{"id":"https://openalex.org/W2025002407","doi":"https://doi.org/10.1186/1471-2105-11-319","title":"Accessing the SEED Genome Databases via Web Services API: Tools for Programmers","display_name":"Accessing the SEED Genome Databases via Web Services API: Tools for Programmers","publication_year":2010,"publication_date":"2010-06-14","ids":{"openalex":"https://openalex.org/W2025002407","doi":"https://doi.org/10.1186/1471-2105-11-319","mag":"2025002407","pmid":"https://pubmed.ncbi.nlm.nih.gov/20546611"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-11-319","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-319","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-319","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/10.1186/1471-2105-11-319","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5111684840","display_name":"Terry Disz","orcid":null},"institutions":[{"id":"https://openalex.org/I1282105669","display_name":"Argonne National Laboratory","ror":"https://ror.org/05gvnxz63","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282105669","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I40347166"]},{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Terry Disz","raw_affiliation_strings":["Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA","Computation Institute, University of Chicago, Chicago, USA","Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA","institution_ids":["https://openalex.org/I1282105669"]},{"raw_affiliation_string":"Computation Institute, University of Chicago, Chicago, USA","institution_ids":["https://openalex.org/I40347166"]},{"raw_affiliation_string":"Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, USA","institution_ids":["https://openalex.org/I1282105669"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001954627","display_name":"Sajia Akhter","orcid":"https://orcid.org/0000-0003-0793-0625"},"institutions":[{"id":"https://openalex.org/I26538001","display_name":"San Diego State University","ror":"https://ror.org/0264fdx42","country_code":"US","type":"education","lineage":["https://openalex.org/I26538001"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sajia Akhter","raw_affiliation_strings":["Computational Sciences Research Center, San Diego State University, San Diego, CA, 92182, USA","San Diego State University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Sciences Research Center, San Diego State University, San Diego, CA, 92182, USA","institution_ids":["https://openalex.org/I26538001"]},{"raw_affiliation_string":"San Diego State University","institution_ids":["https://openalex.org/I26538001"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038629940","display_name":"Daniel Cuevas","orcid":"https://orcid.org/0000-0003-2326-3199"},"institutions":[{"id":"https://openalex.org/I26538001","display_name":"San Diego State University","ror":"https://ror.org/0264fdx42","country_code":"US","type":"education","lineage":["https://openalex.org/I26538001"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Daniel Cuevas","raw_affiliation_strings":["Department of Computer Science, San Diego State University, San Diego, CA, 92182, USA","San Diego State University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, San Diego State University, San Diego, CA, 92182, USA","institution_ids":["https://openalex.org/I26538001"]},{"raw_affiliation_string":"San Diego State University","institution_ids":["https://openalex.org/I26538001"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015210172","display_name":"Robert Olson","orcid":"https://orcid.org/0000-0001-9751-4734"},"institutions":[{"id":"https://openalex.org/I1282105669","display_name":"Argonne National Laboratory","ror":"https://ror.org/05gvnxz63","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282105669","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Robert Olson","raw_affiliation_strings":["Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA","[Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, USA]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA","institution_ids":["https://openalex.org/I1282105669"]},{"raw_affiliation_string":"[Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, USA]","institution_ids":["https://openalex.org/I1282105669"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085138988","display_name":"Ross Overbeek","orcid":null},"institutions":[{"id":"https://openalex.org/I4210124484","display_name":"Directorate-General for Interpretation","ror":"https://ror.org/03728bb41","country_code":"BE","type":"government","lineage":["https://openalex.org/I1320481043","https://openalex.org/I2800387288","https://openalex.org/I4210124484"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Ross Overbeek","raw_affiliation_strings":["Fellowship for the Interpretation of Genomes, Burr Ridge, IL, 60527, USA","Fellowship for the Interpretation of Genomes"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Fellowship for the Interpretation of Genomes, Burr Ridge, IL, 60527, USA","institution_ids":[]},{"raw_affiliation_string":"Fellowship for the Interpretation of Genomes","institution_ids":["https://openalex.org/I4210124484"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036781580","display_name":"Veronika Vonstein","orcid":null},"institutions":[{"id":"https://openalex.org/I4210124484","display_name":"Directorate-General for Interpretation","ror":"https://ror.org/03728bb41","country_code":"BE","type":"government","lineage":["https://openalex.org/I1320481043","https://openalex.org/I2800387288","https://openalex.org/I4210124484"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Veronika Vonstein","raw_affiliation_strings":["Fellowship for the Interpretation of Genomes, Burr Ridge, IL, 60527, USA","Fellowship for the Interpretation of Genomes"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Fellowship for the Interpretation of Genomes, Burr Ridge, IL, 60527, USA","institution_ids":[]},{"raw_affiliation_string":"Fellowship for the Interpretation of Genomes","institution_ids":["https://openalex.org/I4210124484"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053682943","display_name":"Rick Stevens","orcid":"https://orcid.org/0000-0002-4268-4020"},"institutions":[{"id":"https://openalex.org/I1282105669","display_name":"Argonne National Laboratory","ror":"https://ror.org/05gvnxz63","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282105669","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rick Stevens","raw_affiliation_strings":["Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA","[Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, USA]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA","institution_ids":["https://openalex.org/I1282105669"]},{"raw_affiliation_string":"[Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, USA]","institution_ids":["https://openalex.org/I1282105669"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5036802114","display_name":"Robert A. Edwards","orcid":"https://orcid.org/0000-0001-8383-8949"},"institutions":[{"id":"https://openalex.org/I1282105669","display_name":"Argonne National Laboratory","ror":"https://ror.org/05gvnxz63","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282105669","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I40347166"]},{"id":"https://openalex.org/I26538001","display_name":"San Diego State University","ror":"https://ror.org/0264fdx42","country_code":"US","type":"education","lineage":["https://openalex.org/I26538001"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Robert A Edwards","raw_affiliation_strings":["Computational Sciences Research Center, San Diego State University, San Diego, CA, 92182, USA","Department of Computer Science, San Diego State University, San Diego, CA, 92182, USA","Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA","Department of Computer Science, San Diego State University, San Diego, USA","Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Sciences Research Center, San Diego State University, San Diego, CA, 92182, USA","institution_ids":["https://openalex.org/I26538001"]},{"raw_affiliation_string":"Department of Computer Science, San Diego State University, San Diego, CA, 92182, USA","institution_ids":["https://openalex.org/I26538001"]},{"raw_affiliation_string":"Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA","institution_ids":["https://openalex.org/I1282105669"]},{"raw_affiliation_string":"Department of Computer Science, San Diego State University, San Diego, USA","institution_ids":["https://openalex.org/I26538001"]},{"raw_affiliation_string":"Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, USA","institution_ids":["https://openalex.org/I1282105669"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5036802114"],"corresponding_institution_ids":["https://openalex.org/I1282105669","https://openalex.org/I26538001"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":4.7275,"has_fulltext":true,"cited_by_count":125,"citation_normalized_percentile":{"value":0.95843024,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"11","issue":"1","first_page":"319","last_page":"319"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.7422000169754028,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.7422000169754028,"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":0.028599999845027924,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.02669999934732914,"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":0.7640395164489746},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.6649985313415527},{"id":"https://openalex.org/keywords/perl","display_name":"Perl","score":0.6205605268478394},{"id":"https://openalex.org/keywords/web-service","display_name":"Web service","score":0.6149536967277527},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.5760496854782104},{"id":"https://openalex.org/keywords/genome-browser","display_name":"Genome browser","score":0.5118126273155212},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.5083779692649841},{"id":"https://openalex.org/keywords/application-programming-interface","display_name":"Application programming interface","score":0.4842047691345215},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.4769510328769684},{"id":"https://openalex.org/keywords/java","display_name":"Java","score":0.46989011764526367},{"id":"https://openalex.org/keywords/web-api","display_name":"Web API","score":0.4569362699985504},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.42476963996887207},{"id":"https://openalex.org/keywords/web-resource","display_name":"Web resource","score":0.42418068647384644},{"id":"https://openalex.org/keywords/programmer","display_name":"Programmer","score":0.42358654737472534},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.41064250469207764},{"id":"https://openalex.org/keywords/web-modeling","display_name":"Web modeling","score":0.3041137456893921},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.2706076502799988},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.20899927616119385},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.12688875198364258},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11588490009307861}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7640395164489746},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6649985313415527},{"id":"https://openalex.org/C2777002779","wikidata":"https://www.wikidata.org/wiki/Q42478","display_name":"Perl","level":2,"score":0.6205605268478394},{"id":"https://openalex.org/C35578498","wikidata":"https://www.wikidata.org/wiki/Q193424","display_name":"Web service","level":2,"score":0.6149536967277527},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.5760496854782104},{"id":"https://openalex.org/C2781148417","wikidata":"https://www.wikidata.org/wiki/Q5533486","display_name":"Genome browser","level":5,"score":0.5118126273155212},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.5083779692649841},{"id":"https://openalex.org/C99613125","wikidata":"https://www.wikidata.org/wiki/Q165194","display_name":"Application programming interface","level":2,"score":0.4842047691345215},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.4769510328769684},{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.46989011764526367},{"id":"https://openalex.org/C127613066","wikidata":"https://www.wikidata.org/wiki/Q557770","display_name":"Web API","level":4,"score":0.4569362699985504},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.42476963996887207},{"id":"https://openalex.org/C65603577","wikidata":"https://www.wikidata.org/wiki/Q3427877","display_name":"Web resource","level":2,"score":0.42418068647384644},{"id":"https://openalex.org/C2778514511","wikidata":"https://www.wikidata.org/wiki/Q1374194","display_name":"Programmer","level":2,"score":0.42358654737472534},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.41064250469207764},{"id":"https://openalex.org/C130436687","wikidata":"https://www.wikidata.org/wiki/Q7978591","display_name":"Web modeling","level":3,"score":0.3041137456893921},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.2706076502799988},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.20899927616119385},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.12688875198364258},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11588490009307861},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.0}],"mesh":[{"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":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1186/1471-2105-11-319","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-319","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-319","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:20546611","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20546611","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:oai:doaj.org/article:981aef45c4fa4131a57576d09aa7f94b","is_oa":true,"landing_page_url":"https://doaj.org/article/981aef45c4fa4131a57576d09aa7f94b","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 11, Iss 1, p 319 (2010)","raw_type":"article"},{"id":"pmh:oai:escholarship.org/ark:/13030/qt07g0k4r8","is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/07g0k4r8","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 11, iss 1","raw_type":"article"},{"id":"pmh:oai:osti.gov:1626269","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1626269","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:2900279","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2900279","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":"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:10.1186/1471-2105-11-319","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-319","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-319","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/G2950853548","display_name":null,"funder_award_id":"HHSN266200400042C","funder_id":"https://openalex.org/F4320332505","funder_display_name":"U.S. Public Health Service"},{"id":"https://openalex.org/G7581547835","display_name":null,"funder_award_id":"HHSN266200400042C","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"}],"funders":[{"id":"https://openalex.org/F4320306085","display_name":"U.S. Department of Health and Human Services","ror":"https://ror.org/033jnv181"},{"id":"https://openalex.org/F4320309507","display_name":"San Diego State University","ror":"https://ror.org/0264fdx42"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332505","display_name":"U.S. Public Health Service","ror":"https://ror.org/05xf94514"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2025002407.pdf","grobid_xml":"https://content.openalex.org/works/W2025002407.grobid-xml"},"referenced_works_count":18,"referenced_works":["https://openalex.org/W1634075213","https://openalex.org/W1989348205","https://openalex.org/W1995117714","https://openalex.org/W1995875735","https://openalex.org/W2004548026","https://openalex.org/W2013469333","https://openalex.org/W2042938763","https://openalex.org/W2053636710","https://openalex.org/W2055043387","https://openalex.org/W2096525273","https://openalex.org/W2103017472","https://openalex.org/W2114034054","https://openalex.org/W2141626941","https://openalex.org/W2142237411","https://openalex.org/W2143395586","https://openalex.org/W2171437346","https://openalex.org/W2343468826","https://openalex.org/W4231041617"],"related_works":["https://openalex.org/W2991583567","https://openalex.org/W116073624","https://openalex.org/W3084665889","https://openalex.org/W2028108227","https://openalex.org/W3133165613","https://openalex.org/W2298263910","https://openalex.org/W1002123358","https://openalex.org/W839602675","https://openalex.org/W2525660525","https://openalex.org/W1986150280"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,13,40,118,136,160,241],"SEED":[2,93,197,218],"integrates":[3],"many":[4,48],"publicly":[5],"available":[6],"genome":[7,49,64,73,134,157],"sequences":[8],"into":[9],"a":[10,88,166,212,223],"single":[11],"resource.":[12],"database":[14,144],"contains":[15],"accurate":[16,156],"and":[17,30,35,75,115,155,207],"up-to-date":[18],"annotations":[19,81,158],"based":[20,98],"on":[21],"the":[22,45,54,66,76,92,104,107,110,143,152,173,177,196,217,247,253],"subsystems":[23],"concept":[24],"that":[25,171,188],"leverages":[26],"clustering":[27],"between":[28],"genomes":[29,255],"other":[31],"clues":[32],"to":[33,87,103,132,142,151,175,194,215,228,246],"accurately":[34],"efficiently":[36],"annotate":[37],"microbial":[38,133],"genomes.":[39],"backend":[41],"is":[42,231],"used":[43,193],"as":[44,53,204,256,258],"foundation":[46],"for":[47,62,70,79,100,128,182,226],"annotation":[50,77],"tools,":[51],"such":[52,203],"Rapid":[55],"Annotation":[56],"using":[57,165,198],"Subsystems":[58],"Technology":[59],"(RAST)":[60],"server":[61,69],"whole":[63],"annotation,":[65],"metagenomics":[67],"RAST":[68],"random":[71],"community":[72],"annotations,":[74],"clearinghouse":[78],"exchanging":[80],"from":[82],"different":[83,126],"resources.":[84],"In":[85],"addition":[86],"web":[89],"user":[90,174],"interface,":[91],"also":[94],"provides":[95],"Web":[96,121,137,161,189,221],"services":[97,122,138,162,190],"API":[99,225,242],"programmatic":[101],"access":[102,141,150,195,216,227,245],"data":[105,130,230],"in":[106],"SEED,":[108],"allowing":[109,147],"development":[111],"of":[112],"third-party":[113],"tools":[114],"mash-ups.":[116],"RESULTS:":[117],"currently":[119],"exposed":[120],"encompass":[123],"over":[124],"forty":[125],"methods":[127],"accessing":[129],"related":[131],"annotations.":[135],"provide":[139],"comprehensive":[140],"back":[145],"end,":[146],"any":[148],"programmer":[149],"most":[153,178,248],"consistent":[154],"available.":[159],"are":[163],"deployed":[164],"platform":[167,181],"independent":[168],"service-oriented":[169],"approach":[170,214],"allows":[172],"choose":[176],"suitable":[179],"programming":[180,201],"their":[183],"application.":[184],"Example":[185],"code":[186],"demonstrate":[187],"can":[191],"be":[192],"common":[199],"bioinformatics":[200],"languages":[202],"Perl,":[205],"Python,":[206],"Java.":[208],"CONCLUSIONS:":[209],"We":[210],"present":[211],"novel":[213],"database.":[219],"Using":[220],"services,":[222],"robust":[224],"genomics":[229],"provided,":[232],"without":[233],"requiring":[234],"large":[235],"volume":[236],"downloads":[237],"all":[238],"at":[239],"once.":[240],"ensures":[243],"timely":[244],"current":[249],"datasets":[250],"available,":[251],"including":[252],"new":[254],"soon":[257],"they":[259],"come":[260],"online.":[261]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":13},{"year":2019,"cited_by_count":11},{"year":2018,"cited_by_count":6},{"year":2017,"cited_by_count":9},{"year":2016,"cited_by_count":8},{"year":2015,"cited_by_count":15},{"year":2014,"cited_by_count":8},{"year":2013,"cited_by_count":11},{"year":2012,"cited_by_count":17}],"updated_date":"2026-07-26T07:53:14.480251","created_date":"2025-10-10T00:00:00"}