{"id":"https://openalex.org/W2140001356","doi":"https://doi.org/10.1093/bioinformatics/btp259","title":"Application and evaluation of automated semantic annotation of gene expression experiments","display_name":"Application and evaluation of automated semantic annotation of gene expression experiments","publication_year":2009,"publication_date":"2009-04-17","ids":{"openalex":"https://openalex.org/W2140001356","doi":"https://doi.org/10.1093/bioinformatics/btp259","mag":"2140001356","pmid":"https://pubmed.ncbi.nlm.nih.gov/19376825"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btp259","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp259","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/12/1543/482937/btp259.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/25/12/1543/482937/btp259.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5074657982","display_name":"Leon French","orcid":"https://orcid.org/0000-0002-9409-4583"},"institutions":[{"id":"https://openalex.org/I141945490","display_name":"University of British Columbia","ror":"https://ror.org/03rmrcq20","country_code":"CA","type":"education","lineage":["https://openalex.org/I141945490"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Leon French","raw_affiliation_strings":["1 Bioinformatics Graduate Program, 2Department of Psychiatry and 3Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC, Canada"],"affiliations":[{"raw_affiliation_string":"1 Bioinformatics Graduate Program, 2Department of Psychiatry and 3Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC, Canada","institution_ids":["https://openalex.org/I141945490"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084367319","display_name":"Suzanne Lane","orcid":null},"institutions":[{"id":"https://openalex.org/I141945490","display_name":"University of British Columbia","ror":"https://ror.org/03rmrcq20","country_code":"CA","type":"education","lineage":["https://openalex.org/I141945490"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Suzanne Lane","raw_affiliation_strings":["1 Bioinformatics Graduate Program, 2Department of Psychiatry and 3Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC, Canada"],"affiliations":[{"raw_affiliation_string":"1 Bioinformatics Graduate Program, 2Department of Psychiatry and 3Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC, Canada","institution_ids":["https://openalex.org/I141945490"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111720029","display_name":"Tamryn K. Law","orcid":null},"institutions":[{"id":"https://openalex.org/I141945490","display_name":"University of British Columbia","ror":"https://ror.org/03rmrcq20","country_code":"CA","type":"education","lineage":["https://openalex.org/I141945490"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Tamryn Law","raw_affiliation_strings":["1 Bioinformatics Graduate Program, 2Department of Psychiatry and 3Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC, Canada"],"affiliations":[{"raw_affiliation_string":"1 Bioinformatics Graduate Program, 2Department of Psychiatry and 3Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC, Canada","institution_ids":["https://openalex.org/I141945490"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100296880","display_name":"Lydia Xu","orcid":null},"institutions":[{"id":"https://openalex.org/I141945490","display_name":"University of British Columbia","ror":"https://ror.org/03rmrcq20","country_code":"CA","type":"education","lineage":["https://openalex.org/I141945490"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Lydia Xu","raw_affiliation_strings":["1 Bioinformatics Graduate Program, 2Department of Psychiatry and 3Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC, Canada"],"affiliations":[{"raw_affiliation_string":"1 Bioinformatics Graduate Program, 2Department of Psychiatry and 3Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC, Canada","institution_ids":["https://openalex.org/I141945490"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5012991069","display_name":"Paul Pavlidis","orcid":"https://orcid.org/0000-0002-0426-5028"},"institutions":[{"id":"https://openalex.org/I141945490","display_name":"University of British Columbia","ror":"https://ror.org/03rmrcq20","country_code":"CA","type":"education","lineage":["https://openalex.org/I141945490"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Paul Pavlidis","raw_affiliation_strings":["1 Bioinformatics Graduate Program, 2Department of Psychiatry and 3Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC, Canada"],"affiliations":[{"raw_affiliation_string":"1 Bioinformatics Graduate Program, 2Department of Psychiatry and 3Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC, Canada","institution_ids":["https://openalex.org/I141945490"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5074657982"],"corresponding_institution_ids":["https://openalex.org/I141945490"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.348,"has_fulltext":true,"cited_by_count":13,"citation_normalized_percentile":{"value":0.80349596,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"25","issue":"12","first_page":"1543","last_page":"1549"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9962999820709229,"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":0.9952999949455261,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8233827948570251},{"id":"https://openalex.org/keywords/unified-medical-language-system","display_name":"Unified Medical Language System","score":0.7618687152862549},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.7340571880340576},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.5957258939743042},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.5564296841621399},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.5241318345069885},{"id":"https://openalex.org/keywords/controlled-vocabulary","display_name":"Controlled vocabulary","score":0.5099972486495972},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.47730743885040283},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.47396084666252136},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.4679481089115143},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.46518009901046753},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.45446059107780457},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.4430595636367798},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.21184036135673523}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8233827948570251},{"id":"https://openalex.org/C69505689","wikidata":"https://www.wikidata.org/wiki/Q455338","display_name":"Unified Medical Language System","level":2,"score":0.7618687152862549},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.7340571880340576},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.5957258939743042},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.5564296841621399},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.5241318345069885},{"id":"https://openalex.org/C110615152","wikidata":"https://www.wikidata.org/wiki/Q1469824","display_name":"Controlled vocabulary","level":2,"score":0.5099972486495972},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.47730743885040283},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.47396084666252136},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.4679481089115143},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.46518009901046753},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.45446059107780457},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4430595636367798},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.21184036135673523},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017432","descriptor_name":"Unified Medical Language System","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D017432","descriptor_name":"Unified Medical Language System","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D017432","descriptor_name":"Unified Medical Language System","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btp259","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp259","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/12/1543/482937/btp259.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:19376825","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19376825","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:europepmc.org:1856013","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2687992","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btp259","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp259","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/12/1543/482937/btp259.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2165548363","display_name":null,"funder_award_id":"Canada","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G3969565085","display_name":null,"funder_award_id":"Foundation","funder_id":"https://openalex.org/F4320334506","funder_display_name":"Canadian Institutes of Health Research"},{"id":"https://openalex.org/G4389354971","display_name":null,"funder_award_id":"Research","funder_id":"https://openalex.org/F4320334506","funder_display_name":"Canadian Institutes of Health Research"},{"id":"https://openalex.org/G5782839332","display_name":null,"funder_award_id":"New Investigator","funder_id":"https://openalex.org/F4320334506","funder_display_name":"Canadian Institutes of Health Research"},{"id":"https://openalex.org/G6082334676","display_name":null,"funder_award_id":"GM076990","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6282788884","display_name":null,"funder_award_id":"Canadian Institutes of Health","funder_id":"https://openalex.org/F4320334506","funder_display_name":"Canadian Institutes of Health Research"},{"id":"https://openalex.org/G727862659","display_name":null,"funder_award_id":"Canadian Institutes of Health Research (CIHR)","funder_id":"https://openalex.org/F4320334506","funder_display_name":"Canadian Institutes of Health Research"}],"funders":[{"id":"https://openalex.org/F4320319965","display_name":"Michael Smith Health Research BC","ror":"https://ror.org/020x39229"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320334506","display_name":"Canadian Institutes of Health Research","ror":"https://ror.org/01gavpb45"},{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2140001356.pdf","grobid_xml":"https://content.openalex.org/works/W2140001356.grobid-xml"},"referenced_works_count":29,"referenced_works":["https://openalex.org/W1550258693","https://openalex.org/W1602694398","https://openalex.org/W2004884668","https://openalex.org/W2045016337","https://openalex.org/W2064930103","https://openalex.org/W2087779040","https://openalex.org/W2090566980","https://openalex.org/W2091729411","https://openalex.org/W2096525273","https://openalex.org/W2101727078","https://openalex.org/W2103017472","https://openalex.org/W2105883975","https://openalex.org/W2113142309","https://openalex.org/W2127241285","https://openalex.org/W2134725489","https://openalex.org/W2137999759","https://openalex.org/W2142741334","https://openalex.org/W2144303444","https://openalex.org/W2144949988","https://openalex.org/W2152545090","https://openalex.org/W2154362705","https://openalex.org/W2159583324","https://openalex.org/W2162311237","https://openalex.org/W2162348425","https://openalex.org/W2163670493","https://openalex.org/W4241827326","https://openalex.org/W4390854702","https://openalex.org/W6632766574","https://openalex.org/W6860437399"],"related_works":["https://openalex.org/W2509297716","https://openalex.org/W1508778694","https://openalex.org/W138082899","https://openalex.org/W2114373757","https://openalex.org/W2159583324","https://openalex.org/W2036729745","https://openalex.org/W2010487328","https://openalex.org/W2340589664","https://openalex.org/W2264448939","https://openalex.org/W2052511096"],"abstract_inverted_index":{"The":[0,11,38],"source":[1],"code,":[2],"documentation":[3],"and":[4,24,30],"Supplementary":[5,20],"Materials":[6],"are":[7,17],"available":[8,45],"at":[9,36],"http://www.chibi.ubc.ca/GEOMMTX.":[10],"results":[12],"of":[13,41],"the":[14,33],"manual":[15,23],"evaluations":[16],"provided":[18],"as":[19,46],"Material.":[21],"Both":[22],"predicted":[25,42],"annotations":[26,43],"can":[27],"be":[28],"viewed":[29],"searched":[31],"via":[32],"Gemma":[34],"website":[35],"http://www.chibi.ubc.ca/Gemma.":[37],"complete":[39],"set":[40],"is":[44],"a":[47],"machine":[48],"readable":[49],"resource":[50],"description":[51],"framework":[52],"graph.":[53]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2012,"cited_by_count":4}],"updated_date":"2026-04-15T08:11:43.952461","created_date":"2025-10-10T00:00:00"}