{"id":"https://openalex.org/W2003614537","doi":"https://doi.org/10.1186/1471-2105-13-217","title":"Process attributes in bio-ontologies","display_name":"Process attributes in bio-ontologies","publication_year":2012,"publication_date":"2012-08-28","ids":{"openalex":"https://openalex.org/W2003614537","doi":"https://doi.org/10.1186/1471-2105-13-217","mag":"2003614537","pmid":"https://pubmed.ncbi.nlm.nih.gov/22928880"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-13-217","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-217","pdf_url":"https://link.springer.com/content/pdf/10.1186/1471-2105-13-217.pdf","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://link.springer.com/content/pdf/10.1186/1471-2105-13-217.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5020628326","display_name":"Andr\u00e9 Q Andrade","orcid":"https://orcid.org/0000-0001-6587-3169"},"institutions":[{"id":"https://openalex.org/I110200422","display_name":"Universidade Federal de Minas Gerais","ror":"https://ror.org/0176yjw32","country_code":"BR","type":"education","lineage":["https://openalex.org/I110200422"]},{"id":"https://openalex.org/I202276237","display_name":"Medical University of Graz","ror":"https://ror.org/02n0bts35","country_code":"AT","type":"education","lineage":["https://openalex.org/I202276237"]}],"countries":["AT","BR"],"is_corresponding":false,"raw_author_name":"Andr\u00e9 Q Andrade","raw_affiliation_strings":["Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Graz, Austria","School of Information Science, Federal University of Minas Gerais, Belo Horizonte, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Graz, Austria","institution_ids":["https://openalex.org/I202276237"]},{"raw_affiliation_string":"School of Information Science, Federal University of Minas Gerais, Belo Horizonte, Brazil","institution_ids":["https://openalex.org/I110200422"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083985501","display_name":"Ward Blond\u00e9","orcid":"https://orcid.org/0000-0001-7624-4069"},"institutions":[{"id":"https://openalex.org/I202276237","display_name":"Medical University of Graz","ror":"https://ror.org/02n0bts35","country_code":"AT","type":"education","lineage":["https://openalex.org/I202276237"]}],"countries":["AT"],"is_corresponding":false,"raw_author_name":"Ward Blond\u00e9","raw_affiliation_strings":["Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Graz, Austria","Institute for Medical Informatics Statistics and Documentation Medical University of Graz Graz Austria"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Graz, Austria","institution_ids":["https://openalex.org/I202276237"]},{"raw_affiliation_string":"Institute for Medical Informatics Statistics and Documentation Medical University of Graz Graz Austria","institution_ids":["https://openalex.org/I202276237"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044072805","display_name":"Janna Hastings","orcid":"https://orcid.org/0000-0002-3469-4923"},"institutions":[{"id":"https://openalex.org/I114457229","display_name":"University of Geneva","ror":"https://ror.org/01swzsf04","country_code":"CH","type":"education","lineage":["https://openalex.org/I114457229"]},{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]}],"countries":["CH","GB"],"is_corresponding":false,"raw_author_name":"Janna Hastings","raw_affiliation_strings":["Cheminformatics and Metabolism, European Bioinformatics Institute, Hinxton, UK","Swiss Centre for Affective Sciences, University of Geneva, Geneva, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Cheminformatics and Metabolism, European Bioinformatics Institute, Hinxton, UK","institution_ids":["https://openalex.org/I1303153112"]},{"raw_affiliation_string":"Swiss Centre for Affective Sciences, University of Geneva, Geneva, Switzerland","institution_ids":["https://openalex.org/I114457229"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101773732","display_name":"Stefan Schulz","orcid":"https://orcid.org/0000-0001-7222-3287"},"institutions":[{"id":"https://openalex.org/I202276237","display_name":"Medical University of Graz","ror":"https://ror.org/02n0bts35","country_code":"AT","type":"education","lineage":["https://openalex.org/I202276237"]},{"id":"https://openalex.org/I2801240073","display_name":"University Medical Center Freiburg","ror":"https://ror.org/03vzbgh69","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I2801240073"]}],"countries":["AT","DE"],"is_corresponding":true,"raw_author_name":"Stefan Schulz","raw_affiliation_strings":["Institute for Medical Biometry and Medical Informatics, University Medical Center, Freiburg, Germany","Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Graz, Austria"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Medical Biometry and Medical Informatics, University Medical Center, Freiburg, Germany","institution_ids":["https://openalex.org/I2801240073"]},{"raw_affiliation_string":"Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Graz, Austria","institution_ids":["https://openalex.org/I202276237"]}]}],"institutions":[],"countries_distinct_count":5,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5101773732"],"corresponding_institution_ids":["https://openalex.org/I202276237","https://openalex.org/I2801240073"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1404,"currency":"EUR","value_usd":1514},"fwci":0.0,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.0716957,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"13","issue":"1","first_page":"217","last_page":"217"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9477999806404114,"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":0.9477999806404114,"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":0.028300000354647636,"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":0.004600000102072954,"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":0.5844096541404724},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.538159191608429},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.476028710603714},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4480668306350708},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3852362036705017},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.24121174216270447},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.15116235613822937},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1372278928756714},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.09367850422859192}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5844096541404724},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.538159191608429},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.476028710603714},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4480668306350708},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3852362036705017},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.24121174216270447},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.15116235613822937},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1372278928756714},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09367850422859192},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D035843","descriptor_name":"Biomedical Research","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D035843","descriptor_name":"Biomedical Research","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D035843","descriptor_name":"Biomedical Research","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":6,"locations":[{"id":"doi:10.1186/1471-2105-13-217","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-217","pdf_url":"https://link.springer.com/content/pdf/10.1186/1471-2105-13-217.pdf","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:22928880","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22928880","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:06ed4f7d30454882b9714579829ef865","is_oa":false,"landing_page_url":"https://doaj.org/article/06ed4f7d30454882b9714579829ef865","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 13, Iss 1, p 217 (2012)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2593522","is_oa":true,"landing_page_url":"http://europepmc.org/articles/PMC3585786","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:freidok.uni-freiburg.de:12430","is_oa":false,"landing_page_url":"https://freidok.uni-freiburg.de/data/12430","pdf_url":null,"source":{"id":"https://openalex.org/S4306401057","display_name":"FreiDok plus (Universit\u00e4tsbibliothek Freiburg)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I161046081","host_organization_name":"University of Freiburg","host_organization_lineage":["https://openalex.org/I161046081"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC bioinformatics. 13 (2012), 217, DOI 10.1186/1471-2105-13-217, issn: 1471-2105","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:3585786","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3585786","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:10.1186/1471-2105-13-217","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-217","pdf_url":"https://link.springer.com/content/pdf/10.1186/1471-2105-13-217.pdf","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":[],"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/F4320321091","display_name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior","ror":"https://ror.org/00x0ma614"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2003614537.pdf","grobid_xml":"https://content.openalex.org/works/W2003614537.grobid-xml"},"referenced_works_count":22,"referenced_works":["https://openalex.org/W165350299","https://openalex.org/W176700763","https://openalex.org/W1480447656","https://openalex.org/W1501546233","https://openalex.org/W1516237339","https://openalex.org/W1574496698","https://openalex.org/W1628054318","https://openalex.org/W1681831155","https://openalex.org/W1976894668","https://openalex.org/W2003550891","https://openalex.org/W2048495389","https://openalex.org/W2103017472","https://openalex.org/W2113142309","https://openalex.org/W2133589238","https://openalex.org/W2135140530","https://openalex.org/W2178026535","https://openalex.org/W2285072859","https://openalex.org/W2397297646","https://openalex.org/W2397733741","https://openalex.org/W4285719527","https://openalex.org/W4298441315","https://openalex.org/W4407687382"],"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/W2359140296"],"abstract_inverted_index":{"BACKGROUND:":[0],"Biomedical":[1],"processes":[2,31,134],"can":[3,123,150],"provide":[4,202],"essential":[5],"information":[6],"about":[7],"the":[8,25,86,114,127,171,192,196,229,236],"(mal-)":[9],"functioning":[10],"of":[11,41,52,88,113,116,132,173,179,186,211,221,231,238,254],"an":[12,138],"organism":[13],"and":[14,22,37,64,76,101,175,181,184,190,258],"are":[15,120],"thus":[16],"frequently":[17],"represented":[18],"in":[19,39,61,136,195],"biomedical":[20],"terminologies":[21],"ontologies,":[23],"including":[24],"GO":[26],"Biological":[27],"Process":[28],"branch.":[29],"These":[30],"often":[32],"need":[33,155],"to":[34,156,170],"be":[35,124,151,157],"described":[36],"categorised":[38],"terms":[40],"their":[42],"attributes,":[43],"such":[44,53,98,133],"as":[45,99,159,251],"rates":[46,183],"or":[47],"regularities.":[48],"The":[49],"adequate":[50],"representation":[51,87,199],"process":[54,89,117,206,222],"attributes":[55,90,118,207,223],"has":[56],"been":[57],"a":[58,82,146,162,218,252],"contentious":[59],"issue":[60],"bio-ontologies":[62],"recently;":[63],"domain":[65,212],"ontologies":[66],"have":[67],"correspondingly":[68],"developed":[69],"ad":[70],"hoc":[71],"workarounds":[72],"that":[73,91,111,129,142,217,235],"compromise":[74],"interoperability":[75,257],"logical":[77,148,219],"consistency.":[78],"RESULTS:":[79],"We":[80,166,201,215],"present":[81],"design":[83],"pattern":[84],"for":[85,144,205],"is":[92,224,240],"compatible":[93],"with":[94],"upper":[95],"ontology":[96,164,198],"frameworks":[97,250],"BFO":[100],"BioTop.":[102],"Our":[103],"solution":[104],"rests":[105],"on":[106],"two":[107],"key":[108],"tenets:":[109],"firstly,":[110],"many":[112],"sorts":[115],"which":[119,145],"biomedically":[121],"interesting":[122],"characterised":[125],"by":[126,228],"ways":[128],"repeated":[130],"parts":[131],"constitute,":[135],"combination,":[137],"overall":[139],"process;":[140],"secondly,":[141],"entities":[143],"full":[147,203],"definition":[149,220],"assigned":[152],"do":[153],"not":[154],"treated":[158],"primitive":[160],"within":[161],"formal":[163,248],"framework.":[165],"apply":[167],"this":[168],"approach":[169],"challenge":[172],"modelling":[174],"automatically":[176],"classifying":[177],"examples":[178],"normal":[180],"abnormal":[182],"patterns":[185],"heart":[187],"beating":[188],"processes,":[189],"discuss":[191],"expressivity":[193,230],"required":[194],"underlying":[197],"language.":[200],"definitions":[204],"at":[208],"increasing":[209],"levels":[210],"complexity.":[213],"CONCLUSIONS:":[214],"show":[216],"feasible,":[225],"though":[226],"limited":[227],"DL":[232],"languages":[233],"so":[234],"creation":[237],"primitives":[239],"still":[241],"necessary.":[242],"This":[243],"finding":[244],"may":[245],"endorse":[246],"current":[247],"upper-ontology":[249],"way":[253],"ensuring":[255],"consistency,":[256],"clarity.":[259]},"counts_by_year":[{"year":2016,"cited_by_count":1}],"updated_date":"2026-06-16T07:32:37.131356","created_date":"2025-10-10T00:00:00"}
