{"id":"https://openalex.org/W2102486637","doi":"https://doi.org/10.1093/bioinformatics/btn018","title":"Flexible informatics for linking experimental data to mathematical models via <i>DataRail</i>","display_name":"Flexible informatics for linking experimental data to mathematical models via <i>DataRail</i>","publication_year":2008,"publication_date":"2008-01-24","ids":{"openalex":"https://openalex.org/W2102486637","doi":"https://doi.org/10.1093/bioinformatics/btn018","mag":"2102486637","pmid":"https://pubmed.ncbi.nlm.nih.gov/18218655"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btn018","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn018","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/6/840/49047048/bioinformatics_24_6_840.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/24/6/840/49047048/bioinformatics_24_6_840.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5005499510","display_name":"Julio S\u00e1ez-Rodr\u00edguez","orcid":"https://orcid.org/0000-0002-8552-8976"},"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/I4210143601","display_name":"Decision Systems (United States)","ror":"https://ror.org/0434dpa13","country_code":"US","type":"company","lineage":["https://openalex.org/I4210143601"]},{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Julio Saez-Rodriguez","raw_affiliation_strings":["1 Center for Cell Decision Processes, 2Department of Systems Biology, Harvard Medical School, Boston, MA 02115 and 3Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Center for Cell Decision Processes, 2Department of Systems Biology, Harvard Medical School, Boston, MA 02115 and 3Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139","institution_ids":["https://openalex.org/I4210143601","https://openalex.org/I136199984","https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044653603","display_name":"Arthur Goldsipe","orcid":null},"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/I4210143601","display_name":"Decision Systems (United States)","ror":"https://ror.org/0434dpa13","country_code":"US","type":"company","lineage":["https://openalex.org/I4210143601"]},{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Arthur Goldsipe","raw_affiliation_strings":["1 Center for Cell Decision Processes, 2Department of Systems Biology, Harvard Medical School, Boston, MA 02115 and 3Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Center for Cell Decision Processes, 2Department of Systems Biology, Harvard Medical School, Boston, MA 02115 and 3Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139","institution_ids":["https://openalex.org/I4210143601","https://openalex.org/I136199984","https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008170279","display_name":"Jeremy L. Muhlich","orcid":"https://orcid.org/0000-0002-0811-637X"},"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/I4210143601","display_name":"Decision Systems (United States)","ror":"https://ror.org/0434dpa13","country_code":"US","type":"company","lineage":["https://openalex.org/I4210143601"]},{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jeremy Muhlich","raw_affiliation_strings":["1 Center for Cell Decision Processes, 2Department of Systems Biology, Harvard Medical School, Boston, MA 02115 and 3Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Center for Cell Decision Processes, 2Department of Systems Biology, Harvard Medical School, Boston, MA 02115 and 3Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139","institution_ids":["https://openalex.org/I4210143601","https://openalex.org/I136199984","https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053848151","display_name":"Leonidas G. Alexopoulos","orcid":"https://orcid.org/0000-0003-0425-166X"},"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/I4210143601","display_name":"Decision Systems (United States)","ror":"https://ror.org/0434dpa13","country_code":"US","type":"company","lineage":["https://openalex.org/I4210143601"]},{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Leonidas G. Alexopoulos","raw_affiliation_strings":["1 Center for Cell Decision Processes, 2Department of Systems Biology, Harvard Medical School, Boston, MA 02115 and 3Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Center for Cell Decision Processes, 2Department of Systems Biology, Harvard Medical School, Boston, MA 02115 and 3Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139","institution_ids":["https://openalex.org/I4210143601","https://openalex.org/I136199984","https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079038334","display_name":"Bjorn L. Millard","orcid":null},"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/I4210143601","display_name":"Decision Systems (United States)","ror":"https://ror.org/0434dpa13","country_code":"US","type":"company","lineage":["https://openalex.org/I4210143601"]},{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bjorn Millard","raw_affiliation_strings":["1 Center for Cell Decision Processes, 2Department of Systems Biology, Harvard Medical School, Boston, MA 02115 and 3Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Center for Cell Decision Processes, 2Department of Systems Biology, Harvard Medical School, Boston, MA 02115 and 3Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139","institution_ids":["https://openalex.org/I4210143601","https://openalex.org/I136199984","https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060106170","display_name":"Douglas A. Lauffenburger","orcid":"https://orcid.org/0000-0002-0050-989X"},"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/I4210143601","display_name":"Decision Systems (United States)","ror":"https://ror.org/0434dpa13","country_code":"US","type":"company","lineage":["https://openalex.org/I4210143601"]},{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Douglas A. Lauffenburger","raw_affiliation_strings":["1 Center for Cell Decision Processes, 2Department of Systems Biology, Harvard Medical School, Boston, MA 02115 and 3Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Center for Cell Decision Processes, 2Department of Systems Biology, Harvard Medical School, Boston, MA 02115 and 3Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139","institution_ids":["https://openalex.org/I4210143601","https://openalex.org/I136199984","https://openalex.org/I63966007"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5063426870","display_name":"Peter K. Sorger","orcid":"https://orcid.org/0000-0002-3364-1838"},"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/I4210143601","display_name":"Decision Systems (United States)","ror":"https://ror.org/0434dpa13","country_code":"US","type":"company","lineage":["https://openalex.org/I4210143601"]},{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Peter K. Sorger","raw_affiliation_strings":["1 Center for Cell Decision Processes, 2Department of Systems Biology, Harvard Medical School, Boston, MA 02115 and 3Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Center for Cell Decision Processes, 2Department of Systems Biology, Harvard Medical School, Boston, MA 02115 and 3Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139","institution_ids":["https://openalex.org/I4210143601","https://openalex.org/I136199984","https://openalex.org/I63966007"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5063426870"],"corresponding_institution_ids":["https://openalex.org/I136199984","https://openalex.org/I4210143601","https://openalex.org/I63966007"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":4.212,"has_fulltext":true,"cited_by_count":82,"citation_normalized_percentile":{"value":0.947705,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"24","issue":"6","first_page":"840","last_page":"847"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.3449000120162964,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.3449000120162964,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.05920000001788139,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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":0.05559999868273735,"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":0.8178117275238037},{"id":"https://openalex.org/keywords/metadata","display_name":"Metadata","score":0.6460045576095581},{"id":"https://openalex.org/keywords/normalization","display_name":"Normalization (sociology)","score":0.5924860835075378},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5215303897857666},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.510394275188446},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5038222670555115},{"id":"https://openalex.org/keywords/sbml","display_name":"SBML","score":0.46730518341064453},{"id":"https://openalex.org/keywords/identifier","display_name":"Identifier","score":0.4549200236797333},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.41853490471839905},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4128956198692322},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.33546966314315796},{"id":"https://openalex.org/keywords/markup-language","display_name":"Markup language","score":0.27838820219039917},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.22573915123939514},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.1461806297302246}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8178117275238037},{"id":"https://openalex.org/C93518851","wikidata":"https://www.wikidata.org/wiki/Q180160","display_name":"Metadata","level":2,"score":0.6460045576095581},{"id":"https://openalex.org/C136886441","wikidata":"https://www.wikidata.org/wiki/Q926129","display_name":"Normalization (sociology)","level":2,"score":0.5924860835075378},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5215303897857666},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.510394275188446},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5038222670555115},{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.46730518341064453},{"id":"https://openalex.org/C154504017","wikidata":"https://www.wikidata.org/wiki/Q853614","display_name":"Identifier","level":2,"score":0.4549200236797333},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.41853490471839905},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4128956198692322},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.33546966314315796},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.27838820219039917},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.22573915123939514},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.1461806297302246},{"id":"https://openalex.org/C19165224","wikidata":"https://www.wikidata.org/wiki/Q23404","display_name":"Anthropology","level":1,"score":0.0},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","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":true},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","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":true},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","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":"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":"D011381","descriptor_name":"Programming Languages","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":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","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":false},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012107","descriptor_name":"Research Design","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":"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":"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":"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},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btn018","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn018","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/6/840/49047048/bioinformatics_24_6_840.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:18218655","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18218655","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:dspace.lib.ntua.gr:123456789/28235","is_oa":true,"landing_page_url":"http://doi.org/10.1093/bioinformatics/btn018","pdf_url":null,"source":{"id":"https://openalex.org/S4377196837","display_name":"DSpace - NTUA (National Technical University of Athens)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I174458059","host_organization_name":"National Technical University of Athens","host_organization_lineage":["https://openalex.org/I174458059"],"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":"Bioinformatics/computer Applications in The Biosciences","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2617752","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2617752","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btn018","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn018","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/6/840/49047048/bioinformatics_24_6_840.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.44999998807907104,"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals"}],"awards":[{"id":"https://openalex.org/G1964169749","display_name":null,"funder_award_id":"GM68762","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320307765","display_name":"Pfizer","ror":"https://ror.org/01xdqrp08"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2102486637.pdf","grobid_xml":"https://content.openalex.org/works/W2102486637.grobid-xml"},"referenced_works_count":13,"referenced_works":["https://openalex.org/W1522423564","https://openalex.org/W1812401750","https://openalex.org/W2052522161","https://openalex.org/W2086988962","https://openalex.org/W2103201239","https://openalex.org/W2116271446","https://openalex.org/W2127020923","https://openalex.org/W2147385427","https://openalex.org/W2151163584","https://openalex.org/W2160697532","https://openalex.org/W2274895364","https://openalex.org/W2314522446","https://openalex.org/W4239696231"],"related_works":["https://openalex.org/W1833372769","https://openalex.org/W2128782793","https://openalex.org/W1994518768","https://openalex.org/W104010570","https://openalex.org/W2082621456","https://openalex.org/W2150908245","https://openalex.org/W2069162648","https://openalex.org/W2099969795","https://openalex.org/W3120493416","https://openalex.org/W2098192829"],"abstract_inverted_index":{"MOTIVATION:":[0],"Linking":[1],"experimental":[2,76],"data":[3,41,58,77],"to":[4,17,36,39,54,86],"mathematical":[5],"models":[6,28,93],"in":[7,31,78],"biology":[8],"is":[9,101,173],"impeded":[10],"by":[11,148],"the":[12,56,65,134,140,144,176],"lack":[13],"of":[14,46,67,110,122,129,136,146,154,159],"suitable":[15],"software":[16],"manage":[18],"and":[19,27,50,90,127,166,181],"transform":[20],"data.":[21],"Model":[22],"calibration":[23],"would":[24,29],"be":[25],"facilitated":[26],"increase":[30],"value":[32],"were":[33],"it":[34],"possible":[35],"preserve":[37],"links":[38],"training":[40,57],"along":[42],"with":[43,139],"a":[44,104,111,116,130,150],"record":[45],"all":[47,137],"normalization,":[48],"scaling,":[49],"fusion":[51],"routines":[52],"used":[53],"assemble":[55],"from":[59,163],"primary":[60,165],"results.":[61],"RESULTS:":[62],"We":[63,142],"describe":[64],"implementation":[66,128],"DataRail,":[68],"an":[69],"open":[70],"source":[71],"MATLAB-based":[72],"toolbox":[73],"that":[74],"stores":[75],"flexible":[79],"multi-dimensional":[80],"arrays,":[81,108],"transforms":[82],"arrays":[83],"so":[84],"as":[85],"maximize":[87],"information":[88],"content,":[89],"then":[91],"constructs":[92],"using":[94],"internal":[95],"or":[96],"external":[97],"tools.":[98],"Data":[99],"integrity":[100],"maintained":[102],"via":[103],"containment":[105],"hierarchy":[106],"for":[107,132],"imposition":[109],"metadata":[112],"standard":[113],"based":[114],"on":[115],"newly":[117,151],"proposed":[118],"MIDAS":[119],"format,":[120],"assignment":[121],"semantically":[123],"typed":[124],"universal":[125],"identifiers,":[126],"procedure":[131],"storing":[133],"history":[135],"transformations":[138],"array.":[141],"illustrate":[143],"utility":[145],"DataRail":[147,172],"processing":[149],"collected":[152],"set":[153],"approximately":[155],"22":[156],"000":[157],"measurements":[158],"protein":[160],"activities":[161],"obtained":[162],"cytokine-stimulated":[164],"transformed":[167],"human":[168],"liver":[169],"cells.":[170],"AVAILABILITY:":[171],"distributed":[174],"under":[175],"GNU":[177],"General":[178],"Public":[179],"License":[180],"available":[182],"at":[183],"http://code.google.com/p/sbpipeline/":[184]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":3},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":9},{"year":2013,"cited_by_count":5},{"year":2012,"cited_by_count":9}],"updated_date":"2026-06-16T07:32:37.131356","created_date":"2016-06-24T00:00:00"}