diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..b3c003b --- /dev/null +++ b/.gitignore @@ -0,0 +1,167 @@ +# MAC +.DS_Store + +.vscode/ + +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +share/python-wheels/ +*.egg-info/ +.installed.cfg +*.egg +MANIFEST + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.nox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*.cover +*.py,cover +.hypothesis/ +.pytest_cache/ +cover/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py +db.sqlite3 +db.sqlite3-journal + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +.pybuilder/ +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# IPython +profile_default/ +ipython_config.py + +# pyenv +# For a library or package, you might want to ignore these files since the code is +# intended to run in multiple environments; otherwise, check them in: +# .python-version + +# pipenv +# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. +# However, in case of collaboration, if having platform-specific dependencies or dependencies +# having no cross-platform support, pipenv may install dependencies that don't work, or not +# install all needed dependencies. +#Pipfile.lock + +# poetry +# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control. +# This is especially recommended for binary packages to ensure reproducibility, and is more +# commonly ignored for libraries. +# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control +#poetry.lock + +# pdm +# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control. +#pdm.lock +# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it +# in version control. +# https://pdm.fming.dev/#use-with-ide +.pdm.toml + +# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm +__pypackages__/ + +# Celery stuff +celerybeat-schedule +celerybeat.pid + +# SageMath parsed files +*.sage.py + +# Environments +.env +.venv +env/ +venv/ +ENV/ +env.bak/ +venv.bak/ + +# Spyder project settings +.spyderproject +.spyproject + +# Rope project settings +.ropeproject + +# mkdocs documentation +/site + +# mypy +.mypy_cache/ +.dmypy.json +dmypy.json + +# Pyre type checker +.pyre/ + +# pytype static type analyzer +.pytype/ + +# Cython debug symbols +cython_debug/ + +# PyCharm +# JetBrains specific template is maintained in a separate JetBrains.gitignore that can +# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore +# and can be added to the global gitignore or merged into this file. For a more nuclear +# option (not recommended) you can uncomment the following to ignore the entire idea folder. +#.idea/ + +nb/ diff --git a/ontology/BIKO/BIKO_v0_5.ttl b/ontology/BIKO/BIKO_v0_5.ttl index edcc60c..325ee11 100755 --- a/ontology/BIKO/BIKO_v0_5.ttl +++ b/ontology/BIKO/BIKO_v0_5.ttl @@ -1137,8 +1137,6 @@ uri:BIKO_0000266 a owl:Class ; oboInOwl:creation_date "2022-09-07T05:13:33.947178Z"^^xsd:string ; rdfs:subClassOf uri:BIKO_0000014 . - a owl:Ontology . - uri:BIKO_0000024 a owl:Class ; rdfs:label "Strain" ; oboInOwl:created_by "MCSZ"^^xsd:string ; diff --git a/plots/class-plots.ipynb b/plots/class-plots.ipynb new file mode 100644 index 0000000..825d511 --- /dev/null +++ b/plots/class-plots.ipynb @@ -0,0 +1,1084 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "id": "2bc12381-629b-4e4b-8450-0851e5c3bf6f", + "metadata": {}, + "outputs": [], + "source": [ + "import ontospy" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "id": "38effe26-0c84-449c-a7fb-2ffd6aacb0cf", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "'2.1.1'" + ] + }, + "execution_count": 2, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "ontospy.__version__" + ] + }, + { + "cell_type": "code", + "execution_count": 20, + "id": "b738cdbb-468f-4d21-9168-c8514430db48", + "metadata": {}, + "outputs": [], + "source": [ + "ontology_file_path = \"http://xmlns.com/foaf/0.1/\"\n", + "ontology_file_path = \"../ontology/BIKO/BIKO_v0_5.ttl\"" + ] + }, + { + "cell_type": "code", + "execution_count": 21, + "id": "a8f80d4b-4dea-4861-9d0e-3f2157e8a230", + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "\u001b[32mReading: <../ontology/BIKO/BIKO_v0_5.ttl>\u001b[0m\n", + ".. trying rdf serialization: \u001b[0m\n", + "\u001b[1m..... success!\u001b[0m\n", + "\u001b[37m----------\n", + "Loaded 1381 triples.\n", + "----------\u001b[0m\n", + "\u001b[32mRDF sources loaded successfully: 1 of 1.\u001b[0m\n", + "\u001b[37m..... '../ontology/BIKO/BIKO_v0_5.ttl'\u001b[0m\n", + "\u001b[37m----------\u001b[0m\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\u001b[32mScanning entities...\u001b[0m\n", + "\u001b[2m----------\u001b[0m\n", + "\u001b[2mOntologies.........: 1\u001b[0m\n", + "\u001b[2mClasses............: 255\u001b[0m\n", + "\u001b[2mProperties.........: 14\u001b[0m\n", + "\u001b[2m..annotation.......: 4\u001b[0m\n", + "\u001b[2m..datatype.........: 0\u001b[0m\n", + "\u001b[2m..object...........: 10\u001b[0m\n", + "\u001b[2mConcepts (SKOS)....: 0\u001b[0m\n", + "\u001b[2mShapes (SHACL).....: 0\u001b[0m\n", + "\u001b[2m----------\u001b[0m\n" + ] + } + ], + "source": [ + "# example load\n", + "model = ontospy.Ontospy(ontology_file_path, verbose=True)" + ] + }, + { + "cell_type": "code", + "execution_count": 37, + "id": "9319b3b2-3ca0-4ad3-8310-ac0226270458", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[('Ontologies', 1),\n", + " ('Triples', 1381),\n", + " ('Classes', 255),\n", + " ('Properties', 14),\n", + " ('Annotation Properties', 4),\n", + " ('Object Properties', 10),\n", + " ('Datatype Properties', 0),\n", + " ('Skos Concepts', 0),\n", + " ('Data Shapes', 0),\n", + " ('Data Sources', 1)]" + ] + }, + "execution_count": 37, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "model.stats()" + ] + }, + { + "cell_type": "code", + "execution_count": 23, + "id": "7d61a505-d812-4548-8d29-a9b3a3944b29", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[,\n", + " ,\n", + " ,\n", + " ,\n", + " ,\n", + " ,\n", + " ,\n", + " ,\n", + " ,\n", + " ]" + ] + }, + "execution_count": 23, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "model.all_classes[:10]" + ] + }, + { + "cell_type": "code", + "execution_count": 24, + "id": "8e2ea20d-2d51-443f-b47c-948d1012d00f", + "metadata": { + "collapsed": true, + "jupyter": { + "outputs_hidden": true + } + }, + "outputs": [ + { + 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"--------------------------------uri:BIKO_0000118\u001b[0m\n", + "--------------------------------uri:BIKO_0000119\u001b[0m\n", + "--------------------------------uri:BIKO_0000120\u001b[0m\n", + "--------------------------------uri:BIKO_0000121\u001b[0m\n", + "--------------------------------uri:BIKO_0000122\u001b[0m\n", + "--------------------------------uri:BIKO_0000123\u001b[0m\n", + "--------------------------------uri:BIKO_0000124\u001b[0m\n", + "--------------------------------uri:BIKO_0000125\u001b[0m\n", + "----------------------------uri:BIKO_0000114\u001b[0m\n", + "------------------------uri:BIKO_0000099\u001b[0m\n", + "----------------------------uri:BIKO_0000111\u001b[0m\n", + "------------------------uri:BIKO_0000100\u001b[0m\n", + "--------------------uri:BIKO_0000095\u001b[0m\n", + "--------------------uri:BIKO_0000096\u001b[0m\n", + "--------------------uri:BIKO_0000097\u001b[0m\n", + "----------------uri:BIKO_0000090\u001b[0m\n", + "----------------uri:BIKO_0000091\u001b[0m\n", + "----------------uri:BIKO_0000092\u001b[0m\n", + "----------------uri:BIKO_0000093\u001b[0m\n", + "------------uri:BIKO_0000083\u001b[0m\n", + "------------uri:BIKO_0000084\u001b[0m\n", + "------------uri:BIKO_0000085\u001b[0m\n", + "------------uri:BIKO_0000086\u001b[0m\n", + "------------uri:BIKO_0000087\u001b[0m\n", + "----uri:BIKO_0000014\u001b[0m\n", + "--------uri:BIKO_0000246\u001b[0m\n", + "--------uri:BIKO_0000247\u001b[0m\n", + "--------uri:BIKO_0000265\u001b[0m\n", + "--------uri:BIKO_0000266\u001b[0m\n", + "----uri:BIKO_0000015\u001b[0m\n" + ] + } + ], + "source": [ + "model.printClassTree()" + ] + }, + { + "cell_type": "code", + "execution_count": 25, + "id": "696d63e1-a7d0-457a-8139-9fd7afab316e", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[,\n", + " ,\n", + " ,\n", + " ]" + ] + }, + "execution_count": 25, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "model.toplayer_classes" + ] + }, + { + "cell_type": "code", + "execution_count": 76, + "id": "1b42a489-d7a5-4531-afa7-da2b1bbf0ed9", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[]" + ] + }, + "execution_count": 76, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + " model.get_class('BIKO_0000246')" + ] + }, + { + "cell_type": "code", + "execution_count": 77, + "id": "164d27e6-e0c4-44ae-9d3d-8dc485848cd2", + "metadata": {}, + "outputs": [], + "source": [ + "c1 = model.get_class('BIKO_0000246')[-1]" + ] + }, + { + "cell_type": "code", + "execution_count": 78, + "id": "7641924b-80df-42b9-a9d7-7b808b42d179", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "@prefix oboInOwl: .\n", + "@prefix owl: .\n", + "@prefix rdfs: .\n", + "@prefix uri: .\n", + "@prefix xsd: .\n", + "\n", + "uri:BIKO_0000246 a owl:Class ;\n", + " rdfs:label \"Controlled cortical impact device\" ;\n", + " oboInOwl:created_by \"MCSZ\"^^xsd:string ;\n", + " oboInOwl:creation_date \"2022-08-29T07:19:02.16796Z\"^^xsd:string ;\n", + " rdfs:subClassOf uri:BIKO_0000014 .\n", + "\n", + "\n" + ] + } + ], + "source": [ + "print(c1.rdf_source())" + ] + }, + { + "cell_type": "code", + "execution_count": 79, + "id": "bf9af642-41e0-4ab6-9125-99d9979ae7ac", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[]" + ] + }, + "execution_count": 79, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "c1.parents()" + ] + }, + { + "cell_type": "markdown", + "id": "bf8cbec6-9af0-4d4e-be8a-c95b6c5b21fa", + "metadata": {}, + "source": [ + "# Terminal" + ] + }, + { + "cell_type": "code", + "execution_count": 40, + "id": "5ce95075-7f11-46f0-b349-e73b92e51c4b", + "metadata": { + "collapsed": true, + "jupyter": { + "outputs_hidden": true + }, + "scrolled": true + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\u001b[2mOntospy v2.1.1\u001b[0m\n", + "\u001b[37mParsing ...\u001b[0m\n", + "\u001b[37m# ../ontology/BIKO/BIKO_v0_5.ttl\u001b[0m\n", + "\u001b[0m\n", + "\u001b[1mNamespaces\n", + "-----------\u001b[0m\u001b[0m\n", + "\u001b[32mbrick\u001b[30m https://brickschema.org/schema/Brick#\u001b[39m\u001b[0m\n", + "\u001b[32mcsvw\u001b[30m http://www.w3.org/ns/csvw#\u001b[39m\u001b[0m\n", + "\u001b[32mdc\u001b[30m http://purl.org/dc/elements/1.1/\u001b[39m\u001b[0m\n", + "\u001b[32mdcam\u001b[30m http://purl.org/dc/dcam/\u001b[39m\u001b[0m\n", + "\u001b[32mdcat\u001b[30m http://www.w3.org/ns/dcat#\u001b[39m\u001b[0m\n", + "\u001b[32mdcmitype\u001b[30m http://purl.org/dc/dcmitype/\u001b[39m\u001b[0m\n", + "\u001b[32mdcterms\u001b[30m http://purl.org/dc/terms/\u001b[39m\u001b[0m\n", + "\u001b[32mdoap\u001b[30m http://usefulinc.com/ns/doap#\u001b[39m\u001b[0m\n", + "\u001b[32mfoaf\u001b[30m http://xmlns.com/foaf/0.1/\u001b[39m\u001b[0m\n", + "\u001b[32mgeo\u001b[30m http://www.opengis.net/ont/geosparql#\u001b[39m\u001b[0m\n", + "\u001b[32moboInOwl\u001b[30m http://www.geneontology.org/formats/oboInOwl#\u001b[39m\u001b[0m\n", + "\u001b[32modrl\u001b[30m http://www.w3.org/ns/odrl/2/\u001b[39m\u001b[0m\n", + "\u001b[32morg\u001b[30m http://www.w3.org/ns/org#\u001b[39m\u001b[0m\n", + "\u001b[32mowl\u001b[30m http://www.w3.org/2002/07/owl#\u001b[39m\u001b[0m\n", + "\u001b[32mprof\u001b[30m http://www.w3.org/ns/dx/prof/\u001b[39m\u001b[0m\n", + "\u001b[32mprov\u001b[30m http://www.w3.org/ns/prov#\u001b[39m\u001b[0m\n", + "\u001b[32mqb\u001b[30m http://purl.org/linked-data/cube#\u001b[39m\u001b[0m\n", + "\u001b[32mrdf\u001b[30m http://www.w3.org/1999/02/22-rdf-syntax-ns#\u001b[39m\u001b[0m\n", + "\u001b[32mrdfs\u001b[30m http://www.w3.org/2000/01/rdf-schema#\u001b[39m\u001b[0m\n", + "\u001b[32mschema\u001b[30m https://schema.org/\u001b[39m\u001b[0m\n", + "\u001b[32msh\u001b[30m http://www.w3.org/ns/shacl#\u001b[39m\u001b[0m\n", + "\u001b[32mskos\u001b[30m http://www.w3.org/2004/02/skos/core#\u001b[39m\u001b[0m\n", + "\u001b[32msosa\u001b[30m http://www.w3.org/ns/sosa/\u001b[39m\u001b[0m\n", + "\u001b[32mssn\u001b[30m http://www.w3.org/ns/ssn/\u001b[39m\u001b[0m\n", + "\u001b[32mtime\u001b[30m http://www.w3.org/2006/time#\u001b[39m\u001b[0m\n", + "\u001b[32muri\u001b[30m https://www.bikotbi.org/uri/\u001b[39m\u001b[0m\n", + "\u001b[32mvann\u001b[30m http://purl.org/vocab/vann/\u001b[39m\u001b[0m\n", + "\u001b[32mvoid\u001b[30m http://rdfs.org/ns/void#\u001b[39m\u001b[0m\n", + "\u001b[32mwgs\u001b[30m https://www.w3.org/2003/01/geo/wgs84_pos#\u001b[39m\u001b[0m\n", + "\u001b[32mxml\u001b[30m http://www.w3.org/XML/1998/namespace\u001b[39m\u001b[0m\n", + "\u001b[32mxsd\u001b[30m http://www.w3.org/2001/XMLSchema#\u001b[39m\u001b[0m\n", + "\u001b[1m\n", + "Ontologies\n", + "-----------\u001b[0m\u001b[0m\n", + "\u001b[31murn:webprotege:ontology:f11172a8-959d-4250-be04-4c0bb15a4569\u001b[0m\u001b[0m\n", + "\u001b[30m=> http://www.w3.org/1999/02/22-rdf-syntax-ns#type\u001b[0m\n", + "\u001b[2m.... http://www.w3.org/2002/07/owl#Ontology\u001b[39m\u001b[0m\n", + "\u001b[0m\n", + "\u001b[1m\n", + "Classes\n", + "----------\u001b[0m\u001b[0m\n", + "uri:BIKO_0000001\u001b[0m\n", + "----uri:BIKO_0000006\u001b[0m\n", + "----uri:BIKO_0000007\u001b[0m\n", + "--------uri:BIKO_0000126\u001b[0m\n", + "------------uri:BIKO_0000127\u001b[0m\n", + "------------uri:BIKO_0000128\u001b[0m\n", + "----------------uri:BIKO_0000129\u001b[0m\n", + "--------------------uri:BIKO_0000258\u001b[0m\n", + "----------------uri:BIKO_0000130\u001b[0m\n", + "--------------------uri:BIKO_0000131\u001b[0m\n", + "--------------------uri:BIKO_0000132\u001b[0m\n", + "----------------uri:BIKO_0000133\u001b[0m\n", + "--------------------uri:BIKO_0000134\u001b[0m\n", + "------------------------uri:BIKO_0000135\u001b[0m\n", + "--------------------uri:BIKO_0000136\u001b[0m\n", + "--------------------uri:BIKO_0000137\u001b[0m\n", + "----------------uri:BIKO_0000138\u001b[0m\n", + "----------------uri:BIKO_0000139\u001b[0m\n", + "----------------uri:BIKO_0000252\u001b[0m\n", + "----------------uri:BIKO_0000253\u001b[0m\n", + "----------------uri:BIKO_0000254\u001b[0m\n", + "----------------uri:BIKO_0000259\u001b[0m\n", + "----------------uri:BIKO_0000260\u001b[0m\n", + "--------uri:BIKO_0000148\u001b[0m\n", + "------------uri:BIKO_0000149\u001b[0m\n", + "----------------uri:BIKO_0000140\u001b[0m\n", + "----------------uri:BIKO_0000141\u001b[0m\n", + "----------------uri:BIKO_0000143\u001b[0m\n", + "----------------uri:BIKO_0000144\u001b[0m\n", + "--------------------uri:BIKO_0000142\u001b[0m\n", + "----------------uri:BIKO_0000145\u001b[0m\n", + "----------------uri:BIKO_0000146\u001b[0m\n", + "----uri:BIKO_0000008\u001b[0m\n", + "--------uri:BIKO_0000214\u001b[0m\n", + "------------uri:BIKO_0000215\u001b[0m\n", + "----------------uri:BIKO_0000216\u001b[0m\n", + "----------------uri:BIKO_0000217\u001b[0m\n", + "----------------uri:BIKO_0000218\u001b[0m\n", + "--------uri:BIKO_0000219\u001b[0m\n", + "------------uri:BIKO_0000220\u001b[0m\n", + "----------------uri:BIKO_0000221\u001b[0m\n", + "--------------------uri:BIKO_0000222\u001b[0m\n", + "--------------------uri:BIKO_0000223\u001b[0m\n", + "--------------------uri:BIKO_0000224\u001b[0m\n", + "--------------------uri:BIKO_0000225\u001b[0m\n", + "--------------------uri:BIKO_0000226\u001b[0m\n", + "--------------------uri:BIKO_0000227\u001b[0m\n", + "------------------------uri:BIKO_0000228\u001b[0m\n", + "------------------------uri:BIKO_0000229\u001b[0m\n", + "------------------------uri:BIKO_0000230\u001b[0m\n", + "--------------------uri:BIKO_0000231\u001b[0m\n", + "----------------uri:BIKO_0000232\u001b[0m\n", + "--------------------uri:BIKO_0000233\u001b[0m\n", + "--------------------uri:BIKO_0000234\u001b[0m\n", + "----------------uri:BIKO_0000235\u001b[0m\n", + "--------------------uri:BIKO_0000236\u001b[0m\n", + "--------------------uri:BIKO_0000237\u001b[0m\n", + "--------------------uri:BIKO_0000238\u001b[0m\n", + "------------------------uri:BIKO_0000239\u001b[0m\n", + "------------------------uri:BIKO_0000240\u001b[0m\n", + "----------------------------uri:BIKO_0000241\u001b[0m\n", + "----------------uri:BIKO_0000242\u001b[0m\n", + "----------------uri:BIKO_0000243\u001b[0m\n", + "--------------------uri:BIKO_0000244\u001b[0m\n", + "----uri:BIKO_0000009\u001b[0m\n", + "--------uri:BIKO_0000147\u001b[0m\n", + "------------uri:BIKO_0000150\u001b[0m\n", + "------------uri:BIKO_0000151\u001b[0m\n", + "--------uri:BIKO_0000152\u001b[0m\n", + "------------uri:BIKO_0000153\u001b[0m\n", + "------------uri:BIKO_0000154\u001b[0m\n", + "--------uri:BIKO_0000155\u001b[0m\n", + "------------uri:BIKO_0000158\u001b[0m\n", + "------------uri:BIKO_0000159\u001b[0m\n", + "------------uri:BIKO_0000160\u001b[0m\n", + "------------uri:BIKO_0000161\u001b[0m\n", + "------------uri:BIKO_0000162\u001b[0m\n", + "------------uri:BIKO_0000163\u001b[0m\n", + "------------uri:BIKO_0000164\u001b[0m\n", + "------------uri:BIKO_0000165\u001b[0m\n", + "------------uri:BIKO_0000166\u001b[0m\n", + "------------uri:BIKO_0000167\u001b[0m\n", + "------------uri:BIKO_0000168\u001b[0m\n", + "------------uri:BIKO_0000169\u001b[0m\n", + "------------uri:BIKO_0000170\u001b[0m\n", + "------------uri:BIKO_0000171\u001b[0m\n", + "------------uri:BIKO_0000172\u001b[0m\n", + "------------uri:BIKO_0000173\u001b[0m\n", + "----------------uri:BIKO_0000204\u001b[0m\n", + "------------uri:BIKO_0000174\u001b[0m\n", + "------------uri:BIKO_0000175\u001b[0m\n", + "------------uri:BIKO_0000176\u001b[0m\n", + "------------uri:BIKO_0000177\u001b[0m\n", + "------------uri:BIKO_0000178\u001b[0m\n", + "------------uri:BIKO_0000179\u001b[0m\n", + "------------uri:BIKO_0000180\u001b[0m\n", + "------------uri:BIKO_0000181\u001b[0m\n", + "------------uri:BIKO_0000182\u001b[0m\n", + "------------uri:BIKO_0000183\u001b[0m\n", + "------------uri:BIKO_0000184\u001b[0m\n", + "------------uri:BIKO_0000185\u001b[0m\n", + "------------uri:BIKO_0000186\u001b[0m\n", + "------------uri:BIKO_0000187\u001b[0m\n", + "------------uri:BIKO_0000188\u001b[0m\n", + "------------uri:BIKO_0000189\u001b[0m\n", + "------------uri:BIKO_0000190\u001b[0m\n", + "------------uri:BIKO_0000191\u001b[0m\n", + "------------uri:BIKO_0000192\u001b[0m\n", + "------------uri:BIKO_0000193\u001b[0m\n", + "------------uri:BIKO_0000194\u001b[0m\n", + "------------uri:BIKO_0000195\u001b[0m\n", + "------------uri:BIKO_0000196\u001b[0m\n", + "------------uri:BIKO_0000197\u001b[0m\n", + "------------uri:BIKO_0000198\u001b[0m\n", + "------------uri:BIKO_0000199\u001b[0m\n", + "------------uri:BIKO_0000200\u001b[0m\n", + "------------uri:BIKO_0000201\u001b[0m\n", + "------------uri:BIKO_0000202\u001b[0m\n", + "------------uri:BIKO_0000203\u001b[0m\n", + "------------uri:BIKO_0000205\u001b[0m\n", + "------------uri:BIKO_0000206\u001b[0m\n", + "------------uri:BIKO_0000207\u001b[0m\n", + "------------uri:BIKO_0000208\u001b[0m\n", + "------------uri:BIKO_0000209\u001b[0m\n", + "------------uri:BIKO_0000210\u001b[0m\n", + "------------uri:BIKO_0000211\u001b[0m\n", + "------------uri:BIKO_0000212\u001b[0m\n", + "------------uri:BIKO_0000213\u001b[0m\n", + "--------uri:BIKO_0000156\u001b[0m\n", + "------------uri:BIKO_0000157\u001b[0m\n", + "--------uri:BIKO_0000248\u001b[0m\n", + "------------uri:BIKO_0000249\u001b[0m\n", + "------------uri:BIKO_0000250\u001b[0m\n", + "------------uri:BIKO_0000251\u001b[0m\n", + "----uri:BIKO_0000027\u001b[0m\n", + "--------uri:BIKO_0000028\u001b[0m\n", + "--------uri:BIKO_0000032\u001b[0m\n", + "------------uri:BIKO_0000030\u001b[0m\n", + "----------------uri:BIKO_0000029\u001b[0m\n", + "------------uri:BIKO_0000031\u001b[0m\n", + "----------------uri:BIKO_0000035\u001b[0m\n", + "------------uri:BIKO_0000033\u001b[0m\n", + "------------uri:BIKO_0000034\u001b[0m\n", + "------------uri:BIKO_0000036\u001b[0m\n", + "--------uri:BIKO_0000037\u001b[0m\n", + "--------uri:BIKO_0000038\u001b[0m\n", + "--------uri:BIKO_0000039\u001b[0m\n", + "--------uri:BIKO_0000040\u001b[0m\n", + "----uri:BIKO_0000106\u001b[0m\n", + "uri:BIKO_0000002\u001b[0m\n", + "----uri:BIKO_0000010\u001b[0m\n", + "----uri:BIKO_0000011\u001b[0m\n", + "----uri:BIKO_0000012\u001b[0m\n", + "--------uri:BIKO_0000019\u001b[0m\n", + "--------uri:BIKO_0000021\u001b[0m\n", + "--------uri:BIKO_0000022\u001b[0m\n", + "--------uri:BIKO_0000026\u001b[0m\n", + "------------uri:BIKO_0000023\u001b[0m\n", + "------------uri:BIKO_0000024\u001b[0m\n", + "----------------uri:BIKO_0000025\u001b[0m\n", + "----uri:BIKO_0000020\u001b[0m\n", + "----uri:BIKO_0000107\u001b[0m\n", + "--------uri:BIKO_0000108\u001b[0m\n", + "------------uri:BIKO_0000110\u001b[0m\n", + "uri:BIKO_0000004\u001b[0m\n", + "----uri:BIKO_0000016\u001b[0m\n", + "----uri:BIKO_0000017\u001b[0m\n", + "----uri:BIKO_0000018\u001b[0m\n", + "uri:BIKO_0000005\u001b[0m\n", + "----uri:BIKO_0000003\u001b[0m\n", + "--------uri:BIKO_0000263\u001b[0m\n", + "------------uri:BIKO_0000264\u001b[0m\n", + "----------------uri:BIKO_0000245\u001b[0m\n", + "----uri:BIKO_0000013\u001b[0m\n", + "--------uri:BIKO_0000041\u001b[0m\n", + "------------uri:BIKO_0000042\u001b[0m\n", + "----------------uri:BIKO_0000057\u001b[0m\n", + "--------------------uri:BIKO_0000058\u001b[0m\n", + "------------------------uri:BIKO_0000059\u001b[0m\n", + "--------------------uri:BIKO_0000060\u001b[0m\n", + "------------------------uri:BIKO_0000062\u001b[0m\n", + "--------------------uri:BIKO_0000061\u001b[0m\n", + "------------------------uri:BIKO_0000063\u001b[0m\n", + "------------------------uri:BIKO_0000064\u001b[0m\n", + "----------------------------uri:BIKO_0000065\u001b[0m\n", + "------------uri:BIKO_0000043\u001b[0m\n", + "----------------uri:BIKO_0000045\u001b[0m\n", + "----------------uri:BIKO_0000046\u001b[0m\n", + "----------------uri:BIKO_0000047\u001b[0m\n", + "----------------uri:BIKO_0000048\u001b[0m\n", + "----------------uri:BIKO_0000049\u001b[0m\n", + "----------------uri:BIKO_0000050\u001b[0m\n", + "--------------------uri:BIKO_0000051\u001b[0m\n", + "----------------uri:BIKO_0000052\u001b[0m\n", + "--------------------uri:BIKO_0000053\u001b[0m\n", + "----------------uri:BIKO_0000054\u001b[0m\n", + "----------------uri:BIKO_0000055\u001b[0m\n", + "----------------uri:BIKO_0000056\u001b[0m\n", + "------------uri:BIKO_0000044\u001b[0m\n", + "----------------uri:BIKO_0000066\u001b[0m\n", + "--------------------uri:BIKO_0000067\u001b[0m\n", + "------------------------uri:BIKO_0000068\u001b[0m\n", + "----------------------------uri:BIKO_0000069\u001b[0m\n", + "----------------------------uri:BIKO_0000070\u001b[0m\n", + "----------------------------uri:BIKO_0000071\u001b[0m\n", + "------------------------uri:BIKO_0000072\u001b[0m\n", + "----------------------------uri:BIKO_0000073\u001b[0m\n", + "----------------------------uri:BIKO_0000074\u001b[0m\n", + "----------------------------uri:BIKO_0000075\u001b[0m\n", + "----------------------------uri:BIKO_0000076\u001b[0m\n", + "------------------------uri:BIKO_0000077\u001b[0m\n", + "----------------------------uri:BIKO_0000078\u001b[0m\n", + "----------------------------uri:BIKO_0000079\u001b[0m\n", + "------------------------uri:BIKO_0000080\u001b[0m\n", + "----------------------------uri:BIKO_0000081\u001b[0m\n", + "------------uri:BIKO_0000082\u001b[0m\n", + "----------------uri:BIKO_0000088\u001b[0m\n", + "----------------uri:BIKO_0000089\u001b[0m\n", + "--------------------uri:BIKO_0000094\u001b[0m\n", + "------------------------uri:BIKO_0000098\u001b[0m\n", + "----------------------------uri:BIKO_0000112\u001b[0m\n", + "----------------------------uri:BIKO_0000113\u001b[0m\n", + "--------------------------------uri:BIKO_0000115\u001b[0m\n", + "--------------------------------uri:BIKO_0000116\u001b[0m\n", + "--------------------------------uri:BIKO_0000117\u001b[0m\n", + "--------------------------------uri:BIKO_0000118\u001b[0m\n", + "--------------------------------uri:BIKO_0000119\u001b[0m\n", + "--------------------------------uri:BIKO_0000120\u001b[0m\n", + "--------------------------------uri:BIKO_0000121\u001b[0m\n", + "--------------------------------uri:BIKO_0000122\u001b[0m\n", + "--------------------------------uri:BIKO_0000123\u001b[0m\n", + "--------------------------------uri:BIKO_0000124\u001b[0m\n", + "--------------------------------uri:BIKO_0000125\u001b[0m\n", + "----------------------------uri:BIKO_0000114\u001b[0m\n", + "------------------------uri:BIKO_0000099\u001b[0m\n", + "----------------------------uri:BIKO_0000111\u001b[0m\n", + "------------------------uri:BIKO_0000100\u001b[0m\n", + "--------------------uri:BIKO_0000095\u001b[0m\n", + "--------------------uri:BIKO_0000096\u001b[0m\n", + "--------------------uri:BIKO_0000097\u001b[0m\n", + "----------------uri:BIKO_0000090\u001b[0m\n", + "----------------uri:BIKO_0000091\u001b[0m\n", + "----------------uri:BIKO_0000092\u001b[0m\n", + "----------------uri:BIKO_0000093\u001b[0m\n", + "------------uri:BIKO_0000083\u001b[0m\n", + "------------uri:BIKO_0000084\u001b[0m\n", + "------------uri:BIKO_0000085\u001b[0m\n", + "------------uri:BIKO_0000086\u001b[0m\n", + "------------uri:BIKO_0000087\u001b[0m\n", + "----uri:BIKO_0000014\u001b[0m\n", + "--------uri:BIKO_0000246\u001b[0m\n", + "--------uri:BIKO_0000247\u001b[0m\n", + "--------uri:BIKO_0000265\u001b[0m\n", + "--------uri:BIKO_0000266\u001b[0m\n", + "----uri:BIKO_0000015\u001b[0m\n", + "\u001b[1m\n", + "Properties\n", + "----------\u001b[0m\u001b[0m\n", + "oboInOwl:created_by\u001b[0m\n", + "oboInOwl:creation_date\u001b[0m\n", + "skos:definition\u001b[0m\n", + "uri:BIKO_0000101\u001b[0m\n", + "uri:BIKO_0000102\u001b[0m\n", + "uri:BIKO_0000103\u001b[0m\n", + "uri:BIKO_0000104\u001b[0m\n", + "uri:BIKO_0000105\u001b[0m\n", + "uri:BIKO_0000109\u001b[0m\n", + "uri:BIKO_0000267\u001b[0m\n", + "uri:BIKO_0000268\u001b[0m\n", + "uri:BIKO_0000269\u001b[0m\n", + "uri:BIKO_0000270\u001b[0m\n", + "uri:BIKO_0000271\u001b[0m\n", + "\u001b[1m\n", + "SKOS Concepts\n", + "----------\u001b[0m\u001b[0m\n", + "\u001b[2mNone found\u001b[0m\n", + "\u001b[1m\n", + "SHACL Shapes\n", + "----------\u001b[0m\u001b[0m\n", + "\u001b[2mNone found\u001b[0m\n", + "\u001b[2m\n", + "-----------\n", + "Time:\t 4.25s\u001b[0m\n" + ] + } + ], + "source": [ + "!ontospy scan $ontology_file_path" + ] + }, + { + "cell_type": "code", + "execution_count": 80, + "id": "58e83fbc-8d03-4c0a-9880-97f424be0249", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\u001b[2mOntospy v2.1.1\u001b[0m\n", + "Usage: ontospy gendocs [OPTIONS] [SOURCE]...\n", + "\n", + " GENDOCS: generate documentation in html or markdown format.\n", + "\n", + "Options:\n", + " -l, --lib LIBRARY: choose an ontology from your local library.\n", + " -o, --outputpath TEXT OUTPUT-PATH: where to save the visualization files\n", + " (default: home folder).\n", + " -x, --extra EXTRA-DATA: extract implicit types and predicates\n", + " using basic inference rules. Note: by default ontospy\n", + " extracts only classes/properties which are explictly\n", + " declared.\n", + " -i, --individuals INDIVIDUALS: extract class instances as well. Note:\n", + " by default ontospy extracts only instances of\n", + " explicitly declared classes. Use with -x option to\n", + " get all possible instances.\n", + " --type TEXT VIZ-TYPE: specify which viz type to use as an integer\n", + " (eg 1=single-page html, 2=multi-page etc..).\n", + " --title TEXT TITLE: custom title for the visualization\n", + " (default=graph uri).\n", + " --theme TEXT THEME: select bootstrap style (only for the html-\n", + " multi-page visualization). Default: simplex\n", + " (random=use a random theme).\n", + " --preflabel TEXT PREF-LABEL: default value to use for entity titles\n", + " (qname|label - default=qname).\n", + " --preflang TEXT PREF-LANGUAGE: default language for multilingual\n", + " strings (default=en).\n", + " --nobrowser NO-BROWSER: prevents opening the html output in the\n", + " browser by default.\n", + " --showtypes SHOW-TYPES: show the available visualization types.\n", + " --showthemes SHOW-THEMES: show the available css theme choices.\n", + " -v, --verbose VERBOSE: print out debug messages.\n", + " -h, --help Show this message and exit.\u001b[0m\n" + ] + } + ], + "source": [ + "!ontospy gendocs" + ] + }, + { + "cell_type": "code", + "execution_count": 57, + "id": "f54e2fbe-2e01-4577-b4d7-9a6a16635534", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\u001b[2mOntospy v2.1.1\u001b[0m\n", + "\u001b[32m1. Html: single page\u001b[0m\n", + "\u001b[32m2. Html: multi page\u001b[0m\n", + "\u001b[32m3. Markdown: multi page\u001b[0m\n", + "\u001b[32m4. D3 Dendogram\u001b[0m\n", + "\u001b[32m5. D3 Bubble chart\u001b[0m\n", + "\u001b[32m6. D3 Pack hierarchy\u001b[0m\n", + "\u001b[32m7. D3 Bar hierarchy\u001b[0m\n", + "\u001b[32m8. D3 Partition table [alpha]\u001b[0m\n", + "\u001b[32m9. D3 Rotating cluster [alpha]\u001b[0m\n", + "\u001b[32m10. Sigma.js Force directed graph [alpha]\u001b[0m\n", + "\u001b[2mNote: select a viz type by using its numerical index.\u001b[0m\n" + ] + } + ], + "source": [ + "!ontospy gendocs --showtypes" + ] + }, + { + "cell_type": "code", + "execution_count": 64, + "id": "15b81484-d492-45df-be68-ae10a24f4d59", + "metadata": { + "jp-MarkdownHeadingCollapsed": true + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\u001b[2mOntospy v2.1.1\u001b[0m\n", + "\u001b[1mPlease choose an output format for the ontology visualization: (q=quit)\n", + "\u001b[0m\n", + "1) Html: single page\n", + "2) Html: multi page\n", + "3) Markdown: multi page\n", + "4) D3 Dendogram\n", + "5) D3 Bubble chart\n", + "6) D3 Pack hierarchy\n", + "7) D3 Bar hierarchy\n", + "8) D3 Partition table [alpha]\n", + "9) D3 Rotating cluster [alpha]\n", + "10) Sigma.js Force directed graph [alpha]\n", + ">\u001b[2mLoading graph...\u001b[0m\n", + "\u001b[2mBuilding visualization...\u001b[0m\n", + "\u001b[2mDone.\u001b[0m\n", + "\u001b[2m=> file:///Users/tmsincomb/ontospy-viz/ontologybikobiko_v0_5ttl/sigmajs-force-directed-graph-alpha/index.html\u001b[0m\n", + "\u001b[2m\n", + "-----------\n", + "Time:\t 4.40s\u001b[0m\n" + ] + } + ], + "source": [ + "!echo \"10\" | ontospy gendocs $ontology_file_path " + ] + }, + { + "cell_type": "code", + "execution_count": 70, + "id": "578051dc-0de5-4a92-82eb-6897f2e916a0", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "'7.0.0'" + ] + }, + "execution_count": 70, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "import rdflib\n", + "rdflib.__version__" + ] + }, + { + "cell_type": "code", + "execution_count": 81, + "id": "33682bdd-cb71-445c-9faa-fa323f44f882", + "metadata": {}, + "outputs": [], + "source": [ + "!./ontology-visualization/ontology_viz.py -o test.dot $ontology_file_path" + ] + }, + { + "cell_type": "code", + "execution_count": 83, + "id": "bb7c71f1-67a5-48ce-86ab-5a39ecf0c3bf", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "dot: graph is too large for cairo-renderer bitmaps. Scaling by 0.36223 to fit\n" + ] + } + ], + "source": [ + "!dot -Tpng -o test.png test.dot" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python [conda env:ilx] *", + "language": "python", + "name": "conda-env-ilx-py" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.11.0" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/plots/ontology-visualization b/plots/ontology-visualization new file mode 160000 index 0000000..bdddb08 --- /dev/null +++ b/plots/ontology-visualization @@ -0,0 +1 @@ +Subproject commit bdddb08e141eff911bd873960a138b56b86801c4 diff --git a/plots/test.dot b/plots/test.dot new file mode 100644 index 0000000..0c362fb --- /dev/null +++ b/plots/test.dot @@ -0,0 +1,2292 @@ +digraph G { + rankdir=BT + node[style="filled" height=.3] 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