{"id":"https://openalex.org/W1812401750","doi":"https://doi.org/10.1186/1471-2105-7-176","title":"The Gaggle: An open-source software system for integrating bioinformatics software and data sources","display_name":"The Gaggle: An open-source software system for integrating bioinformatics software and data sources","publication_year":2006,"publication_date":"2006-03-28","ids":{"openalex":"https://openalex.org/W1812401750","doi":"https://doi.org/10.1186/1471-2105-7-176","mag":"1812401750","pmid":"https://pubmed.ncbi.nlm.nih.gov/16569235"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-7-176","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-176","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-176","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/10.1186/1471-2105-7-176","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102926868","display_name":"Paul Shannon","orcid":"https://orcid.org/0009-0003-6641-3115"},"institutions":[{"id":"https://openalex.org/I3148997608","display_name":"Institute for Systems Biology","ror":"https://ror.org/02tpgw303","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I3148997608"]},{"id":"https://openalex.org/I58610484","display_name":"Seattle University","ror":"https://ror.org/02jqc0m91","country_code":"US","type":"education","lineage":["https://openalex.org/I58610484"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Paul T Shannon","raw_affiliation_strings":["Institute for Systems Biology, Seattle, WA 98103, USA. pshannon@systemsbiology.org","Institute for Systems Biology, Seattle, USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Systems Biology, Seattle, WA 98103, USA. pshannon@systemsbiology.org","institution_ids":["https://openalex.org/I3148997608"]},{"raw_affiliation_string":"Institute for Systems Biology, Seattle, USA#TAB#","institution_ids":["https://openalex.org/I3148997608","https://openalex.org/I58610484"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087598092","display_name":"David J. Reiss","orcid":"https://orcid.org/0000-0001-5392-3034"},"institutions":[{"id":"https://openalex.org/I3148997608","display_name":"Institute for Systems Biology","ror":"https://ror.org/02tpgw303","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I3148997608"]},{"id":"https://openalex.org/I58610484","display_name":"Seattle University","ror":"https://ror.org/02jqc0m91","country_code":"US","type":"education","lineage":["https://openalex.org/I58610484"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David J Reiss","raw_affiliation_strings":["Institute for Systems Biology, 1441 N 34th Street, Seattle, WA, 98103, USA","Institute for Systems Biology, Seattle, USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Systems Biology, 1441 N 34th Street, Seattle, WA, 98103, USA","institution_ids":["https://openalex.org/I3148997608"]},{"raw_affiliation_string":"Institute for Systems Biology, Seattle, USA#TAB#","institution_ids":["https://openalex.org/I3148997608","https://openalex.org/I58610484"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055203249","display_name":"Richard Bonneau","orcid":"https://orcid.org/0000-0003-4354-7906"},"institutions":[{"id":"https://openalex.org/I3148997608","display_name":"Institute for Systems Biology","ror":"https://ror.org/02tpgw303","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I3148997608"]},{"id":"https://openalex.org/I57206974","display_name":"New York University","ror":"https://ror.org/0190ak572","country_code":"US","type":"education","lineage":["https://openalex.org/I57206974"]},{"id":"https://openalex.org/I58610484","display_name":"Seattle University","ror":"https://ror.org/02jqc0m91","country_code":"US","type":"education","lineage":["https://openalex.org/I58610484"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Richard Bonneau","raw_affiliation_strings":["Department of Biology, New York University, 100 Washington Square E, New York, NY, 10003, USA","Institute for Systems Biology, 1441 N 34th Street, Seattle, WA, 98103, USA","Department of Biology, New York University, New York, USA","Institute for Systems Biology, Seattle, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, New York University, 100 Washington Square E, New York, NY, 10003, USA","institution_ids":["https://openalex.org/I57206974"]},{"raw_affiliation_string":"Institute for Systems Biology, 1441 N 34th Street, Seattle, WA, 98103, USA","institution_ids":["https://openalex.org/I3148997608"]},{"raw_affiliation_string":"Department of Biology, New York University, New York, USA","institution_ids":["https://openalex.org/I57206974"]},{"raw_affiliation_string":"Institute for Systems Biology, Seattle, USA","institution_ids":["https://openalex.org/I3148997608","https://openalex.org/I58610484"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5005287667","display_name":"Nitin S. Baliga","orcid":"https://orcid.org/0000-0001-9157-5974"},"institutions":[{"id":"https://openalex.org/I3148997608","display_name":"Institute for Systems Biology","ror":"https://ror.org/02tpgw303","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I3148997608"]},{"id":"https://openalex.org/I58610484","display_name":"Seattle University","ror":"https://ror.org/02jqc0m91","country_code":"US","type":"education","lineage":["https://openalex.org/I58610484"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Nitin S Baliga","raw_affiliation_strings":["Institute for Systems Biology, 1441 N 34th Street, Seattle, WA, 98103, USA","Institute for Systems Biology, Seattle, USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Systems Biology, 1441 N 34th Street, Seattle, WA, 98103, USA","institution_ids":["https://openalex.org/I3148997608"]},{"raw_affiliation_string":"Institute for Systems Biology, Seattle, USA#TAB#","institution_ids":["https://openalex.org/I3148997608","https://openalex.org/I58610484"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5005287667"],"corresponding_institution_ids":["https://openalex.org/I3148997608","https://openalex.org/I58610484"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":5.849,"has_fulltext":true,"cited_by_count":158,"citation_normalized_percentile":{"value":0.97046171,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"7","issue":"1","first_page":"176","last_page":"176"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12477","display_name":"Toxin Mechanisms and Immunotoxins","score":0.15119999647140503,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T12477","display_name":"Toxin Mechanisms and Immunotoxins","score":0.15119999647140503,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10602","display_name":"Glycosylation and Glycoproteins Research","score":0.07519999891519547,"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":0.04820000007748604,"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":0.7411761283874512},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5987924933433533},{"id":"https://openalex.org/keywords/variety","display_name":"Variety (cybernetics)","score":0.5619795322418213},{"id":"https://openalex.org/keywords/data-integration","display_name":"Data integration","score":0.4722679853439331},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.4332898259162903},{"id":"https://openalex.org/keywords/software-system","display_name":"Software system","score":0.41334325075149536},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.40519794821739197},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.32884716987609863},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.14790406823158264},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.12943485379219055}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7411761283874512},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5987924933433533},{"id":"https://openalex.org/C136197465","wikidata":"https://www.wikidata.org/wiki/Q1729295","display_name":"Variety (cybernetics)","level":2,"score":0.5619795322418213},{"id":"https://openalex.org/C72634772","wikidata":"https://www.wikidata.org/wiki/Q386824","display_name":"Data integration","level":2,"score":0.4722679853439331},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.4332898259162903},{"id":"https://openalex.org/C149091818","wikidata":"https://www.wikidata.org/wiki/Q2429814","display_name":"Software system","level":3,"score":0.41334325075149536},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.40519794821739197},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32884716987609863},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.14790406823158264},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.12943485379219055}],"mesh":[{"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":"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":"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":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","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":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1186/1471-2105-7-176","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-176","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-176","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:16569235","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16569235","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:osti.gov:1626316","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1626316","pdf_url":"https://www.osti.gov/servlets/purl/1626316","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:doaj.org/article:4f08409fc00a4d49971aa46dab329a29","is_oa":true,"landing_page_url":"https://doaj.org/article/4f08409fc00a4d49971aa46dab329a29","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 7, Iss 1, p 176 (2006)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:262647","is_oa":false,"landing_page_url":"http://europepmc.org/pmc/articles/PMC1464137","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:1464137","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1464137","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":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-7-176","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-176","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-176","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/G179655095","display_name":null,"funder_award_id":"R01 GM070743","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G5015013786","display_name":"BE/Gen-En:  The Oxygen-stress Response in the Extremophile Halobacterium sp. NRC-1: Systems Analysis and Development of Supplemental High School Instruction Modules","funder_award_id":"0313754","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320320875","display_name":"Deutscher Akademischer Austauschdienst","ror":"https://ror.org/039djdh30"},{"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/W1812401750.pdf","grobid_xml":"https://content.openalex.org/works/W1812401750.grobid-xml"},"referenced_works_count":26,"referenced_works":["https://openalex.org/W45534775","https://openalex.org/W1482582909","https://openalex.org/W1578104218","https://openalex.org/W1910666671","https://openalex.org/W1976366515","https://openalex.org/W1996902131","https://openalex.org/W2013751835","https://openalex.org/W2022948175","https://openalex.org/W2040941311","https://openalex.org/W2096144498","https://openalex.org/W2096608686","https://openalex.org/W2120789186","https://openalex.org/W2123500593","https://openalex.org/W2126952238","https://openalex.org/W2126991359","https://openalex.org/W2130402885","https://openalex.org/W2134119432","https://openalex.org/W2134310257","https://openalex.org/W2135174809","https://openalex.org/W2137970956","https://openalex.org/W2145149019","https://openalex.org/W2150908245","https://openalex.org/W2159675211","https://openalex.org/W2160697532","https://openalex.org/W2168103533","https://openalex.org/W4388123360"],"related_works":["https://openalex.org/W2032233321","https://openalex.org/W3121970507","https://openalex.org/W2110028391","https://openalex.org/W54497855","https://openalex.org/W2367207301","https://openalex.org/W2164098295","https://openalex.org/W4294754599","https://openalex.org/W2118743872","https://openalex.org/W2039681720","https://openalex.org/W4255658034"],"abstract_inverted_index":{"BACKGROUND:":[0],"Systems":[1],"biologists":[2],"work":[3],"with":[4,187],"many":[5,10],"kinds":[6],"of":[7,16,20,28,32,34,38,50,75,98,123,135,137,142,184,190,215,222,254,264],"data,":[8],"from":[9],"different":[11],"sources,":[12],"using":[13,211],"a":[14,61,140,154,199,212,220],"variety":[15,72,221],"software":[17,92,115,124,132,225,239,256],"tools.":[18,226],"Each":[19],"these":[21,51],"tools":[22,58],"typically":[23],"excels":[24],"at":[25,325],"one":[26],"type":[27],"analysis,":[29],"such":[30],"as":[31],"microarrays,":[33],"metabolic":[35,282],"networks":[36],"and":[37,57,64,73,91,125,139,150,168,178,219,238,245,257,268,272,285,299,307,316,321],"predicted":[39],"protein":[40,202,269],"structure.":[41],"A":[42,80],"crucial":[43],"challenge":[44],"is":[45],"to":[46,59,70,82,119,173,296,302],"combine":[47],"the":[48,71,109,121,130,185,259],"capabilities":[49,183],"(and":[52],"other":[53],"forthcoming)":[54],"data":[55,62,78,88,163,209,218,266],"resources":[56,152],"create":[60],"exploration":[63,189,210,263],"analysis":[65],"environment":[66,116,294],"that":[67,87,117,160],"does":[68],"justice":[69],"complexity":[74],"systems":[76],"biology":[77,99],"sets.":[79],"solution":[81],"this":[83,94,105,251],"problem":[84,122],"should":[85],"recognize":[86],"types,":[89],"formats":[90],"in":[93,195,309],"high":[95],"throughput":[96],"age":[97],"are":[100,171],"constantly":[101],"changing.":[102],"RESULTS:":[103],"In":[104],"paper":[106],"we":[107,197],"describe":[108],"Gaggle":[110,186,260,312],"-a":[111,203],"simple,":[112],"open-source":[113],"Java":[114,314,317],"helps":[118],"solve":[120],"database":[126],"integration.":[127],"Guided":[128],"by":[129,207],"classic":[131],"engineering":[133],"strategy":[134],"separation":[136],"concerns":[138],"policy":[141],"semantic":[143],"flexibility,":[144],"it":[145],"integrates":[146],"existing":[147],"popular":[148,223],"programs":[149],"web":[151,289],"into":[153],"user-friendly,":[155],"easily-extended":[156],"environment.":[157],"We":[158,180,228],"demonstrate":[159],"four":[161],"simple":[162],"types":[164],"(names,":[165],"matrices,":[166],"networks,":[167],"associative":[169],"arrays)":[170],"sufficient":[172],"bring":[174],"together":[175],"diverse":[176,231,255],"databases":[177,232,258],"software.":[179],"highlight":[181],"some":[182],"an":[188,292],"Helicobacter":[191],"pylori":[192],"pathogenesis":[193],"genes,":[194],"which":[196],"identify":[198],"putative":[200],"ricin-like":[201],"discovery":[204],"made":[205],"possible":[206],"simultaneous":[208,262],"wide":[213],"range":[214],"publicly":[216],"available":[217],"bioinformatics":[224],"CONCLUSION:":[227],"have":[229],"integrated":[230],"(for":[233],"example,":[234],"KEGG,":[235],"BioCyc,":[236],"String)":[237],"(Cytoscape,":[240],"DataMatrixViewer,":[241],"R":[242],"statistical":[243],"environment,":[244],"TIGR":[246],"Microarray":[247],"Expression":[248],"Viewer).":[249],"Through":[250],"loose":[252],"coupling":[253],"enables":[261],"experimental":[265],"(mRNA":[267],"abundance,":[270],"protein-protein":[271],"protein-DNA":[273],"interactions),":[274],"functional":[275],"associations":[276],"(operon,":[277],"chromosomal":[278],"proximity,":[279],"phylogenetic":[280],"pattern),":[281],"pathways":[283],"(KEGG)":[284],"Pubmed":[286],"abstracts":[287],"(STRING":[288],"resource),":[290],"creating":[291],"exploratory":[293],"useful":[295],"'web":[297],"browser":[298],"spreadsheet":[300],"biologists',":[301],"statistically":[303],"savvy":[304],"computational":[305],"biologists,":[306],"those":[308],"between.":[310],"The":[311],"uses":[313],"RMI":[315],"Web":[318],"Start":[319],"technologies":[320],"can":[322],"be":[323],"found":[324],"http://gaggle.systemsbiology.net.":[326]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":7},{"year":2015,"cited_by_count":7},{"year":2014,"cited_by_count":9},{"year":2013,"cited_by_count":13},{"year":2012,"cited_by_count":13}],"updated_date":"2026-07-28T07:46:37.118299","created_date":"2025-10-10T00:00:00"}
