{"id":"https://openalex.org/W2106483935","doi":"https://doi.org/10.1186/s12918-014-0115-1","title":"A computational platform to maintain and migrate manual functional annotations for BioCyc databases","display_name":"A computational platform to maintain and migrate manual functional annotations for BioCyc databases","publication_year":2014,"publication_date":"2014-10-11","ids":{"openalex":"https://openalex.org/W2106483935","doi":"https://doi.org/10.1186/s12918-014-0115-1","mag":"2106483935","pmid":"https://pubmed.ncbi.nlm.nih.gov/25304126"},"language":"en","primary_location":{"id":"doi:10.1186/s12918-014-0115-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12918-014-0115-1","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/s12918-014-0115-1","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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 Systems Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/s12918-014-0115-1","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5047506227","display_name":"Jesse R. Walsh","orcid":"https://orcid.org/0000-0001-6048-1166"},"institutions":[{"id":"https://openalex.org/I173911158","display_name":"Iowa State University","ror":"https://ror.org/04rswrd78","country_code":"US","type":"education","lineage":["https://openalex.org/I173911158"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jesse R Walsh","raw_affiliation_strings":["Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, USA. jrwalsh@iastate.edu","Electrical and Computer Engineering Department, Iowa State University, Ames, IA, USA. jrwalsh@iastate.edu","Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, USA. jrwalsh@iastate.edu","institution_ids":[]},{"raw_affiliation_string":"Electrical and Computer Engineering Department, Iowa State University, Ames, IA, USA. jrwalsh@iastate.edu","institution_ids":[]},{"raw_affiliation_string":"Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, USA","institution_ids":["https://openalex.org/I173911158"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022049098","display_name":"Taner Z. Sen","orcid":"https://orcid.org/0000-0002-5553-6190"},"institutions":[{"id":"https://openalex.org/I173911158","display_name":"Iowa State University","ror":"https://ror.org/04rswrd78","country_code":"US","type":"education","lineage":["https://openalex.org/I173911158"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Taner Z Sen","raw_affiliation_strings":["Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, USA. taner@iastate.edu","Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA. taner@iastate.edu","USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA, USA. taner@iastate.edu","Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, USA. taner@iastate.edu","institution_ids":[]},{"raw_affiliation_string":"Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA. taner@iastate.edu","institution_ids":[]},{"raw_affiliation_string":"USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA, USA. taner@iastate.edu","institution_ids":[]},{"raw_affiliation_string":"Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, USA","institution_ids":["https://openalex.org/I173911158"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5077949687","display_name":"Julie Dickerson","orcid":"https://orcid.org/0000-0003-4973-5641"},"institutions":[{"id":"https://openalex.org/I173911158","display_name":"Iowa State University","ror":"https://ror.org/04rswrd78","country_code":"US","type":"education","lineage":["https://openalex.org/I173911158"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Julie A Dickerson","raw_affiliation_strings":["Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, USA. julied@iastate.edu","Electrical and Computer Engineering Department, Iowa State University, Ames, IA, USA. julied@iastate.edu","Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, USA. julied@iastate.edu","institution_ids":[]},{"raw_affiliation_string":"Electrical and Computer Engineering Department, Iowa State University, Ames, IA, USA. julied@iastate.edu","institution_ids":[]},{"raw_affiliation_string":"Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, USA","institution_ids":["https://openalex.org/I173911158"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5047506227"],"corresponding_institution_ids":["https://openalex.org/I173911158"],"apc_list":null,"apc_paid":null,"fwci":0.4268,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.64444051,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"8","issue":"1","first_page":"115","last_page":"115"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.7921000123023987,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.7921000123023987,"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":0.038600001484155655,"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/T10497","display_name":"Fungal and yeast genetics research","score":0.03739999979734421,"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/identifier","display_name":"Identifier","score":0.7869517803192139},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7751583456993103},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.718205988407135},{"id":"https://openalex.org/keywords/biological-database","display_name":"Biological database","score":0.7060331106185913},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.6615471839904785},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.5442379713058472},{"id":"https://openalex.org/keywords/biological-data","display_name":"Biological data","score":0.5153777003288269},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5013790130615234},{"id":"https://openalex.org/keywords/unique-identifier","display_name":"Unique identifier","score":0.47854334115982056},{"id":"https://openalex.org/keywords/data-integration","display_name":"Data integration","score":0.4766605496406555},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.424100786447525},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.33811384439468384},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.20853033661842346},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.11363163590431213},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.08398017287254333}],"concepts":[{"id":"https://openalex.org/C154504017","wikidata":"https://www.wikidata.org/wiki/Q853614","display_name":"Identifier","level":2,"score":0.7869517803192139},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7751583456993103},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.718205988407135},{"id":"https://openalex.org/C20901353","wikidata":"https://www.wikidata.org/wiki/Q4117139","display_name":"Biological database","level":2,"score":0.7060331106185913},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6615471839904785},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.5442379713058472},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.5153777003288269},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5013790130615234},{"id":"https://openalex.org/C119839945","wikidata":"https://www.wikidata.org/wiki/Q6545185","display_name":"Unique identifier","level":3,"score":0.47854334115982056},{"id":"https://openalex.org/C72634772","wikidata":"https://www.wikidata.org/wiki/Q386824","display_name":"Data integration","level":2,"score":0.4766605496406555},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.424100786447525},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.33811384439468384},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.20853033661842346},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.11363163590431213},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.08398017287254333},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","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":"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":"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":"D066289","descriptor_name":"Data Curation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D066289","descriptor_name":"Data Curation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D066289","descriptor_name":"Data Curation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12918-014-0115-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12918-014-0115-1","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/s12918-014-0115-1","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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 Systems Biology","raw_type":"journal-article"},{"id":"pmid:25304126","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25304126","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 systems biology","raw_type":null},{"id":"pmh:oai:lib.dr.iastate.edu:ece_pubs-1075","is_oa":false,"landing_page_url":"https://lib.dr.iastate.edu/ece_pubs/77","pdf_url":null,"source":{"id":"https://openalex.org/S4377196104","display_name":"Iowa State University Digital Repository (Iowa State University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I173911158","host_organization_name":"Iowa State University","host_organization_lineage":["https://openalex.org/I173911158"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Electrical and Computer Engineering Publications","raw_type":"text"},{"id":"pmh:oai:pubmedcentral.nih.gov:4203924","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4203924","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 Syst Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12918-014-0115-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12918-014-0115-1","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/s12918-014-0115-1","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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 Systems Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6658813440","display_name":null,"funder_award_id":"0813570","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8774199850","display_name":null,"funder_award_id":"EEC-0813570","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"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2106483935.pdf","grobid_xml":"https://content.openalex.org/works/W2106483935.grobid-xml"},"referenced_works_count":13,"referenced_works":["https://openalex.org/W1993025082","https://openalex.org/W2003016664","https://openalex.org/W2010803653","https://openalex.org/W2013620058","https://openalex.org/W2014704298","https://openalex.org/W2041995829","https://openalex.org/W2060797027","https://openalex.org/W2093890109","https://openalex.org/W2096144498","https://openalex.org/W2119298353","https://openalex.org/W2151874233","https://openalex.org/W2155331065","https://openalex.org/W2164686527"],"related_works":["https://openalex.org/W2307569040","https://openalex.org/W2541393756","https://openalex.org/W2060096282","https://openalex.org/W2131941936","https://openalex.org/W2385643360","https://openalex.org/W2739872940","https://openalex.org/W115596161","https://openalex.org/W1983206747","https://openalex.org/W2167730203","https://openalex.org/W1537750021"],"abstract_inverted_index":{"BACKGROUND:":[0],"BioCyc":[1,71,111],"databases":[2,16,37,169,178],"are":[3,51,55],"an":[4],"important":[5],"resource":[6],"for":[7,57,143,179],"information":[8],"on":[9,96],"biological":[10,21,145],"pathways":[11],"and":[12,101,118,173],"genomic":[13],"data.":[14],"Such":[15],"represent":[17],"the":[18,39,66,70,123,126,134],"accumulation":[19],"of":[20,24,35,65,69,106,149],"data,":[22],"some":[23],"which":[25,81],"has":[26],"been":[27],"manually":[28],"curated":[29],"from":[30,158],"literature.":[31],"An":[32],"essential":[33],"feature":[34],"these":[36],"is":[38,46,151],"continuing":[40],"data":[41,104,109,136],"integration":[42],"as":[43],"new":[44],"knowledge":[45,64],"discovered.":[47],"As":[48],"functional":[49,86],"annotations":[50,61,87,157],"improved,":[52],"scalable":[53],"methods":[54],"needed":[56],"curators":[58,83],"to":[59,84,99,160],"manage":[60],"without":[62],"detailed":[63],"specific":[67,177],"design":[68],"database.":[72,92],"RESULTS:":[73],"We":[74],"have":[75],"developed":[76],"CycTools,":[77],"a":[78,89],"software":[79,98],"tool":[80,94],"allows":[82],"maintain":[85],"in":[88,133,163],"model":[90],"organism":[91],"This":[93],"builds":[95],"existing":[97],"improve":[100,140],"simplify":[102],"annotation":[103],"imports":[105],"user":[107],"provided":[108],"into":[110,125],"databases.":[112,146],"Additionally,":[113],"CycTools":[114,150],"automatically":[115],"resolves":[116],"synonyms":[117],"alternate":[119],"identifiers":[120],"contained":[121],"within":[122],"database":[124],"appropriate":[127],"internal":[128],"identifiers.":[129],"CONCLUSIONS:":[130],"Automating":[131],"steps":[132],"manual":[135],"entry":[137],"process":[138],"can":[139],"curation":[141],"efforts":[142],"major":[144],"The":[147],"functionality":[148],"demonstrated":[152],"by":[153,174],"transferring":[154],"GO":[155],"term":[156],"MaizeCyc":[159],"matching":[161],"proteins":[162],"CornCyc,":[164],"both":[165],"maize":[166],"metabolic":[167,180],"pathway":[168],"available":[170],"at":[171],"MaizeGDB,":[172],"creating":[175],"strain":[176],"engineering.":[181]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2}],"updated_date":"2026-04-29T09:16:38.111599","created_date":"2025-10-10T00:00:00"}
