{"id":"https://openalex.org/W2612416799","doi":"https://doi.org/10.1145/2166896.2166900","title":"Translating standards into practice","display_name":"Translating standards into practice","publication_year":2011,"publication_date":"2011-12-07","ids":{"openalex":"https://openalex.org/W2612416799","doi":"https://doi.org/10.1145/2166896.2166900","mag":"2612416799"},"language":"en","primary_location":{"id":"doi:10.1145/2166896.2166900","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2166896.2166900","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 4th International Workshop on Semantic Web Applications and Tools for the Life Sciences","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5086141196","display_name":"Helena Deus","orcid":"https://orcid.org/0000-0003-2995-568X"},"institutions":[{"id":"https://openalex.org/I188760350","display_name":"Ollscoil na Gaillimhe \u2013 University of Galway","ror":"https://ror.org/03bea9k73","country_code":"IE","type":"education","lineage":["https://openalex.org/I188760350"]}],"countries":["IE"],"is_corresponding":true,"raw_author_name":"Helena F. Deus","raw_affiliation_strings":["National University of Ireland, Galway"],"affiliations":[{"raw_affiliation_string":"National University of Ireland, Galway","institution_ids":["https://openalex.org/I188760350"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100744623","display_name":"Jun Zhao","orcid":"https://orcid.org/0000-0001-6935-9028"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Jun Zhao","raw_affiliation_strings":["University of Oxford, Oxford, UK"],"affiliations":[{"raw_affiliation_string":"University of Oxford, Oxford, UK","institution_ids":["https://openalex.org/I40120149"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030875887","display_name":"Jamie P. McCusker","orcid":"https://orcid.org/0000-0003-1085-6059"},"institutions":[{"id":"https://openalex.org/I165799507","display_name":"Rensselaer Polytechnic Institute","ror":"https://ror.org/01rtyzb94","country_code":"US","type":"education","lineage":["https://openalex.org/I165799507"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jamie Patricia McCusker","raw_affiliation_strings":["Rensselaer Polytechnic Institute (RPI), NY"],"affiliations":[{"raw_affiliation_string":"Rensselaer Polytechnic Institute (RPI), NY","institution_ids":["https://openalex.org/I165799507"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040459591","display_name":"Ronan Fox","orcid":null},"institutions":[{"id":"https://openalex.org/I188760350","display_name":"Ollscoil na Gaillimhe \u2013 University of Galway","ror":"https://ror.org/03bea9k73","country_code":"IE","type":"education","lineage":["https://openalex.org/I188760350"]}],"countries":["IE"],"is_corresponding":false,"raw_author_name":"Ronan Fox","raw_affiliation_strings":["National University of Ireland, Galway"],"affiliations":[{"raw_affiliation_string":"National University of Ireland, Galway","institution_ids":["https://openalex.org/I188760350"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057752123","display_name":"Eric Prud\u2019hommeaux","orcid":"https://orcid.org/0000-0003-1775-9921"},"institutions":[{"id":"https://openalex.org/I4210087207","display_name":"World Wide Web Consortium","ror":"https://ror.org/0059y1582","country_code":"US","type":"other","lineage":["https://openalex.org/I4210087207"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Eric Prud'hommeaux","raw_affiliation_strings":["World Wide Web Consortium (W3C), MIT, Cambridge, MA"],"affiliations":[{"raw_affiliation_string":"World Wide Web Consortium (W3C), MIT, Cambridge, MA","institution_ids":["https://openalex.org/I4210087207"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037878913","display_name":"James Malone","orcid":"https://orcid.org/0000-0002-1615-2899"},"institutions":[{"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":["GB"],"is_corresponding":false,"raw_author_name":"James Malone","raw_affiliation_strings":["European Bioinformatics Institute (EBI), Cambridge, UK"],"affiliations":[{"raw_affiliation_string":"European Bioinformatics Institute (EBI), Cambridge, UK","institution_ids":["https://openalex.org/I1303153112"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062048275","display_name":"Sudeshna Das","orcid":"https://orcid.org/0000-0002-9486-6811"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I4210087915","display_name":"Massachusetts General Hospital","ror":"https://ror.org/002pd6e78","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210087915","https://openalex.org/I48633490"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sudeshna Das","raw_affiliation_strings":["Massachusetts General Hospital &amp; Harvard Medical School, Boston MA"],"affiliations":[{"raw_affiliation_string":"Massachusetts General Hospital &amp; Harvard Medical School, Boston MA","institution_ids":["https://openalex.org/I4210087915","https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058054350","display_name":"Michael Miller","orcid":"https://orcid.org/0000-0003-0781-7868"},"institutions":[{"id":"https://openalex.org/I3148997608","display_name":"Institute for Systems Biology","ror":"https://ror.org/02tpgw303","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I3148997608"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael Miller","raw_affiliation_strings":["Institute for Systems Biology (ISB), Seattle, WA"],"affiliations":[{"raw_affiliation_string":"Institute for Systems Biology (ISB), Seattle, WA","institution_ids":["https://openalex.org/I3148997608"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007740400","display_name":"Tomasz Adamusiak","orcid":"https://orcid.org/0000-0002-0746-2916"},"institutions":[{"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":["GB"],"is_corresponding":false,"raw_author_name":"Tomasz Adamusiak","raw_affiliation_strings":["European Bioinformatics Institute (EBI), Cambridge, UK"],"affiliations":[{"raw_affiliation_string":"European Bioinformatics Institute (EBI), Cambridge, UK","institution_ids":["https://openalex.org/I1303153112"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009463654","display_name":"Philippe Rocca Serra","orcid":null},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Philippe Rocca Serra","raw_affiliation_strings":["University of Oxford, Oxford, United Kingdom"],"affiliations":[{"raw_affiliation_string":"University of Oxford, Oxford, United Kingdom","institution_ids":["https://openalex.org/I40120149"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5075308601","display_name":"Michael S. Marshall","orcid":"https://orcid.org/0000-0002-5742-2031"},"institutions":[{"id":"https://openalex.org/I2800006345","display_name":"Leiden University Medical Center","ror":"https://ror.org/05xvt9f17","country_code":"NL","type":"funder","lineage":["https://openalex.org/I2800006345"]},{"id":"https://openalex.org/I887064364","display_name":"University of Amsterdam","ror":"https://ror.org/04dkp9463","country_code":"NL","type":"education","lineage":["https://openalex.org/I887064364"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"M. Scott Marshall","raw_affiliation_strings":["Leiden University Medical Center, University of Amsterdam, Netherlands"],"affiliations":[{"raw_affiliation_string":"Leiden University Medical Center, University of Amsterdam, Netherlands","institution_ids":["https://openalex.org/I2800006345","https://openalex.org/I887064364"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":11,"corresponding_author_ids":["https://openalex.org/A5086141196"],"corresponding_institution_ids":["https://openalex.org/I188760350"],"apc_list":null,"apc_paid":null,"fwci":0.3909,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.63290366,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":null,"issue":null,"first_page":"6","last_page":"7"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9998999834060669,"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":0.9998999834060669,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9970999956130981,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9968000054359436,"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":0.7914551496505737},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.6910756230354309},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.5698288083076477},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5690225958824158},{"id":"https://openalex.org/keywords/sparql","display_name":"SPARQL","score":0.5031129717826843},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.49480241537094116},{"id":"https://openalex.org/keywords/data-integration","display_name":"Data integration","score":0.43408501148223877},{"id":"https://openalex.org/keywords/construct","display_name":"Construct (python library)","score":0.43194055557250977},{"id":"https://openalex.org/keywords/semantic-web","display_name":"Semantic Web","score":0.4029756784439087},{"id":"https://openalex.org/keywords/rdf","display_name":"RDF","score":0.3399461805820465},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.2870570421218872}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7914551496505737},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.6910756230354309},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.5698288083076477},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5690225958824158},{"id":"https://openalex.org/C41009113","wikidata":"https://www.wikidata.org/wiki/Q54871","display_name":"SPARQL","level":4,"score":0.5031129717826843},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.49480241537094116},{"id":"https://openalex.org/C72634772","wikidata":"https://www.wikidata.org/wiki/Q386824","display_name":"Data integration","level":2,"score":0.43408501148223877},{"id":"https://openalex.org/C2780801425","wikidata":"https://www.wikidata.org/wiki/Q5164392","display_name":"Construct (python library)","level":2,"score":0.43194055557250977},{"id":"https://openalex.org/C2129575","wikidata":"https://www.wikidata.org/wiki/Q54837","display_name":"Semantic Web","level":2,"score":0.4029756784439087},{"id":"https://openalex.org/C147497476","wikidata":"https://www.wikidata.org/wiki/Q54872","display_name":"RDF","level":3,"score":0.3399461805820465},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2870570421218872},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","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},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","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/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/2166896.2166900","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2166896.2166900","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 4th International Workshop on Semantic Web Applications and Tools for the Life Sciences","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":36,"referenced_works":["https://openalex.org/W53016874","https://openalex.org/W191751253","https://openalex.org/W1010927513","https://openalex.org/W1486283310","https://openalex.org/W1544923801","https://openalex.org/W1994100378","https://openalex.org/W2002057022","https://openalex.org/W2002607603","https://openalex.org/W2010502047","https://openalex.org/W2015191210","https://openalex.org/W2019149345","https://openalex.org/W2022381538","https://openalex.org/W2024913341","https://openalex.org/W2034792128","https://openalex.org/W2039144282","https://openalex.org/W2050554833","https://openalex.org/W2062926086","https://openalex.org/W2072485437","https://openalex.org/W2083737836","https://openalex.org/W2084975981","https://openalex.org/W2088908026","https://openalex.org/W2090566980","https://openalex.org/W2100453203","https://openalex.org/W2100471807","https://openalex.org/W2113142309","https://openalex.org/W2130430745","https://openalex.org/W2130542009","https://openalex.org/W2131660156","https://openalex.org/W2137999759","https://openalex.org/W2144303444","https://openalex.org/W2145065529","https://openalex.org/W2155232871","https://openalex.org/W2168546553","https://openalex.org/W2259172389","https://openalex.org/W2608145068","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W2615202182","https://openalex.org/W4206665951","https://openalex.org/W3085073370","https://openalex.org/W2904139343","https://openalex.org/W2529794967","https://openalex.org/W2978246852","https://openalex.org/W2604011835","https://openalex.org/W2528203718","https://openalex.org/W2295924417","https://openalex.org/W4243630814"],"abstract_inverted_index":{"Sharing":[0],"and":[1,30,35,58,66,75,79,105,121,148,192,194,219,232],"describing":[2],"experimental":[3,122,230],"results":[4,13,48,120,233],"unambiguously":[5],"with":[6],"sufficient":[7],"detail":[8],"to":[9,117,142,159,170,185],"enable":[10,171],"replication":[11],"of":[12,18,25,33,63,73,88,124,128,145,163,173,190,213,229,234],"is":[14,183,240],"a":[15,115,187],"fundamental":[16],"tenet":[17],"scientific":[19],"research.":[20],"In":[21],"today's":[22],"cluttered":[23],"world":[24],"\"-omics\"":[26],"sciences,":[27],"data":[28,110],"standards":[29,89,165],"standardized":[31],"use":[32],"terminologies":[34],"ontologies":[36,104],"for":[37,70,100,166,222,226],"biomedical":[38],"informatics":[39],"play":[40],"an":[41],"important":[42],"role":[43],"in":[44,49],"reporting":[45,143,228],"high-throughput":[46],"experiment":[47],"formats":[50],"that":[51,197],"can":[52,97,210],"be":[53,98],"interpreted":[54],"by":[55],"both":[56],"researchers":[57],"analytical":[59],"tools.":[60],"Increasing":[61],"adoption":[62],"Semantic":[64],"Web":[65],"Linked":[67],"Data":[68],"technologies":[69],"the":[71,86,119,132,136,149,161,214,220,227],"integration":[72,172],"heterogeneous":[74],"distributed":[76],"Health":[77],"Care":[78],"Life":[80],"Sciences":[81],"(HCLS)":[82],"datasets":[83,175],"has":[84],"made":[85,241],"reuse":[87,212],"even":[90],"more":[91],"pressing;":[92],"dynamic":[93],"semantic":[94],"query":[95,202],"federation":[96],"used":[99,184],"integrative":[101,208],"bioinformatics":[102],"when":[103],"identifiers":[106],"are":[107],"reused":[108],"across":[109],"instances.":[111],"We":[112,204],"present":[113],"here":[114],"methodology":[116],"integrate":[118],"context":[123,231],"three":[125],"different":[126],"representations":[127],"microarray-based":[129,178],"transcriptomic":[130,179],"experiments:":[131],"Gene":[133],"Expression":[134],"Atlas,":[135],"W3C":[137],"BioRDF":[138],"task":[139],"force":[140],"approach":[141,155,209],"provenance":[144],"microarray":[146],"experiments,":[147],"HSCI":[150],"blood":[151],"genomics":[152,167],"project.":[153],"Our":[154],"does":[156],"not":[157],"attempt":[158],"improve":[160],"expressivity":[162],"existing":[164,174],"but,":[168],"instead,":[169],"published":[176],"from":[177],"experiments.":[180],"SPARQL":[181],"Construct":[182],"create":[186],"posteriori":[188],"mappings":[189],"concepts":[191],"properties":[193],"linking":[195],"rules":[196],"match":[198],"entities":[199],"based":[200],"on":[201],"constraints.":[203],"discuss":[205],"how":[206],"our":[207],"encourage":[211],"Experimental":[215],"Factor":[216],"Ontology":[217,221],"(EFO)":[218],"Biomedical":[223],"Investigations":[224],"(OBI)":[225],"gene":[235],"expression":[236],"studies.":[237],"A":[238],"demo":[239],"available":[242],"at":[243],"http://ui.genexpressfusion.googlecode.com/hg/index.html":[244]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
