{"id":"https://openalex.org/W2050624025","doi":"https://doi.org/10.1093/database/bat061","title":"Groups: knowledge spreadsheets for symbolic biocomputing","display_name":"Groups: knowledge spreadsheets for symbolic biocomputing","publication_year":2013,"publication_date":"2013-01-01","ids":{"openalex":"https://openalex.org/W2050624025","doi":"https://doi.org/10.1093/database/bat061","mag":"2050624025","pmid":"https://pubmed.ncbi.nlm.nih.gov/24037025"},"language":"en","primary_location":{"id":"doi:10.1093/database/bat061","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/bat061","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bat061/11197818/bat061.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Database","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bat061/11197818/bat061.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5040794648","display_name":"Michael Travers","orcid":"https://orcid.org/0000-0002-5452-880X"},"institutions":[{"id":"https://openalex.org/I1298353152","display_name":"SRI International","ror":"https://ror.org/05s570m15","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1298353152"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael Travers","raw_affiliation_strings":["Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA","institution_ids":["https://openalex.org/I1298353152"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015212276","display_name":"Suzanne Paley","orcid":"https://orcid.org/0000-0001-5763-8935"},"institutions":[{"id":"https://openalex.org/I1298353152","display_name":"SRI International","ror":"https://ror.org/05s570m15","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1298353152"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Suzanne M. Paley","raw_affiliation_strings":["Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA","institution_ids":["https://openalex.org/I1298353152"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037249015","display_name":"Jeff Shrager","orcid":"https://orcid.org/0000-0002-7007-6305"},"institutions":[{"id":"https://openalex.org/I1298353152","display_name":"SRI International","ror":"https://ror.org/05s570m15","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1298353152"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jeff Shrager","raw_affiliation_strings":["Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA","institution_ids":["https://openalex.org/I1298353152"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037386702","display_name":"Timothy A. Holland","orcid":null},"institutions":[{"id":"https://openalex.org/I1298353152","display_name":"SRI International","ror":"https://ror.org/05s570m15","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1298353152"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Timothy A. Holland","raw_affiliation_strings":["Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA","institution_ids":["https://openalex.org/I1298353152"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082071104","display_name":"Peter D. Karp","orcid":"https://orcid.org/0000-0002-5876-6418"},"institutions":[{"id":"https://openalex.org/I1298353152","display_name":"SRI International","ror":"https://ror.org/05s570m15","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1298353152"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Peter D. Karp","raw_affiliation_strings":["Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA","institution_ids":["https://openalex.org/I1298353152"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5082071104"],"corresponding_institution_ids":["https://openalex.org/I1298353152"],"apc_list":{"value":1415,"currency":"GBP","value_usd":1735},"apc_paid":{"value":1415,"currency":"GBP","value_usd":1735},"fwci":4.8911,"has_fulltext":true,"cited_by_count":27,"citation_normalized_percentile":{"value":0.95227582,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"2013","issue":null,"first_page":"bat061","last_page":"bat061"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.998199999332428,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},"topics":[{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.998199999332428,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9757999777793884,"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/T10715","display_name":"Distributed and Parallel Computing Systems","score":0.96670001745224,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7004855871200562},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.46662437915802},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.32450729608535767}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7004855871200562},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.46662437915802},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.32450729608535767}],"mesh":[{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005798","descriptor_name":"Genes, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005798","descriptor_name":"Genes, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005798","descriptor_name":"Genes, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"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":"D019359","descriptor_name":"Knowledge","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019359","descriptor_name":"Knowledge","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019359","descriptor_name":"Knowledge","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019992","descriptor_name":"Databases as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019992","descriptor_name":"Databases as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019992","descriptor_name":"Databases as Topic","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":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055442","descriptor_name":"Metabolome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055442","descriptor_name":"Metabolome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055442","descriptor_name":"Metabolome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/database/bat061","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/bat061","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bat061/11197818/bat061.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Database","raw_type":"journal-article"},{"id":"pmid:24037025","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24037025","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":"Database : the journal of biological databases and curation","raw_type":null},{"id":"pmh:oai:europepmc.org:2766005","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3773185","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/database/bat061","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/bat061","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bat061/11197818/bat061.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Database","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2653952165","display_name":null,"funder_award_id":"01-GM075742","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G462345482","display_name":null,"funder_award_id":"R01GM075742","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G682688612","display_name":null,"funder_award_id":"U24GM077678","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"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/W2050624025.pdf","grobid_xml":"https://content.openalex.org/works/W2050624025.grobid-xml"},"referenced_works_count":20,"referenced_works":["https://openalex.org/W8528480","https://openalex.org/W1835740130","https://openalex.org/W1937308970","https://openalex.org/W1990098464","https://openalex.org/W1998902445","https://openalex.org/W2050822109","https://openalex.org/W2128601422","https://openalex.org/W2136482257","https://openalex.org/W2137653635","https://openalex.org/W2144741676","https://openalex.org/W2144907278","https://openalex.org/W2152274187","https://openalex.org/W2162091032","https://openalex.org/W2168465568","https://openalex.org/W2600906272","https://openalex.org/W2886769257","https://openalex.org/W4237293127","https://openalex.org/W4285719527","https://openalex.org/W6638693577","https://openalex.org/W6753999818"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2478288626","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655"],"abstract_inverted_index":{"Knowledge":[0],"spreadsheets":[1,17],"(KSs)":[2],"are":[3,98],"a":[4,65,76,86,115,163],"visual":[5],"tool":[6],"for":[7],"interactive":[8],"data":[9,153],"analysis":[10],"and":[11,34,109,132],"exploration.":[12],"They":[13],"differ":[14],"from":[15,75],"traditional":[16],"in":[18,94],"that":[19,37,140,155],"rather":[20],"than":[21],"being":[22],"oriented":[23],"toward":[24],"numeric":[25],"data,":[26],"they":[27],"work":[28],"with":[29],"symbolic":[30],"knowledge":[31],"representation":[32],"structures":[33],"provide":[35],"operations":[36],"take":[38],"into":[39],"account":[40],"the":[41,44,54,90,121,144,160],"semantics":[42],"of":[43,51,67,71,92,120,130,136,146,162],"application":[45],"domain.":[46],"'Groups'":[47],"is":[48],"an":[49,133],"implementation":[50],"KSs":[52],"within":[53],"Pathway":[55,60,122],"Tools":[56,61],"system.":[57],"Groups":[58,79,137,141],"allows":[59],"users":[62,138],"to":[63,89,150],"define":[64],"group":[66,88,91],"objects":[68],"(e.g.":[69,83,105,111],"groups":[70],"genes":[72],"or":[73],"metabolites)":[74],"Pathway/Genome":[77],"Database.":[78],"can":[80],"be":[81],"transformed":[82],"by":[84,112],"transforming":[85],"metabolite":[87],"pathways":[93],"which":[95],"those":[96],"metabolites":[97],"substrates);":[99],"combined":[100],"through":[101,106],"set":[102],"operations;":[103],"analysed":[104],"enrichment":[107],"analysis);":[108],"visualized":[110],"painting":[113],"onto":[114],"metabolic":[116],"map":[117],"diagram).":[118],"Users":[119],"Tools-based":[123],"BioCyc.org":[124],"website":[125],"have":[126,158],"made":[127],"extensive":[128],"use":[129],"Groups,":[131],"informal":[134],"survey":[135],"suggests":[139],"has":[142],"achieved":[143],"goal":[145],"allowing":[147],"biologists":[148],"themselves":[149],"perform":[151],"some":[152],"manipulations":[154],"previously":[156],"would":[157],"required":[159],"assistance":[161],"programmer.":[164],"Database":[165],"URL:":[166],"BioCyc.org.":[167]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":1}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}
