{"id":"https://openalex.org/W2949540143","doi":"https://doi.org/10.1186/s13326-019-0202-8","title":"Predicting instances of pathway ontology classes for pathway integration","display_name":"Predicting instances of pathway ontology classes for pathway integration","publication_year":2019,"publication_date":"2019-06-13","ids":{"openalex":"https://openalex.org/W2949540143","doi":"https://doi.org/10.1186/s13326-019-0202-8","mag":"2949540143","pmid":"https://pubmed.ncbi.nlm.nih.gov/31196182"},"language":"en","primary_location":{"id":"doi:10.1186/s13326-019-0202-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13326-019-0202-8","pdf_url":"https://jbiomedsem.biomedcentral.com/track/pdf/10.1186/s13326-019-0202-8","source":{"id":"https://openalex.org/S172276550","display_name":"Journal of Biomedical Semantics","issn_l":"2041-1480","issn":["2041-1480"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Biomedical Semantics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jbiomedsem.biomedcentral.com/track/pdf/10.1186/s13326-019-0202-8","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5001778694","display_name":"Lucy Lu Wang","orcid":"https://orcid.org/0000-0001-8752-6635"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Lucy Lu Wang","raw_affiliation_strings":["Department of Biomedical Informatics and Medical Education, University of Washington, 850 Republican St, Seattle, 98109, WA, USA. lucylw@uw.edu","Department of Biomedical Informatics and Medical Education, University of Washington, 850 Republican St, Seattle, 98109, WA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics and Medical Education, University of Washington, 850 Republican St, Seattle, 98109, WA, USA. lucylw@uw.edu","institution_ids":[]},{"raw_affiliation_string":"Department of Biomedical Informatics and Medical Education, University of Washington, 850 Republican St, Seattle, 98109, WA, USA","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021887904","display_name":"G. Thomas Hayman","orcid":"https://orcid.org/0000-0002-9553-7227"},"institutions":[{"id":"https://openalex.org/I204308271","display_name":"Medical College of Wisconsin","ror":"https://ror.org/00qqv6244","country_code":"US","type":"education","lineage":["https://openalex.org/I204308271"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"G. Thomas Hayman","raw_affiliation_strings":["Department of Biomedical Engineering, Medical College of Wisconsin, 8701 W Watertown Plank Rd, Milwaukee, 53226, WI, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, Medical College of Wisconsin, 8701 W Watertown Plank Rd, Milwaukee, 53226, WI, USA","institution_ids":["https://openalex.org/I204308271"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101914581","display_name":"Jennifer R. Smith","orcid":null},"institutions":[{"id":"https://openalex.org/I204308271","display_name":"Medical College of Wisconsin","ror":"https://ror.org/00qqv6244","country_code":"US","type":"education","lineage":["https://openalex.org/I204308271"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jennifer R. Smith","raw_affiliation_strings":["Department of Biomedical Engineering, Medical College of Wisconsin, 8701 W Watertown Plank Rd, Milwaukee, 53226, WI, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, Medical College of Wisconsin, 8701 W Watertown Plank Rd, Milwaukee, 53226, WI, USA","institution_ids":["https://openalex.org/I204308271"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028945083","display_name":"Monika Tutaj","orcid":"https://orcid.org/0000-0002-0378-4002"},"institutions":[{"id":"https://openalex.org/I204308271","display_name":"Medical College of Wisconsin","ror":"https://ror.org/00qqv6244","country_code":"US","type":"education","lineage":["https://openalex.org/I204308271"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Monika Tutaj","raw_affiliation_strings":["Department of Biomedical Engineering, Medical College of Wisconsin, 8701 W Watertown Plank Rd, Milwaukee, 53226, WI, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, Medical College of Wisconsin, 8701 W Watertown Plank Rd, Milwaukee, 53226, WI, USA","institution_ids":["https://openalex.org/I204308271"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031193159","display_name":"Mary Shimoyama","orcid":"https://orcid.org/0000-0003-1176-0796"},"institutions":[{"id":"https://openalex.org/I204308271","display_name":"Medical College of Wisconsin","ror":"https://ror.org/00qqv6244","country_code":"US","type":"education","lineage":["https://openalex.org/I204308271"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mary E. Shimoyama","raw_affiliation_strings":["Department of Biomedical Engineering, Medical College of Wisconsin, 8701 W Watertown Plank Rd, Milwaukee, 53226, WI, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, Medical College of Wisconsin, 8701 W Watertown Plank Rd, Milwaukee, 53226, WI, USA","institution_ids":["https://openalex.org/I204308271"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5010618664","display_name":"John H. Gennari","orcid":"https://orcid.org/0000-0001-8254-4957"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"John H. Gennari","raw_affiliation_strings":["Department of Biomedical Informatics and Medical Education, University of Washington, 850 Republican St, Seattle, 98109, WA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics and Medical Education, University of Washington, 850 Republican St, Seattle, 98109, WA, USA","institution_ids":["https://openalex.org/I201448701"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5001778694"],"corresponding_institution_ids":["https://openalex.org/I201448701"],"apc_list":{"value":1190,"currency":"GBP","value_usd":1459},"apc_paid":{"value":1190,"currency":"GBP","value_usd":1459},"fwci":0.0861,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.46553563,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"10","issue":"1","first_page":"11","last_page":"11"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10252","display_name":"Microbial Natural Products and Biosynthesis","score":0.9930999875068665,"subfield":{"id":"https://openalex.org/subfields/2736","display_name":"Pharmacology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7675116062164307},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.735240638256073},{"id":"https://openalex.org/keywords/leverage","display_name":"Leverage (statistics)","score":0.6076288223266602},{"id":"https://openalex.org/keywords/class","display_name":"Class (philosophy)","score":0.5672793388366699},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5523043870925903},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.5187630653381348},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.45277032256126404},{"id":"https://openalex.org/keywords/precision-and-recall","display_name":"Precision and recall","score":0.4190806448459625},{"id":"https://openalex.org/keywords/pathway-analysis","display_name":"Pathway analysis","score":0.416487455368042},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.36079999804496765},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.34436100721359253}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7675116062164307},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.735240638256073},{"id":"https://openalex.org/C153083717","wikidata":"https://www.wikidata.org/wiki/Q6535263","display_name":"Leverage (statistics)","level":2,"score":0.6076288223266602},{"id":"https://openalex.org/C2777212361","wikidata":"https://www.wikidata.org/wiki/Q5127848","display_name":"Class (philosophy)","level":2,"score":0.5672793388366699},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5523043870925903},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.5187630653381348},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.45277032256126404},{"id":"https://openalex.org/C81669768","wikidata":"https://www.wikidata.org/wiki/Q2359161","display_name":"Precision and recall","level":2,"score":0.4190806448459625},{"id":"https://openalex.org/C2779230013","wikidata":"https://www.wikidata.org/wiki/Q25303877","display_name":"Pathway analysis","level":4,"score":0.416487455368042},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.36079999804496765},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.34436100721359253},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000069553","descriptor_name":"Supervised Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069553","descriptor_name":"Supervised Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069553","descriptor_name":"Supervised Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1186/s13326-019-0202-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13326-019-0202-8","pdf_url":"https://jbiomedsem.biomedcentral.com/track/pdf/10.1186/s13326-019-0202-8","source":{"id":"https://openalex.org/S172276550","display_name":"Journal of Biomedical Semantics","issn_l":"2041-1480","issn":["2041-1480"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Biomedical Semantics","raw_type":"journal-article"},{"id":"pmid:31196182","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31196182","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of biomedical semantics","raw_type":null},{"id":"pmh:oai:doaj.org/article:a48580a1c17f422ba60351f47a585c74","is_oa":true,"landing_page_url":"https://doaj.org/article/a48580a1c17f422ba60351f47a585c74","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Biomedical Semantics, Vol 10, Iss 1, Pp 1-11 (2019)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:5548070","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6567466","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13326-019-0202-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13326-019-0202-8","pdf_url":"https://jbiomedsem.biomedcentral.com/track/pdf/10.1186/s13326-019-0202-8","source":{"id":"https://openalex.org/S172276550","display_name":"Journal of Biomedical Semantics","issn_l":"2041-1480","issn":["2041-1480"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Biomedical Semantics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1732705454","display_name":null,"funder_award_id":"R01LM011969","funder_id":"https://openalex.org/F4320337372","funder_display_name":"U.S. National Library of Medicine"},{"id":"https://openalex.org/G6247589191","display_name":null,"funder_award_id":"R01HL064541","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"}],"funders":[{"id":"https://openalex.org/F4320310094","display_name":"University of Washington","ror":"https://ror.org/00cvxb145"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337338","display_name":"National Heart, Lung, and Blood Institute","ror":"https://ror.org/012pb6c26"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2949540143.pdf","grobid_xml":"https://content.openalex.org/works/W2949540143.grobid-xml"},"referenced_works_count":34,"referenced_works":["https://openalex.org/W21497345","https://openalex.org/W1964572291","https://openalex.org/W1969709265","https://openalex.org/W1970594207","https://openalex.org/W1989108446","https://openalex.org/W1989277387","https://openalex.org/W2010457001","https://openalex.org/W2031218556","https://openalex.org/W2044689550","https://openalex.org/W2064675550","https://openalex.org/W2102899487","https://openalex.org/W2103017472","https://openalex.org/W2108798001","https://openalex.org/W2109337529","https://openalex.org/W2120433529","https://openalex.org/W2126997165","https://openalex.org/W2128601422","https://openalex.org/W2130410032","https://openalex.org/W2138776746","https://openalex.org/W2142302575","https://openalex.org/W2148866288","https://openalex.org/W2150908245","https://openalex.org/W2151014102","https://openalex.org/W2159583324","https://openalex.org/W2164298117","https://openalex.org/W2164508904","https://openalex.org/W2170637386","https://openalex.org/W2493916176","https://openalex.org/W2558643140","https://openalex.org/W2591703969","https://openalex.org/W2886143135","https://openalex.org/W4230770774","https://openalex.org/W4237335579","https://openalex.org/W6819133582"],"related_works":["https://openalex.org/W2003333417","https://openalex.org/W2378862226","https://openalex.org/W118236634","https://openalex.org/W2355326633","https://openalex.org/W2804669904","https://openalex.org/W2149777447","https://openalex.org/W2347456287","https://openalex.org/W2121651557","https://openalex.org/W2787993192","https://openalex.org/W2782969047"],"abstract_inverted_index":null,"counts_by_year":[{"year":2019,"cited_by_count":1}],"updated_date":"2026-03-05T09:29:38.588285","created_date":"2025-10-10T00:00:00"}
