{"id":"https://openalex.org/W2030103067","doi":"https://doi.org/10.1186/2041-1480-2-6","title":"GOMMA: a component-based infrastructure for managing and analyzing life science ontologies and their evolution","display_name":"GOMMA: a component-based infrastructure for managing and analyzing life science ontologies and their evolution","publication_year":2011,"publication_date":"2011-01-01","ids":{"openalex":"https://openalex.org/W2030103067","doi":"https://doi.org/10.1186/2041-1480-2-6","mag":"2030103067","pmid":"https://pubmed.ncbi.nlm.nih.gov/21914205"},"language":"en","primary_location":{"id":"doi:10.1186/2041-1480-2-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/2041-1480-2-6","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/2041-1480-2-6","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/10.1186/2041-1480-2-6","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5018641933","display_name":"Toralf Kirsten","orcid":"https://orcid.org/0000-0001-7117-4268"},"institutions":[{"id":"https://openalex.org/I926574661","display_name":"Leipzig University","ror":"https://ror.org/03s7gtk40","country_code":"DE","type":"education","lineage":["https://openalex.org/I926574661"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Toralf Kirsten","raw_affiliation_strings":["Interdisciplinary Centre for Bioinformatics, Universit\u00e4t Leipzig, H\u00e4rtelstra\u00dfe 16-18, 04107 Leipzig, Germany. tkirsten@izbi.uni-leipzig.de","Interdisciplinary Centre for Bioinformatics, Universit\u00e4t Leipzig, H\u00e4rtelstra\u00dfe 16-18, 04107, Leipzig, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Interdisciplinary Centre for Bioinformatics, Universit\u00e4t Leipzig, H\u00e4rtelstra\u00dfe 16-18, 04107 Leipzig, Germany. tkirsten@izbi.uni-leipzig.de","institution_ids":["https://openalex.org/I926574661"]},{"raw_affiliation_string":"Interdisciplinary Centre for Bioinformatics, Universit\u00e4t Leipzig, H\u00e4rtelstra\u00dfe 16-18, 04107, Leipzig, Germany","institution_ids":["https://openalex.org/I926574661"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004046987","display_name":"Anika Gro\u00df","orcid":"https://orcid.org/0000-0002-2684-8427"},"institutions":[{"id":"https://openalex.org/I926574661","display_name":"Leipzig University","ror":"https://ror.org/03s7gtk40","country_code":"DE","type":"education","lineage":["https://openalex.org/I926574661"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Anika Gross","raw_affiliation_strings":["Department of Computer Science, Universit\u00e4t Leipzig, Johannisgasse 26, 04103, Leipzig, Germany","Interdisciplinary Centre for Bioinformatics, Universit\u00e4t Leipzig, H\u00e4rtelstra\u00dfe 16-18, 04107, Leipzig, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Universit\u00e4t Leipzig, Johannisgasse 26, 04103, Leipzig, Germany","institution_ids":["https://openalex.org/I926574661"]},{"raw_affiliation_string":"Interdisciplinary Centre for Bioinformatics, Universit\u00e4t Leipzig, H\u00e4rtelstra\u00dfe 16-18, 04107, Leipzig, Germany","institution_ids":["https://openalex.org/I926574661"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102879929","display_name":"Michael Hartung","orcid":"https://orcid.org/0000-0002-3992-0125"},"institutions":[{"id":"https://openalex.org/I926574661","display_name":"Leipzig University","ror":"https://ror.org/03s7gtk40","country_code":"DE","type":"education","lineage":["https://openalex.org/I926574661"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Michael Hartung","raw_affiliation_strings":["Department of Computer Science, Universit\u00e4t Leipzig, Johannisgasse 26, 04103, Leipzig, Germany","Interdisciplinary Centre for Bioinformatics, Universit\u00e4t Leipzig, H\u00e4rtelstra\u00dfe 16-18, 04107, Leipzig, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Universit\u00e4t Leipzig, Johannisgasse 26, 04103, Leipzig, Germany","institution_ids":["https://openalex.org/I926574661"]},{"raw_affiliation_string":"Interdisciplinary Centre for Bioinformatics, Universit\u00e4t Leipzig, H\u00e4rtelstra\u00dfe 16-18, 04107, Leipzig, Germany","institution_ids":["https://openalex.org/I926574661"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5075756237","display_name":"Erhard Rahm","orcid":"https://orcid.org/0000-0002-2665-1114"},"institutions":[{"id":"https://openalex.org/I926574661","display_name":"Leipzig University","ror":"https://ror.org/03s7gtk40","country_code":"DE","type":"education","lineage":["https://openalex.org/I926574661"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Erhard Rahm","raw_affiliation_strings":["Department of Computer Science, Universit\u00e4t Leipzig, Johannisgasse 26, 04103, Leipzig, Germany","Interdisciplinary Centre for Bioinformatics, Universit\u00e4t Leipzig, H\u00e4rtelstra\u00dfe 16-18, 04107, Leipzig, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Universit\u00e4t Leipzig, Johannisgasse 26, 04103, Leipzig, Germany","institution_ids":["https://openalex.org/I926574661"]},{"raw_affiliation_string":"Interdisciplinary Centre for Bioinformatics, Universit\u00e4t Leipzig, H\u00e4rtelstra\u00dfe 16-18, 04107, Leipzig, Germany","institution_ids":["https://openalex.org/I926574661"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5018641933"],"corresponding_institution_ids":["https://openalex.org/I926574661"],"apc_list":{"value":1340,"currency":"USD","value_usd":1340},"apc_paid":{"value":1340,"currency":"USD","value_usd":1340},"fwci":5.1093,"has_fulltext":true,"cited_by_count":89,"citation_normalized_percentile":{"value":0.96561632,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"2","issue":"1","first_page":"6","last_page":"6"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.8603000044822693,"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":0.8603000044822693,"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":0.09679999947547913,"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":0.031700000166893005,"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":0.8094059228897095},{"id":"https://openalex.org/keywords/component","display_name":"Component (thermodynamics)","score":0.7428117990493774},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.6040143966674805}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8094059228897095},{"id":"https://openalex.org/C168167062","wikidata":"https://www.wikidata.org/wiki/Q1117970","display_name":"Component (thermodynamics)","level":2,"score":0.7428117990493774},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.6040143966674805},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/2041-1480-2-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/2041-1480-2-6","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/2041-1480-2-6","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:21914205","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21914205","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of biomedical semantics","raw_type":null},{"id":"pmh:oai:doaj.org/article:7ffe66d7bece4e72a7da96519107dd3b","is_oa":true,"landing_page_url":"https://doaj.org/article/7ffe66d7bece4e72a7da96519107dd3b","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":"Journal of Biomedical Semantics, Vol 2, Iss 1, p 6 (2011)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2200774","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3198872","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"}],"best_oa_location":{"id":"doi:10.1186/2041-1480-2-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/2041-1480-2-6","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/2041-1480-2-6","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":[{"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9","score":0.6399999856948853}],"awards":[],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"},{"id":"https://openalex.org/F4320325298","display_name":"Universit\u00e4t Leipzig","ror":"https://ror.org/03s7gtk40"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2030103067.pdf","grobid_xml":"https://content.openalex.org/works/W2030103067.grobid-xml"},"referenced_works_count":63,"referenced_works":["https://openalex.org/W509898","https://openalex.org/W91108659","https://openalex.org/W1480700989","https://openalex.org/W1489291989","https://openalex.org/W1500717163","https://openalex.org/W1505011908","https://openalex.org/W1525293890","https://openalex.org/W1530162452","https://openalex.org/W1542417898","https://openalex.org/W1555563750","https://openalex.org/W1569665785","https://openalex.org/W1588213250","https://openalex.org/W1588413769","https://openalex.org/W1596947943","https://openalex.org/W1604962959","https://openalex.org/W1607633708","https://openalex.org/W1620530708","https://openalex.org/W1646048262","https://openalex.org/W1679882079","https://openalex.org/W1786194602","https://openalex.org/W1941101184","https://openalex.org/W1956929876","https://openalex.org/W1969713547","https://openalex.org/W1998671175","https://openalex.org/W1998982581","https://openalex.org/W2008896880","https://openalex.org/W2020490061","https://openalex.org/W2033377040","https://openalex.org/W2035707461","https://openalex.org/W2039386673","https://openalex.org/W2047253404","https://openalex.org/W2062040469","https://openalex.org/W2067926721","https://openalex.org/W2088387316","https://openalex.org/W2091631218","https://openalex.org/W2096704019","https://openalex.org/W2096939566","https://openalex.org/W2102992354","https://openalex.org/W2103260426","https://openalex.org/W2111601482","https://openalex.org/W2111903862","https://openalex.org/W2113142309","https://openalex.org/W2119710029","https://openalex.org/W2119733112","https://openalex.org/W2122733285","https://openalex.org/W2124890217","https://openalex.org/W2126434293","https://openalex.org/W2126742636","https://openalex.org/W2127480960","https://openalex.org/W2131660156","https://openalex.org/W2133465414","https://openalex.org/W2134868174","https://openalex.org/W2137946607","https://openalex.org/W2138247507","https://openalex.org/W2156510574","https://openalex.org/W2161529001","https://openalex.org/W2166574880","https://openalex.org/W2171030481","https://openalex.org/W2290620050","https://openalex.org/W2406556598","https://openalex.org/W2495004097","https://openalex.org/W2604823638","https://openalex.org/W2611894836"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655","https://openalex.org/W2357256365"],"abstract_inverted_index":{"BACKGROUND:":[0],"Ontologies":[1],"are":[2,94,178],"increasingly":[3],"used":[4,95],"to":[5,68,142,180,198],"structure":[6],"and":[7,16,24,41,55,60,70,75,87,106,118,125,139,148,161,167,207],"semantically":[8],"describe":[9],"entities":[10],"of":[11,28,35,43,78,109,158,202],"domains,":[12],"such":[13,99,187],"as":[14,100,188],"genes":[15],"proteins":[17],"in":[18,31],"life":[19,57,126,145],"sciences.":[20],"Their":[21],"increasing":[22],"size":[23],"the":[25,101,107,115],"high":[26],"frequency":[27],"updates":[29],"resulting":[30],"a":[32,50,65,137,155],"large":[33,144],"set":[34],"ontology":[36,73,85,90,111,159,165,169,176],"versions":[37,74,160,201],"necessitates":[38],"efficient":[39],"management":[40],"analysis":[42,97,120],"this":[44],"data.":[45],"RESULTS:":[46],"We":[47,113],"present":[48],"GOMMA,":[49],"generic":[51,66,156],"infrastructure":[52,117,141],"for":[53,84,122,164,174,189],"managing":[54],"analyzing":[56,175],"science":[58,127,146],"ontologies":[59,147,206],"their":[61,150,182],"evolution.":[62,151],"GOMMA":[63,129,135,192],"utilizes":[64],"repository":[67],"uniformly":[69],"efficiently":[71],"manage":[72,143,199],"different":[76,210],"kinds":[77],"mappings.":[79],"Furthermore,":[80],"it":[81],"provides":[82,136],"components":[83,93,124],"matching,":[86],"determining":[88,168],"evolutionary":[89],"changes.":[91,170],"These":[92],"by":[96,195],"tools,":[98],"Ontology":[102],"Evolution":[103],"Explorer":[104],"(OnEX)":[105],"detection":[108],"unstable":[110],"regions.":[112],"introduce":[114],"component-based":[116],"show":[119],"results":[121],"selected":[123],"applications.":[128],"is":[130],"available":[131],"at":[132],"http://dbs.uni-leipzig.de/GOMMA.":[133],"CONCLUSIONS:":[134],"comprehensive":[138],"scalable":[140],"analyze":[149],"Key":[152],"functions":[153],"include":[154],"storage":[157],"mappings,":[162],"support":[163],"matching":[166],"The":[171],"supported":[172],"features":[173],"changes":[177],"helpful":[179],"assess":[181],"impact":[183],"on":[184],"ontology-dependent":[185],"applications":[186],"term":[190],"enrichment.":[191],"complements":[193],"OnEX":[194],"providing":[196],"functionalities":[197],"various":[200],"mappings":[203],"between":[204],"two":[205],"allows":[208],"combining":[209],"match":[211],"approaches.":[212]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":6},{"year":2016,"cited_by_count":7},{"year":2015,"cited_by_count":16},{"year":2014,"cited_by_count":19},{"year":2013,"cited_by_count":12},{"year":2012,"cited_by_count":10}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
