Merge pull request #21 from TheJacksonLaboratory/release_v0.1.4

Release v0.1.4
ielis · Apr 14, 2023 · 12104ff · 12104ff
2 parents 171cdd6 + 9c1d10e
commit 12104ff
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diff --git a/notebooks/Tutorial.ipynb b/notebooks/Tutorial.ipynb
@@ -27,7 +27,9 @@
   {
    "cell_type": "markdown",
    "id": "6e41fb89-d16e-427f-8e53-ec92710af8c8",
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "source": [
     "# Load HPO\n",
     "\n",
@@ -49,7 +51,7 @@
     "from hpotk.ontology import Ontology\n",
     "from hpotk.ontology.load.obographs import load_ontology\n",
     "\n",
-    "o: Ontology = load_ontology('https://raw.githubusercontent.com/obophenotype/human-phenotype-ontology/master/hp.json')"
+    "o: Ontology = load_ontology('http://purl.obolibrary.org/obo/hp.json')"
    ]
   },
   {
@@ -65,7 +67,9 @@
   {
    "cell_type": "markdown",
    "id": "a98ea987-741a-42fa-8ae1-5924d77647ff",
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "source": [
     "# Ontology data model and functionality\n",
     "\n",
@@ -77,8 +81,11 @@
     "  - `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 `definition` and `comment`\n",
-    "\n",
+    "- `hpotk.model.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",
@@ -132,7 +139,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Term(identifier=HP:0000001, name=\"All\", definition=None, comment=Root of all terms in the Human Phenotype Ontology., is_obsolete=False, alt_term_ids=\"[]\")\n"
+      "Term(identifier=HP:0000001, name=\"All\", definition=None, comment=Root of all terms in the Human Phenotype Ontology., synonyms=None, xrefs=[DefaultTermId(idx=4, value=UMLS:C0444868)], is_obsolete=False, alt_term_ids=\"[]\")\n"
      ]
     }
    ],
@@ -157,7 +164,7 @@
     {
      "data": {
       "text/plain": [
-       "16874"
+       "17138"
       ]
      },
      "execution_count": 4,
@@ -252,7 +259,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Term(identifier=HP:0001166, name=\"Arachnodactyly\", definition=Abnormally long and slender fingers (\"spider fingers\")., comment=None, is_obsolete=False, alt_term_ids=\"[DefaultTermId(idx=2, value=HP:0001505)]\")\n"
+      "Term(identifier=HP:0001166, name=\"Arachnodactyly\", definition=Abnormally long and slender fingers (\"spider fingers\")., comment=None, synonyms=[Synonym(name=\"Long slender fingers\", category=SynonymCategory.EXACT, synonym_type=SynonymType.LAYPERSON_TERM, xrefs=\"None\"), Synonym(name=\"Long, slender fingers\", category=SynonymCategory.EXACT, synonym_type=None, xrefs=\"None\"), Synonym(name=\"Spider fingers\", category=SynonymCategory.EXACT, synonym_type=SynonymType.LAYPERSON_TERM, xrefs=\"None\")], xrefs=[DefaultTermId(idx=3, value=MSH:D054119), DefaultTermId(idx=11, value=SNOMEDCT_US:62250003), DefaultTermId(idx=4, value=UMLS:C0003706)], is_obsolete=False, alt_term_ids=\"[DefaultTermId(idx=2, value=HP:0001505)]\")\n"
      ]
     }
    ],
@@ -261,42 +268,6 @@
     "print(arachnodactyly)"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "id": "68f50a4f-bef6-4cfc-afbe-ebeb1dbdc298",
-   "metadata": {},
-   "source": [
-    "As described above, each term has:\n",
-    "- `identifier` - a `hpotk.model.TermId` corresponding to term's CURIE \n",
-    "- `name` - term's name (e.g. *\"Hypertension\"*)\n",
-    "- `alt_term_ids` - alternative term IDs - term ids of obsoleted terms that have been replaced by this term\n",
-    "- `is_obsolete` - obsoletion status"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 9,
-   "id": "b9285dbf-4248-4fe1-821c-732dfe1c90f8",
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "ID: HP:0001166\n",
-      "Name: Arachnodactyly\n",
-      "Alt ids: ['HP:0001505']\n",
-      "Is obsolete: False\n"
-     ]
-    }
-   ],
-   "source": [
-    "print(f'ID: {arachnodactyly.identifier.value}')\n",
-    "print(f'Name: {arachnodactyly.name}')\n",
-    "print(f'Alt ids: {[str(at) for at in arachnodactyly.alt_term_ids]}')\n",
-    "print(f'Is obsolete: {arachnodactyly.is_obsolete}')"
-   ]
-  },
   {
    "cell_type": "markdown",
    "id": "70d5ee3d-2329-4094-8b9a-1c09dde7147f",
@@ -307,7 +278,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 9,
    "id": "7763a3f8-9487-4ccc-ac20-06333fe3fd37",
    "metadata": {},
    "outputs": [],
@@ -331,7 +302,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 10,
    "id": "fd90ffa7-9cd4-4557-8c36-e7c1ba7b5c64",
    "metadata": {},
    "outputs": [
@@ -344,21 +315,21 @@
       "HP:0001238 - Slender finger\n",
       "\n",
       "#################### Ancestors ##################\n",
-      "HP:0000118 - Phenotypic abnormality\n",
       "HP:0000924 - Abnormality of the skeletal system\n",
+      "HP:0000001 - All\n",
+      "HP:0040064 - Abnormality of limbs\n",
+      "HP:0002817 - Abnormality of the upper limb\n",
       "HP:0040068 - Abnormality of limb bone\n",
-      "HP:0011842 - Abnormal skeletal morphology\n",
-      "HP:0011844 - Abnormal appendicular skeleton morphology\n",
+      "HP:0001167 - Abnormal finger morphology\n",
+      "HP:0033127 - Abnormality of the musculoskeletal system\n",
       "HP:0100807 - Long fingers\n",
-      "HP:0001167 - Abnormality of finger\n",
-      "HP:0000001 - All\n",
+      "HP:0011844 - Abnormal appendicular skeleton morphology\n",
+      "HP:0001238 - Slender finger\n",
+      "HP:0002813 - Abnormality of limb bone morphology\n",
+      "HP:0000118 - Phenotypic abnormality\n",
       "HP:0001155 - Abnormality of the hand\n",
-      "HP:0033127 - Abnormality of the musculoskeletal system\n",
-      "HP:0002817 - Abnormality of the upper limb\n",
       "HP:0011297 - Abnormal digit morphology\n",
-      "HP:0002813 - Abnormality of limb bone morphology\n",
-      "HP:0040064 - Abnormality of limbs\n",
-      "HP:0001238 - Slender finger\n"
+      "HP:0011842 - Abnormal skeletal morphology\n"
      ]
     }
    ],
@@ -386,7 +357,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 11,
    "id": "e74d9f8c-20af-4a1d-a8b2-81ec90708b30",
    "metadata": {
     "tags": []
@@ -397,8 +368,8 @@
      "output_type": "stream",
      "text": [
       "#################### Children ####################\n",
-      "HP:0001166 - Arachnodactyly\n",
       "HP:0001182 - Tapered finger\n",
+      "HP:0001166 - Arachnodactyly\n",
       "\n",
       "#################### Descendants #################\n",
       "HP:0006216 - Single interphalangeal crease of fifth finger\n",
@@ -439,7 +410,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
+   "execution_count": 12,
    "id": "3b2f58cc-e008-4153-96b5-1abbd4db9e47",
    "metadata": {},
    "outputs": [],
@@ -487,7 +458,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 14,
+   "execution_count": 13,
    "id": "0e668a54-c146-47be-921e-72ab29ee7d28",
    "metadata": {},
    "outputs": [],
@@ -531,7 +502,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 15,
+   "execution_count": 14,
    "id": "b575229e-1c08-4d02-aaa3-012c9a8c80bd",
    "metadata": {},
    "outputs": [],
@@ -571,7 +542,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 16,
+   "execution_count": 15,
    "id": "654026c8-0e98-45ee-b245-0fa72f8498c3",
    "metadata": {},
    "outputs": [
@@ -616,7 +587,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 17,
+   "execution_count": 16,
    "id": "215903d1-5c3f-4b0f-8fa0-486ef272f5a8",
    "metadata": {},
    "outputs": [
@@ -645,7 +616,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 18,
+   "execution_count": 17,
    "id": "0b1e1b30-e70e-4ec9-89c9-5c702d24ea25",
    "metadata": {},
    "outputs": [
@@ -672,7 +643,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 19,
+   "execution_count": 18,
    "id": "5c4bf517-3e4c-4444-9ada-8bdd9cdcbbbe",
    "metadata": {
     "tags": []
@@ -684,7 +655,7 @@
        "HpoFrequency(identifier=HP:0040283, lower_bound=0.05, upper_bound=0.29)"
       ]
      },
-     "execution_count": 19,
+     "execution_count": 18,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -705,7 +676,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 20,
+   "execution_count": 19,
    "id": "03e7bc93-a58e-422e-a9e1-b04f40956dfb",
    "metadata": {
     "tags": []
@@ -728,7 +699,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 21,
+   "execution_count": 20,
    "id": "7daaab3e-6ead-4230-88d5-b8c080b3730b",
    "metadata": {
     "tags": []
@@ -759,7 +730,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 22,
+   "execution_count": 21,
    "id": "d7bf2281-d8ed-4373-b094-ef7df0c60aa8",
    "metadata": {
     "tags": []
@@ -790,7 +761,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 23,
+   "execution_count": 22,
    "id": "2ddccd09-43d8-448d-8df1-f55ae8eeb658",
    "metadata": {
     "tags": []
@@ -821,7 +792,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 24,
+   "execution_count": 23,
    "id": "0c183a9c-802b-43a1-8bf9-b0e81e5a26f1",
    "metadata": {
     "tags": []
@@ -867,7 +838,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 25,
+   "execution_count": 24,
    "id": "9b5e5216-abde-4b8e-888b-fd12b43ce92e",
    "metadata": {
     "tags": []
@@ -876,10 +847,10 @@
     {
      "data": {
       "text/plain": [
-       "'Parsed 12606 diseases'"
+       "'Parsed 12429 diseases'"
       ]
      },
-     "execution_count": 25,
+     "execution_count": 24,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -905,7 +876,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 26,
+   "execution_count": 25,
    "id": "b4303dc6-a653-4720-8a50-0600d655b679",
    "metadata": {
     "tags": []
@@ -915,7 +886,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "HpoDisease(identifier=OMIM:203400, name=Corticosterone methyloxidase type I deficiency, n_annotations=12)\n"
+      "HpoDisease(identifier=OMIM:619340, name=Developmental and epileptic encephalopathy 96, n_annotations=9)\n"
      ]
     }
    ],
@@ -933,7 +904,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 27,
+   "execution_count": 26,
    "id": "45035d68-baad-4e69-ab51-5e9c9e0aad86",
    "metadata": {
     "tags": []
@@ -943,7 +914,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "OMIM:203400\n"
+      "OMIM:619340\n"
      ]
     }
    ],
@@ -962,7 +933,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 28,
+   "execution_count": 27,
    "id": "e061b854-2218-4355-8a9f-d6ef9988f588",
    "metadata": {
     "tags": []
@@ -995,7 +966,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 29,
+   "execution_count": 28,
    "id": "2faad640-4765-49c5-9eba-535018782e5b",
    "metadata": {
     "tags": []

diff --git a/recipe/meta.yaml b/recipe/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "hpo-toolkit" %}
-{% set version = "0.1.3post0" %}
+{% set version = "0.1.4" %}
 
 package:
   name: {{ name|lower }}

diff --git a/src/hpotk/__init__.py b/src/hpotk/__init__.py
@@ -1,4 +1,4 @@
-__version__ = "0.1.3post0"
+__version__ = "0.1.4"
 
 from . import model
 from . import constants