{"id":"https://openalex.org/W2134015035","doi":"https://doi.org/10.1186/1471-2105-10-s2-s1","title":"Ontology-driven indexing of public datasets for translational bioinformatics","display_name":"Ontology-driven indexing of public datasets for translational bioinformatics","publication_year":2009,"publication_date":"2009-02-01","ids":{"openalex":"https://openalex.org/W2134015035","doi":"https://doi.org/10.1186/1471-2105-10-s2-s1","mag":"2134015035","pmid":"https://pubmed.ncbi.nlm.nih.gov/19208184"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-10-s2-s1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-s2-s1","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-S2-S1","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://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-S2-S1","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5041175834","display_name":"Nigam H. Shah","orcid":"https://orcid.org/0000-0001-9385-7158"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]},{"id":"https://openalex.org/I4210137306","display_name":"Stanford Medicine","ror":"https://ror.org/03mtd9a03","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210137306","https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Nigam H Shah","raw_affiliation_strings":["Centre for Biomedical Informatics, School of Medicine, Stanford University, Stanford, CA 94305, USA. nigam@stanford.edu","Centre for Biomedical Informatics, School of Medicine, Stanford University, Stanford, USA"],"affiliations":[{"raw_affiliation_string":"Centre for Biomedical Informatics, School of Medicine, Stanford University, Stanford, CA 94305, USA. nigam@stanford.edu","institution_ids":["https://openalex.org/I97018004","https://openalex.org/I4210137306"]},{"raw_affiliation_string":"Centre for Biomedical Informatics, School of Medicine, Stanford University, Stanford, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064022148","display_name":"Cl\u00e9ment Jonquet","orcid":"https://orcid.org/0000-0002-2404-1582"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Clement Jonquet","raw_affiliation_strings":["Centre for Biomedical Informatics, School of Medicine, Stanford University, Stanford, CA, 94305, USA","Centre for Biomedical Informatics, School of Medicine, Stanford University, Stanford, USA"],"affiliations":[{"raw_affiliation_string":"Centre for Biomedical Informatics, School of Medicine, Stanford University, Stanford, CA, 94305, USA","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Centre for Biomedical Informatics, School of Medicine, Stanford University, Stanford, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068270301","display_name":"Annie Chiang","orcid":"https://orcid.org/0000-0003-0188-1586"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Annie P Chiang","raw_affiliation_strings":["Centre for Biomedical Informatics, School of Medicine, Stanford University, Stanford, CA, 94305, USA","Centre for Biomedical Informatics, School of Medicine, Stanford University, Stanford, USA"],"affiliations":[{"raw_affiliation_string":"Centre for Biomedical Informatics, School of Medicine, Stanford University, Stanford, CA, 94305, USA","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Centre for Biomedical Informatics, School of Medicine, Stanford University, Stanford, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036068985","display_name":"Atul J. Butte","orcid":"https://orcid.org/0000-0002-7433-2740"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Atul J Butte","raw_affiliation_strings":["Centre for Biomedical Informatics, School of Medicine, Stanford University, Stanford, CA, 94305, USA","Centre for Biomedical Informatics, School of Medicine, Stanford University, Stanford, USA"],"affiliations":[{"raw_affiliation_string":"Centre for Biomedical Informatics, School of Medicine, Stanford University, Stanford, CA, 94305, USA","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Centre for Biomedical Informatics, School of Medicine, Stanford University, Stanford, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100419014","display_name":"Rong Chen","orcid":"https://orcid.org/0000-0002-4019-9304"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rong Chen","raw_affiliation_strings":["Centre for Biomedical Informatics, School of Medicine, Stanford University, Stanford, CA, 94305, USA","Centre for Biomedical Informatics, School of Medicine, Stanford University, Stanford, USA"],"affiliations":[{"raw_affiliation_string":"Centre for Biomedical Informatics, School of Medicine, Stanford University, Stanford, CA, 94305, USA","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Centre for Biomedical Informatics, School of Medicine, Stanford University, Stanford, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5009128820","display_name":"Mark A. Musen","orcid":"https://orcid.org/0000-0003-3325-793X"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mark A Musen","raw_affiliation_strings":["Centre for Biomedical Informatics, School of Medicine, Stanford University, Stanford, CA, 94305, USA","Centre for Biomedical Informatics, School of Medicine, Stanford University, Stanford, USA"],"affiliations":[{"raw_affiliation_string":"Centre for Biomedical Informatics, School of Medicine, Stanford University, Stanford, CA, 94305, USA","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Centre for Biomedical Informatics, School of Medicine, Stanford University, Stanford, USA","institution_ids":["https://openalex.org/I97018004"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5041175834"],"corresponding_institution_ids":["https://openalex.org/I4210137306","https://openalex.org/I97018004"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":6.8746,"has_fulltext":true,"cited_by_count":121,"citation_normalized_percentile":{"value":0.97738197,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"10","issue":"S2","first_page":"S1","last_page":"S1"},"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/T10215","display_name":"Semantic Web and Ontologies","score":0.9939000010490417,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9897000193595886,"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":0.7193628549575806},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.667856752872467},{"id":"https://openalex.org/keywords/unified-medical-language-system","display_name":"Unified Medical Language System","score":0.6391133666038513},{"id":"https://openalex.org/keywords/open-biomedical-ontologies","display_name":"Open Biomedical Ontologies","score":0.628785252571106},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.6203716397285461},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.6185171604156494},{"id":"https://openalex.org/keywords/metadata","display_name":"Metadata","score":0.5493155121803284},{"id":"https://openalex.org/keywords/controlled-vocabulary","display_name":"Controlled vocabulary","score":0.5275686979293823},{"id":"https://openalex.org/keywords/search-engine-indexing","display_name":"Search engine indexing","score":0.49703434109687805},{"id":"https://openalex.org/keywords/microarray-databases","display_name":"Microarray databases","score":0.4541877508163452},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.4015113413333893},{"id":"https://openalex.org/keywords/ontology-based-data-integration","display_name":"Ontology-based data integration","score":0.345417857170105},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3286956548690796},{"id":"https://openalex.org/keywords/suggested-upper-merged-ontology","display_name":"Suggested Upper Merged Ontology","score":0.27021968364715576},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.21593257784843445},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.1851074993610382},{"id":"https://openalex.org/keywords/semantic-web","display_name":"Semantic Web","score":0.11830216646194458},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.10681849718093872},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.0916222333908081},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.08347979187965393}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7193628549575806},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.667856752872467},{"id":"https://openalex.org/C69505689","wikidata":"https://www.wikidata.org/wiki/Q455338","display_name":"Unified Medical Language System","level":2,"score":0.6391133666038513},{"id":"https://openalex.org/C137982476","wikidata":"https://www.wikidata.org/wiki/Q7072326","display_name":"Open Biomedical Ontologies","level":5,"score":0.628785252571106},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.6203716397285461},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6185171604156494},{"id":"https://openalex.org/C93518851","wikidata":"https://www.wikidata.org/wiki/Q180160","display_name":"Metadata","level":2,"score":0.5493155121803284},{"id":"https://openalex.org/C110615152","wikidata":"https://www.wikidata.org/wiki/Q1469824","display_name":"Controlled vocabulary","level":2,"score":0.5275686979293823},{"id":"https://openalex.org/C75165309","wikidata":"https://www.wikidata.org/wiki/Q2258979","display_name":"Search engine indexing","level":2,"score":0.49703434109687805},{"id":"https://openalex.org/C548314002","wikidata":"https://www.wikidata.org/wiki/Q6839218","display_name":"Microarray databases","level":5,"score":0.4541877508163452},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.4015113413333893},{"id":"https://openalex.org/C22550185","wikidata":"https://www.wikidata.org/wiki/Q7095047","display_name":"Ontology-based data integration","level":3,"score":0.345417857170105},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3286956548690796},{"id":"https://openalex.org/C50971890","wikidata":"https://www.wikidata.org/wiki/Q7635093","display_name":"Suggested Upper Merged Ontology","level":4,"score":0.27021968364715576},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.21593257784843445},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.1851074993610382},{"id":"https://openalex.org/C2129575","wikidata":"https://www.wikidata.org/wiki/Q54837","display_name":"Semantic Web","level":2,"score":0.11830216646194458},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.10681849718093872},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0916222333908081},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.08347979187965393},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","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/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017432","descriptor_name":"Unified Medical Language System","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017432","descriptor_name":"Unified Medical Language System","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017432","descriptor_name":"Unified Medical Language System","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":7,"locations":[{"id":"doi:10.1186/1471-2105-10-s2-s1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-s2-s1","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-S2-S1","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:19208184","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19208184","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:ark:/13030/qt5rp3q8p1","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:HAL:hal-00492025v2","is_oa":true,"landing_page_url":"https://hal.science/hal-00492025","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, 2009, 10 (2:S1), pp.1-10. &#x27E8;10.1186/1471-2105-10-S2-S1&#x27E9;","raw_type":"Journal articles"},{"id":"pmh:oai:doaj.org/article:f122afb26d11465f9316b371aa582ea5","is_oa":true,"landing_page_url":"https://doaj.org/article/f122afb26d11465f9316b371aa582ea5","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 10, Iss Suppl 2, p S1 (2009)","raw_type":"article"},{"id":"pmh:oai:escholarship.org/ark:/13030/qt5rp3q8p1","is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/5rp3q8p1","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"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 10 Suppl 2, iss S2","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2646250","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2646250","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"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:10.1186/1471-2105-10-s2-s1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-s2-s1","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-S2-S1","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":[{"id":"https://openalex.org/G1857259337","display_name":null,"funder_award_id":"U54 HG004028","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320308571","display_name":"North Carolina Biotechnology Center","ror":"https://ror.org/03hj4jr80"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2134015035.pdf","grobid_xml":"https://content.openalex.org/works/W2134015035.grobid-xml"},"referenced_works_count":16,"referenced_works":["https://openalex.org/W64604996","https://openalex.org/W116062262","https://openalex.org/W1550258693","https://openalex.org/W1642278221","https://openalex.org/W1985098533","https://openalex.org/W1999278192","https://openalex.org/W2034978601","https://openalex.org/W2090566980","https://openalex.org/W2105713982","https://openalex.org/W2127581560","https://openalex.org/W2128424000","https://openalex.org/W2134725489","https://openalex.org/W2144949988","https://openalex.org/W2154708031","https://openalex.org/W2159583324","https://openalex.org/W6646748417"],"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/W1801798365","https://openalex.org/W2036729745","https://openalex.org/W2064177607","https://openalex.org/W2157272674","https://openalex.org/W2068800403"],"abstract_inverted_index":{"The":[0,167,203],"volume":[1],"of":[2,24,55,77,90,96,112,122,164,173,184,206],"publicly":[3],"available":[4],"genomic":[5],"scale":[6],"data":[7,137,181,216],"is":[8,209],"increasing.":[9],"Genomic":[10],"datasets":[11,44,80,97,123],"in":[12,35,60,83,98],"public":[13],"repositories":[14],"are":[15,30],"annotated":[16],"with":[17,198],"free-text":[18],"fields":[19],"describing":[20],"the":[21,25,61,84,88,99,133,170],"pathological":[22],"state":[23],"studied":[26],"sample.":[27],"These":[28],"annotations":[29,76,95],"not":[31],"mapped":[32],"to":[33,41,52,58,73,81,193,210,213,219],"concepts":[34,59,82,199],"any":[36],"ontology,":[37],"making":[38],"it":[39],"difficult":[40],"integrate":[42],"these":[43],"across":[45,127],"repositories.":[46,129],"We":[47,86,103,119],"have":[48,153],"previously":[49],"developed":[50],"methods":[51,72,92],"map":[53,74],"text-annotations":[54],"tissue":[56,113],"microarrays":[57],"NCI":[62],"thesaurus":[63],"and":[64,110,114,144,162,189,195],"SNOMED-CT.":[65],"In":[66],"this":[67,150,207],"work":[68,151],"we":[69,106,152],"generalize":[70],"our":[71,91],"text":[75,171],"gene":[78,115,143,179],"expression":[79,116,146,180],"UMLS.":[85],"demonstrate":[87,104],"utility":[89],"by":[93],"processing":[94],"Gene":[100],"Expression":[101],"Omnibus.":[102],"that":[105],"enable":[107,120,211],"ontology-based":[108],"querying":[109],"integration":[111,138],"microarray":[117],"data.":[118,147,166],"identification":[121],"on":[124,142,149],"specific":[125],"diseases":[126],"both":[128],"Our":[130],"approach":[131],"provides":[132],"basis":[134],"for":[135,139,158],"ontology-driven":[136],"translational":[140],"research":[141],"protein":[145],"Based":[148],"built":[154],"a":[155],"prototype":[156],"system":[157,168,208],"ontology":[159,221],"based":[160],"annotation":[161],"indexing":[163],"biomedical":[165,215],"processes":[169],"metadata":[172],"diverse":[174],"resource":[175],"elements":[176],"such":[177],"as":[178],"sets,":[182],"descriptions":[183],"radiology":[185],"images,":[186],"clinical-trial":[187],"reports,":[188],"PubMed":[190],"article":[191],"abstracts":[192],"annotate":[194],"index":[196],"them":[197],"from":[200],"appropriate":[201],"ontologies.":[202],"key":[204],"functionality":[205],"users":[212],"locate":[214],"resources":[217],"related":[218],"particular":[220],"concepts.":[222]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":5},{"year":2017,"cited_by_count":7},{"year":2016,"cited_by_count":10},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":10},{"year":2013,"cited_by_count":7},{"year":2012,"cited_by_count":13}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
