{"id":"https://openalex.org/W2112390719","doi":"https://doi.org/10.1186/2041-1480-4-41","title":"Ontology of physics for biology: representing physical dependencies as a basis for biological processes","display_name":"Ontology of physics for biology: representing physical dependencies as a basis for biological processes","publication_year":2013,"publication_date":"2013-01-01","ids":{"openalex":"https://openalex.org/W2112390719","doi":"https://doi.org/10.1186/2041-1480-4-41","mag":"2112390719","pmid":"https://pubmed.ncbi.nlm.nih.gov/24295137"},"language":"en","primary_location":{"id":"doi:10.1186/2041-1480-4-41","is_oa":true,"landing_page_url":"https://doi.org/10.1186/2041-1480-4-41","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/2041-1480-4-41","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/counter/pdf/10.1186/2041-1480-4-41","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5103723179","display_name":"Daniel L. Cook","orcid":null},"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":"Daniel L Cook","raw_affiliation_strings":["Department of Physiology & Biophysics, University of Washington, Seattle 98195, USA. dcook@uw.edu","University of Washington"],"affiliations":[{"raw_affiliation_string":"Department of Physiology & Biophysics, University of Washington, Seattle 98195, USA. dcook@uw.edu","institution_ids":[]},{"raw_affiliation_string":"University of Washington","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031987031","display_name":"Maxwell L. Neal","orcid":"https://orcid.org/0000-0002-2390-6572"},"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":"Maxwell L Neal","raw_affiliation_strings":["Department of Bioengineering, University of Washington, Seattle, 98195, USA","University of Washington"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of Washington, Seattle, 98195, USA","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"University of Washington","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090763434","display_name":"Fred L. Bookstein","orcid":"https://orcid.org/0000-0003-2716-8471"},"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":"Fred L Bookstein","raw_affiliation_strings":["Department of Statistics, University of Washington, Seattle, 98195, USA","University of Washington"],"affiliations":[{"raw_affiliation_string":"Department of Statistics, University of Washington, Seattle, 98195, USA","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"University of Washington","institution_ids":["https://openalex.org/I201448701"]}]},{"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 & Health Informatics, University of Washington, Seattle, 98195, USA","University of Washington"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical & Health Informatics, University of Washington, Seattle, 98195, USA","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"University of Washington","institution_ids":["https://openalex.org/I201448701"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5103723179"],"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":0.5979,"has_fulltext":true,"cited_by_count":33,"citation_normalized_percentile":{"value":0.69446,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"4","issue":"1","first_page":"41","last_page":"41"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9952999949455261,"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":0.9952999949455261,"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/T10621","display_name":"Gene Regulatory Network Analysis","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"}},{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9908000230789185,"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/ontology","display_name":"Ontology","score":0.6923152208328247},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6779755353927612},{"id":"https://openalex.org/keywords/physical-law","display_name":"Physical law","score":0.631572961807251},{"id":"https://openalex.org/keywords/physical-science","display_name":"Physical science","score":0.5744019746780396},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.534175455570221},{"id":"https://openalex.org/keywords/physical-system","display_name":"Physical system","score":0.45171454548835754},{"id":"https://openalex.org/keywords/knowledge-representation-and-reasoning","display_name":"Knowledge representation and reasoning","score":0.4303404688835144},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.4259892702102661},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.41830864548683167},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3650907278060913},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.36002880334854126},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.21881607174873352}],"concepts":[{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.6923152208328247},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6779755353927612},{"id":"https://openalex.org/C194583477","wikidata":"https://www.wikidata.org/wiki/Q408891","display_name":"Physical law","level":2,"score":0.631572961807251},{"id":"https://openalex.org/C6314898","wikidata":"https://www.wikidata.org/wiki/Q14632398","display_name":"Physical science","level":2,"score":0.5744019746780396},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.534175455570221},{"id":"https://openalex.org/C116672817","wikidata":"https://www.wikidata.org/wiki/Q1454986","display_name":"Physical system","level":2,"score":0.45171454548835754},{"id":"https://openalex.org/C161301231","wikidata":"https://www.wikidata.org/wiki/Q3478658","display_name":"Knowledge representation and reasoning","level":2,"score":0.4303404688835144},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.4259892702102661},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.41830864548683167},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3650907278060913},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.36002880334854126},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.21881607174873352},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","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/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"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/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","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":[],"locations_count":4,"locations":[{"id":"doi:10.1186/2041-1480-4-41","is_oa":true,"landing_page_url":"https://doi.org/10.1186/2041-1480-4-41","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/2041-1480-4-41","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:24295137","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24295137","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:europepmc.org:2888706","is_oa":true,"landing_page_url":"http://europepmc.org/articles/PMC3904761","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3904761","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3904761","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Biomed Semantics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/2041-1480-4-41","is_oa":true,"landing_page_url":"https://doi.org/10.1186/2041-1480-4-41","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/2041-1480-4-41","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":[{"score":0.4699999988079071,"id":"https://metadata.un.org/sdg/16","display_name":"Peace, Justice and strong institutions"}],"awards":[{"id":"https://openalex.org/G3777599518","display_name":null,"funder_award_id":"NIH-NIGMS","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4359693134","display_name":null,"funder_award_id":"NIGMS","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7175982441","display_name":null,"funder_award_id":"GM094503","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2112390719.pdf","grobid_xml":"https://content.openalex.org/works/W2112390719.grobid-xml"},"referenced_works_count":33,"referenced_works":["https://openalex.org/W102398446","https://openalex.org/W124759080","https://openalex.org/W131090992","https://openalex.org/W1501546233","https://openalex.org/W1571433676","https://openalex.org/W1967930981","https://openalex.org/W1969709265","https://openalex.org/W1977875710","https://openalex.org/W2007924064","https://openalex.org/W2011346323","https://openalex.org/W2024741923","https://openalex.org/W2027082381","https://openalex.org/W2045808901","https://openalex.org/W2047480488","https://openalex.org/W2090469206","https://openalex.org/W2103260426","https://openalex.org/W2104942450","https://openalex.org/W2111299816","https://openalex.org/W2114124738","https://openalex.org/W2120134656","https://openalex.org/W2123903656","https://openalex.org/W2131294353","https://openalex.org/W2145435867","https://openalex.org/W2150908245","https://openalex.org/W2170122529","https://openalex.org/W2171926758","https://openalex.org/W2406774182","https://openalex.org/W2471568356","https://openalex.org/W2577373959","https://openalex.org/W2914859070","https://openalex.org/W3196492948","https://openalex.org/W4246991885","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W3037664319","https://openalex.org/W2945599743","https://openalex.org/W3149970480","https://openalex.org/W1659546960","https://openalex.org/W3176289043","https://openalex.org/W2543363198","https://openalex.org/W4252762046","https://openalex.org/W4229780500","https://openalex.org/W2350068154","https://openalex.org/W2386652184"],"abstract_inverted_index":{"We":[0],"have":[1],"developed":[2],"the":[3,10,14,21,49],"OPB":[4],"and":[5,20,26,31,44],"annotation":[6],"methods":[7],"to":[8,35],"represent":[9],"meaning-the":[11],"biophysical":[12,22,53],"semantics-of":[13],"mathematical":[15,50],"statements":[16],"of":[17,24,39,52],"physiological":[18],"analysis":[19,51],"content":[23],"models":[25],"datasets.":[27],"Here":[28],"we":[29],"describe":[30],"discuss":[32],"our":[33],"approach":[34],"an":[36],"ontological":[37],"representation":[38],"physical":[40],"laws":[41],"(as":[42],"dependencies)":[43],"properties":[45],"as":[46],"encoded":[47],"for":[48],"processes.":[54]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":12},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
