{"id":"https://openalex.org/W1965822196","doi":"https://doi.org/10.1109/bibmw.2012.6470377","title":"Pathway curation: Application of text-mining tools eGIFT and RLIMS-P","display_name":"Pathway curation: Application of text-mining tools eGIFT and RLIMS-P","publication_year":2012,"publication_date":"2012-10-01","ids":{"openalex":"https://openalex.org/W1965822196","doi":"https://doi.org/10.1109/bibmw.2012.6470377","mag":"1965822196"},"language":"en","primary_location":{"id":"doi:10.1109/bibmw.2012.6470377","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibmw.2012.6470377","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5004246605","display_name":"Carl J. Schmidt","orcid":"https://orcid.org/0000-0002-8386-4781"},"institutions":[{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Carl J Schmidt","raw_affiliation_strings":["Dept. of Animal & Food Sciences","Department of Animal and Food Sciences University of Delaware Newark DE USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept. of Animal & Food Sciences","institution_ids":[]},{"raw_affiliation_string":"Department of Animal and Food Sciences University of Delaware Newark DE USA","institution_ids":["https://openalex.org/I86501945"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101475441","display_name":"Liang Sun","orcid":"https://orcid.org/0000-0003-1634-4716"},"institutions":[{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Liang Sun","raw_affiliation_strings":["Dept. of Animal & Food Sciences","Department of Animal and Food Sciences University of Delaware Newark DE USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept. of Animal & Food Sciences","institution_ids":[]},{"raw_affiliation_string":"Department of Animal and Food Sciences University of Delaware Newark DE USA","institution_ids":["https://openalex.org/I86501945"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001355963","display_name":"Cecilia N. Arighi","orcid":"https://orcid.org/0000-0002-0803-4817"},"institutions":[{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Cecilia N. Arighi","raw_affiliation_strings":["Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA","Department of Computer and Information Sciences, University of Delaware , Newark, DE, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA","institution_ids":["https://openalex.org/I86501945"]},{"raw_affiliation_string":"Department of Computer and Information Sciences, University of Delaware , Newark, DE, USA","institution_ids":["https://openalex.org/I86501945"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053733472","display_name":"Keith Decker","orcid":"https://orcid.org/0000-0003-2707-5769"},"institutions":[{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Keith Decker","raw_affiliation_strings":["Dept. of Computer and Information Sciences","Department of Computer and Information Sciences, University of Delaware , Newark, DE, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept. of Computer and Information Sciences","institution_ids":[]},{"raw_affiliation_string":"Department of Computer and Information Sciences, University of Delaware , Newark, DE, USA","institution_ids":["https://openalex.org/I86501945"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027009667","display_name":"K. Vijay\u2010Shanker","orcid":"https://orcid.org/0000-0003-0958-3073"},"institutions":[{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"K. Vijay-Shanker","raw_affiliation_strings":["Dept. of Computer and Information Sciences","Department of Computer and Information Sciences, University of Delaware , Newark, DE, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept. of Computer and Information Sciences","institution_ids":[]},{"raw_affiliation_string":"Department of Computer and Information Sciences, University of Delaware , Newark, DE, USA","institution_ids":["https://openalex.org/I86501945"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028161578","display_name":"Manabu Torii","orcid":"https://orcid.org/0000-0002-4825-0696"},"institutions":[{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Manabu Torii","raw_affiliation_strings":["Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA","Department of Computer and Information Sciences, University of Delaware , Newark, DE, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA","institution_ids":["https://openalex.org/I86501945"]},{"raw_affiliation_string":"Department of Computer and Information Sciences, University of Delaware , Newark, DE, USA","institution_ids":["https://openalex.org/I86501945"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019996064","display_name":"Catalina O. Tudor","orcid":"https://orcid.org/0009-0002-0420-7589"},"institutions":[{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Catalina O. Tudor","raw_affiliation_strings":["Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA","Center for Bioinformatics & Computational Biology, University of Delaware, Newark, DE, USA;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA","institution_ids":["https://openalex.org/I86501945"]},{"raw_affiliation_string":"Center for Bioinformatics & Computational Biology, University of Delaware, Newark, DE, USA;","institution_ids":["https://openalex.org/I86501945"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053761444","display_name":"Cathy Wu","orcid":"https://orcid.org/0000-0001-6379-8601"},"institutions":[{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Cathy Wu","raw_affiliation_strings":["Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA","Department of Computer and Information Sciences, University of Delaware , Newark, DE, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA","institution_ids":["https://openalex.org/I86501945"]},{"raw_affiliation_string":"Department of Computer and Information Sciences, University of Delaware , Newark, DE, USA","institution_ids":["https://openalex.org/I86501945"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5074201106","display_name":"Peter D\u2019Eustachio","orcid":"https://orcid.org/0000-0002-5494-626X"},"institutions":[{"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"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Peter D'Eustachio","raw_affiliation_strings":["Dept. of Biochemistry, New York University School of Medicine, New York, NY, USA","Dept. of Biochemistry, New York University School of Medicine, New York, NY USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept. of Biochemistry, New York University School of Medicine, New York, NY, USA","institution_ids":["https://openalex.org/I57206974"]},{"raw_affiliation_string":"Dept. of Biochemistry, New York University School of Medicine, New York, NY USA","institution_ids":["https://openalex.org/I57206974"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":9,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.2688,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.56583672,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"199","issue":null,"first_page":"523","last_page":"528"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9972000122070312,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9972000122070312,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.982699990272522,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9812999963760376,"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":0.719426155090332},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.6752957105636597},{"id":"https://openalex.org/keywords/data-curation","display_name":"Data curation","score":0.5397058725357056},{"id":"https://openalex.org/keywords/resource","display_name":"Resource (disambiguation)","score":0.5052295327186584},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.42338910698890686},{"id":"https://openalex.org/keywords/quality","display_name":"Quality (philosophy)","score":0.42081621289253235},{"id":"https://openalex.org/keywords/information-extraction","display_name":"Information extraction","score":0.4144079089164734},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.39374399185180664},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.37901583313941956},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1725958287715912}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.719426155090332},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.6752957105636597},{"id":"https://openalex.org/C91632574","wikidata":"https://www.wikidata.org/wiki/Q15088675","display_name":"Data curation","level":2,"score":0.5397058725357056},{"id":"https://openalex.org/C206345919","wikidata":"https://www.wikidata.org/wiki/Q20380951","display_name":"Resource (disambiguation)","level":2,"score":0.5052295327186584},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.42338910698890686},{"id":"https://openalex.org/C2779530757","wikidata":"https://www.wikidata.org/wiki/Q1207505","display_name":"Quality (philosophy)","level":2,"score":0.42081621289253235},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.4144079089164734},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.39374399185180664},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.37901583313941956},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1725958287715912},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibmw.2012.6470377","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibmw.2012.6470377","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":25,"referenced_works":["https://openalex.org/W138570049","https://openalex.org/W1858586091","https://openalex.org/W1965102380","https://openalex.org/W1966822396","https://openalex.org/W1986576216","https://openalex.org/W1999895438","https://openalex.org/W2001790050","https://openalex.org/W2007397565","https://openalex.org/W2028348480","https://openalex.org/W2051725757","https://openalex.org/W2075027317","https://openalex.org/W2086364694","https://openalex.org/W2102778729","https://openalex.org/W2104965688","https://openalex.org/W2105683352","https://openalex.org/W2110014419","https://openalex.org/W2115118514","https://openalex.org/W2125278742","https://openalex.org/W2129578971","https://openalex.org/W2131924932","https://openalex.org/W2133889507","https://openalex.org/W2146486983","https://openalex.org/W2164666853","https://openalex.org/W2166057395","https://openalex.org/W2400486633"],"related_works":["https://openalex.org/W2701062589","https://openalex.org/W4308914582","https://openalex.org/W4388126069","https://openalex.org/W2567393658","https://openalex.org/W3200944274","https://openalex.org/W4306317641","https://openalex.org/W1488337274","https://openalex.org/W2216178707","https://openalex.org/W3095602079","https://openalex.org/W4287611188"],"abstract_inverted_index":{"Gallus":[0],"Reactome":[1],"provides":[2],"a":[3,16],"manually":[4],"curated":[5],"reference":[6,18],"database":[7,19],"for":[8],"chicken":[9,74],"signaling":[10,77],"and":[11,27,44],"metabolic":[12],"pathways.":[13],"Providing":[14],"such":[15],"high-quality":[17],"requires":[20],"significant":[21],"time":[22],"input":[23],"from":[24,52],"both":[25],"curators":[26],"pathway":[28,59],"experts.":[29],"This":[30],"paper":[31],"describes":[32],"the":[33,53,69,73],"application":[34],"of":[35,71],"orthology":[36],"prediction,":[37],"computational":[38],"linguistic":[39],"tools":[40],"including":[41],"text":[42],"mining":[43],"information":[45],"extraction":[46],"applications,":[47],"along":[48],"with":[49],"resources":[50],"available":[51],"Protein":[54],"Information":[55],"Resource,":[56],"to":[57],"facilitate":[58],"curation.":[60],"In":[61],"this":[62],"paper,":[63],"we":[64],"describe":[65],"these":[66],"methods":[67],"in":[68],"context":[70],"curating":[72],"TGF":[75],"beta":[76],"pathway.":[78]},"counts_by_year":[{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
