{"id":"https://openalex.org/W2099007946","doi":"https://doi.org/10.1093/bioinformatics/btg416","title":"An ontology for collaborative construction and analysis of cellular pathways","display_name":"An ontology for collaborative construction and analysis of cellular pathways","publication_year":2004,"publication_date":"2004-02-11","ids":{"openalex":"https://openalex.org/W2099007946","doi":"https://doi.org/10.1093/bioinformatics/btg416","mag":"2099007946","pmid":"https://pubmed.ncbi.nlm.nih.gov/14960461"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btg416","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg416","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/20/3/349/48905259/bioinformatics_20_3_349.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/20/3/349/48905259/bioinformatics_20_3_349.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5037803004","display_name":"Emek Demir","orcid":"https://orcid.org/0000-0002-3663-7113"},"institutions":[{"id":"https://openalex.org/I168864056","display_name":"Bilkent University","ror":"https://ror.org/02vh8a032","country_code":"TR","type":"education","lineage":["https://openalex.org/I168864056"]},{"id":"https://openalex.org/I4210148697","display_name":"Institute of Bioinformatics","ror":"https://ror.org/04hqfvm50","country_code":"IN","type":"nonprofit","lineage":["https://openalex.org/I4210148697"]}],"countries":["IN","TR"],"is_corresponding":true,"raw_author_name":"E. Demir","raw_affiliation_strings":["Center for Bioinformatics, Bilkent University, Ankara, Turkey","Center for Bioinformatics,#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics, Bilkent University, Ankara, Turkey","institution_ids":["https://openalex.org/I168864056"]},{"raw_affiliation_string":"Center for Bioinformatics,#TAB#","institution_ids":["https://openalex.org/I4210148697"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006448195","display_name":"\u00d6zg\u00fcn Babur","orcid":"https://orcid.org/0000-0002-0239-5259"},"institutions":[{"id":"https://openalex.org/I4210148697","display_name":"Institute of Bioinformatics","ror":"https://ror.org/04hqfvm50","country_code":"IN","type":"nonprofit","lineage":["https://openalex.org/I4210148697"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"O. Babur","raw_affiliation_strings":["Center for Bioinformatics,#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics,#TAB#","institution_ids":["https://openalex.org/I4210148697"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006798669","display_name":"U\u011fur Do\u011frus\u00f6z","orcid":"https://orcid.org/0000-0002-7153-0784"},"institutions":[{"id":"https://openalex.org/I4210148697","display_name":"Institute of Bioinformatics","ror":"https://ror.org/04hqfvm50","country_code":"IN","type":"nonprofit","lineage":["https://openalex.org/I4210148697"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"U. Dogrusoz","raw_affiliation_strings":["Center for Bioinformatics,#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics,#TAB#","institution_ids":["https://openalex.org/I4210148697"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036278069","display_name":"Attila G\u00fcrsoy","orcid":"https://orcid.org/0000-0002-2297-2113"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"A. Gursoy","raw_affiliation_strings":["Computer Engineering Department#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Engineering Department#TAB#","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016420508","display_name":"Asl\u0131 Ayaz","orcid":"https://orcid.org/0000-0002-6276-2516"},"institutions":[{"id":"https://openalex.org/I4210148697","display_name":"Institute of Bioinformatics","ror":"https://ror.org/04hqfvm50","country_code":"IN","type":"nonprofit","lineage":["https://openalex.org/I4210148697"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"A. Ayaz","raw_affiliation_strings":["Center for Bioinformatics,#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics,#TAB#","institution_ids":["https://openalex.org/I4210148697"]}]},{"author_position":"middle","author":{"id":null,"display_name":"G. Gulesir","orcid":null},"institutions":[{"id":"https://openalex.org/I4210148697","display_name":"Institute of Bioinformatics","ror":"https://ror.org/04hqfvm50","country_code":"IN","type":"nonprofit","lineage":["https://openalex.org/I4210148697"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"G. Gulesir","raw_affiliation_strings":["Center for Bioinformatics,#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics,#TAB#","institution_ids":["https://openalex.org/I4210148697"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065310718","display_name":"G. Nisanci","orcid":null},"institutions":[{"id":"https://openalex.org/I4210148697","display_name":"Institute of Bioinformatics","ror":"https://ror.org/04hqfvm50","country_code":"IN","type":"nonprofit","lineage":["https://openalex.org/I4210148697"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"G. Nisanci","raw_affiliation_strings":["Center for Bioinformatics,#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics,#TAB#","institution_ids":["https://openalex.org/I4210148697"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5037440533","display_name":"Reng\u00fcl \u00c7etin-Atalay","orcid":"https://orcid.org/0000-0003-2408-6606"},"institutions":[{"id":"https://openalex.org/I4210148697","display_name":"Institute of Bioinformatics","ror":"https://ror.org/04hqfvm50","country_code":"IN","type":"nonprofit","lineage":["https://openalex.org/I4210148697"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"R. Cetin-Atalay","raw_affiliation_strings":["Center for Bioinformatics,#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics,#TAB#","institution_ids":["https://openalex.org/I4210148697"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5037803004"],"corresponding_institution_ids":["https://openalex.org/I168864056","https://openalex.org/I4210148697"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":3.406,"has_fulltext":false,"cited_by_count":58,"citation_normalized_percentile":{"value":0.93121626,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"20","issue":"3","first_page":"349","last_page":"356"},"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":0.9987000226974487,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9934999942779541,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8070400953292847},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.8029078245162964},{"id":"https://openalex.org/keywords/ontology-based-data-integration","display_name":"Ontology-based data integration","score":0.6610539555549622},{"id":"https://openalex.org/keywords/consistency","display_name":"Consistency (knowledge bases)","score":0.5802301168441772},{"id":"https://openalex.org/keywords/abstraction","display_name":"Abstraction","score":0.5469919443130493},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5298464298248291},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.4999828338623047},{"id":"https://openalex.org/keywords/data-integration","display_name":"Data integration","score":0.49471375346183777},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.44349098205566406},{"id":"https://openalex.org/keywords/process-ontology","display_name":"Process ontology","score":0.4109155833721161},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.31242120265960693},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.28727102279663086},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.17214533686637878},{"id":"https://openalex.org/keywords/semantic-web","display_name":"Semantic Web","score":0.12795719504356384},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.12250968813896179}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8070400953292847},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.8029078245162964},{"id":"https://openalex.org/C22550185","wikidata":"https://www.wikidata.org/wiki/Q7095047","display_name":"Ontology-based data integration","level":3,"score":0.6610539555549622},{"id":"https://openalex.org/C2776436953","wikidata":"https://www.wikidata.org/wiki/Q5163215","display_name":"Consistency (knowledge bases)","level":2,"score":0.5802301168441772},{"id":"https://openalex.org/C124304363","wikidata":"https://www.wikidata.org/wiki/Q673661","display_name":"Abstraction","level":2,"score":0.5469919443130493},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5298464298248291},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.4999828338623047},{"id":"https://openalex.org/C72634772","wikidata":"https://www.wikidata.org/wiki/Q386824","display_name":"Data integration","level":2,"score":0.49471375346183777},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.44349098205566406},{"id":"https://openalex.org/C137003198","wikidata":"https://www.wikidata.org/wiki/Q7247296","display_name":"Process ontology","level":3,"score":0.4109155833721161},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.31242120265960693},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.28727102279663086},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.17214533686637878},{"id":"https://openalex.org/C2129575","wikidata":"https://www.wikidata.org/wiki/Q54837","display_name":"Semantic Web","level":2,"score":0.12795719504356384},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.12250968813896179},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"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":"D001704","descriptor_name":"Biopolymers","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001704","descriptor_name":"Biopolymers","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001704","descriptor_name":"Biopolymers","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002468","descriptor_name":"Cell Physiological Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002468","descriptor_name":"Cell Physiological Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002468","descriptor_name":"Cell Physiological Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btg416","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg416","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/20/3/349/48905259/bioinformatics_20_3_349.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:14960461","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/14960461","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:ris.utwente.nl:openaire_cris_publications/107ea71e-c377-4413-ab94-d46d2e5a8733","is_oa":false,"landing_page_url":"https://research.utwente.nl/en/publications/107ea71e-c377-4413-ab94-d46d2e5a8733","pdf_url":null,"source":{"id":"https://openalex.org/S4406922991","display_name":"University of Twente Research Information","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Demir, E, Babur, O, Dogrusoz, U, Gursoy, A, Ayaz, A, G\u00fclesir, G, Nisanci, G & Cetin-Atalay, R 2004, 'An Ontology for Collaborative Construction and Analysis of Cellular Pathways', Bioinformatics, vol. 20, no. 3, 10.1093/bioinformatics/btg416, pp. 349-356. https://doi.org/10.1093/bioinformatics/btg416","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.602.190","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.602.190","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bioinformatics.oxfordjournals.org/content/20/3/349.full.pdf","raw_type":"text"},{"id":"pmh:oai:repository.bilkent.edu.tr:11693/24320","is_oa":false,"landing_page_url":"http://hdl.handle.net/11693/24320","pdf_url":null,"source":{"id":"https://openalex.org/S4306400079","display_name":"Bilkent University Institutional Repository (Bilkent University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I168864056","host_organization_name":"Bilkent University","host_organization_lineage":["https://openalex.org/I168864056"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btg416","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg416","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/20/3/349/48905259/bioinformatics_20_3_349.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W2099007946.pdf"},"referenced_works_count":26,"referenced_works":["https://openalex.org/W1744968466","https://openalex.org/W1758628264","https://openalex.org/W1780615788","https://openalex.org/W1884509322","https://openalex.org/W1978319180","https://openalex.org/W1991613592","https://openalex.org/W1999866856","https://openalex.org/W2003144438","https://openalex.org/W2007006124","https://openalex.org/W2074906123","https://openalex.org/W2103017472","https://openalex.org/W2105941683","https://openalex.org/W2113221321","https://openalex.org/W2121905803","https://openalex.org/W2123280311","https://openalex.org/W2124025352","https://openalex.org/W2125713713","https://openalex.org/W2130687290","https://openalex.org/W2133298156","https://openalex.org/W2140115103","https://openalex.org/W2150908245","https://openalex.org/W2155320925","https://openalex.org/W2159482845","https://openalex.org/W2160453515","https://openalex.org/W2160540739","https://openalex.org/W2167869241"],"related_works":["https://openalex.org/W2114954739","https://openalex.org/W2159818280","https://openalex.org/W1506177826","https://openalex.org/W2889792096","https://openalex.org/W1794266373","https://openalex.org/W4251889114","https://openalex.org/W2363188691","https://openalex.org/W1953363106","https://openalex.org/W176267515","https://openalex.org/W4255991504"],"abstract_inverted_index":{"MOTIVATION:":[0],"As":[1],"the":[2,14,53,103,113,180],"scientific":[3],"curiosity":[4],"in":[5,16],"genome":[6],"studies":[7],"shifts":[8],"toward":[9],"identification":[10],"of":[11,13,55,82,91,102,126,129,143,146,175,182],"functions":[12],"genomes":[15],"large":[17,144],"scale,":[18],"data":[19,50,114],"produced":[20],"about":[21],"cellular":[22,83,176],"processes":[23],"at":[24],"molecular":[25],"level":[26],"has":[27],"been":[28],"accumulating":[29],"with":[30,52],"an":[31,73,76,166],"accelerating":[32],"rate.":[33],"In":[34,106],"this":[35,49,59],"regard,":[36],"it":[37,108],"is":[38,65,135],"essential":[39],"to":[40,43,112],"be":[41],"able":[42],"store,":[44],"integrate,":[45],"access":[46],"and":[47,68,79,99,119,133,161,172],"analyze":[48],"effectively":[51],"help":[54],"software":[56,153],"tools.":[57],"Clearly":[58],"requires":[60],"a":[61,152],"strong":[62],"ontology":[63,74,86,139],"that":[64],"intuitive,":[66,77],"comprehensive":[67,78],"uncomplicated.":[69],"RESULTS:":[70],"We":[71,148],"define":[72],"for":[75,124,131,159,170],"uncomplicated":[80],"representation":[81,125],"events.":[84,177],"The":[85],"presented":[87],"here":[88],"enables":[89],"integration":[90,160],"fragmented":[92],"or":[93],"incomplete":[94],"pathway":[95,156],"information":[96],"via":[97],"collaboration,":[98],"supports":[100,140],"manipulation":[101],"stored":[104],"data.":[105,147],"addition,":[107],"facilitates":[109],"concurrent":[110],"modifications":[111],"while":[115],"maintaining":[116],"its":[117],"validity":[118],"consistency.":[120],"Furthermore,":[121],"novel":[122],"structures":[123],"multiple":[127],"levels":[128],"abstraction":[130],"pathways":[132],"homologies":[134],"provided.":[136],"Lastly,":[137],"our":[138,183],"efficient":[141],"querying":[142],"amounts":[145],"have":[149],"also":[150],"developed":[151],"tool":[154,158],"named":[155],"analysis":[157],"knowledge":[162],"acquisition":[163],"(PATIKA)":[164],"providing":[165],"integrated,":[167],"multi-user":[168],"environment":[169],"visualizing":[171],"manipulating":[173],"network":[174],"PATIKA":[178],"implements":[179],"basics":[181],"ontology.":[184]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2012,"cited_by_count":3}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}
