{"id":"https://openalex.org/W2148529794","doi":"https://doi.org/10.1186/2041-1480-4-25","title":"Using ontologies to study cell transitions","display_name":"Using ontologies to study cell transitions","publication_year":2013,"publication_date":"2013-01-01","ids":{"openalex":"https://openalex.org/W2148529794","doi":"https://doi.org/10.1186/2041-1480-4-25","mag":"2148529794","pmid":"https://pubmed.ncbi.nlm.nih.gov/24103098"},"language":"en","primary_location":{"id":"doi:10.1186/2041-1480-4-25","is_oa":true,"landing_page_url":"https://doi.org/10.1186/2041-1480-4-25","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/2041-1480-4-25","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/10.1186/2041-1480-4-25","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5089023752","display_name":"Georg Fuellen","orcid":"https://orcid.org/0000-0002-4994-9829"},"institutions":[{"id":"https://openalex.org/I4665924","display_name":"University of Rostock","ror":"https://ror.org/03zdwsf69","country_code":"DE","type":"education","lineage":["https://openalex.org/I4665924"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Georg Fuellen","raw_affiliation_strings":["Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock Medical School, Ernst-Heydemann-Str, 8, 18057 Rostock, Germany. fuellen@uni-rostock.de","Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock Medical School, Ernst-Heydemann-Str. 8, 18057, Rostock, Germany"],"affiliations":[{"raw_affiliation_string":"Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock Medical School, Ernst-Heydemann-Str, 8, 18057 Rostock, Germany. fuellen@uni-rostock.de","institution_ids":[]},{"raw_affiliation_string":"Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock Medical School, Ernst-Heydemann-Str. 8, 18057, Rostock, Germany","institution_ids":["https://openalex.org/I4665924"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044902964","display_name":"Ludger Jansen","orcid":"https://orcid.org/0000-0002-0097-6359"},"institutions":[{"id":"https://openalex.org/I4665924","display_name":"University of Rostock","ror":"https://ror.org/03zdwsf69","country_code":"DE","type":"education","lineage":["https://openalex.org/I4665924"]},{"id":"https://openalex.org/I63274643","display_name":"FH M\u00fcnster","ror":"https://ror.org/00pv45a02","country_code":"DE","type":"education","lineage":["https://openalex.org/I63274643"]},{"id":"https://openalex.org/I22465464","display_name":"University of M\u00fcnster","ror":"https://ror.org/00pd74e08","country_code":"DE","type":"education","lineage":["https://openalex.org/I22465464"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Ludger Jansen","raw_affiliation_strings":["Department of Philosophy, University of M\u00fcnster, Domplatz 6, 48143, M\u00fcnster, Germany","Institute of Philosophy, University of Rostock, 18051, Rostock, Germany"],"affiliations":[{"raw_affiliation_string":"Department of Philosophy, University of M\u00fcnster, Domplatz 6, 48143, M\u00fcnster, Germany","institution_ids":["https://openalex.org/I22465464","https://openalex.org/I63274643"]},{"raw_affiliation_string":"Institute of Philosophy, University of Rostock, 18051, Rostock, Germany","institution_ids":["https://openalex.org/I4665924"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055236937","display_name":"Ulf Leser","orcid":"https://orcid.org/0000-0003-2166-9582"},"institutions":[{"id":"https://openalex.org/I39343248","display_name":"Humboldt-Universit\u00e4t zu Berlin","ror":"https://ror.org/01hcx6992","country_code":"DE","type":"education","lineage":["https://openalex.org/I39343248"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Ulf Leser","raw_affiliation_strings":["Humboldt Universit\u00e4t zu Berlin, Unter den Linden 6, 10099, Berlin, Germany"],"affiliations":[{"raw_affiliation_string":"Humboldt Universit\u00e4t zu Berlin, Unter den Linden 6, 10099, Berlin, Germany","institution_ids":["https://openalex.org/I39343248"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5070999479","display_name":"Armin Kurtz","orcid":"https://orcid.org/0000-0003-3301-6546"},"institutions":[{"id":"https://openalex.org/I7877124","display_name":"Charit\u00e9 - Universit\u00e4tsmedizin Berlin","ror":"https://ror.org/001w7jn25","country_code":"DE","type":"funder","lineage":["https://openalex.org/I7877124"]},{"id":"https://openalex.org/I139264467","display_name":"Seoul National University","ror":"https://ror.org/04h9pn542","country_code":"KR","type":"education","lineage":["https://openalex.org/I139264467"]}],"countries":["DE","KR"],"is_corresponding":false,"raw_author_name":"Andreas Kurtz","raw_affiliation_strings":["Charite Berlin, BCRT, Augustenburger Platz 1, 13353, Berlin, Germany","College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, Republic of Korea"],"affiliations":[{"raw_affiliation_string":"Charite Berlin, BCRT, Augustenburger Platz 1, 13353, Berlin, Germany","institution_ids":["https://openalex.org/I7877124"]},{"raw_affiliation_string":"College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, Republic of Korea","institution_ids":["https://openalex.org/I139264467"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5089023752"],"corresponding_institution_ids":["https://openalex.org/I4665924"],"apc_list":{"value":1190,"currency":"GBP","value_usd":1459},"apc_paid":{"value":1190,"currency":"GBP","value_usd":1459},"fwci":0.1497,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.58220176,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"4","issue":"1","first_page":"25","last_page":"25"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9973000288009644,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9973000288009644,"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/T10215","display_name":"Semantic Web and Ontologies","score":0.975600004196167,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9664999842643738,"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/reprogramming","display_name":"Reprogramming","score":0.7205725908279419},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7165369391441345},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.5738813281059265},{"id":"https://openalex.org/keywords/mechanism","display_name":"Mechanism (biology)","score":0.49339666962623596},{"id":"https://openalex.org/keywords/knowledge-base","display_name":"Knowledge base","score":0.44800928235054016},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.4390820562839508},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.38282710313796997},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3815881311893463},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.221576988697052},{"id":"https://openalex.org/keywords/cell","display_name":"Cell","score":0.21985605359077454},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.18529614806175232},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.0831301212310791}],"concepts":[{"id":"https://openalex.org/C77255625","wikidata":"https://www.wikidata.org/wiki/Q402093","display_name":"Reprogramming","level":3,"score":0.7205725908279419},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7165369391441345},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.5738813281059265},{"id":"https://openalex.org/C89611455","wikidata":"https://www.wikidata.org/wiki/Q6804646","display_name":"Mechanism (biology)","level":2,"score":0.49339666962623596},{"id":"https://openalex.org/C4554734","wikidata":"https://www.wikidata.org/wiki/Q593744","display_name":"Knowledge base","level":2,"score":0.44800928235054016},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.4390820562839508},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.38282710313796997},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3815881311893463},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.221576988697052},{"id":"https://openalex.org/C1491633281","wikidata":"https://www.wikidata.org/wiki/Q7868","display_name":"Cell","level":2,"score":0.21985605359077454},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.18529614806175232},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0831301212310791},{"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/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"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/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:10.1186/2041-1480-4-25","is_oa":true,"landing_page_url":"https://doi.org/10.1186/2041-1480-4-25","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/2041-1480-4-25","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:24103098","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24103098","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:3097433","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4128511","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":null,"raw_type":"Text"},{"id":"pmh:oai:s-space.snu.ac.kr:10371/192315","is_oa":false,"landing_page_url":"https://hdl.handle.net/10371/192315","pdf_url":null,"source":{"id":"https://openalex.org/S4306401345","display_name":"Seoul National University Open Repository (Seoul National University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139264467","host_organization_name":"Seoul National University","host_organization_lineage":["https://openalex.org/I139264467"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1186/2041-1480-4-25","is_oa":true,"landing_page_url":"https://doi.org/10.1186/2041-1480-4-25","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/2041-1480-4-25","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":0.75,"display_name":"Quality Education","id":"https://metadata.un.org/sdg/4"}],"awards":[{"id":"https://openalex.org/G3260707992","display_name":null,"funder_award_id":"FU 583/2-2","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2148529794.pdf","grobid_xml":"https://content.openalex.org/works/W2148529794.grobid-xml"},"referenced_works_count":24,"referenced_works":["https://openalex.org/W1757909678","https://openalex.org/W1982789882","https://openalex.org/W1994698160","https://openalex.org/W1998028266","https://openalex.org/W2018840791","https://openalex.org/W2022451103","https://openalex.org/W2044257395","https://openalex.org/W2048024098","https://openalex.org/W2048438929","https://openalex.org/W2056827131","https://openalex.org/W2080008467","https://openalex.org/W2103017472","https://openalex.org/W2108241558","https://openalex.org/W2110233415","https://openalex.org/W2112811019","https://openalex.org/W2124991490","https://openalex.org/W2125987139","https://openalex.org/W2131555431","https://openalex.org/W2136961946","https://openalex.org/W2140551998","https://openalex.org/W2145290999","https://openalex.org/W2146495783","https://openalex.org/W2159444728","https://openalex.org/W2162361752"],"related_works":["https://openalex.org/W1631979401","https://openalex.org/W2395945797","https://openalex.org/W2129470469","https://openalex.org/W2368295610","https://openalex.org/W1543102035","https://openalex.org/W1497716427","https://openalex.org/W3014941007","https://openalex.org/W2972394710","https://openalex.org/W2183075003","https://openalex.org/W2946692299"],"abstract_inverted_index":{"We":[0],"show":[1],"that":[2,47],"the":[3,17,20,25,49,56],"principles":[4,43],"for":[5,37],"building":[6],"cellular":[7,32,71],"ontologies":[8,46],"published":[9],"in":[10,31,55],"this":[11],"work":[12],"allow":[13,48],"deeper":[14],"insights":[15],"into":[16],"relations":[18],"between":[19],"continuants":[21],"(cell":[22,27],"phenotypes)":[23],"and":[24,61],"occurrents":[26],"mechanism":[28],"changes)":[29],"involved":[30],"reprogramming,":[33],"although":[34],"implementation":[35],"remains":[36],"future":[38],"work.":[39],"Further,":[40],"our":[41],"design":[42],"lead":[44],"to":[45],"meaningful":[50],"application":[51],"of":[52,58,62,66,68],"similarity":[53],"searches":[54],"spaces":[57],"cell":[59],"phenotypes":[60],"mechanisms,":[63],"and,":[64],"especially,":[65],"changes":[67],"mechanisms":[69],"during":[70],"transitions.":[72]},"counts_by_year":[{"year":2018,"cited_by_count":1},{"year":2013,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
