{"id":"https://openalex.org/W2162561781","doi":"https://doi.org/10.1093/bioinformatics/btt567","title":"A C library for retrieving specific reactions from the BioModels database","display_name":"A C library for retrieving specific reactions from the BioModels database","publication_year":2013,"publication_date":"2013-09-29","ids":{"openalex":"https://openalex.org/W2162561781","doi":"https://doi.org/10.1093/bioinformatics/btt567","mag":"2162561781","pmid":"https://pubmed.ncbi.nlm.nih.gov/24078714"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btt567","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt567","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/1/129/48913192/bioinformatics_30_1_129.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/30/1/129/48913192/bioinformatics_30_1_129.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5031987031","display_name":"Maxwell L. Neal","orcid":"https://orcid.org/0000-0002-2390-6572"},"institutions":[{"id":"https://openalex.org/I130905186","display_name":"Wofford College","ror":"https://ror.org/04dzs7b08","country_code":"US","type":"education","lineage":["https://openalex.org/I130905186"]},{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"M. L. Neal","raw_affiliation_strings":["1 Department of Bioengineering, University of Washington, Seattle, WA 98195, USA and 2Department of Computer Science, Wofford College, Spartanburg, SC 29303, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Bioengineering, University of Washington, Seattle, WA 98195, USA and 2Department of Computer Science, Wofford College, Spartanburg, SC 29303, USA","institution_ids":["https://openalex.org/I130905186","https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075592645","display_name":"Michal Galdzicki","orcid":"https://orcid.org/0000-0002-8392-8183"},"institutions":[{"id":"https://openalex.org/I130905186","display_name":"Wofford College","ror":"https://ror.org/04dzs7b08","country_code":"US","type":"education","lineage":["https://openalex.org/I130905186"]},{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"M. Galdzicki","raw_affiliation_strings":["1 Department of Bioengineering, University of Washington, Seattle, WA 98195, USA and 2Department of Computer Science, Wofford College, Spartanburg, SC 29303, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Bioengineering, University of Washington, Seattle, WA 98195, USA and 2Department of Computer Science, Wofford College, Spartanburg, SC 29303, USA","institution_ids":["https://openalex.org/I130905186","https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033654726","display_name":"J. T. Gallimore","orcid":null},"institutions":[{"id":"https://openalex.org/I130905186","display_name":"Wofford College","ror":"https://ror.org/04dzs7b08","country_code":"US","type":"education","lineage":["https://openalex.org/I130905186"]},{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"J. T. Gallimore","raw_affiliation_strings":["1 Department of Bioengineering, University of Washington, Seattle, WA 98195, USA and 2Department of Computer Science, Wofford College, Spartanburg, SC 29303, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Bioengineering, University of Washington, Seattle, WA 98195, USA and 2Department of Computer Science, Wofford College, Spartanburg, SC 29303, USA","institution_ids":["https://openalex.org/I130905186","https://openalex.org/I201448701"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5044484291","display_name":"Herbert M. Sauro","orcid":"https://orcid.org/0000-0002-3659-6817"},"institutions":[{"id":"https://openalex.org/I130905186","display_name":"Wofford College","ror":"https://ror.org/04dzs7b08","country_code":"US","type":"education","lineage":["https://openalex.org/I130905186"]},{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"H. M. Sauro","raw_affiliation_strings":["1 Department of Bioengineering, University of Washington, Seattle, WA 98195, USA and 2Department of Computer Science, Wofford College, Spartanburg, SC 29303, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Bioengineering, University of Washington, Seattle, WA 98195, USA and 2Department of Computer Science, Wofford College, Spartanburg, SC 29303, USA","institution_ids":["https://openalex.org/I130905186","https://openalex.org/I201448701"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5031987031"],"corresponding_institution_ids":["https://openalex.org/I130905186","https://openalex.org/I201448701"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":0.5498,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.67300137,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"30","issue":"1","first_page":"129","last_page":"130"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9997000098228455,"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":0.9997000098228455,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9988999962806702,"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":0.995199978351593,"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":0.8389173150062561},{"id":"https://openalex.org/keywords/sbml","display_name":"SBML","score":0.7255029678344727},{"id":"https://openalex.org/keywords/markup-language","display_name":"Markup language","score":0.7088209390640259},{"id":"https://openalex.org/keywords/license","display_name":"License","score":0.6237158179283142},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.6120148301124573},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.5552788376808167},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5439791679382324},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.5052943825721741},{"id":"https://openalex.org/keywords/string","display_name":"String (physics)","score":0.4513850808143616},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.4459910988807678},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.39775747060775757},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.3672829270362854},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.3414287567138672},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.12452837824821472},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.07564175128936768}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8389173150062561},{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.7255029678344727},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.7088209390640259},{"id":"https://openalex.org/C2780560020","wikidata":"https://www.wikidata.org/wiki/Q79719","display_name":"License","level":2,"score":0.6237158179283142},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.6120148301124573},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.5552788376808167},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5439791679382324},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.5052943825721741},{"id":"https://openalex.org/C157486923","wikidata":"https://www.wikidata.org/wiki/Q1376436","display_name":"String (physics)","level":2,"score":0.4513850808143616},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.4459910988807678},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.39775747060775757},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.3672829270362854},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.3414287567138672},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.12452837824821472},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.07564175128936768},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D001669","descriptor_name":"Biochemical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001669","descriptor_name":"Biochemical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001669","descriptor_name":"Biochemical Phenomena","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":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","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":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":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btt567","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt567","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/1/129/48913192/bioinformatics_30_1_129.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":"pmh:oai:pubmedcentral.nih.gov:3866552","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3866552","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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmid:24078714","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24078714","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":"Journal Article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btt567","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt567","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/1/129/48913192/bioinformatics_30_1_129.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/G5513879771","display_name":null,"funder_award_id":"P50-GM094503","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G5646925778","display_name":null,"funder_award_id":"GM081070","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G7217935269","display_name":"PROJECT 4","funder_award_id":"5p50gm094503-06","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G798009823","display_name":null,"funder_award_id":"R01 GM081070","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G8430477637","display_name":"Continued Development and Maintenance of the Systems Biology Workbench","funder_award_id":"5r01gm081070-07","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2162561781.pdf","grobid_xml":"https://content.openalex.org/works/W2162561781.grobid-xml"},"referenced_works_count":6,"referenced_works":["https://openalex.org/W2016238670","https://openalex.org/W2041228025","https://openalex.org/W2097203094","https://openalex.org/W2114124738","https://openalex.org/W2134221731","https://openalex.org/W2150908245"],"related_works":["https://openalex.org/W2082621456","https://openalex.org/W2150908245","https://openalex.org/W2981332207","https://openalex.org/W2211443823","https://openalex.org/W2100525485","https://openalex.org/W2040642413","https://openalex.org/W3048335229","https://openalex.org/W2146744007","https://openalex.org/W1546010648","https://openalex.org/W2890725831"],"abstract_inverted_index":{"SUMMARY:":[0],"We":[1],"describe":[2],"libSBMLReactionFinder,":[3],"a":[4,52],"C":[5],"library":[6,26,79],"for":[7,55],"retrieving":[8],"specific":[9,72],"biochemical":[10],"reactions":[11,35,41],"from":[12],"the":[13,22,31,40,65,86],"curated":[14],"systems":[15],"biology":[16],"markup":[17],"language":[18],"models":[19],"contained":[20],"in":[21,30],"BioModels":[23],"database.":[24],"The":[25,78],"leverages":[27],"semantic":[28],"annotations":[29],"database":[32],"to":[33,50,60],"associate":[34],"with":[36],"human-readable":[37],"descriptions,":[38],"making":[39],"retrievable":[42],"through":[43,64],"simple":[44],"string":[45],"searches.":[46],"Our":[47],"goal":[48],"is":[49,80],"provide":[51],"useful":[53],"tool":[54],"quantitative":[56],"modelers":[57],"who":[58],"seek":[59],"accelerate":[61],"modeling":[62],"efforts":[63],"reuse":[66],"of":[67,71],"previously":[68],"published":[69],"representations":[70],"chemical":[73],"reactions.":[74],"AVAILABILITY":[75],"AND":[76],"IMPLEMENTATION:":[77],"open-source":[81],"and":[82,92,103],"dual":[83],"licensed":[84],"under":[85],"Mozilla":[87],"Public":[88,95],"License":[89,96],"Version":[90,97],"2.0":[91],"GNU":[93],"General":[94],"2.0.":[98],"Project":[99],"source":[100],"code,":[101],"downloads":[102],"documentation":[104],"are":[105],"available":[106],"at":[107],"http://code.google.com/p/lib-sbml-reaction-finder.":[108]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":1}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2016-06-24T00:00:00"}
