Absent toe" + }, { + "pred" : "hasExactSynonym", + "val" : "Aplasia of toe" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasRelatedSynonym", + "val" : "Absent toes", + "xrefs" : [ "https://orcid.org/0000-0002-5316-1399" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "Aplasia of the toes" + } ], + "xrefs" : [ { + "val" : "UMLS:C3553754" + } ], + "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" : "2010-04-23T03:58:25Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0008084" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0010108" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0011306" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0010766", + "lbl" : "Ectopic calcification", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Deposition of calcium salts in a tissue or location in which calcification does not normally occur.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "xrefs" : [ { + "val" : "UMLS:C3806226" + } ], + "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" : "2010-04-27T09:52:59Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0010779", + "lbl" : "Large pelvis bone", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The presence of an abnormally large pelvis.", + "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" : "Large pelvis", + "xrefs" : [ "https://orcid.org/0000-0002-5316-1399" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Large pelvis bone" + } ], + "xrefs" : [ { + "val" : "UMLS:C4019074" + }, { + "val" : "UMLS:C4072882" + } ], + "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" : "2010-04-29T11:03:39Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0010866", + "lbl" : "Abdominal wall defect", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An incomplete closure of the abdominal wall.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abdominal wall defect" + }, { + "pred" : "hasExactSynonym", + "val" : "Congenital anterior abdominal wall defect" + } ], + "xrefs" : [ { + "val" : "UMLS:C0238577" + } ], + "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" : "2010-08-03T09:55:15Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0010978", + "lbl" : "Abnormality of immune system physiology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A functional abnormality of the immune system.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199", "MP:0001790" ] + }, + "xrefs" : [ { + "val" : "UMLS:C4023616" + } ], + "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" : "2011-02-07T04:28:55Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0010991", + "lbl" : "Abnormal morphology of the abdominal musculature", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An abnormality of the abdominal musculature.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Abnormality of the abdominal musculature" + } ], + "xrefs" : [ { + "val" : "UMLS:C4023608" + } ], + "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" : "2011-02-09T08:05:11Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0011001", + "lbl" : "Increased bone mineral density", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An abnormal increase of bone mineral density, that is, of the amount of matter per cubic centimeter of bones which is often referred to as osteosclerosis. 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" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2011-02-13T11:58:36Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0011004", + "lbl" : "Abnormal systemic arterial morphology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An abnormality of the systemic arterial tree, which consists of the aorta and other systemic arteries.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Abnormal systemic artery morphology" + }, { + "pred" : "hasExactSynonym", + "val" : "Abnormality of the systemic arterial tree" + }, { + "pred" : "hasExactSynonym", + "val" : "Systemic artery abnormality" + }, { + "pred" : "hasRelatedSynonym", + "val" : "Arterial abnormalities" + } ], + "xrefs" : [ { + "val" : "Fyler:2600" + }, { + "val" : "SNOMEDCT_US:234119001" + }, { + "val" : "UMLS:C0151489" + }, { + "val" : "UMLS:C4021205" + } ], + "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" : "2011-02-16T08:46:49Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0002620" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0005114" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0011024", + "lbl" : "Abnormality of the gastrointestinal tract", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An abnormality of the gastrointestinal tract.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#abbreviation", + "pred" : "hasExactSynonym", + "val" : "Abnormality of the GI tract" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormality of the 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", + "meta" : { + "definition" : { + "val" : "Abnormal functionality of the cardiovascular system.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Abnormality of cardiovascular system physiology" + } ], + "xrefs" : [ { + "val" : "UMLS:C4023587" + } ], + "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" : "2011-03-03T10:23:19Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0011061", + "lbl" : "Abnormality of dental structure", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An abnormality of the structure or composition of the teeth.", + "xrefs" : [ "https://orcid.org/0000-0002-9338-3017" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "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. A supernumerary tooth present between the maxillary central incisors is called mesiodens." ], + "subsets" : [ "http://purl.obolibrary.org/obo/hp#hposlim_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Extra teeth", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Hyperdontia", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Increased number of teeth" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Increased tooth count", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Supernumerary teeth" + }, { + "pred" : "hasExactSynonym", + "val" : "Supplemental dentition", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Supplemental teeth", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Tooth, supernumerary" + }, { + "pred" : "hasNarrowSynonym", + "val" : "Supernumary dentition", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "Supernumary teeth", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasRelatedSynonym", + "val" : "More teeth than normal", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + } ], + "xrefs" : [ { + "val" : "MSH:D014096" + }, { + "val" : "SNOMEDCT_US:266414008" + }, { + "val" : "SNOMEDCT_US:367534004" + }, { + "val" : "SNOMEDCT_US:8666004" + }, { + "val" : "UMLS:C0040457" + } ], + "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" : "2011-03-10T02:52:19Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0000672" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0011121", + "lbl" : "Abnormality of skin morphology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any morphological abnormality of the skin.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Abnormal skin morphology", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormal skin structure", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + } ], + "xrefs" : [ { + "val" : "Fyler:4133" + }, { + "val" : "UMLS:C4023528" + } ], + "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" : "2011-06-12T10:03:23Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0011122", + "lbl" : "Abnormality of skin physiology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any abnormality of the physiological function of the skin.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormality of skin physiology" + } ], + "xrefs" : [ { + "val" : "UMLS:C4023527" + } ], + "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" : "2011-06-12T10:05:14Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0011123", + "lbl" : "Inflammatory abnormality of the skin", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The presence of inflammation of the skin. 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. 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+ "val" : "2012-04-24T07:46:05Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0040199" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0011804", + "lbl" : "Abnormal muscle physiology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A functional abnormality of a skeletal muscle.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Abnormality of muscle physiology" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Issue with muscle function" + } ], + "xrefs" : [ { + "val" : "UMLS:C4023182" + } ], + "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" : "2012-04-25T02:00:15Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0011805", + "lbl" : "Abnormal skeletal muscle morphology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A structural abnormality of a skeletal muscle.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Abnormal muscle morphology" + }, { + "pred" : "hasExactSynonym", + "val" : "Abnormality of muscle morphology" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormally shaped muscle", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Issue with muscle structure" + } ], + "xrefs" : [ { + "val" : "UMLS:C4023181" + } ], + "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" : "2012-04-25T02:00:34Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "HP:0003735" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0011821", + "lbl" : "Abnormal facial skeleton morphology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An abnormality of one or more of the set of bones that make up the facial skeleton.", + "xrefs" : [ "https://orcid.org/0000-0002-2972-5481" ] + }, + "comments" : [ "The facial skeleton comprises the mandible, maxilla, frontal bone, nasal bones, and zygoma, as well as the inferior nasal concha, the lacrimal bones, the palatine bone, and the vomer." ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormality of facial skeleton" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Anomaly of facial skeleton", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasNarrowSynonym", + "val" : "Abnormality of facial bones", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasNarrowSynonym", + "val" : "Anomaly of facial bones", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasNarrowSynonym", + "val" : "Deformity of facial skeleton", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasNarrowSynonym", + "val" : "Deformity of the facial bones", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasNarrowSynonym", + "val" : "Malformation of facial bones", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasNarrowSynonym", + "val" : "Malformation of facial skeleton", + "xrefs" : [ "https://orcid.org/0000-0001-5889-4463" ] + } ], + "xrefs" : [ { + "val" : "SNOMEDCT_US:433096001" + }, { + "val" : "UMLS:C2315229" + } ], + "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" : "2012-04-29T04:37:30Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0011842", + "lbl" : "Abnormal skeletal morphology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An abnormality of the form, structure, or size of the skeletal system.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Abnormality of skeletal morphology" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormally shaped skeletal", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + } ], + "xrefs" : [ { + "val" : "UMLS:C4023165" + } ], + "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" : "2012-05-07T08:08:37Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0011843", + "lbl" : "Abnormal musculoskeletal physiology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An abnormality of the function of the skeletal system.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "Abnormality of musculoskeletal physiology" + } ], + "xrefs" : [ { + "val" : "UMLS:C4023164" + } ], + "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" : "2012-05-07T08:09:43Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0011844", + "lbl" : "Abnormal appendicular skeleton morphology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An abnormality of the appendicular skeletal system, consisting of the of the limbs, shoulder and pelvic girdles.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "xrefs" : [ { + "val" : "UMLS:C4023163" + } ], + "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" : "2012-05-07T08:12:26Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0011849", + "lbl" : "Abnormal bone 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. Hypertropia is a manifest deviation in which the eyes are not aligned under binocular conditions." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/date", + "val" : "2018-01-13T19:45:45Z" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025590", + "lbl" : "Abnormal extraocular muscle physiology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A functional anomaly of the muscles of the eye." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/date", + "val" : "2018-01-13T20:11:20Z" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025596", + "lbl" : "Abnormal inferior oblique muscle physiology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A functional anomaly of the inferior oblique muscle, an extraocular muscle that has its origin on the maxillary bone just posterior to the inferior medial orbital rim and lateral to the nasolacrimal canal and that is innervated by the inferior branch of the oculomotor nerve.", + "xrefs" : [ "https://orcid.org/0000-0003-0986-4123" ] + }, + "comments" : [ "The major functions of the inferior oblique muscle are extorsion (external rotation), elevation, and abduction." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/date", + "val" : "2018-01-13T20:54:37Z" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0025599", + "lbl" : "Inferior oblique muscle overaction", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A common ocular motility disorder characterized by vertical incomitance of the eyes in lateral gaze. 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 monocular cover-uncover test is the most important test for detecting the presence of manifest strabismus and for differentiating a heterophoria from a heterotropia." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/date", + "val" : "2018-07-22T15:46:55Z" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0032039", + "lbl" : "Abnormality of the ocular adnexa", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An 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." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/date", + "val" : "2018-09-03T00:17:49Z" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0032040", + "lbl" : "Abnormal ocular adnexa physiology", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A functional 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." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/date", + "val" : "2018-09-03T00:18:45Z" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0032934", + "lbl" : "Spontaneous cerebrospinal fluid leak", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A spontaneous cerebrospinal fluid leak (SCSFL) is a spontaneous and unexplained leak of the cerebrospinal fluid from the dura surrounding either the brain (cranial leak) or spine (spinal leak).", + "xrefs" : [ "PMID:19225307", "PMID:22929030" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-0736-9199" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0033127", + "lbl" : "Abnormality of the musculoskeletal system", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An anomaly of the musculoskeletal system, which consists of the bones of the skeleton, muscles, cartilage, tendons, ligaments, joints, and other connective tissue. 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. 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telencephalon, diencephalon, lateral ventricles and third ventricle.", + "xrefs" : [ "https://orcid.org/0000-0002-0736-9199" ] + }, + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/hp#layperson", + "pred" : "hasExactSynonym", + "val" : "Abnormal shape of forebrain", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Abnormality of forebrain morphology" + }, { + "pred" : "hasExactSynonym", + "val" : "Abnormality of the forebrain" + } ], + "xrefs" : [ { + "val" : "UMLS:C4020967" + } ], + "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" : "2010-12-21T02:12:53Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0100614", + "lbl" : "Myositis", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A general term for inflammation of the muscles without respect to the underlying cause.", + "xrefs" : [ "https://orcid.org/0009-0006-4530-3154" ] + }, + "comments" : [ "Many such conditions are considered likely to be caused by autoimmune conditions, rather than directly due to infection, although autoimmune conditions can be activated or exacerbated by infections. 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..8e36cd4 --- /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 +#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] 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..3d0ed6c --- /dev/null +++ b/tests/ontology/load/test_obographs.py @@ -0,0 +1,146 @@ +import os +import unittest + +from pkg_resources import resource_filename + +import hpotk as hp +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() + + +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')]) 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. 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