{"id":"https://openalex.org/W2025998497","doi":"https://doi.org/10.1186/1471-2105-10-s12-s5","title":"Phenotypic and genotypic data integration and exploration through a web-service architecture","display_name":"Phenotypic and genotypic data integration and exploration through a web-service architecture","publication_year":2009,"publication_date":"2009-10-01","ids":{"openalex":"https://openalex.org/W2025998497","doi":"https://doi.org/10.1186/1471-2105-10-s12-s5","mag":"2025998497","pmid":"https://pubmed.ncbi.nlm.nih.gov/19828081"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-10-s12-s5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-s12-s5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-S12-S5","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-S12-S5","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5009977600","display_name":"Angelo Nuzzo","orcid":null},"institutions":[{"id":"https://openalex.org/I25217355","display_name":"University of Pavia","ror":"https://ror.org/00s6t1f81","country_code":"IT","type":"education","lineage":["https://openalex.org/I25217355"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Angelo Nuzzo","raw_affiliation_strings":["Department of Computer Engineering and Systems Science, University of Pavia, Via Ferrata 1, Pavia, Italy. angelo.nuzzo@unipv.it","Dept. of Computer Engineering and Systems Science, University of Pavia, Pavia, Italy#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Engineering and Systems Science, University of Pavia, Via Ferrata 1, Pavia, Italy. angelo.nuzzo@unipv.it","institution_ids":["https://openalex.org/I25217355"]},{"raw_affiliation_string":"Dept. of Computer Engineering and Systems Science, University of Pavia, Pavia, Italy#TAB#","institution_ids":["https://openalex.org/I25217355"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012026856","display_name":"Alberto Riva","orcid":"https://orcid.org/0000-0001-9150-8333"},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alberto Riva","raw_affiliation_strings":["Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, USA","Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, USA","institution_ids":["https://openalex.org/I33213144"]},{"raw_affiliation_string":"Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, USA","institution_ids":["https://openalex.org/I33213144"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5050932220","display_name":"Riccardo Bellazzi","orcid":"https://orcid.org/0000-0002-6974-9808"},"institutions":[{"id":"https://openalex.org/I25217355","display_name":"University of Pavia","ror":"https://ror.org/00s6t1f81","country_code":"IT","type":"education","lineage":["https://openalex.org/I25217355"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Riccardo Bellazzi","raw_affiliation_strings":["Department of Computer Engineering and Systems Science, University of Pavia, Via Ferrata 1, 27100, Pavia, Italy","Dept. of Computer Engineering and Systems Science, University of Pavia, Pavia, Italy#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Engineering and Systems Science, University of Pavia, Via Ferrata 1, 27100, Pavia, Italy","institution_ids":["https://openalex.org/I25217355"]},{"raw_affiliation_string":"Dept. of Computer Engineering and Systems Science, University of Pavia, Pavia, Italy#TAB#","institution_ids":["https://openalex.org/I25217355"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5050932220"],"corresponding_institution_ids":["https://openalex.org/I25217355"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":0.5037,"has_fulltext":true,"cited_by_count":11,"citation_normalized_percentile":{"value":0.63614757,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"10","issue":"S12","first_page":"S5","last_page":"S5"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.5835999846458435,"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":0.5835999846458435,"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/T10350","display_name":"Electronic Health Records Systems","score":0.0738999992609024,"subfield":{"id":"https://openalex.org/subfields/3605","display_name":"Health Information Management"},"field":{"id":"https://openalex.org/fields/36","display_name":"Health Professions"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.053199999034404755,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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":0.5652647614479065},{"id":"https://openalex.org/keywords/workbench","display_name":"Workbench","score":0.5210292339324951},{"id":"https://openalex.org/keywords/upload","display_name":"Upload","score":0.5112268924713135},{"id":"https://openalex.org/keywords/phenotypic-trait","display_name":"Phenotypic trait","score":0.45365917682647705},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.444624125957489},{"id":"https://openalex.org/keywords/web-service","display_name":"Web service","score":0.41740506887435913},{"id":"https://openalex.org/keywords/phenotype","display_name":"Phenotype","score":0.3659800887107849},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.29386383295059204},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.281309574842453},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.24858158826828003},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.13404759764671326},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.11694705486297607}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5652647614479065},{"id":"https://openalex.org/C2779145975","wikidata":"https://www.wikidata.org/wiki/Q347690","display_name":"Workbench","level":3,"score":0.5210292339324951},{"id":"https://openalex.org/C71901391","wikidata":"https://www.wikidata.org/wiki/Q7126699","display_name":"Upload","level":2,"score":0.5112268924713135},{"id":"https://openalex.org/C130073038","wikidata":"https://www.wikidata.org/wiki/Q1211967","display_name":"Phenotypic trait","level":4,"score":0.45365917682647705},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.444624125957489},{"id":"https://openalex.org/C35578498","wikidata":"https://www.wikidata.org/wiki/Q193424","display_name":"Web service","level":2,"score":0.41740506887435913},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.3659800887107849},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.29386383295059204},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.281309574842453},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.24858158826828003},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.13404759764671326},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.11694705486297607},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-10-s12-s5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-s12-s5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-S12-S5","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:19828081","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19828081","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:92e5e75ebe754d6d8e4c705dcc6aecee","is_oa":true,"landing_page_url":"https://doaj.org/article/92e5e75ebe754d6d8e4c705dcc6aecee","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 10, Iss Suppl 12, p S5 (2009)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2762070","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2762070","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-10-s12-s5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-s12-s5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-S12-S5","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","score":0.6399999856948853,"id":"https://metadata.un.org/sdg/9"}],"awards":[{"id":"https://openalex.org/G4701717143","display_name":null,"funder_award_id":"R01 HL087681","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G5331206282","display_name":null,"funder_award_id":"R01 HL87681-01","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G722919562","display_name":null,"funder_award_id":"R01 HL87681","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337338","display_name":"National Heart, Lung, and Blood Institute","ror":"https://ror.org/012pb6c26"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2025998497.pdf","grobid_xml":"https://content.openalex.org/works/W2025998497.grobid-xml"},"referenced_works_count":9,"referenced_works":["https://openalex.org/W1480316328","https://openalex.org/W1985849948","https://openalex.org/W2048296798","https://openalex.org/W2050821039","https://openalex.org/W2073527744","https://openalex.org/W2133413127","https://openalex.org/W2169294950","https://openalex.org/W2403838977","https://openalex.org/W2965465701"],"related_works":["https://openalex.org/W2388509490","https://openalex.org/W2109648960","https://openalex.org/W1787347804","https://openalex.org/W2583262180","https://openalex.org/W2052001298","https://openalex.org/W3014691397","https://openalex.org/W2342312410","https://openalex.org/W2143131037","https://openalex.org/W4245102296","https://openalex.org/W4376271000"],"abstract_inverted_index":{"BACKGROUND:":[0],"Linking":[1],"genotypic":[2,50,89],"and":[3,29,47,74,84,88,96,111,122,144,192,197,202],"phenotypic":[4,87,109,127],"information":[5,51,118],"is":[6,58],"one":[7],"of":[8,12,18,27,37,44,62,70,86,98,171],"the":[9,35,42,48,54,68,81,94,99,142,164,172,204],"greatest":[10],"challenges":[11],"current":[13],"genetics":[14],"research.":[15],"The":[16],"definition":[17,43],"an":[19,168],"Information":[20,71],"Technology":[21,72],"infrastructure":[22],"to":[23,52,76,106,115,123,126,136,149],"support":[24],"this":[25,130,159,184],"kind":[26],"studies,":[28],"in":[30,174],"particular":[31],"studies":[32],"aimed":[33],"at":[34],"analysis":[36],"complex":[38],"traits,":[39],"which":[40,175],"require":[41],"multifaceted":[45],"phenotypes":[46],"integration":[49,85,199],"discover":[53],"most":[55],"prevalent":[56],"diseases,":[57],"a":[59,78,102,134,145,189],"paradigmatic":[60],"goal":[61],"Biomedical":[63],"Informatics.":[64],"This":[65],"paper":[66,160,185],"describes":[67],"use":[69],"methods":[73],"tools":[75],"develop":[77],"system":[79,104,165,173],"for":[80,195],"management,":[82],"inspection":[83],"data.":[90,128],"RESULTS:":[91],"We":[92],"present":[93],"design":[95],"architecture":[97],"Phenotype":[100],"Miner,":[101],"software":[103],"able":[105],"flexibly":[107],"manage":[108],"information,":[110],"its":[112],"extended":[113],"functionalities":[114],"retrieve":[116,150],"genotype":[117,196],"from":[119,152],"external":[120],"repositories":[121],"relate":[124],"it":[125],"For":[129],"purpose":[131],"we":[132,161,176,186],"developed":[133],"module":[135],"allow":[137],"customized":[138],"data":[139,151],"upload":[140],"by":[141,167],"user":[143],"SOAP-based":[146],"communications":[147],"layer":[148],"existing":[153],"biomedical":[154],"knowledge":[155],"management":[156],"tools.":[157],"In":[158,183],"also":[162],"demonstrate":[163],"functionality":[166],"example":[169],"application":[170],"analyze":[177],"two":[178],"related":[179],"genomic":[180],"datasets.":[181],"CONCLUSION:":[182],"show":[187],"how":[188],"comprehensive,":[190],"integrated":[191],"automated":[193],"workbench":[194],"phenotype":[198],"can":[200],"facilitate":[201],"improve":[203],"hypothesis":[205],"generation":[206],"process":[207],"underlying":[208],"modern":[209],"genetic":[210],"studies.":[211]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
