{"id":"https://openalex.org/W2130262775","doi":"https://doi.org/10.2390/biecoll-jib-2012-203","title":"Computational approaches to standard-compliant biofilm data for reliable analysis and integration","display_name":"Computational approaches to standard-compliant biofilm data for reliable analysis and integration","publication_year":2012,"publication_date":"2012-01-01","ids":{"openalex":"https://openalex.org/W2130262775","doi":"https://doi.org/10.2390/biecoll-jib-2012-203","mag":"2130262775","pmid":"https://pubmed.ncbi.nlm.nih.gov/22829574"},"language":"en","primary_location":{"id":"pmid:22829574","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22829574","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/1822/22372","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5018709423","display_name":"Ana Margarida Sousa","orcid":"https://orcid.org/0000-0002-8900-2656"},"institutions":[{"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"],"is_corresponding":true,"raw_author_name":"Sousa, Ana Margarida","raw_affiliation_strings":["IBB - Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IBB - Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal","institution_ids":["https://openalex.org/I4210167387","https://openalex.org/I99682543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050223713","display_name":"Andreia Ferreira","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ferreira, Andreia","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035712663","display_name":"Nuno F. Azevedo","orcid":"https://orcid.org/0000-0001-5864-3250"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Azevedo, Nuno","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100751103","display_name":"Maria Ol\u00edvia Pereira","orcid":"https://orcid.org/0000-0002-4307-3985"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Pereira, Maria Olivia","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5033016354","display_name":"An\u00e1lia Louren\u00e7o","orcid":"https://orcid.org/0000-0001-8401-5362"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Lourenco, Analia","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5018709423"],"corresponding_institution_ids":["https://openalex.org/I4210167387","https://openalex.org/I99682543"],"apc_list":null,"apc_paid":null,"fwci":0.6718,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.69361044,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"9","issue":"3","first_page":"203","last_page":"203"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9973999857902527,"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":0.9973999857902527,"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/T11791","display_name":"Microbial Community Ecology and Physiology","score":0.9377999901771545,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/biofilm","display_name":"Biofilm","score":0.9199652075767517},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.6580203771591187},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6198012232780457},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.33838409185409546},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.28623491525650024},{"id":"https://openalex.org/keywords/bacteria","display_name":"Bacteria","score":0.11630263924598694},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.07539010047912598}],"concepts":[{"id":"https://openalex.org/C58123911","wikidata":"https://www.wikidata.org/wiki/Q467410","display_name":"Biofilm","level":3,"score":0.9199652075767517},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.6580203771591187},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6198012232780457},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.33838409185409546},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.28623491525650024},{"id":"https://openalex.org/C523546767","wikidata":"https://www.wikidata.org/wiki/Q10876","display_name":"Bacteria","level":2,"score":0.11630263924598694},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.07539010047912598},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","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}],"mesh":[{"descriptor_ui":"D001330","descriptor_name":"Electronic Data Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001330","descriptor_name":"Electronic Data Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001330","descriptor_name":"Electronic Data Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000254","qualifier_name":"growth & development","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000254","qualifier_name":"growth & development","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000254","qualifier_name":"growth & development","is_major_topic":false},{"descriptor_ui":"D012015","descriptor_name":"Reference Standards","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012015","descriptor_name":"Reference Standards","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012015","descriptor_name":"Reference Standards","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013223","descriptor_name":"Statistics as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013223","descriptor_name":"Statistics as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013223","descriptor_name":"Statistics as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015169","descriptor_name":"Colony Count, Microbial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015169","descriptor_name":"Colony Count, Microbial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015169","descriptor_name":"Colony Count, Microbial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018441","descriptor_name":"Biofilms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018441","descriptor_name":"Biofilms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018441","descriptor_name":"Biofilms","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}],"locations_count":6,"locations":[{"id":"pmid:22829574","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22829574","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:biecoll.ub.uni-bielefeld.de:5213","is_oa":false,"landing_page_url":"http://biecoll.ub.uni-bielefeld.de/volltexte/2012/5213/","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://journal.imbio.de/article.php?aid=203","raw_type":"Journal Article"},{"id":"pmh:oai:repositorio-aberto.up.pt:10216/104649","is_oa":false,"landing_page_url":"https://hdl.handle.net/10216/104649","pdf_url":null,"source":{"id":"https://openalex.org/S4306401934","display_name":"Open Repository of the University of Porto (University of Porto)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I182534213","host_organization_name":"Universidade do Porto","host_organization_lineage":["https://openalex.org/I182534213"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":null},{"id":"pmh:oai:repositorium.sdum.uminho.pt:1822/22372","is_oa":true,"landing_page_url":"http://hdl.handle.net/1822/22372","pdf_url":null,"source":{"id":"https://openalex.org/S4306401240","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:1822/22372","is_oa":true,"landing_page_url":"https://hdl.handle.net/1822/22372","pdf_url":null,"source":{"id":"https://openalex.org/S4306400624","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":null,"raw_type":"journal article"},{"id":"doi:10.2390/biecoll-jib-2012-203","is_oa":true,"landing_page_url":"https://doi.org/10.2390/biecoll-jib-2012-203","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:1822/22372","is_oa":true,"landing_page_url":"http://hdl.handle.net/1822/22372","pdf_url":null,"source":{"id":"https://openalex.org/S4306401240","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"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1578237752","display_name":null,"funder_award_id":"COMPETE","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G8868700560","display_name":null,"funder_award_id":"FCOMP-01-0124-FEDER","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":24,"referenced_works":["https://openalex.org/W77226232","https://openalex.org/W1894776803","https://openalex.org/W1922424370","https://openalex.org/W1970939575","https://openalex.org/W2004589632","https://openalex.org/W2005628297","https://openalex.org/W2011904099","https://openalex.org/W2036414366","https://openalex.org/W2052813877","https://openalex.org/W2062816144","https://openalex.org/W2077351059","https://openalex.org/W2093430945","https://openalex.org/W2098809087","https://openalex.org/W2113142309","https://openalex.org/W2115534487","https://openalex.org/W2120069425","https://openalex.org/W2127371670","https://openalex.org/W2127535305","https://openalex.org/W2128835519","https://openalex.org/W2139664090","https://openalex.org/W2155572331","https://openalex.org/W2159880526","https://openalex.org/W2166101181","https://openalex.org/W2233369658"],"related_works":["https://openalex.org/W2362192218","https://openalex.org/W2381477132","https://openalex.org/W1802100029","https://openalex.org/W2386636980","https://openalex.org/W1523602405","https://openalex.org/W2269907498","https://openalex.org/W1867395701","https://openalex.org/W1560807622","https://openalex.org/W2348324746","https://openalex.org/W2377000990"],"abstract_inverted_index":{"The":[0,55,93,136],"study":[1],"of":[2,14,32,36,47,57,100,102,172],"microorganism":[3,123],"consortia,":[4],"also":[5,166],"known":[6],"as":[7],"biofilms,":[8],"is":[9,61,79,95,141],"associated":[10],"to":[11,44,142,146],"a":[12,42,62,98,158,168,183],"number":[13,99],"applications":[15],"in":[16,157,170],"biotechnology,":[17],"ecotechnology":[18],"and":[19,27,50,69,74,125,133,149,154,176,182],"clinical":[20],"domains.":[21],"Nowadays,":[22],"biofilm":[23,37,52,67,71,112,129,173],"studies":[24,38,68],"are":[25],"heterogeneous":[26],"data-intensive,":[28],"encompassing":[29],"different":[30],"levels":[31],"analysis.":[33],"Computational":[34],"modelling":[35],"has":[39],"become":[40],"thus":[41],"requirement":[43],"make":[45],"sense":[46],"these":[48],"vast":[49],"ever-expanding":[51],"data":[53,72,75,151,174],"volumes.":[54],"rationale":[56],"the":[58,82,87,105,115,163],"present":[59,164],"work":[60,165],"machine-readable":[63],"format":[64,78],"for":[65],"representing":[66],"supporting":[70],"interchange":[73,175],"integration.":[76],"This":[77],"supported":[80],"by":[81],"Biofilm":[83],"Science":[84],"Ontology":[85,108,118],"(BSO),":[86],"first":[88],"ontology":[89,94],"on":[90,152,186],"biofilms":[91,153],"information.":[92],"decomposed":[96],"into":[97],"areas":[101],"interest,":[103],"namely:":[104],"Experimental":[106],"Procedure":[107],"(EPO)":[109],"which":[110,120],"describes":[111],"experimental":[113],"procedures;":[114],"Colony":[116],"Morphology":[117],"(CMO)":[119],"characterises":[121],"morphologically":[122],"colonies;":[124],"other":[126],"modules":[127],"concerning":[128],"phenotype,":[130],"antimicrobial":[131],"susceptibility":[132],"virulence":[134],"traits.":[135],"overall":[137],"objective":[138],"behind":[139],"BSO":[140],"develop":[143],"semantic":[144],"resources":[145],"capture,":[147],"represent":[148],"share":[150],"related":[155],"experiments":[156],"regularized":[159],"fashion":[160],"manner.":[161],"Furthermore,":[162],"introduces":[167],"framework":[169],"assistance":[171],"analysis":[177],"-":[178,181,190],"BiofOmics":[179],"(http://biofomics.org)":[180],"public":[184],"repository":[185],"colony":[187],"morphology":[188],"signatures":[189],"MorphoCol":[191],"(http://stardust.deb.uminho.pt/morphocol).":[192]},"counts_by_year":[{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":1}],"updated_date":"2026-05-16T08:24:45.110214","created_date":"2025-10-10T00:00:00"}
