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Moved Jupter notebooks to be part of sphinx docs (#816)
* Moved Jupter notebooks to be part of sphinx docs Fixes #758 * format * format * codespell * updated test to sync with labels being included * fixed test label
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.. _adapters_examples: | ||
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Adapter Examples | ||
================ | ||
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.. toctree:: | ||
:maxdepth: 2 | ||
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Ubergraph/Ubergraph-Tutorial |
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.. _commands_notebooks: | ||
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Commands | ||
======== | ||
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.. toctree:: | ||
:maxdepth: 2 | ||
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Apply | ||
Associations | ||
DiffViaMappings | ||
Disjoints | ||
Enrichment | ||
LogicalDefinitions | ||
Mappings | ||
Obsoletes | ||
Paths | ||
Relationships | ||
Rollup | ||
Statistics | ||
TaxonConstraints | ||
TermsetSimilarity | ||
ValidateDefinitions | ||
ValidateMappings |
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15 changes: 11 additions & 4 deletions
15
notebooks/mappings.ipynb → ...Interfaces/MappingProviderInterface.ipynb
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.. _interfaces_examples: | ||
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Interfaces Examples | ||
=================== | ||
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.. toctree:: | ||
:maxdepth: 2 | ||
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BasicOntologyInterface | ||
ClassEnrichmentCalculationInterface | ||
MappingProviderInterface |
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{ | ||
"cells": [ | ||
{ | ||
"cell_type": "code", | ||
"execution_count": 4, | ||
"id": "bf0c4518", | ||
"metadata": {}, | ||
"outputs": [], | ||
"source": [ | ||
"%alias chiro runoak -i sqlite:obo:chiro" | ||
] | ||
}, | ||
{ | ||
"cell_type": "code", | ||
"execution_count": 5, | ||
"id": "c726f3db", | ||
"metadata": {}, | ||
"outputs": [ | ||
{ | ||
"name": "stdout", | ||
"output_type": "stream", | ||
"text": [ | ||
"subject\tsubject_label\tpredicate\tpredicate_label\tobject\tobject_label\n", | ||
"CHEBI:22180\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0003984\tNone\n", | ||
"CHEBI:22587\tNone\tobo:chiro#inhibitor_of\tNone\tNCBITaxon:10239\tNone\n", | ||
"CHEBI:23018\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004089\tNone\n", | ||
"CHEBI:23100\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0006031\tNone\n", | ||
"CHEBI:23529\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0009512\tNone\n", | ||
"CHEBI:23924\tNone\tobo:chiro#inhibitor_of\tNone\t<http://purl.obolibrary.org/GO_0003824>\tNone\n", | ||
"CHEBI:24319\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004356\tNone\n", | ||
"CHEBI:25355\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0005746\tNone\n", | ||
"CHEBI:26087\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0009767\tNone\n", | ||
"CHEBI:26088\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0009522\tNone\n", | ||
"CHEBI:26089\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0009523\tNone\n", | ||
"CHEBI:33282\tNone\tobo:chiro#inhibitor_of\tNone\tNCBITaxon:2\tNone\n", | ||
"CHEBI:35472\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0006954\tNone\n", | ||
"CHEBI:35493\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0001660\tNone\n", | ||
"CHEBI:35608\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004725\tNone\n", | ||
"CHEBI:35634\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004855\tNone\n", | ||
"CHEBI:35842\tNone\tobo:chiro#inhibitor_of\tNone\tMP:0003561\tNone\n", | ||
"CHEBI:35856\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0016165\tNone\n", | ||
"CHEBI:36044\tNone\tobo:chiro#inhibitor_of\tNone\tNCBITaxon:10239\tNone\n", | ||
"CHEBI:36047\tNone\tobo:chiro#inhibitor_of\tNone\t<http://purl.obolibrary.org/NCBITaxon_2>\tNone\n", | ||
"CHEBI:37153\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0016791\tNone\n", | ||
"CHEBI:37416\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0034062\tNone\n", | ||
"CHEBI:37670\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004175\tNone\n", | ||
"CHEBI:37699\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004672\tNone\n", | ||
"CHEBI:37700\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004697\tNone\n", | ||
"CHEBI:37733\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004104\tNone\n", | ||
"CHEBI:38070\tNone\tobo:chiro#inhibitor_of\tNone\tHP:0011675\tNone\n", | ||
"CHEBI:38234\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0034061\tNone\n", | ||
"CHEBI:38462\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0003990\tNone\n", | ||
"CHEBI:38496\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0022900\tNone\n", | ||
"CHEBI:38497\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0070469\tNone\n", | ||
"CHEBI:38498\tNone\tobo:chiro#inhibitor_of\tNone\t_:riog00000282\tNone\n", | ||
"CHEBI:38499\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0005750\tNone\n", | ||
"CHEBI:38500\tNone\tobo:chiro#inhibitor_of\tNone\t_:riog00000306\tNone\n", | ||
"CHEBI:38501\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004129\tNone\n", | ||
"CHEBI:38502\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0045275\tNone\n", | ||
"CHEBI:38503\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0008137\tNone\n", | ||
"CHEBI:38637\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004713\tNone\n", | ||
"CHEBI:39456\tNone\tobo:chiro#inhibitor_of\tNone\tHP:0000501\tNone\n", | ||
"CHEBI:48001\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0006412\tNone\n", | ||
"CHEBI:48406\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0016206\tNone\n", | ||
"CHEBI:48422\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0001525\tNone\n", | ||
"CHEBI:48550\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004032\tNone\n", | ||
"CHEBI:49200\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0022804\tNone\n", | ||
"CHEBI:49205\tNone\tobo:chiro#inhibitor_of\tNone\tPR:000005373\tNone\n", | ||
"CHEBI:50184\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0006811\tNone\n", | ||
"CHEBI:50185\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0006633\tNone\n", | ||
"CHEBI:50380\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0003868\tNone\n", | ||
"CHEBI:50382\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0008120\tNone\n", | ||
"CHEBI:50390\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0003955\tNone\n", | ||
"CHEBI:50427\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0070527\tNone\n", | ||
"CHEBI:50445\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004000\tNone\n", | ||
"CHEBI:50469\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004623\tNone\n", | ||
"CHEBI:50502\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004156\tNone\n", | ||
"CHEBI:50627\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004556\tNone\n", | ||
"CHEBI:50628\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004558\tNone\n", | ||
"CHEBI:50635\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0009039\tNone\n", | ||
"CHEBI:50643\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004337\tNone\n", | ||
"CHEBI:50664\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0008237\tNone\n", | ||
"CHEBI:50683\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004146\tNone\n", | ||
"CHEBI:50750\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0003918\tNone\n", | ||
"CHEBI:50790\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0070330\tNone\n", | ||
"CHEBI:50914\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0035004\tNone\n", | ||
"CHEBI:50916\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0001727\tNone\n", | ||
"CHEBI:50925\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004674\tNone\n", | ||
"CHEBI:50949\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0051610\tNone\n", | ||
"CHEBI:51039\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0051583\tNone\n", | ||
"CHEBI:52303\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0003838\tNone\n", | ||
"CHEBI:52425\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004308\tNone\n", | ||
"CHEBI:52629\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004523\tNone\n", | ||
"CHEBI:52629\tNone\tobo:chiro#inhibitor_of\tNone\tNCBITaxon:11676\tNone\n", | ||
"CHEBI:52726\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0000502\tNone\n", | ||
"CHEBI:53659\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0052597\tNone\n", | ||
"CHEBI:53746\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0003938\tNone\n", | ||
"CHEBI:53756\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0003964\tNone\n", | ||
"CHEBI:53756\tNone\tobo:chiro#inhibitor_of\tNone\tNCBITaxon:11676\tNone\n", | ||
"CHEBI:59105\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0016881\tNone\n", | ||
"CHEBI:59107\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004222\tNone\n", | ||
"CHEBI:5924\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004252\tNone\n", | ||
"CHEBI:59285\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004506\tNone\n", | ||
"CHEBI:59321\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004058\tNone\n", | ||
"CHEBI:59499\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0016805\tNone\n", | ||
"CHEBI:59517\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0071897\tNone\n", | ||
"CHEBI:59647\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004758\tNone\n", | ||
"CHEBI:59672\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004100\tNone\n", | ||
"CHEBI:59897\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0003964\tNone\n", | ||
"CHEBI:59997\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004503\tNone\n", | ||
"CHEBI:60186\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0005388\tNone\n", | ||
"CHEBI:60258\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0008233\tNone\n", | ||
"CHEBI:60280\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004359\tNone\n", | ||
"CHEBI:60688\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004834\tNone\n", | ||
"CHEBI:60901\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004746\tNone\n", | ||
"CHEBI:61115\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004407\tNone\n", | ||
"CHEBI:61908\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004517\tNone\n", | ||
"CHEBI:62089\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0015930\tNone\n", | ||
"CHEBI:62434\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004714\tNone\n", | ||
"CHEBI:62530\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0050291\tNone\n", | ||
"CHEBI:62608\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0003994\tNone\n", | ||
"CHEBI:62609\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0033978\tNone\n", | ||
"CHEBI:62670\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004721\tNone\n", | ||
"CHEBI:62871\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0045548\tNone\n", | ||
"CHEBI:62915\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0008373\tNone\n", | ||
"CHEBI:63090\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004731\tNone\n", | ||
"CHEBI:63146\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0030073\tNone\n", | ||
"CHEBI:63156\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0047639\tNone\n", | ||
"CHEBI:63173\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0042098\tNone\n", | ||
"CHEBI:63330\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0044341\tNone\n", | ||
"CHEBI:63332\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004035\tNone\n", | ||
"CHEBI:63510\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0005391\tNone\n", | ||
"CHEBI:63674\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0003867\tNone\n", | ||
"CHEBI:63720\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004799\tNone\n", | ||
"CHEBI:63932\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004511\tNone\n", | ||
"CHEBI:63958\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0030244\tNone\n", | ||
"CHEBI:63962\tNone\tobo:chiro#inhibitor_of\tNone\tPR:000025350\tNone\n", | ||
"CHEBI:64133\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004660\tNone\n", | ||
"CHEBI:64152\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0008234\tNone\n", | ||
"CHEBI:64411\tNone\tobo:chiro#inhibitor_of\tNone\tPR:000007961\tNone\n", | ||
"CHEBI:64416\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0047794\tNone\n", | ||
"CHEBI:64570\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004372\tNone\n", | ||
"CHEBI:64670\tNone\tobo:chiro#inhibitor_of\tNone\tPR:000024130\tNone\n", | ||
"CHEBI:64696\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0008415\tNone\n", | ||
"CHEBI:64697\tNone\tobo:chiro#inhibitor_of\tNone\tPR:000015390\tNone\n", | ||
"CHEBI:64763\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004435\tNone\n", | ||
"CHEBI:64919\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004144\tNone\n", | ||
"CHEBI:64920\tNone\tobo:chiro#inhibitor_of\tNone\tPR:000023089\tNone\n", | ||
"CHEBI:64924\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0008233\tNone\n", | ||
"CHEBI:64924\tNone\tobo:chiro#inhibitor_of\tNone\tNCBITaxon:11103\tNone\n", | ||
"CHEBI:64933\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0042438\tNone\n", | ||
"CHEBI:64947\tNone\tobo:chiro#inhibitor_of\tNone\tNCBITaxon:11676\tNone\n", | ||
"CHEBI:64955\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0030305\tNone\n", | ||
"CHEBI:64964\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004051\tNone\n", | ||
"CHEBI:64995\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004052\tNone\n", | ||
"CHEBI:64996\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0050473\tNone\n", | ||
"CHEBI:65001\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004806\tNone\n", | ||
"CHEBI:65053\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0008792\tNone\n", | ||
"CHEBI:65064\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0008825\tNone\n", | ||
"CHEBI:65065\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0009008\tNone\n", | ||
"CHEBI:65232\tNone\tobo:chiro#inhibitor_of\tNone\t<http://purl.obolibrary.org/GO_0003809>\tNone\n", | ||
"CHEBI:66921\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0004718\tNone\n", | ||
"CHEBI:66956\tNone\tobo:chiro#inhibitor_of\tNone\tHP:0100660\tNone\n" | ||
] | ||
}, | ||
{ | ||
"name": "stdout", | ||
"output_type": "stream", | ||
"text": [ | ||
"CHEBI:67079\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0006954\tNone\r", | ||
"\r\n", | ||
"CHEBI:67195\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0005243\tNone\r", | ||
"\r\n", | ||
"CHEBI:67268\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0008907\tNone\r", | ||
"\r\n", | ||
"CHEBI:68494\tNone\tobo:chiro#inhibitor_of\tNone\tGO:0006915\tNone\r", | ||
"\r\n" | ||
] | ||
} | ||
], | ||
"source": [ | ||
"chiro relationships -p obo:chiro#inhibitor_of" | ||
] | ||
}, | ||
{ | ||
"cell_type": "code", | ||
"execution_count": null, | ||
"id": "5619e51c", | ||
"metadata": {}, | ||
"outputs": [], | ||
"source": [] | ||
} | ||
], | ||
"metadata": { | ||
"kernelspec": { | ||
"display_name": "Python 3 (ipykernel)", | ||
"language": "python", | ||
"name": "python3" | ||
}, | ||
"language_info": { | ||
"codemirror_mode": { | ||
"name": "ipython", | ||
"version": 3 | ||
}, | ||
"file_extension": ".py", | ||
"mimetype": "text/x-python", | ||
"name": "python", | ||
"nbconvert_exporter": "python", | ||
"pygments_lexer": "ipython3", | ||
"version": "3.9.5" | ||
} | ||
}, | ||
"nbformat": 4, | ||
"nbformat_minor": 5 | ||
} |
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.. _chebi_examples: | ||
|
||
CHEBI Examples | ||
============== | ||
|
||
.. toctree:: | ||
:maxdepth: 2 | ||
|
||
CHEBI-Predicates | ||
CHEBI-Slimmer | ||
|
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.. _cl_examples: | ||
|
||
CL Examples | ||
============== | ||
|
||
.. toctree:: | ||
:maxdepth: 2 | ||
|
||
CL-Neuro-Tutorial | ||
Lung-Epithelial-Cell-Types | ||
|
||
|
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