{"id":"https://openalex.org/W2192214268","doi":"https://doi.org/10.2390/biecoll-jib-2015-282","title":"Extracting kinetic information from literature with KineticRE","display_name":"Extracting kinetic information from literature with KineticRE","publication_year":2015,"publication_date":"2015-01-01","ids":{"openalex":"https://openalex.org/W2192214268","doi":"https://doi.org/10.2390/biecoll-jib-2015-282","mag":"2192214268","pmid":"https://pubmed.ncbi.nlm.nih.gov/26673933"},"language":"en","primary_location":{"id":"pmid:26673933","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26673933","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":"Journal of integrative bioinformatics","raw_type":null},"type":"article","indexed_in":["datacite","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"http://hdl.handle.net/1822/38891","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5047026171","display_name":"Ana Al\u00e3o Freitas","orcid":"https://orcid.org/0000-0001-9454-4874"},"institutions":[{"id":"https://openalex.org/I99682543","display_name":"University of Minho","ror":"https://ror.org/037wpkx04","country_code":"PT","type":"education","lineage":["https://openalex.org/I99682543"]}],"countries":["PT"],"is_corresponding":true,"raw_author_name":"Alao Freitas, Ana","raw_affiliation_strings":["1Centre of Biological Engineering, University of Minho, Braga, Portugal"],"affiliations":[{"raw_affiliation_string":"1Centre of Biological Engineering, University of Minho, Braga, Portugal","institution_ids":["https://openalex.org/I99682543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090172347","display_name":"Hugo Costa","orcid":"https://orcid.org/0000-0002-3155-2110"},"institutions":[{"id":"https://openalex.org/I4210114428","display_name":"SilicoLife (Portugal)","ror":"https://ror.org/029gksr15","country_code":"PT","type":"company","lineage":["https://openalex.org/I4210114428"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Costa, Hugo","raw_affiliation_strings":["2SilicoLife Lda, Rua do Canastreiro, 15, 4715-387, Braga, Portugal"],"affiliations":[{"raw_affiliation_string":"2SilicoLife Lda, Rua do Canastreiro, 15, 4715-387, Braga, Portugal","institution_ids":["https://openalex.org/I4210114428"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040524717","display_name":"Miguel Rocha","orcid":"https://orcid.org/0000-0001-8439-8172"},"institutions":[{"id":"https://openalex.org/I99682543","display_name":"University of Minho","ror":"https://ror.org/037wpkx04","country_code":"PT","type":"education","lineage":["https://openalex.org/I99682543"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Rocha, Miguel","raw_affiliation_strings":["3Centre of Biological Engineering, University of Minho, Braga, Portugal 2SilicoLife Lda, Rua do Canastreiro, 15, 4715-387, Braga, Portugal"],"affiliations":[{"raw_affiliation_string":"3Centre of Biological Engineering, University of Minho, Braga, Portugal 2SilicoLife Lda, Rua do Canastreiro, 15, 4715-387, Braga, Portugal","institution_ids":["https://openalex.org/I99682543"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5079343705","display_name":"Isabel Rocha","orcid":"https://orcid.org/0000-0001-9494-3410"},"institutions":[{"id":"https://openalex.org/I99682543","display_name":"University of Minho","ror":"https://ror.org/037wpkx04","country_code":"PT","type":"education","lineage":["https://openalex.org/I99682543"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Rocha, Isabel","raw_affiliation_strings":["3Centre of Biological Engineering, University of Minho, Braga, Portugal 2SilicoLife Lda, Rua do Canastreiro, 15, 4715-387, Braga, Portugal"],"affiliations":[{"raw_affiliation_string":"3Centre of Biological Engineering, University of Minho, Braga, Portugal 2SilicoLife Lda, Rua do Canastreiro, 15, 4715-387, Braga, Portugal","institution_ids":["https://openalex.org/I99682543"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5047026171"],"corresponding_institution_ids":["https://openalex.org/I99682543"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.06673123,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"12","issue":"4","first_page":"282","last_page":"282"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9994000196456909,"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":0.9994000196456909,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.995199978351593,"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":0.9904000163078308,"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":0.7514907121658325},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.6370404958724976},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.6128517389297485},{"id":"https://openalex.org/keywords/variety","display_name":"Variety (cybernetics)","score":0.5934139490127563},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.5584685802459717},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.47595760226249695},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.47489041090011597},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3651995062828064},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.12983372807502747},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.10236996412277222},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.0814867615699768}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7514907121658325},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.6370404958724976},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.6128517389297485},{"id":"https://openalex.org/C136197465","wikidata":"https://www.wikidata.org/wiki/Q1729295","display_name":"Variety (cybernetics)","level":2,"score":0.5934139490127563},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.5584685802459717},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.47595760226249695},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.47489041090011597},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3651995062828064},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.12983372807502747},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.10236996412277222},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0814867615699768},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"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/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007716","descriptor_name":"Kluyveromyces","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D007716","descriptor_name":"Kluyveromyces","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D007716","descriptor_name":"Kluyveromyces","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":5,"locations":[{"id":"pmid:26673933","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26673933","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":"Journal of integrative bioinformatics","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.738.676","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.738.676","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://repositorium.sdum.uminho.pt/bitstream/1822/38891/1/document_26628_1.pdf","raw_type":"text"},{"id":"pmh:oai:repositorium.sdum.uminho.pt:1822/38891","is_oa":true,"landing_page_url":"http://hdl.handle.net/1822/38891","pdf_url":null,"source":{"id":"https://openalex.org/S4306402433","display_name":"Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT)","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"journal article"},{"id":"pmh:oai:repositorium.uminho.pt:1822/38891","is_oa":true,"landing_page_url":"https://hdl.handle.net/1822/38891","pdf_url":null,"source":null,"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"doi:10.2390/biecoll-jib-2015-282","is_oa":true,"landing_page_url":"https://doi.org/10.2390/biecoll-jib-2015-282","pdf_url":null,"source":{"id":"https://openalex.org/S4306401670","display_name":"PUB \u2013 Publications at Bielefeld University (Bielefeld University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I20121455","host_organization_name":"Bielefeld University","host_organization_lineage":["https://openalex.org/I20121455"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"pmh:oai:repositorium.sdum.uminho.pt:1822/38891","is_oa":true,"landing_page_url":"http://hdl.handle.net/1822/38891","pdf_url":null,"source":{"id":"https://openalex.org/S4306402433","display_name":"Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT)","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"journal article"},"sustainable_development_goals":[{"score":0.6000000238418579,"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education"}],"awards":[{"id":"https://openalex.org/G1176428255","display_name":null,"funder_award_id":"PTDC/QUI-BIQ/119657/2010","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G1716593420","display_name":null,"funder_award_id":"-FEDER-","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G220245157","display_name":null,"funder_award_id":"NORTE-07-0124-FEDER-000028","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G5348594205","display_name":null,"funder_award_id":"FEDER","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G6299983296","display_name":null,"funder_award_id":"PTDC/","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G7049410507","display_name":null,"funder_award_id":"Portuguese Foundation for Science","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G943999617","display_name":null,"funder_award_id":"Technology","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"}],"funders":[{"id":"https://openalex.org/F4320334779","display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","ror":"https://ror.org/00snfqn58"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":20,"referenced_works":["https://openalex.org/W590716758","https://openalex.org/W1972863608","https://openalex.org/W1976353541","https://openalex.org/W1987939469","https://openalex.org/W1989263028","https://openalex.org/W2010579377","https://openalex.org/W2014358138","https://openalex.org/W2014849717","https://openalex.org/W2028232771","https://openalex.org/W2051689038","https://openalex.org/W2053339983","https://openalex.org/W2078775934","https://openalex.org/W2100627415","https://openalex.org/W2103397879","https://openalex.org/W2111925240","https://openalex.org/W2125396196","https://openalex.org/W2128601422","https://openalex.org/W2137450588","https://openalex.org/W2151023149","https://openalex.org/W2157641143"],"related_works":["https://openalex.org/W1595868330","https://openalex.org/W2883542984","https://openalex.org/W2384888906","https://openalex.org/W2147536281","https://openalex.org/W2992516105","https://openalex.org/W2144190808","https://openalex.org/W2792109275","https://openalex.org/W2464280762","https://openalex.org/W2416260158","https://openalex.org/W2378298813"],"abstract_inverted_index":{"To":[0],"better":[1],"understand":[2],"the":[3,15,25,50,54,64,90,118,125,131,133,146],"dynamic":[4],"behavior":[5],"of":[6,13,17,27,49,56,92,120,150],"metabolic":[7],"networks":[8],"in":[9,24,63],"a":[10,46,93,121,139],"wide":[11,61],"variety":[12],"conditions,":[14],"field":[16],"Systems":[18],"Biology":[19],"has":[20,86],"increased":[21],"its":[22],"interest":[23],"use":[26],"kinetic":[28,102],"models.":[29],"The":[30,114],"different":[31],"databases,":[32],"available":[33],"these":[34,79],"days,":[35],"do":[36],"not":[37],"contain":[38],"enough":[39],"data":[40],"regarding":[41],"this":[42,82,84],"topic.":[43],"Given":[44],"that":[45],"significant":[47],"part":[48],"relevant":[51],"information":[52],"for":[53],"development":[55,91,119],"such":[57],"models":[58],"is":[59],"still":[60],"spread":[62],"literature,":[65,101],"it":[66],"becomes":[67],"essential":[68],"to":[69,77,97],"develop":[70],"specific":[71],"and":[72,107,112,148],"powerful":[73],"text":[74,94,126,153],"mining":[75,95,127],"tools":[76],"collect":[78],"data.":[80],"In":[81,130],"context,":[83],"work":[85],"as":[87],"main":[88],"objective":[89],"tool":[96],"extract,":[98],"from":[99],"scientific":[100],"parameters,":[103],"their":[104,108],"respective":[105],"values":[106],"relations":[109],"with":[110,138],"enzymes":[111],"metabolites.":[113],"approach":[115],"proposed":[116],"integrates":[117],"novel":[122],"plug-in":[123],"over":[124],"framework":[128],"@Note2.":[129],"end,":[132],"pipeline":[134],"developed":[135],"was":[136],"validated":[137],"case":[140],"study":[141],"on":[142],"Kluyveromyces":[143],"lactis,":[144],"spanning":[145],"analysis":[147],"results":[149],"20":[151],"full":[152],"documents.":[154]},"counts_by_year":[],"updated_date":"2026-04-14T08:04:32.555800","created_date":"2025-10-10T00:00:00"}
