{"id":"https://openalex.org/W2951846550","doi":"https://doi.org/10.1186/s12859-019-2863-9","title":"PathMe: merging and exploring mechanistic pathway knowledge","display_name":"PathMe: merging and exploring mechanistic pathway knowledge","publication_year":2019,"publication_date":"2019-05-15","ids":{"openalex":"https://openalex.org/W2951846550","doi":"https://doi.org/10.1186/s12859-019-2863-9","mag":"2951846550","pmid":"https://pubmed.ncbi.nlm.nih.gov/31092193"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-019-2863-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2863-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2863-9","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2863-9","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5043459521","display_name":"Daniel Domingo\u2010Fern\u00e1nd\u00e9z","orcid":"https://orcid.org/0000-0002-2046-6145"},"institutions":[{"id":"https://openalex.org/I4210098248","display_name":"Fraunhofer Institute for Algorithms and Scientific Computing","ror":"https://ror.org/00trw9c49","country_code":"DE","type":"facility","lineage":["https://openalex.org/I4210098248","https://openalex.org/I4923324"]},{"id":"https://openalex.org/I4210164149","display_name":"Bonn Aachen International Center for Information Technology","ror":"https://ror.org/054zhq066","country_code":"DE","type":"facility","lineage":["https://openalex.org/I135140700","https://openalex.org/I155417937","https://openalex.org/I4210164149","https://openalex.org/I4923324"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Daniel Domingo-Fern\u00e1ndez","raw_affiliation_strings":["Bonn-Aachen International Center for IT, Rheinische Friedrich-Wilhelms-Universit\u00e4t Bonn, 53115, Bonn, Germany. daniel.domingo.fernandez@scai.fraunhofer.de","Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, 53754, Sankt Augustin, Germany. daniel.domingo.fernandez@scai.fraunhofer.de","Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, 53754, Sankt Augustin, Germany"],"raw_orcid":"https://orcid.org/0000-0002-2046-6145","affiliations":[{"raw_affiliation_string":"Bonn-Aachen International Center for IT, Rheinische Friedrich-Wilhelms-Universit\u00e4t Bonn, 53115, Bonn, Germany. daniel.domingo.fernandez@scai.fraunhofer.de","institution_ids":["https://openalex.org/I4210164149"]},{"raw_affiliation_string":"Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, 53754, Sankt Augustin, Germany. daniel.domingo.fernandez@scai.fraunhofer.de","institution_ids":["https://openalex.org/I4210098248"]},{"raw_affiliation_string":"Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, 53754, Sankt Augustin, Germany","institution_ids":["https://openalex.org/I4210098248"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012235619","display_name":"Sarah Mubeen","orcid":"https://orcid.org/0000-0002-9858-3755"},"institutions":[{"id":"https://openalex.org/I135140700","display_name":"University of Bonn","ror":"https://ror.org/041nas322","country_code":"DE","type":"education","lineage":["https://openalex.org/I135140700"]},{"id":"https://openalex.org/I4210098248","display_name":"Fraunhofer Institute for Algorithms and Scientific Computing","ror":"https://ror.org/00trw9c49","country_code":"DE","type":"facility","lineage":["https://openalex.org/I4210098248","https://openalex.org/I4923324"]},{"id":"https://openalex.org/I4210164149","display_name":"Bonn Aachen International Center for Information Technology","ror":"https://ror.org/054zhq066","country_code":"DE","type":"facility","lineage":["https://openalex.org/I135140700","https://openalex.org/I155417937","https://openalex.org/I4210164149","https://openalex.org/I4923324"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Sarah Mubeen","raw_affiliation_strings":["Bonn-Aachen International Center for IT, Rheinische Friedrich-Wilhelms-Universit\u00e4t Bonn, 53115, Bonn, Germany","Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, 53754, Sankt Augustin, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bonn-Aachen International Center for IT, Rheinische Friedrich-Wilhelms-Universit\u00e4t Bonn, 53115, Bonn, Germany","institution_ids":["https://openalex.org/I135140700","https://openalex.org/I4210164149"]},{"raw_affiliation_string":"Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, 53754, Sankt Augustin, Germany","institution_ids":["https://openalex.org/I4210098248"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076832365","display_name":"Josep Mar\u00edn-Lla\u00f3","orcid":null},"institutions":[{"id":"https://openalex.org/I4210098248","display_name":"Fraunhofer Institute for Algorithms and Scientific Computing","ror":"https://ror.org/00trw9c49","country_code":"DE","type":"facility","lineage":["https://openalex.org/I4210098248","https://openalex.org/I4923324"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Josep Mar\u00edn-Lla\u00f3","raw_affiliation_strings":["Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, 53754, Sankt Augustin, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, 53754, Sankt Augustin, Germany","institution_ids":["https://openalex.org/I4210098248"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065488553","display_name":"Charles Tapley Hoyt","orcid":"https://orcid.org/0000-0003-4423-4370"},"institutions":[{"id":"https://openalex.org/I135140700","display_name":"University of Bonn","ror":"https://ror.org/041nas322","country_code":"DE","type":"education","lineage":["https://openalex.org/I135140700"]},{"id":"https://openalex.org/I4210098248","display_name":"Fraunhofer Institute for Algorithms and Scientific Computing","ror":"https://ror.org/00trw9c49","country_code":"DE","type":"facility","lineage":["https://openalex.org/I4210098248","https://openalex.org/I4923324"]},{"id":"https://openalex.org/I4210164149","display_name":"Bonn Aachen International Center for Information Technology","ror":"https://ror.org/054zhq066","country_code":"DE","type":"facility","lineage":["https://openalex.org/I135140700","https://openalex.org/I155417937","https://openalex.org/I4210164149","https://openalex.org/I4923324"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Charles Tapley Hoyt","raw_affiliation_strings":["Bonn-Aachen International Center for IT, Rheinische Friedrich-Wilhelms-Universit\u00e4t Bonn, 53115, Bonn, Germany","Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, 53754, Sankt Augustin, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bonn-Aachen International Center for IT, Rheinische Friedrich-Wilhelms-Universit\u00e4t Bonn, 53115, Bonn, Germany","institution_ids":["https://openalex.org/I135140700","https://openalex.org/I4210164149"]},{"raw_affiliation_string":"Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, 53754, Sankt Augustin, Germany","institution_ids":["https://openalex.org/I4210098248"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5003139478","display_name":"Martin Hofmann\u2010Apitius","orcid":"https://orcid.org/0000-0001-9012-6720"},"institutions":[{"id":"https://openalex.org/I135140700","display_name":"University of Bonn","ror":"https://ror.org/041nas322","country_code":"DE","type":"education","lineage":["https://openalex.org/I135140700"]},{"id":"https://openalex.org/I4210098248","display_name":"Fraunhofer Institute for Algorithms and Scientific Computing","ror":"https://ror.org/00trw9c49","country_code":"DE","type":"facility","lineage":["https://openalex.org/I4210098248","https://openalex.org/I4923324"]},{"id":"https://openalex.org/I4210164149","display_name":"Bonn Aachen International Center for Information Technology","ror":"https://ror.org/054zhq066","country_code":"DE","type":"facility","lineage":["https://openalex.org/I135140700","https://openalex.org/I155417937","https://openalex.org/I4210164149","https://openalex.org/I4923324"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Martin Hofmann-Apitius","raw_affiliation_strings":["Bonn-Aachen International Center for IT, Rheinische Friedrich-Wilhelms-Universit\u00e4t Bonn, 53115, Bonn, Germany","Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, 53754, Sankt Augustin, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bonn-Aachen International Center for IT, Rheinische Friedrich-Wilhelms-Universit\u00e4t Bonn, 53115, Bonn, Germany","institution_ids":["https://openalex.org/I135140700","https://openalex.org/I4210164149"]},{"raw_affiliation_string":"Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, 53754, Sankt Augustin, Germany","institution_ids":["https://openalex.org/I4210098248"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5043459521"],"corresponding_institution_ids":["https://openalex.org/I4210098248","https://openalex.org/I4210164149"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":2.8827,"has_fulltext":true,"cited_by_count":58,"citation_normalized_percentile":{"value":0.92117165,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"20","issue":"1","first_page":"243","last_page":"243"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.8657000064849854,"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":0.8657000064849854,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.040699999779462814,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.011900000274181366,"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":0.677283525466919},{"id":"https://openalex.org/keywords/interoperability","display_name":"Interoperability","score":0.5677540302276611},{"id":"https://openalex.org/keywords/exploit","display_name":"Exploit","score":0.5601816773414612},{"id":"https://openalex.org/keywords/schema","display_name":"Schema (genetic algorithms)","score":0.5263121128082275},{"id":"https://openalex.org/keywords/biological-pathway","display_name":"Biological pathway","score":0.4842964708805084},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.4287324845790863},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3710246980190277},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3632034361362457},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.24563825130462646},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.16457441449165344},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.1482623815536499}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.677283525466919},{"id":"https://openalex.org/C20136886","wikidata":"https://www.wikidata.org/wiki/Q749647","display_name":"Interoperability","level":2,"score":0.5677540302276611},{"id":"https://openalex.org/C165696696","wikidata":"https://www.wikidata.org/wiki/Q11287","display_name":"Exploit","level":2,"score":0.5601816773414612},{"id":"https://openalex.org/C52146309","wikidata":"https://www.wikidata.org/wiki/Q7431116","display_name":"Schema (genetic algorithms)","level":2,"score":0.5263121128082275},{"id":"https://openalex.org/C9927688","wikidata":"https://www.wikidata.org/wiki/Q4915012","display_name":"Biological pathway","level":4,"score":0.4842964708805084},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.4287324845790863},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3710246980190277},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3632034361362457},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.24563825130462646},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16457441449165344},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.1482623815536499},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"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/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019992","descriptor_name":"Databases as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019992","descriptor_name":"Databases as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019992","descriptor_name":"Databases as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058570","descriptor_name":"TOR Serine-Threonine Kinases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D058570","descriptor_name":"TOR Serine-Threonine Kinases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D058570","descriptor_name":"TOR Serine-Threonine Kinases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1186/s12859-019-2863-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2863-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2863-9","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31092193","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31092193","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:94cf8a1a217947e29d9813632bb51626","is_oa":true,"landing_page_url":"https://doaj.org/article/94cf8a1a217947e29d9813632bb51626","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 20, Iss 1, Pp 1-12 (2019)","raw_type":"article"},{"id":"pmh:oai:fraunhofer.de:N-558606","is_oa":true,"landing_page_url":"http://publica.fraunhofer.de/documents/N-558606.html","pdf_url":null,"source":{"id":"https://openalex.org/S4306400801","display_name":"Publikationsdatenbank der Fraunhofer-Gesellschaft (Fraunhofer-Gesellschaft)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4923324","host_organization_name":"Fraunhofer-Gesellschaft","host_organization_lineage":["https://openalex.org/I4923324"],"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":"Fraunhofer SCAI","raw_type":"Journal Article"},{"id":"pmh:oai:publica.fraunhofer.de:publica/259526","is_oa":false,"landing_page_url":"https://publica.fraunhofer.de/handle/publica/259526","pdf_url":null,"source":{"id":"https://openalex.org/S4306400318","display_name":"Fraunhofer-Publica (Fraunhofer-Gesellschaft)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4923324","host_organization_name":"Fraunhofer-Gesellschaft","host_organization_lineage":["https://openalex.org/I4923324"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"journal article"},{"id":"pmh:oai:pubmedcentral.nih.gov:6521546","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6521546","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-019-2863-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2863-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2863-9","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3130801505","display_name":"Aetionomy \u2013 Organising Mechanistic Knowledge about Neurodegenerative Diseases for the Improvement of Drug Development and Therapy","funder_award_id":"115568","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G3829048491","display_name":null,"funder_award_id":"FP7/2007-2013","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G5593277320","display_name":null,"funder_award_id":"2007-2013","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G5702163051","display_name":null,"funder_award_id":"FP7/2007","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G6002116566","display_name":null,"funder_award_id":"115568","funder_id":"https://openalex.org/F4320314178","funder_display_name":"European Federation of Pharmaceutical Industries and Associations"},{"id":"https://openalex.org/G6651150684","display_name":null,"funder_award_id":"115568","funder_id":"https://openalex.org/F4320326631","funder_display_name":"Innovative Medicines Initiative"},{"id":"https://openalex.org/G7364720146","display_name":null,"funder_award_id":"FP7/2007-2013","funder_id":"https://openalex.org/F4320314178","funder_display_name":"European Federation of Pharmaceutical Industries and Associations"}],"funders":[{"id":"https://openalex.org/F4320314178","display_name":"European Federation of Pharmaceutical Industries and Associations","ror":"https://ror.org/00g1x4v36"},{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320326631","display_name":"Innovative Medicines Initiative","ror":"https://ror.org/019af4n30"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2951846550.pdf","grobid_xml":"https://content.openalex.org/works/W2951846550.grobid-xml"},"referenced_works_count":47,"referenced_works":["https://openalex.org/W1601495365","https://openalex.org/W1871096589","https://openalex.org/W1935434993","https://openalex.org/W1969709265","https://openalex.org/W1978608178","https://openalex.org/W1986365650","https://openalex.org/W1989277387","https://openalex.org/W1999758530","https://openalex.org/W1999999605","https://openalex.org/W2022005587","https://openalex.org/W2031218556","https://openalex.org/W2062584010","https://openalex.org/W2069157810","https://openalex.org/W2081563597","https://openalex.org/W2096541451","https://openalex.org/W2102899487","https://openalex.org/W2107580398","https://openalex.org/W2110687686","https://openalex.org/W2119876770","https://openalex.org/W2120680184","https://openalex.org/W2131581981","https://openalex.org/W2139424276","https://openalex.org/W2146737319","https://openalex.org/W2150908245","https://openalex.org/W2151014102","https://openalex.org/W2154139219","https://openalex.org/W2164298117","https://openalex.org/W2170637386","https://openalex.org/W2179127114","https://openalex.org/W2224056471","https://openalex.org/W2396056682","https://openalex.org/W2517051411","https://openalex.org/W2557833574","https://openalex.org/W2559588208","https://openalex.org/W2604808360","https://openalex.org/W2766482558","https://openalex.org/W2767914218","https://openalex.org/W2771692618","https://openalex.org/W2789581023","https://openalex.org/W2810419619","https://openalex.org/W2890947828","https://openalex.org/W2907209357","https://openalex.org/W2912621306","https://openalex.org/W2949333191","https://openalex.org/W2952755768","https://openalex.org/W4213060373","https://openalex.org/W4233698560"],"related_works":["https://openalex.org/W17155033","https://openalex.org/W3207760230","https://openalex.org/W1496222301","https://openalex.org/W4312814274","https://openalex.org/W2105734437","https://openalex.org/W312342747","https://openalex.org/W641470716","https://openalex.org/W1760163131","https://openalex.org/W78967844","https://openalex.org/W3002676839"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1],"complexity":[2],"of":[3,13,21,33,43,65,76,133,160,167,184],"representing":[4],"biological":[5,77],"systems":[6],"is":[7,68,110],"compounded":[8],"by":[9,37,112],"an":[10],"ever-expanding":[11],"body":[12],"knowledge":[14,67,90],"emerging":[15],"from":[16,91],"multi-omics":[17],"experiments.":[18,39],"A":[19],"number":[20],"pathway":[22,46,66,89,94,128,144,161,174,188,193],"databases":[23,47,95,145],"have":[24],"facilitated":[25],"pathway-centric":[26],"approaches":[27],"that":[28,87],"assist":[29],"in":[30,70,153],"the":[31,41,50,72,105,165,168,177,182,187,199],"interpretation":[32],"molecular":[34,200],"signatures":[35],"yielded":[36],"these":[38,54],"However,":[40],"lack":[42],"interoperability":[44],"between":[45],"has":[48,140],"hindered":[49],"ability":[51],"to":[52,57,125,155],"harmonize":[53],"resources":[55],"and":[56,74,130,135,146,190,195],"exploit":[58],"their":[59],"consolidated":[60],"knowledge.":[61,162],"Such":[62],"a":[63,84,97,113,150,157],"unification":[64],"imperative":[69],"enhancing":[71],"comprehension":[73],"modeling":[75],"abstractions.":[78],"RESULTS:":[79],"Here,":[80],"we":[81],"present":[82],"PathMe,":[83],"Python":[85],"package":[86],"transforms":[88],"three":[92,142],"major":[93,143],"into":[96,149],"unified":[98,151],"abstraction":[99],"using":[100],"Biological":[101],"Expression":[102],"Language":[103],"as":[104],"pivotal,":[106],"integrative":[107],"schema.":[108],"PathMe":[109,169],"complemented":[111],"novel":[114],"web":[115],"application":[116],"(freely":[117],"available":[118],"at":[119,176,186,198],"https://pathme.scai.fraunhofer.de/":[120],")":[121],"which":[122],"allows":[123],"users":[124],"comprehensively":[126],"explore":[127],"crosstalk":[129,194],"compare":[131],"areas":[132],"consensus":[134,185,197],"discrepancies.":[136],"CONCLUSIONS:":[137],"This":[138],"work":[139],"harmonized":[141],"transformed":[147],"them":[148],"schema":[152],"order":[154],"gain":[156],"holistic":[158],"picture":[159],"We":[163],"demonstrate":[164],"utility":[166],"framework":[170],"in:":[171],"i)":[172],"integrating":[173],"landscapes":[175],"database":[178],"level,":[179,189],"ii)":[180],"comparing":[181],"degree":[183],"iii)":[191],"exploring":[192],"investigating":[196],"level.":[201]},"counts_by_year":[{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":10},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":8},{"year":2021,"cited_by_count":9},{"year":2020,"cited_by_count":15},{"year":2019,"cited_by_count":6}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
