{"id":"https://openalex.org/W2103832753","doi":"https://doi.org/10.1093/bib/bbq067","title":"Challenges in integrating Escherichia coli molecular biology data","display_name":"Challenges in integrating Escherichia coli molecular biology data","publication_year":2010,"publication_date":"2010-11-07","ids":{"openalex":"https://openalex.org/W2103832753","doi":"https://doi.org/10.1093/bib/bbq067","mag":"2103832753","pmid":"https://pubmed.ncbi.nlm.nih.gov/21059604"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbq067","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbq067","pdf_url":"https://academic.oup.com/bib/article-pdf/12/2/91/726675/bbq067.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bib/article-pdf/12/2/91/726675/bbq067.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5033016354","display_name":"An\u00e1lia Louren\u00e7o","orcid":"https://orcid.org/0000-0001-8401-5362"},"institutions":[{"id":"https://openalex.org/I4210145583","display_name":"Bioengineering Center","ror":"https://ror.org/04f0ydx59","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210145583"]},{"id":"https://openalex.org/I4210167387","display_name":"Institute for Biotechnology and Bioengineering","ror":"https://ror.org/05ws8g470","country_code":"PT","type":"facility","lineage":["https://openalex.org/I4210167387"]},{"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","RU"],"is_corresponding":false,"raw_author_name":"A. Lourenco","raw_affiliation_strings":["Institute for Biotechnology and Bioengineering, Center of Biological Engineering, University of Minho. analia@deb.uminho.pt","Institute for Biotechnology and Bioengineering, Center of Biological Engineering, University of Minho"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Biotechnology and Bioengineering, Center of Biological Engineering, University of Minho. analia@deb.uminho.pt","institution_ids":["https://openalex.org/I4210167387","https://openalex.org/I4210145583","https://openalex.org/I99682543"]},{"raw_affiliation_string":"Institute for Biotechnology and Bioengineering, Center of Biological Engineering, University of Minho","institution_ids":["https://openalex.org/I4210167387"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054642116","display_name":"S\u00f3nia Carneiro","orcid":"https://orcid.org/0000-0001-8037-937X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"S. Carneiro","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040524717","display_name":"Miguel Rocha","orcid":"https://orcid.org/0000-0001-8439-8172"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"M. Rocha","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064824604","display_name":"Eug\u00e9nio C. Ferreira","orcid":"https://orcid.org/0000-0002-5400-3333"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"E. C. Ferreira","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5079343705","display_name":"Isabel Rocha","orcid":"https://orcid.org/0000-0001-9494-3410"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"I. Rocha","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":0.5445,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.66940221,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"12","issue":"2","first_page":"91","last_page":"103"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9993000030517578,"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":0.9993000030517578,"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":0.9972000122070312,"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":0.9922999739646912,"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/data-integration","display_name":"Data integration","score":0.7492538690567017},{"id":"https://openalex.org/keywords/metadata","display_name":"Metadata","score":0.7292251586914062},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7136144638061523},{"id":"https://openalex.org/keywords/interoperability","display_name":"Interoperability","score":0.6928597688674927},{"id":"https://openalex.org/keywords/data-curation","display_name":"Data curation","score":0.6756529808044434},{"id":"https://openalex.org/keywords/uniprot","display_name":"UniProt","score":0.6026173233985901},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.5428329706192017},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.5320801734924316},{"id":"https://openalex.org/keywords/organism","display_name":"Organism","score":0.5196634531021118},{"id":"https://openalex.org/keywords/information-integration","display_name":"Information integration","score":0.4233509302139282},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.42061564326286316},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.38169997930526733},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.36099421977996826},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.34606698155403137},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.21349245309829712},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.19008290767669678},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.13893330097198486},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.08437454700469971}],"concepts":[{"id":"https://openalex.org/C72634772","wikidata":"https://www.wikidata.org/wiki/Q386824","display_name":"Data integration","level":2,"score":0.7492538690567017},{"id":"https://openalex.org/C93518851","wikidata":"https://www.wikidata.org/wiki/Q180160","display_name":"Metadata","level":2,"score":0.7292251586914062},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7136144638061523},{"id":"https://openalex.org/C20136886","wikidata":"https://www.wikidata.org/wiki/Q749647","display_name":"Interoperability","level":2,"score":0.6928597688674927},{"id":"https://openalex.org/C91632574","wikidata":"https://www.wikidata.org/wiki/Q15088675","display_name":"Data curation","level":2,"score":0.6756529808044434},{"id":"https://openalex.org/C202264299","wikidata":"https://www.wikidata.org/wiki/Q905695","display_name":"UniProt","level":3,"score":0.6026173233985901},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.5428329706192017},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5320801734924316},{"id":"https://openalex.org/C137858568","wikidata":"https://www.wikidata.org/wiki/Q7239","display_name":"Organism","level":2,"score":0.5196634531021118},{"id":"https://openalex.org/C33326189","wikidata":"https://www.wikidata.org/wiki/Q17092450","display_name":"Information integration","level":2,"score":0.4233509302139282},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.42061564326286316},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.38169997930526733},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.36099421977996826},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.34606698155403137},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.21349245309829712},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.19008290767669678},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.13893330097198486},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.08437454700469971},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"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":"D048168","descriptor_name":"Escherichia coli K12","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D048168","descriptor_name":"Escherichia coli K12","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D048168","descriptor_name":"Escherichia coli K12","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D048168","descriptor_name":"Escherichia coli K12","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D048168","descriptor_name":"Escherichia coli K12","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D048168","descriptor_name":"Escherichia coli K12","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D048168","descriptor_name":"Escherichia coli K12","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D048168","descriptor_name":"Escherichia coli K12","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D048168","descriptor_name":"Escherichia coli K12","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bib/bbq067","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbq067","pdf_url":"https://academic.oup.com/bib/article-pdf/12/2/91/726675/bbq067.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:21059604","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21059604","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:repositorium.sdum.uminho.pt:1822/14330","is_oa":true,"landing_page_url":"https://hdl.handle.net/1822/14330","pdf_url":null,"source":{"id":"https://openalex.org/S4306400354","display_name":"Reposit\u00f3riUM (Universidade do Minho)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I99682543","host_organization_name":"University of Minho","host_organization_lineage":["https://openalex.org/I99682543"],"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:1822/14330","is_oa":true,"landing_page_url":"http://doi.org/10.1093/bib/bbq067","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"}],"best_oa_location":{"id":"doi:10.1093/bib/bbq067","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbq067","pdf_url":"https://academic.oup.com/bib/article-pdf/12/2/91/726675/bbq067.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":50,"referenced_works":["https://openalex.org/W77347155","https://openalex.org/W119851965","https://openalex.org/W198352279","https://openalex.org/W616284349","https://openalex.org/W1562433595","https://openalex.org/W1584775655","https://openalex.org/W1594937218","https://openalex.org/W1730348256","https://openalex.org/W1835571316","https://openalex.org/W1963841093","https://openalex.org/W1965893904","https://openalex.org/W1975004479","https://openalex.org/W1975147762","https://openalex.org/W1976026861","https://openalex.org/W1999895438","https://openalex.org/W2002107667","https://openalex.org/W2003516452","https://openalex.org/W2033377040","https://openalex.org/W2061636126","https://openalex.org/W2063007776","https://openalex.org/W2080235847","https://openalex.org/W2094236735","https://openalex.org/W2095596879","https://openalex.org/W2107580398","https://openalex.org/W2108078368","https://openalex.org/W2108671185","https://openalex.org/W2118640842","https://openalex.org/W2122264917","https://openalex.org/W2124926885","https://openalex.org/W2128601422","https://openalex.org/W2131152203","https://openalex.org/W2134089435","https://openalex.org/W2134153749","https://openalex.org/W2141132558","https://openalex.org/W2146856779","https://openalex.org/W2149194035","https://openalex.org/W2155592392","https://openalex.org/W2155972151","https://openalex.org/W2159482845","https://openalex.org/W2160948978","https://openalex.org/W2161062388","https://openalex.org/W2167708455","https://openalex.org/W2257914311","https://openalex.org/W2555756618","https://openalex.org/W2916767477","https://openalex.org/W2917375902","https://openalex.org/W2917431650","https://openalex.org/W4230392683","https://openalex.org/W4240231372","https://openalex.org/W4294216483"],"related_works":["https://openalex.org/W2129800387","https://openalex.org/W2080497949","https://openalex.org/W2397655851","https://openalex.org/W4287199895","https://openalex.org/W2064717691","https://openalex.org/W2355440778","https://openalex.org/W2164160537","https://openalex.org/W4244644848","https://openalex.org/W2341628596","https://openalex.org/W2372493300"],"abstract_inverted_index":{"One":[0],"key":[1],"challenge":[2],"in":[3,133,223],"Systems":[4],"Biology":[5],"is":[6,36,66],"to":[7,10,17,20,67,78,89,144,191,218,221],"provide":[8],"mechanisms":[9],"collect":[11],"and":[12,34,50,53,82,97,112,121,156,185,212],"integrate":[13],"the":[14,58,69,125,129,146,152,203,208,232,242],"necessary":[15,245],"data":[16,32,43,99,196],"be":[18,183,213,219,229],"able":[19,220],"meet":[21],"multiple":[22,31],"analysis":[23,211],"requirements.":[24],"Typically,":[25],"biological":[26],"contents":[27,172],"are":[28,173],"scattered":[29],"over":[30,105],"sources":[33,204],"there":[35],"no":[37,134],"easy":[38],"way":[39],"of":[40,94,118,139,154,210,215,231,234,244],"comparing":[41],"heterogeneous":[42],"contents.":[44,114],"This":[45],"work":[46],"discusses":[47],"ongoing":[48],"standardisation":[49],"interoperability":[51],"efforts":[52],"exposes":[54],"integration":[55,74,131,140,153,197,236],"challenges":[56],"for":[57,128,166,248],"model":[59,169],"organism":[60],"Escherichia":[61],"coli":[62],"K-12.":[63],"The":[64],"goal":[65],"analyse":[68],"major":[70],"obstacles":[71],"faced":[72],"by":[73,102,148],"processes,":[75],"suggest":[76],"ways":[77],"systematically":[79],"identify":[80],"them,":[81],"whenever":[83],"possible,":[84],"propose":[85],"solutions":[86],"or":[87],"means":[88],"assist":[90],"manual":[91,246],"curation.":[92,161],"Integration":[93],"gene,":[95],"protein":[96],"compound":[98,157],"was":[100],"evaluated":[101],"performing":[103],"comparisons":[104],"EcoCyc,":[106],"KEGG,":[107],"BRENDA,":[108],"ChEBI,":[109],"Entrez":[110],"Gene":[111],"UniProt":[113],"Cross-links,":[115],"a":[116,167],"number":[117],"standard":[119],"nomenclatures":[120],"name":[122],"information":[123],"supported":[124],"comparisons.":[126],"Except":[127],"gene":[130],"scenario,":[132],"other":[135],"scenario":[136],"an":[137],"element":[138],"performed":[141],"well":[142],"enough":[143],"support":[145],"process":[147],"itself.":[149],"Indeed,":[150],"both":[151],"enzyme":[155],"records":[158],"imply":[159],"considerable":[160],"Results":[162],"evidenced":[163],"that,":[164],"even":[165],"well-studied":[168],"organism,":[170],"source":[171,190],"still":[174],"far":[175],"from":[176,189],"being":[177],"as":[178,180],"standardized":[179],"it":[181],"would":[182],"desired":[184],"metadata":[186],"varies":[187],"considerably":[188],"source.":[192],"Before":[193],"designing":[194],"any":[195],"pipeline,":[198],"researchers":[199],"should":[200,228],"decide":[201],"on":[202],"that":[205,238],"best":[206],"fit":[207],"purpose":[209],"aware":[214,230],"existing":[216],"conflicts/inconsistencies":[217],"intervene":[222],"their":[224],"resolution.":[225],"Moreover,":[226],"they":[227,239],"limits":[233],"automatic":[235],"such":[237],"can":[240],"define":[241],"extent":[243],"curation":[247],"each":[249],"application.":[250]},"counts_by_year":[{"year":2015,"cited_by_count":1},{"year":2012,"cited_by_count":2}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
