{"id":"https://openalex.org/W2138107070","doi":"https://doi.org/10.1093/bioinformatics/bth465","title":"BioLingua: a programmable knowledge environment for biologists","display_name":"BioLingua: a programmable knowledge environment for biologists","publication_year":2004,"publication_date":"2004-08-12","ids":{"openalex":"https://openalex.org/W2138107070","doi":"https://doi.org/10.1093/bioinformatics/bth465","mag":"2138107070","pmid":"https://pubmed.ncbi.nlm.nih.gov/15308539"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bth465","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bth465","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/2/199/457010/bth465.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/21/2/199/457010/bth465.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5110254188","display_name":"J. P. Massar","orcid":null},"institutions":[{"id":"https://openalex.org/I4210143426","display_name":"Institute for the Study of Learning and Expertise","ror":"https://ror.org/036zxgb71","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210143426"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"J. P. Massar","raw_affiliation_strings":["Institute for Study of Learning and Expertise Palo Alto, CA, USA","Institute for Study of Learning and Expertise Palo Alto, CA, USA#TAB#"],"affiliations":[{"raw_affiliation_string":"Institute for Study of Learning and Expertise Palo Alto, CA, USA","institution_ids":[]},{"raw_affiliation_string":"Institute for Study of Learning and Expertise Palo Alto, CA, USA#TAB#","institution_ids":["https://openalex.org/I4210143426"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040794648","display_name":"Michael Travers","orcid":"https://orcid.org/0000-0002-5452-880X"},"institutions":[{"id":"https://openalex.org/I4210143426","display_name":"Institute for the Study of Learning and Expertise","ror":"https://ror.org/036zxgb71","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210143426"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael Travers","raw_affiliation_strings":["Institute for Study of Learning and Expertise, Palo Alto, CA, USA,","Institute for Study of Learning and Expertise Palo Alto, CA, USA#TAB#"],"affiliations":[{"raw_affiliation_string":"Institute for Study of Learning and Expertise, Palo Alto, CA, USA,","institution_ids":["https://openalex.org/I4210143426"]},{"raw_affiliation_string":"Institute for Study of Learning and Expertise Palo Alto, CA, USA#TAB#","institution_ids":["https://openalex.org/I4210143426"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085075626","display_name":"Jeff Elhai","orcid":"https://orcid.org/0000-0003-0424-9236"},"institutions":[{"id":"https://openalex.org/I184840846","display_name":"Virginia Commonwealth University","ror":"https://ror.org/02nkdxk79","country_code":"US","type":"education","lineage":["https://openalex.org/I184840846"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jeff Elhai","raw_affiliation_strings":["Virginia Commonwealth University, Center for the Study of Biological Complexity, Richmond, VA, USA","Virginia Commonwealth University Center for the Study of Biological Complexity Richmond VA USA"],"affiliations":[{"raw_affiliation_string":"Virginia Commonwealth University, Center for the Study of Biological Complexity, Richmond, VA, USA","institution_ids":["https://openalex.org/I184840846"]},{"raw_affiliation_string":"Virginia Commonwealth University Center for the Study of Biological Complexity Richmond VA USA","institution_ids":["https://openalex.org/I184840846"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5037249015","display_name":"Jeff Shrager","orcid":"https://orcid.org/0000-0002-7007-6305"},"institutions":[{"id":"https://openalex.org/I196817621","display_name":"Carnegie Institution for Science","ror":"https://ror.org/04jr01610","country_code":"US","type":"funder","lineage":["https://openalex.org/I196817621"]},{"id":"https://openalex.org/I4210095419","display_name":"Department of Plant Biology","ror":"https://ror.org/00tdyb139","country_code":"US","type":"facility","lineage":["https://openalex.org/I196817621","https://openalex.org/I4210095419"]},{"id":"https://openalex.org/I4210143426","display_name":"Institute for the Study of Learning and Expertise","ror":"https://ror.org/036zxgb71","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210143426"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jeff Shrager","raw_affiliation_strings":["Carnegie Institute of Washington, Department of Plant Biology, Stanford, CA, USA and","Institute for Study of Learning and Expertise, Palo Alto, CA, USA,","Institute for Study of Learning and Expertise Palo Alto, CA, USA#TAB#"],"affiliations":[{"raw_affiliation_string":"Carnegie Institute of Washington, Department of Plant Biology, Stanford, CA, USA and","institution_ids":["https://openalex.org/I196817621","https://openalex.org/I4210095419"]},{"raw_affiliation_string":"Institute for Study of Learning and Expertise, Palo Alto, CA, USA,","institution_ids":["https://openalex.org/I4210143426"]},{"raw_affiliation_string":"Institute for Study of Learning and Expertise Palo Alto, CA, USA#TAB#","institution_ids":["https://openalex.org/I4210143426"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5110254188"],"corresponding_institution_ids":["https://openalex.org/I4210143426"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.6882,"has_fulltext":true,"cited_by_count":46,"citation_normalized_percentile":{"value":0.83109268,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"21","issue":"2","first_page":"199","last_page":"207"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9940999746322632,"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":0.9940999746322632,"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":0.9868999719619751,"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/T11986","display_name":"Scientific Computing and Data Management","score":0.9801999926567078,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8321529030799866},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.5803861618041992},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.5531618595123291},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.4762152135372162},{"id":"https://openalex.org/keywords/frame","display_name":"Frame (networking)","score":0.4583108127117157},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.36496609449386597},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.33206480741500854}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8321529030799866},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.5803861618041992},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.5531618595123291},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.4762152135372162},{"id":"https://openalex.org/C126042441","wikidata":"https://www.wikidata.org/wiki/Q1324888","display_name":"Frame (networking)","level":2,"score":0.4583108127117157},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.36496609449386597},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.33206480741500854},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","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":[{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/bth465","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bth465","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/2/199/457010/bth465.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:15308539","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15308539","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:CiteSeerX.psu:10.1.1.1.4914","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.1.4914","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://nostoc.stanford.edu/Docs/Paper.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.102.745","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.102.745","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bioinformatics.oxfordjournals.org/cgi/reprint/bth465v1.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.876.8779","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.876.8779","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bioinformatics.oxfordjournals.org/content/21/2/199.full.pdf","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bth465","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bth465","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/2/199/457010/bth465.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":[],"funders":[{"id":"https://openalex.org/F4320306101","display_name":"National Aeronautics and Space Administration","ror":"https://ror.org/027ka1x80"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2138107070.pdf","grobid_xml":"https://content.openalex.org/works/W2138107070.grobid-xml"},"referenced_works_count":19,"referenced_works":["https://openalex.org/W1968766436","https://openalex.org/W1970185999","https://openalex.org/W1982195409","https://openalex.org/W1983594585","https://openalex.org/W2018819346","https://openalex.org/W2032533901","https://openalex.org/W2076864883","https://openalex.org/W2099435674","https://openalex.org/W2102697744","https://openalex.org/W2103017472","https://openalex.org/W2107523227","https://openalex.org/W2113024448","https://openalex.org/W2119680932","https://openalex.org/W2132233302","https://openalex.org/W2151709497","https://openalex.org/W2155487633","https://openalex.org/W2159482845","https://openalex.org/W2175268987","https://openalex.org/W4236038677"],"related_works":["https://openalex.org/W2618286804","https://openalex.org/W2329643025","https://openalex.org/W2002770077","https://openalex.org/W3131163342","https://openalex.org/W2092256833","https://openalex.org/W2142369114","https://openalex.org/W2361728394","https://openalex.org/W2166271660","https://openalex.org/W3089582840","https://openalex.org/W2352631095"],"abstract_inverted_index":{"JShrager@Stanford.edu":[0]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":4}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
