{"id":"https://openalex.org/W1994924643","doi":"https://doi.org/10.1109/bibm.2014.6999292","title":"Storing provenance data of genome project workflows using graph database","display_name":"Storing provenance data of genome project workflows using graph database","publication_year":2014,"publication_date":"2014-11-01","ids":{"openalex":"https://openalex.org/W1994924643","doi":"https://doi.org/10.1109/bibm.2014.6999292","mag":"1994924643"},"language":"en","primary_location":{"id":"doi:10.1109/bibm.2014.6999292","doi":"https://doi.org/10.1109/bibm.2014.6999292","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2014.6999292","pdf_url":null,"source":{"id":"https://openalex.org/S4363607730","display_name":"IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2014 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"volume":null,"type":"conference-paper","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":null,"display_name":"Rodrigo Pinheiro","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I150729083","display_name":"Universidade de Bras\u00edlia","ror":"https://ror.org/02xfp8v59","country_code":"BR","type":"education","lineage":["https://openalex.org/I150729083"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Rodrigo Pinheiro","raw_affiliation_strings":["Computer Science Department, University of Brasilia \u2013 UNB, Bras\u00edlia, Brazil","Computer Science Department, University of Brasilia (UnB), Brasilia, Brazil#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Science Department, University of Brasilia \u2013 UNB, Bras\u00edlia, Brazil","institution_ids":["https://openalex.org/I150729083"]},{"raw_affiliation_string":"Computer Science Department, University of Brasilia (UnB), Brasilia, Brazil#TAB#","institution_ids":["https://openalex.org/I150729083"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085702386","display_name":"Bruno Aires","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I150729083","display_name":"Universidade de Bras\u00edlia","ror":"https://ror.org/02xfp8v59","country_code":"BR","type":"education","lineage":["https://openalex.org/I150729083"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Bruno Aires","raw_affiliation_strings":["Computer Science Department, University of Brasilia \u2013 UNB, Bras\u00edlia, Brazil","Computer Science Department, University of Brasilia (UnB), Brasilia, Brazil#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Science Department, University of Brasilia \u2013 UNB, Bras\u00edlia, Brazil","institution_ids":["https://openalex.org/I150729083"]},{"raw_affiliation_string":"Computer Science Department, University of Brasilia (UnB), Brasilia, Brazil#TAB#","institution_ids":["https://openalex.org/I150729083"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031701924","display_name":"Alet\u00e9ia Ara\u00fajo","orcid":"https://orcid.org/0000-0003-4645-6700","observed_orcids":["https://orcid.org/0000-0003-4645-6700"]},"institutions":[{"id":"https://openalex.org/I150729083","display_name":"Universidade de Bras\u00edlia","ror":"https://ror.org/02xfp8v59","country_code":"BR","type":"education","lineage":["https://openalex.org/I150729083"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Aleteia F. Araujo","raw_affiliation_strings":["Computer Science Department, University of Brasilia \u2013 UNB, Bras\u00edlia, Brazil","Computer Science Department, University of Brasilia (UnB), Brasilia, Brazil#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Science Department, University of Brasilia \u2013 UNB, Bras\u00edlia, Brazil","institution_ids":["https://openalex.org/I150729083"]},{"raw_affiliation_string":"Computer Science Department, University of Brasilia (UnB), Brasilia, Brazil#TAB#","institution_ids":["https://openalex.org/I150729083"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054089208","display_name":"Maristela Terto de Holanda","orcid":"https://orcid.org/0000-0002-0883-2579","observed_orcids":["https://orcid.org/0000-0002-0883-2579"]},"institutions":[{"id":"https://openalex.org/I150729083","display_name":"Universidade de Bras\u00edlia","ror":"https://ror.org/02xfp8v59","country_code":"BR","type":"education","lineage":["https://openalex.org/I150729083"]},{"id":"https://openalex.org/I2699952","display_name":"Pontif\u00edcia Universidade Cat\u00f3lica do Rio de Janeiro","ror":"https://ror.org/01dg47b60","country_code":"BR","type":"education","lineage":["https://openalex.org/I2699952"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Maristela Holanda","raw_affiliation_strings":["Department of Informatics, Pontifical Catholic University \u2013 PUC-Rio, Rio de Janeiro, Brazil","Computer Science Department, University of Brasilia (UnB), Brasilia, Brazil#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Informatics, Pontifical Catholic University \u2013 PUC-Rio, Rio de Janeiro, Brazil","institution_ids":["https://openalex.org/I2699952"]},{"raw_affiliation_string":"Computer Science Department, University of Brasilia (UnB), Brasilia, Brazil#TAB#","institution_ids":["https://openalex.org/I150729083"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071276748","display_name":"Maria Em\u00edlia M. T. Walter","orcid":"https://orcid.org/0000-0001-6822-931X","observed_orcids":["https://orcid.org/0000-0001-6822-931X"]},"institutions":[{"id":"https://openalex.org/I150729083","display_name":"Universidade de Bras\u00edlia","ror":"https://ror.org/02xfp8v59","country_code":"BR","type":"education","lineage":["https://openalex.org/I150729083"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Maria Emilia Walter","raw_affiliation_strings":["Computer Science Department, University of Brasilia \u2013 UNB, Bras\u00edlia, Brazil","Computer Science Department, University of Brasilia (UnB), Brasilia, Brazil#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Science Department, University of Brasilia \u2013 UNB, Bras\u00edlia, Brazil","institution_ids":["https://openalex.org/I150729083"]},{"raw_affiliation_string":"Computer Science Department, University of Brasilia (UnB), Brasilia, Brazil#TAB#","institution_ids":["https://openalex.org/I150729083"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5085416987","display_name":"S\u00e9rgio Lifschitz","orcid":"https://orcid.org/0000-0003-3073-3734","observed_orcids":["https://orcid.org/0000-0003-3073-3734"]},"institutions":[{"id":"https://openalex.org/I150729083","display_name":"Universidade de Bras\u00edlia","ror":"https://ror.org/02xfp8v59","country_code":"BR","type":"education","lineage":["https://openalex.org/I150729083"]},{"id":"https://openalex.org/I2699952","display_name":"Pontif\u00edcia Universidade Cat\u00f3lica do Rio de Janeiro","ror":"https://ror.org/01dg47b60","country_code":"BR","type":"education","lineage":["https://openalex.org/I2699952"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Sergio Lifschitz","raw_affiliation_strings":["Computer Science Department, University of Brasilia \u2013 UNB, Bras\u00edlia, Brazil","Department of Informatics, Pontifical Catholic University - PUC-Rio, Rio de Janeiro, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Science Department, University of Brasilia \u2013 UNB, Bras\u00edlia, Brazil","institution_ids":["https://openalex.org/I150729083"]},{"raw_affiliation_string":"Department of Informatics, Pontifical Catholic University - PUC-Rio, Rio de Janeiro, Brazil","institution_ids":["https://openalex.org/I2699952"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":3.6196,"has_fulltext":false,"cited_by_count":8,"citation_normalized_percentile":{"value":0.92823858,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":88,"max":97},"biblio":{"volume":"27","issue":null,"first_page":"16","last_page":"22"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9984999895095825,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},"topics":[{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9984999895095825,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T11937","display_name":"Research Data Management Practices","score":0.0010000000474974513,"subfield":{"id":"https://openalex.org/subfields/1710","display_name":"Information Systems"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":9.999999747378752e-05,"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-provenance","display_name":"data provenance","score":0.9829999804496765},{"id":"https://openalex.org/keywords/bioinformatics-pipeline","display_name":"bioinformatics pipeline","score":0.8199999928474426},{"id":"https://openalex.org/keywords/graph-databases","display_name":"graph databases","score":0.7590000033378601},{"id":"https://openalex.org/keywords/genome-projects","display_name":"genome projects","score":0.8619999885559082},{"id":"https://openalex.org/keywords/provenance-storage","display_name":"provenance storage","score":0.5849999785423279},{"id":"https://openalex.org/keywords/workflow-simulation","display_name":"workflow simulation","score":0.5720000267028809},{"id":"https://openalex.org/keywords/logbooks","display_name":"logbooks","score":0.6639999747276306},{"id":"https://openalex.org/keywords/genomic-data","display_name":"genomic data","score":0.7269999980926514}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.8729733228683472},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.77787184715271},{"id":"https://openalex.org/C2780049196","wikidata":"https://www.wikidata.org/wiki/Q23582628","display_name":"Provenance","level":2,"score":0.6013507843017578},{"id":"https://openalex.org/C162022261","wikidata":"https://www.wikidata.org/wiki/Q6666827","display_name":"Logbook","level":2,"score":0.5266112089157104},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.5136556029319763},{"id":"https://openalex.org/C176225458","wikidata":"https://www.wikidata.org/wiki/Q595971","display_name":"Graph database","level":3,"score":0.4461987018585205},{"id":"https://openalex.org/C67186912","wikidata":"https://www.wikidata.org/wiki/Q367664","display_name":"Data modeling","level":2,"score":0.4153209626674652},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4054795503616333},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.3724147081375122},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3618204891681671},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3396196961402893},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.1446630358695984},{"id":"https://openalex.org/C5900021","wikidata":"https://www.wikidata.org/wiki/Q163082","display_name":"Petrology","level":1,"score":0.0},{"id":"https://openalex.org/C127313418","wikidata":"https://www.wikidata.org/wiki/Q1069","display_name":"Geology","level":0,"score":0.0},{"id":"https://openalex.org/C111368507","wikidata":"https://www.wikidata.org/wiki/Q43518","display_name":"Oceanography","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm.2014.6999292","doi":"https://doi.org/10.1109/bibm.2014.6999292","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2014.6999292","pdf_url":null,"source":{"id":"https://openalex.org/S4363607730","display_name":"IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2014 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"sustainable_development_goals_aurora":[{"id":"https://metadata.un.org/sdg/9","score":0.4099999964237213,"display_name":"Industry, innovation and infrastructure"}],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":17,"referenced_works":["https://openalex.org/W137781046","https://openalex.org/W177720387","https://openalex.org/W1552694902","https://openalex.org/W1567763640","https://openalex.org/W1575999478","https://openalex.org/W1585868236","https://openalex.org/W1992661051","https://openalex.org/W2020336239","https://openalex.org/W2020391739","https://openalex.org/W2081795602","https://openalex.org/W2093896414","https://openalex.org/W2098805832","https://openalex.org/W2114507260","https://openalex.org/W2502420217","https://openalex.org/W2577790658","https://openalex.org/W2611196248","https://openalex.org/W2727986795"],"related_works":["https://openalex.org/W1971498508","https://openalex.org/W2081795602","https://openalex.org/W2774490160","https://openalex.org/W4256353202","https://openalex.org/W2216827723","https://openalex.org/W2080071958","https://openalex.org/W7097461569","https://openalex.org/W2585932170","https://openalex.org/W2922727097","https://openalex.org/W3212300862"],"abstract_inverted_index":{"Many":[0],"scientific":[1],"experiments":[2],"are":[3],"designed":[4],"as":[5,97],"computational":[6],"workflows":[7],"in":[8,129],"bioinformatics.":[9],"However,":[10],"the":[11,24,27,30,56,65,81,89],"amount":[12],"of":[13,20,26,32,84],"data":[14,45,78,102,109,115],"generated":[15],"increases":[16],"at":[17],"every":[18],"phase":[19],"each":[21],"execution,":[22],"hindering":[23],"identification":[25],"source":[28],"and":[29,50,63],"transformation":[31],"data.":[33],"Therefore,":[34],"it":[35],"has":[36],"become":[37],"necessary":[38],"to":[39,43,54,61,72,76,100],"create":[40],"new":[41],"tools":[42],"store":[44,77],"provenance,":[46],"mainly":[47],"which":[48,119],"resources":[49],"parameters":[51],"were":[52],"used":[53],"generate":[55],"results,":[57],"among":[58],"other":[59],"information,":[60],"validate":[62,88],"publish":[64],"experiment.":[66],"In":[67],"this":[68],"paper,":[69],"we":[70,91],"propose":[71],"use":[73],"graph":[74],"database":[75],"provenance":[79,123],"using":[80],"PROV-DM":[82],"model":[83,124],"bioinformatics":[85],"workflows.":[86],"To":[87],"model,":[90],"developed":[92],"a":[93,98],"simulator":[94],"that":[95,111,121],"worked":[96],"logbook":[99],"capture":[101],"provenance.":[103],"A":[104],"workflow":[105],"with":[106],"real":[107],"genomic":[108],"showed":[110],"very":[112],"little":[113],"additional":[114],"should":[116],"be":[117,126],"stored,":[118],"means":[120],"our":[122],"can":[125],"easily":[127],"included":[128],"genome":[130],"projects.":[131]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":2}],"updated_date":"2026-10-16T09:59:22.235173","created_date":"2016-06-24T00:00:00"}