{ "cells": [ { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [], "source": [ "%reset -f" ] }, { "cell_type": "code", "execution_count": 2, "metadata": { "colab": { "base_uri": "https://localhost:8080/" }, "executionInfo": { "elapsed": 40896, "status": "ok", "timestamp": 1691683724630, "user": { "displayName": "Kevin Schaper", "userId": "12126623141624024195" }, "user_tz": 420 }, "id": "-bIXpdDFMwl-", "outputId": "c2800b96-c29a-451c-9e26-5ca3059a1028" }, "outputs": [], "source": [ "# !pip install oaklib==0.5.16-rc1" ] }, { "cell_type": "code", "execution_count": 3, "metadata": { "colab": { "base_uri": "https://localhost:8080/" }, "executionInfo": { "elapsed": 1277, "status": "ok", "timestamp": 1691683951632, "user": { "displayName": "Kevin Schaper", "userId": "12126623141624024195" }, "user_tz": 420 }, "id": "wXAgttWUNGvk", "outputId": "6f32360f-0b57-4143-c301-67a78363e12c" }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "CPU times: user 3.35 s, sys: 710 ms, total: 4.06 s\n", "Wall time: 3.15 s\n" ] } ], "source": [ "%%time\n", "from oaklib.selector import get_adapter\n", "semsim = get_adapter(f\"semsimian:sqlite:obo:phenio\")" ] }, { "cell_type": "code", "execution_count": 4, "metadata": { "id": "bzGuyJ6KOLFC" }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "CPU times: user 39.8 s, sys: 3.9 s, total: 43.7 s\n", "Wall time: 43.3 s\n" ] }, { "data": { "text/plain": [ "TermSetPairwiseSimilarity(subject_termset=[{'MP:0010771': {'id': 'MP:0010771', 'label': 'integument phenotype (MPO)'}}, {'MP:0005367': {'id': 'MP:0005367', 'label': 'renal/urinary system phenotype (MPO)'}}, {'MP:0002169': {'id': 'MP:0002169', 'label': 'no abnormal phenotype detected (MPO)'}}, {'MP:0005389': {'id': 'MP:0005389', 'label': 'reproductive system phenotype (MPO)'}}, {'MP:0005391': {'id': 'MP:0005391', 'label': 'vision/eye phenotype (MPO)'}}], object_termset=[{'MP:0006144': {'id': 'MP:0006144', 'label': 'increased systemic arterial systolic blood pressure (MPO)'}}, {'HP:0004325': {'id': 'HP:0004325', 'label': 'Decreased body weight (HPO)'}}, {'HP:0000093': {'id': 'HP:0000093', 'label': 'Proteinuria (HPO)'}}], subject_best_matches=JsonObj(similarity=JsonObj(**{'MP:0002169': JsonObj(ancestor_id='MP:0000001', ancestor_information_content='4.4237299124581355', ancestor_label='', cosine_similarity='NaN', jaccard_similarity='0.1', object_id='MP:0006144', phenodigm_score='0.6651112623056488', subject_id='MP:0002169'), 'MP:0005367': JsonObj(ancestor_id='UBERON:0001008', ancestor_information_content='6.050689168215567', ancestor_label='', cosine_similarity='NaN', jaccard_similarity='0.24107142857142858', object_id='HP:0000093', phenodigm_score='1.2077451227901506', subject_id='MP:0005367'), 'MP:0005389': JsonObj(ancestor_id='MP:0000001', ancestor_information_content='4.4237299124581355', ancestor_label='', cosine_similarity='NaN', jaccard_similarity='0.38571428571428573', object_id='MP:0006144', phenodigm_score='1.3062525878928277', subject_id='MP:0005389'), 'MP:0005391': JsonObj(ancestor_id='MP:0000001', ancestor_information_content='4.4237299124581355', ancestor_label='', cosine_similarity='NaN', jaccard_similarity='0.36486486486486486', object_id='MP:0006144', phenodigm_score='1.270458034217462', subject_id='MP:0005391'), 'MP:0010771': JsonObj(ancestor_id='MP:0000001', ancestor_information_content='4.4237299124581355', ancestor_label='', cosine_similarity='NaN', jaccard_similarity='0.38028169014084506', object_id='MP:0006144', phenodigm_score='1.2970210051638302', subject_id='MP:0010771')}), **{'MP:0002169': JsonObj(match_source='MP:0002169', match_source_label='no abnormal phenotype detected (MPO)', match_target='MP:0006144', match_target_label='increased systemic arterial systolic blood pressure (MPO)', score='4.4237299124581355'), 'MP:0005367': JsonObj(match_source='MP:0005367', match_source_label='renal/urinary system phenotype (MPO)', match_target='HP:0000093', match_target_label='Proteinuria (HPO)', score='6.050689168215567'), 'MP:0005389': JsonObj(match_source='MP:0005389', match_source_label='reproductive system phenotype (MPO)', match_target='MP:0006144', match_target_label='increased systemic arterial systolic blood pressure (MPO)', score='4.4237299124581355'), 'MP:0005391': JsonObj(match_source='MP:0005391', match_source_label='vision/eye phenotype (MPO)', match_target='MP:0006144', match_target_label='increased systemic arterial systolic blood pressure (MPO)', score='4.4237299124581355'), 'MP:0010771': JsonObj(match_source='MP:0010771', match_source_label='integument phenotype (MPO)', match_target='MP:0006144', match_target_label='increased systemic arterial systolic blood pressure (MPO)', score='4.4237299124581355')}), object_best_matches=JsonObj(similarity=JsonObj(**{'HP:0000093': JsonObj(ancestor_id='UBERON:0001008', ancestor_information_content='6.050689168215567', ancestor_label='', cosine_similarity='NaN', jaccard_similarity='0.24107142857142858', object_id='MP:0005367', phenodigm_score='1.2077451227901506', subject_id='HP:0000093'), 'HP:0004325': JsonObj(ancestor_id='UPHENO:0001003', ancestor_information_content='1.449244551635026', ancestor_label='', cosine_similarity='NaN', jaccard_similarity='0.13043478260869565', object_id='MP:0002169', phenodigm_score='0.4347779870685166', subject_id='HP:0004325'), 'MP:0006144': JsonObj(ancestor_id='MP:0000001', ancestor_information_content='4.4237299124581355', ancestor_label='', cosine_similarity='NaN', jaccard_similarity='0.38028169014084506', object_id='MP:0010771', phenodigm_score='1.2970210051638302', subject_id='MP:0006144')}), **{'HP:0000093': JsonObj(match_source='HP:0000093', match_source_label='Proteinuria (HPO)', match_target='MP:0005367', match_target_label='renal/urinary system phenotype (MPO)', score='6.050689168215567'), 'HP:0004325': JsonObj(match_source='HP:0004325', match_source_label='Decreased body weight (HPO)', match_target='MP:0002169', match_target_label='no abnormal phenotype detected (MPO)', score='1.449244551635026'), 'MP:0006144': JsonObj(match_source='MP:0006144', match_source_label='increased systemic arterial systolic blood pressure (MPO)', match_target='MP:0010771', match_target_label='integument phenotype (MPO)', score='4.4237299124581355')}), average_score=4.361838153856265, best_score=6.050689168215567, metric='ancestor_information_content')" ] }, "execution_count": 4, "metadata": {}, "output_type": "execute_result" } ], "source": [ "%%time\n", "semsim.termset_pairwise_similarity(\n", " subjects=[\"MP:0010771\",\"MP:0002169\",\"MP:0005391\",\"MP:0005389\",\"MP:0005367\"],\n", " objects=[\"HP:0004325\",\"HP:0000093\",\"MP:0006144\"],\n", " predicates=[\"rdfs:subClassOf\", \"BFO:0000050\", \"UPHENO:0000001\"],\n", " labels=False,\n", " )" ] }, { "cell_type": "code", "execution_count": 5, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "{('BFO:0000050',\n", " 'UPHENO:0000001',\n", " 'rdfs:subClassOf'): }" ] }, "execution_count": 5, "metadata": {}, "output_type": "execute_result" } ], "source": [ "semsim.semsimian_object_cache" ] }, { "cell_type": "code", "execution_count": 6, "metadata": { "id": "tnMEeekQO7Ne" }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "CPU times: user 26 s, sys: 1.74 s, total: 27.7 s\n", "Wall time: 27.6 s\n" ] }, { "data": { "text/plain": [ "TermSetPairwiseSimilarity(subject_termset=[{'MP:0005367': {'id': 'MP:0005367', 'label': 'renal/urinary system phenotype (MPO)'}}, {'MP:0005389': {'id': 'MP:0005389', 'label': 'reproductive system phenotype (MPO)'}}, {'MP:0005391': {'id': 'MP:0005391', 'label': 'vision/eye phenotype (MPO)'}}, {'MP:0010771': {'id': 'MP:0010771', 'label': 'integument phenotype (MPO)'}}, {'MP:0002169': {'id': 'MP:0002169', 'label': 'no abnormal phenotype detected (MPO)'}}], object_termset=[{'HP:0000093': {'id': 'HP:0000093', 'label': 'Proteinuria (HPO)'}}, {'MP:0006144': {'id': 'MP:0006144', 'label': 'increased systemic arterial systolic blood pressure (MPO)'}}, {'HP:0004325': {'id': 'HP:0004325', 'label': 'Decreased body weight (HPO)'}}], subject_best_matches=JsonObj(similarity=JsonObj(**{'MP:0002169': JsonObj(ancestor_id='MP:0000001', ancestor_information_content='4.4237299124581355', ancestor_label='', cosine_similarity='NaN', jaccard_similarity='0.1', object_id='MP:0006144', phenodigm_score='0.6651112623056488', subject_id='MP:0002169'), 'MP:0005367': JsonObj(ancestor_id='UBERON:0001008', ancestor_information_content='6.050689168215567', ancestor_label='', cosine_similarity='NaN', jaccard_similarity='0.24107142857142858', object_id='HP:0000093', phenodigm_score='1.2077451227901506', subject_id='MP:0005367'), 'MP:0005389': JsonObj(ancestor_id='MP:0000001', ancestor_information_content='4.4237299124581355', ancestor_label='', cosine_similarity='NaN', jaccard_similarity='0.38571428571428573', object_id='MP:0006144', phenodigm_score='1.3062525878928277', subject_id='MP:0005389'), 'MP:0005391': JsonObj(ancestor_id='MP:0000001', ancestor_information_content='4.4237299124581355', ancestor_label='', cosine_similarity='NaN', jaccard_similarity='0.36486486486486486', object_id='MP:0006144', phenodigm_score='1.270458034217462', subject_id='MP:0005391'), 'MP:0010771': JsonObj(ancestor_id='MP:0000001', ancestor_information_content='4.4237299124581355', ancestor_label='', cosine_similarity='NaN', jaccard_similarity='0.38028169014084506', object_id='MP:0006144', phenodigm_score='1.2970210051638302', subject_id='MP:0010771')}), **{'MP:0002169': JsonObj(match_source='MP:0002169', match_source_label='no abnormal phenotype detected (MPO)', match_target='MP:0006144', match_target_label='increased systemic arterial systolic blood pressure (MPO)', score='4.4237299124581355'), 'MP:0005367': JsonObj(match_source='MP:0005367', match_source_label='renal/urinary system phenotype (MPO)', match_target='HP:0000093', match_target_label='Proteinuria (HPO)', score='6.050689168215567'), 'MP:0005389': JsonObj(match_source='MP:0005389', match_source_label='reproductive system phenotype (MPO)', match_target='MP:0006144', match_target_label='increased systemic arterial systolic blood pressure (MPO)', score='4.4237299124581355'), 'MP:0005391': JsonObj(match_source='MP:0005391', match_source_label='vision/eye phenotype (MPO)', match_target='MP:0006144', match_target_label='increased systemic arterial systolic blood pressure (MPO)', score='4.4237299124581355'), 'MP:0010771': JsonObj(match_source='MP:0010771', match_source_label='integument phenotype (MPO)', match_target='MP:0006144', match_target_label='increased systemic arterial systolic blood pressure (MPO)', score='4.4237299124581355')}), object_best_matches=JsonObj(similarity=JsonObj(**{'HP:0000093': JsonObj(ancestor_id='UBERON:0001008', ancestor_information_content='6.050689168215567', ancestor_label='', cosine_similarity='NaN', jaccard_similarity='0.24107142857142858', object_id='MP:0005367', phenodigm_score='1.2077451227901506', subject_id='HP:0000093'), 'HP:0004325': JsonObj(ancestor_id='UPHENO:0001003', ancestor_information_content='1.449244551635026', ancestor_label='', cosine_similarity='NaN', jaccard_similarity='0.44', object_id='MP:0005367', phenodigm_score='0.7985409211301644', subject_id='HP:0004325'), 'MP:0006144': JsonObj(ancestor_id='MP:0000001', ancestor_information_content='4.4237299124581355', ancestor_label='', cosine_similarity='NaN', jaccard_similarity='0.36486486486486486', object_id='MP:0005391', phenodigm_score='1.270458034217462', subject_id='MP:0006144')}), **{'HP:0000093': JsonObj(match_source='HP:0000093', match_source_label='Proteinuria (HPO)', match_target='MP:0005367', match_target_label='renal/urinary system phenotype (MPO)', score='6.050689168215567'), 'HP:0004325': JsonObj(match_source='HP:0004325', match_source_label='Decreased body weight (HPO)', match_target='MP:0005367', match_target_label='renal/urinary system phenotype (MPO)', score='1.449244551635026'), 'MP:0006144': JsonObj(match_source='MP:0006144', match_source_label='increased systemic arterial systolic blood pressure (MPO)', match_target='MP:0005391', match_target_label='vision/eye phenotype (MPO)', score='4.4237299124581355')}), average_score=4.361838153856265, best_score=6.050689168215567, metric='ancestor_information_content')" ] }, "execution_count": 6, "metadata": {}, "output_type": "execute_result" } ], "source": [ "%%time\n", "semsim.termset_pairwise_similarity(\n", " subjects=[\"MP:0010771\",\"MP:0002169\",\"MP:0005391\",\"MP:0005389\",\"MP:0005367\"],\n", " objects=[\"HP:0004325\",\"HP:0000093\",\"MP:0006144\"],\n", " predicates=[\"rdfs:subClassOf\", \"BFO:0000050\", \"UPHENO:0000001\"],\n", " labels=False,\n", " )" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Semsimian" ] }, { "cell_type": "code", "execution_count": 7, "metadata": {}, "outputs": [], "source": [ "from semsimian import Semsimian" ] }, { "cell_type": "code", "execution_count": 8, "metadata": {}, "outputs": [], "source": [ "subjects=[\"MP:0010771\",\"MP:0002169\",\"MP:0005391\",\"MP:0005389\",\"MP:0005367\"]\n", "objects=[\"HP:0004325\",\"HP:0000093\",\"MP:0006144\"]\n", "predicates=[\"rdfs:subClassOf\", \"BFO:0000050\", \"UPHENO:0000001\"]" ] }, { "cell_type": "code", "execution_count": 9, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "SemSimianImplementation(resource=OntologyResource(slug='sqlite:obo:phenio', directory=None, scheme='semsimian', format=None, url=None, readonly=False, provider=None, local=False, in_memory=False, data=None, implementation_class=, import_depth=None), strict=False, _multilingual=None, autosave=True, exclude_owl_top_and_bottom=True, ontology_metamodel_mapper=None, _converter=None, auto_relax_axioms=None, cache_lookups=False, _edge_index=None, _entailed_edge_index=None, semsimian_object_cache={('BFO:0000050', 'UPHENO:0000001', 'rdfs:subClassOf'): })" ] }, "execution_count": 9, "metadata": {}, "output_type": "execute_result" } ], "source": [ "semsim" ] }, { "cell_type": "code", "execution_count": 10, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "CPU times: user 25 µs, sys: 1 µs, total: 26 µs\n", "Wall time: 30 µs\n" ] }, { "data": { "text/plain": [ "str" ] }, "execution_count": 10, "metadata": {}, "output_type": "execute_result" } ], "source": [ "%%time\n", "\n", "semsim.resource_path = str(semsim.wrapped_adapter.engine.url).lstrip(\"sqlite:\")\n", "type(semsim.resource_path)" ] }, { "cell_type": "code", "execution_count": 11, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "CPU times: user 15.8 s, sys: 1.62 s, total: 17.5 s\n", "Wall time: 17.4 s\n" ] } ], "source": [ "%%time\n", "new_semsim_obj = Semsimian(spo=None, predicates=predicates, pairwise_similarity_attributes=None, resource_path=semsim.resource_path)" ] }, { "cell_type": "code", "execution_count": 12, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "[('HP:0009582', 'UPHENO:0000001', 'CARO:0010000'),\n", " ('HP:0009582', 'rdfs:subClassOf', 'HP:0005918'),\n", " ('HP:0009582', 'rdfs:subClassOf', 'UPHENO:0080300'),\n", " ('HP:0009582', 'UPHENO:0000001', 'CARO:0000003'),\n", " ('HP:0009582', 'UPHENO:0000001', 'CARO:0000006'),\n", " ('HP:0009582', 'UPHENO:0000001', 'CARO:0030000'),\n", " ('HP:0009582', 'rdfs:subClassOf', 'UPHENO:0041448'),\n", " ('HP:0009582', 'UPHENO:0000001', 'UBERON:0001440'),\n", " ('HP:0009582', 'UPHENO:0000001', 'BFO:0000040'),\n", " ('HP:0009582', 'UPHENO:0000001', 'BFO:0000002'),\n", " ('HP:0009582', 'rdfs:subClassOf', 'UPHENO:0041370'),\n", " ('HP:0009582', 'UPHENO:0000001', 'UBERON:0011582'),\n", " ('HP:0009582', 'UPHENO:0000001', 'UBERON:0000475'),\n", " ('HP:0009582', 'rdfs:subClassOf', 'UPHENO:0041262'),\n", " ('HP:0009582', 'rdfs:subClassOf', 'HP:0040068'),\n", " ('HP:0009582', 'UPHENO:0000001', 'UBERON:0008785'),\n", " ('HP:0009582', 'UPHENO:0000001', 'UBERON:0011216'),\n", " ('HP:0009582', 'rdfs:subClassOf', 'UPHENO:0002964'),\n", " ('HP:0009582', 'rdfs:subClassOf', 'HP:0040070'),\n", " ('HP:0009582', 'UPHENO:0000001', 'UBERON:0000468'),\n", " ('HP:0009582', 'UPHENO:0000001', 'UBERON:0015024'),\n", " ('HP:0009582', 'UPHENO:0000001', 'UBERON:0014502'),\n", " ('HP:0009582', 'rdfs:subClassOf', 'UPHENO:0020651'),\n", " ('HP:0009582', 'rdfs:subClassOf', 'HP:0009853'),\n", " ('HP:0009582', 'UPHENO:0000001', 'UBERON:0015063'),\n", " ('HP:0009582', 'UPHENO:0000001', 'UBERON:0007272'),\n", " ('HP:0009582', 'UPHENO:0000001', 'UBERON:0006049'),\n", " ('HP:0009582', 'rdfs:subClassOf', 'UPHENO:0021800'),\n", " ('HP:0009582', 'rdfs:subClassOf', 'UPHENO:0082129'),\n", " ('HP:0009582', 'UPHENO:0000001', 'UBERON:0010712'),\n", " ('HP:0009582', 'UPHENO:0000001', 'UBERON:5103622'),\n", " ('HP:0009582', 'UPHENO:0000001', 'UBERON:5003622'),\n", " ('HP:0009582', 'rdfs:subClassOf', 'UPHENO:0041311'),\n", " ('HP:0009582', 'rdfs:subClassOf', 'UPHENO:0084448'),\n", " ('HP:0009582', 'UPHENO:0000001', 'UBERON:0003607'),\n", " ('HP:0009582', 'UPHENO:0000001', 'UBERON:0000465'),\n", " ('HP:0009582', 'UPHENO:0000001', 'UBERON:0001009'),\n", " ('HP:0009582', 'UPHENO:0000001', 'UBERON:0019232'),\n", " ('HP:0009582', 'rdfs:subClassOf', 'UPHENO:0041288'),\n", " ('HP:0009582', 'UPHENO:0000001', 'UBERON:0012358'),\n", " ('HP:0009582', 'rdfs:subClassOf', 'HP:0040064'),\n", " ('HP:0009582', 'rdfs:subClassOf', 'HP:0009834'),\n", " ('HP:0009582', 'rdfs:subClassOf', 'UPHENO:0021840'),\n", " ('HP:0009582', 'UPHENO:0000001', 'UBERON:0005897'),\n", " ('HP:0009582', 'UPHENO:0000001', 'UBERON:0011249'),\n", " ('HP:0009582', 'UPHENO:0000001', 'UBERON:0001015'),\n", " ('HP:0009582', 'UPHENO:0000001', 'UBERON:0012141'),\n", " ('HP:0009582', 'UPHENO:0000001', 'UBERON:0010912'),\n", " ('HP:0009582', 'UPHENO:0000001', 'UBERON:0010000'),\n", " ('HP:0009582', 'rdfs:subClassOf', 'UPHENO:0002905'),\n", " ('HP:0009582', 'UPHENO:0000001', 'UBERON:0012140'),\n", " ('HP:0009582', 'UPHENO:0000001', 'BFO:0000001'),\n", " ('HP:0009582', 'rdfs:subClassOf', 'UPHENO:0041346'),\n", " ('HP:0009582', 'UPHENO:0000001', 'UBERON:0012139'),\n", " ('HP:0009582', 'rdfs:subClassOf', 'UPHENO:0020853'),\n", " ('HP:0009582', 'rdfs:subClassOf', 'UPHENO:0076740'),\n", " ('HP:0009582', 'UPHENO:0000001', 'UBERON:5102389'),\n", " ('HP:0009582', 'UPHENO:0000001', 'UBERON:0010741'),\n", " ('HP:0009582', 'UPHENO:0000001', 'CARO:0000032'),\n", " ('HP:0009582', 'UPHENO:0000001', 'UBERON:0015023'),\n", " ('HP:0009582', 'UPHENO:0000001', 'UBERON:0004708'),\n", " ('HP:0009582', 'UPHENO:0000001', 'UBERON:0012475'),\n", " ('HP:0009582', 'UPHENO:0000001', 'UBERON:0000075'),\n", " ('HP:0009582', 'UPHENO:0000001', 'UBERON:0010740'),\n", " ('HP:0009582', 'UPHENO:0000001', 'UBERON:0001436'),\n", " ('HP:0009582', 'rdfs:subClassOf', 'UPHENO:0041226'),\n", " ('HP:0009582', 'rdfs:subClassOf', 'UPHENO:0075817'),\n", " ('HP:0009582', 'rdfs:subClassOf', 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"new_semsim_obj.get_spo()" ] }, { "cell_type": "code", "execution_count": 13, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "CPU times: user 25.8 s, sys: 3.38 s, total: 29.2 s\n", "Wall time: 30 s\n" ] }, { "data": { "text/plain": [ "{'subject_termset': [{'MP:0005391': {'id': 'MP:0005391',\n", " 'label': 'vision/eye phenotype (MPO)'}},\n", " {'MP:0005367': {'id': 'MP:0005367',\n", " 'label': 'renal/urinary system phenotype (MPO)'}},\n", " {'MP:0010771': {'id': 'MP:0010771', 'label': 'integument phenotype (MPO)'}},\n", " {'MP:0005389': {'id': 'MP:0005389',\n", " 'label': 'reproductive system phenotype (MPO)'}},\n", " {'MP:0002169': {'id': 'MP:0002169',\n", " 'label': 'no abnormal phenotype detected (MPO)'}}],\n", " 'object_termset': [{'MP:0006144': {'id': 'MP:0006144',\n", " 'label': 'increased systemic arterial systolic blood pressure (MPO)'}},\n", " {'HP:0000093': {'id': 'HP:0000093', 'label': 'Proteinuria (HPO)'}},\n", " {'HP:0004325': {'id': 'HP:0004325',\n", " 'label': 'Decreased body weight (HPO)'}}],\n", " 'subject_best_matches': {'MP:0002169': {'match_source': 'MP:0002169',\n", " 'match_source_label': 'no abnormal phenotype detected (MPO)',\n", " 'match_target': 'MP:0006144',\n", " 'match_target_label': 'increased systemic arterial systolic blood pressure (MPO)',\n", " 'score': '4.4237299124581355'},\n", " 'MP:0005367': {'match_source': 'MP:0005367',\n", " 'match_source_label': 'renal/urinary system phenotype (MPO)',\n", " 'match_target': 'HP:0000093',\n", " 'match_target_label': 'Proteinuria (HPO)',\n", " 'score': '6.050689168215567'},\n", " 'MP:0005389': {'match_source': 'MP:0005389',\n", " 'match_source_label': 'reproductive system phenotype (MPO)',\n", " 'match_target': 'MP:0006144',\n", " 'match_target_label': 'increased systemic arterial systolic blood pressure (MPO)',\n", " 'score': '4.4237299124581355'},\n", " 'MP:0005391': {'match_source': 'MP:0005391',\n", " 'match_source_label': 'vision/eye phenotype (MPO)',\n", " 'match_target': 'MP:0006144',\n", " 'match_target_label': 'increased systemic arterial systolic blood pressure (MPO)',\n", " 'score': '4.4237299124581355'},\n", " 'MP:0010771': {'match_source': 'MP:0010771',\n", " 'match_source_label': 'integument phenotype (MPO)',\n", " 'match_target': 'MP:0006144',\n", " 'match_target_label': 'increased systemic arterial systolic blood pressure (MPO)',\n", " 'score': '4.4237299124581355'},\n", " 'similarity': {'MP:0002169': {'ancestor_id': 'MP:0000001',\n", " 'ancestor_information_content': '4.4237299124581355',\n", " 'ancestor_label': '',\n", " 'cosine_similarity': 'NaN',\n", " 'jaccard_similarity': '0.1',\n", " 'object_id': 'MP:0006144',\n", " 'phenodigm_score': '0.6651112623056488',\n", " 'subject_id': 'MP:0002169'},\n", " 'MP:0005367': {'ancestor_id': 'UBERON:0001008',\n", " 'ancestor_information_content': '6.050689168215567',\n", " 'ancestor_label': '',\n", " 'cosine_similarity': 'NaN',\n", " 'jaccard_similarity': '0.24107142857142858',\n", " 'object_id': 'HP:0000093',\n", " 'phenodigm_score': '1.2077451227901506',\n", " 'subject_id': 'MP:0005367'},\n", " 'MP:0005389': {'ancestor_id': 'MP:0000001',\n", " 'ancestor_information_content': '4.4237299124581355',\n", " 'ancestor_label': '',\n", " 'cosine_similarity': 'NaN',\n", " 'jaccard_similarity': '0.38571428571428573',\n", " 'object_id': 'MP:0006144',\n", " 'phenodigm_score': '1.3062525878928277',\n", " 'subject_id': 'MP:0005389'},\n", " 'MP:0005391': {'ancestor_id': 'MP:0000001',\n", " 'ancestor_information_content': '4.4237299124581355',\n", " 'ancestor_label': '',\n", " 'cosine_similarity': 'NaN',\n", " 'jaccard_similarity': '0.36486486486486486',\n", " 'object_id': 'MP:0006144',\n", " 'phenodigm_score': '1.270458034217462',\n", " 'subject_id': 'MP:0005391'},\n", " 'MP:0010771': {'ancestor_id': 'MP:0000001',\n", " 'ancestor_information_content': '4.4237299124581355',\n", " 'ancestor_label': '',\n", " 'cosine_similarity': 'NaN',\n", " 'jaccard_similarity': '0.38028169014084506',\n", " 'object_id': 'MP:0006144',\n", " 'phenodigm_score': '1.2970210051638302',\n", " 'subject_id': 'MP:0010771'}}},\n", " 'object_best_matches': {'HP:0000093': {'match_source': 'HP:0000093',\n", " 'match_source_label': 'Proteinuria (HPO)',\n", " 'match_target': 'MP:0005367',\n", " 'match_target_label': 'renal/urinary system phenotype (MPO)',\n", " 'score': '6.050689168215567'},\n", " 'HP:0004325': {'match_source': 'HP:0004325',\n", " 'match_source_label': 'Decreased body weight (HPO)',\n", " 'match_target': 'MP:0010771',\n", " 'match_target_label': 'integument phenotype (MPO)',\n", " 'score': '1.449244551635026'},\n", " 'MP:0006144': {'match_source': 'MP:0006144',\n", " 'match_source_label': 'increased systemic arterial systolic blood pressure (MPO)',\n", " 'match_target': 'MP:0005391',\n", " 'match_target_label': 'vision/eye phenotype (MPO)',\n", " 'score': '4.4237299124581355'},\n", " 'similarity': {'HP:0000093': {'ancestor_id': 'UBERON:0001008',\n", " 'ancestor_information_content': '6.050689168215567',\n", " 'ancestor_label': '',\n", " 'cosine_similarity': 'NaN',\n", " 'jaccard_similarity': '0.24107142857142858',\n", " 'object_id': 'MP:0005367',\n", " 'phenodigm_score': '1.2077451227901506',\n", " 'subject_id': 'HP:0000093'},\n", " 'HP:0004325': {'ancestor_id': 'UPHENO:0001003',\n", " 'ancestor_information_content': '1.449244551635026',\n", " 'ancestor_label': '',\n", " 'cosine_similarity': 'NaN',\n", " 'jaccard_similarity': '0.43137254901960786',\n", " 'object_id': 'MP:0010771',\n", " 'phenodigm_score': '0.7906733310233626',\n", " 'subject_id': 'HP:0004325'},\n", " 'MP:0006144': {'ancestor_id': 'MP:0000001',\n", " 'ancestor_information_content': '4.4237299124581355',\n", " 'ancestor_label': '',\n", " 'cosine_similarity': 'NaN',\n", " 'jaccard_similarity': '0.36486486486486486',\n", " 'object_id': 'MP:0005391',\n", " 'phenodigm_score': '1.270458034217462',\n", " 'subject_id': 'MP:0006144'}}},\n", " 'average_score': 4.361838153856265,\n", " 'best_score': 6.050689168215567,\n", " 'metric': 'ancestor_information_content'}" ] }, "execution_count": 13, "metadata": {}, "output_type": "execute_result" } ], "source": [ "%%time\n", "new_semsim_obj.termset_pairwise_similarity(set(subjects), set(objects))" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [] } ], "metadata": { "colab": { "authorship_tag": "ABX9TyOKblottNzNAVbUXf712AY3", "provenance": [] }, "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": "3.10.12" } }, "nbformat": 4, "nbformat_minor": 4 }