{"id":"https://openalex.org/W3091802260","doi":"https://doi.org/10.12688/f1000research.24427.1","title":"Annotation and curation of human genomic variations: an ELIXIR Implementation Study","display_name":"Annotation and curation of human genomic variations: an ELIXIR Implementation Study","publication_year":2020,"publication_date":"2020-10-08","ids":{"openalex":"https://openalex.org/W3091802260","doi":"https://doi.org/10.12688/f1000research.24427.1","mag":"3091802260"},"language":"en","primary_location":{"id":"doi:10.12688/f1000research.24427.1","is_oa":true,"landing_page_url":"https://doi.org/10.12688/f1000research.24427.1","pdf_url":"https://f1000research.com/articles/9-1207/v1/pdf","source":{"id":"https://openalex.org/S4210239046","display_name":"F1000Research","issn_l":"2046-1402","issn":["2046-1402"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320357","host_organization_name":"Faculty of 1000","host_organization_lineage":["https://openalex.org/P4310320357"],"host_organization_lineage_names":["Faculty of 1000"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"F1000Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://f1000research.com/articles/9-1207/v1/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5071925173","display_name":"Alessia David","orcid":"https://orcid.org/0000-0001-8687-024X"},"institutions":[{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Alessia David","raw_affiliation_strings":["Centre for Integrative Systems Biology and Bioinformatics, Imperial College London, London, SW7 2AZ"],"raw_orcid":"https://orcid.org/0000-0001-8687-024X","affiliations":[{"raw_affiliation_string":"Centre for Integrative Systems Biology and Bioinformatics, Imperial College London, London, SW7 2AZ","institution_ids":["https://openalex.org/I47508984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056896983","display_name":"Val\u00e9rie Barbi\u00e9","orcid":"https://orcid.org/0009-0006-8085-9393"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Val\u00e9rie Barbi\u00e9","raw_affiliation_strings":["Clinical Bioinformatics, Swiss Institute of Bioinformatics, Geneva"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Clinical Bioinformatics, Swiss Institute of Bioinformatics, Geneva","institution_ids":["https://openalex.org/I12708293"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063116840","display_name":"Marcella Attimonelli","orcid":"https://orcid.org/0000-0003-2091-8364"},"institutions":[{"id":"https://openalex.org/I5561750","display_name":"University of Bari Aldo Moro","ror":"https://ror.org/027ynra39","country_code":"IT","type":"education","lineage":["https://openalex.org/I5561750"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Marcella Attimonelli","raw_affiliation_strings":["Department of Biosciences, University of Bari, Bari"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biosciences, University of Bari, Bari","institution_ids":["https://openalex.org/I5561750"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035949695","display_name":"Roberto Preste","orcid":"https://orcid.org/0000-0001-5935-9542"},"institutions":[{"id":"https://openalex.org/I5561750","display_name":"University of Bari Aldo Moro","ror":"https://ror.org/027ynra39","country_code":"IT","type":"education","lineage":["https://openalex.org/I5561750"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Roberto Preste","raw_affiliation_strings":["Department of Biosciences, University of Bari, Bari"],"raw_orcid":"https://orcid.org/0000-0001-5935-9542","affiliations":[{"raw_affiliation_string":"Department of Biosciences, University of Bari, Bari","institution_ids":["https://openalex.org/I5561750"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076611064","display_name":"Enni Makkonen","orcid":null},"institutions":[{"id":"https://openalex.org/I4210150043","display_name":"CSC - IT Center for Science (Finland)","ror":"https://ror.org/04m8m1253","country_code":"FI","type":"company","lineage":["https://openalex.org/I4210150043"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Enni Makkonen","raw_affiliation_strings":["CSC-IT Center for Science, Espoo"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CSC-IT Center for Science, Espoo","institution_ids":["https://openalex.org/I4210150043"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038905495","display_name":"Heidi Marjonen","orcid":"https://orcid.org/0000-0001-5595-9946"},"institutions":[{"id":"https://openalex.org/I39624965","display_name":"Finnish Institute for Health and Welfare","ror":"https://ror.org/03tf0c761","country_code":"FI","type":"funder","lineage":["https://openalex.org/I39624965"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Heidi Marjonen","raw_affiliation_strings":["Finnish Institute for Health and Welfare, Helsinki"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Finnish Institute for Health and Welfare, Helsinki","institution_ids":["https://openalex.org/I39624965"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012951847","display_name":"Mats Lindstedt","orcid":null},"institutions":[{"id":"https://openalex.org/I4210150043","display_name":"CSC - IT Center for Science (Finland)","ror":"https://ror.org/04m8m1253","country_code":"FI","type":"company","lineage":["https://openalex.org/I4210150043"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Mats Lindstedt","raw_affiliation_strings":["CSC-IT Center for Science, Espoo"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CSC-IT Center for Science, Espoo","institution_ids":["https://openalex.org/I4210150043"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019774367","display_name":"Kati Kristiansson","orcid":"https://orcid.org/0000-0003-4688-107X"},"institutions":[{"id":"https://openalex.org/I39624965","display_name":"Finnish Institute for Health and Welfare","ror":"https://ror.org/03tf0c761","country_code":"FI","type":"funder","lineage":["https://openalex.org/I39624965"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Kati Kristiansson","raw_affiliation_strings":["Finnish Institute for Health and Welfare, Helsinki"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Finnish Institute for Health and Welfare, Helsinki","institution_ids":["https://openalex.org/I39624965"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044085246","display_name":"Sarah Hunt","orcid":"https://orcid.org/0000-0002-8350-1235"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Sarah E. Hunt","raw_affiliation_strings":["European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton"],"raw_orcid":"https://orcid.org/0000-0002-8350-1235","affiliations":[{"raw_affiliation_string":"European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton","institution_ids":["https://openalex.org/I1303153112"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007575726","display_name":"Fiona Cunningham","orcid":"https://orcid.org/0000-0002-7445-2419"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Fiona Cunningham","raw_affiliation_strings":["European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton","institution_ids":["https://openalex.org/I1303153112"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053057317","display_name":"Ilkka Lappalainen","orcid":"https://orcid.org/0000-0001-5762-893X"},"institutions":[{"id":"https://openalex.org/I4210150043","display_name":"CSC - IT Center for Science (Finland)","ror":"https://ror.org/04m8m1253","country_code":"FI","type":"company","lineage":["https://openalex.org/I4210150043"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Ilkka Lappalainen","raw_affiliation_strings":["CSC-IT Center for Science, Espoo"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CSC-IT Center for Science, Espoo","institution_ids":["https://openalex.org/I4210150043"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5023619547","display_name":"Michael J.E. Sternberg","orcid":"https://orcid.org/0000-0002-1884-5445"},"institutions":[{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Michael J.E. Sternberg","raw_affiliation_strings":["Centre for Integrative Systems Biology and Bioinformatics, Imperial College London, London, SW7 2AZ"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Integrative Systems Biology and Bioinformatics, Imperial College London, London, SW7 2AZ","institution_ids":["https://openalex.org/I47508984"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":6,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1350,"currency":"USD","value_usd":1350},"apc_paid":{"value":1350,"currency":"USD","value_usd":1350},"fwci":0.0746,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.40723756,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"9","issue":null,"first_page":"1207","last_page":"1207"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9987999796867371,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9987999796867371,"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/T10751","display_name":"Forensic and Genetic Research","score":0.9871000051498413,"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"}},{"id":"https://openalex.org/T11791","display_name":"Microbial Community Ecology and Physiology","score":0.9843000173568726,"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/elixir","display_name":"Elixir (programming language)","score":0.7409006953239441},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.32930684089660645},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.20421946048736572}],"concepts":[{"id":"https://openalex.org/C103472402","wikidata":"https://www.wikidata.org/wiki/Q5362035","display_name":"Elixir (programming language)","level":2,"score":0.7409006953239441},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.32930684089660645},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.20421946048736572},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.12688/f1000research.24427.1","is_oa":true,"landing_page_url":"https://doi.org/10.12688/f1000research.24427.1","pdf_url":"https://f1000research.com/articles/9-1207/v1/pdf","source":{"id":"https://openalex.org/S4210239046","display_name":"F1000Research","issn_l":"2046-1402","issn":["2046-1402"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320357","host_organization_name":"Faculty of 1000","host_organization_lineage":["https://openalex.org/P4310320357"],"host_organization_lineage_names":["Faculty of 1000"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"F1000Research","raw_type":"journal-article"},{"id":"pmh:oai:zenodo.org:137991","is_oa":true,"landing_page_url":"https://www.openaccessrepository.it/record/137991","pdf_url":null,"source":{"id":"https://openalex.org/S4306402478","display_name":"INFM-OAR (INFN Catania)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210116497","host_organization_name":"Istituto Nazionale di Fisica Nucleare, Sezione di Catania","host_organization_lineage":["https://openalex.org/I4210116497"],"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":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.12688/f1000research.24427.1","is_oa":true,"landing_page_url":"https://doi.org/10.12688/f1000research.24427.1","pdf_url":"https://f1000research.com/articles/9-1207/v1/pdf","source":{"id":"https://openalex.org/S4210239046","display_name":"F1000Research","issn_l":"2046-1402","issn":["2046-1402"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320357","host_organization_name":"Faculty of 1000","host_organization_lineage":["https://openalex.org/P4310320357"],"host_organization_lineage_names":["Faculty of 1000"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"F1000Research","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9","score":0.6000000238418579}],"awards":[{"id":"https://openalex.org/G2973693531","display_name":null,"funder_award_id":"BB/P017193/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G3359526469","display_name":null,"funder_award_id":"BB/L005042/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G8466563894","display_name":null,"funder_award_id":"BB/P026001/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320314023","display_name":"European Molecular Biology Laboratory","ror":"https://ror.org/050589e39"},{"id":"https://openalex.org/F4320320283","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10"},{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3091802260.pdf","grobid_xml":"https://content.openalex.org/works/W3091802260.grobid-xml"},"referenced_works_count":29,"referenced_works":["https://openalex.org/W1903713963","https://openalex.org/W1971835681","https://openalex.org/W1992436001","https://openalex.org/W2036253883","https://openalex.org/W2047544230","https://openalex.org/W2051309999","https://openalex.org/W2051978340","https://openalex.org/W2059145105","https://openalex.org/W2099085143","https://openalex.org/W2112480941","https://openalex.org/W2112589398","https://openalex.org/W2123340910","https://openalex.org/W2126807072","https://openalex.org/W2143988400","https://openalex.org/W2146112039","https://openalex.org/W2158412800","https://openalex.org/W2180760460","https://openalex.org/W2336818861","https://openalex.org/W2417483443","https://openalex.org/W2558885334","https://openalex.org/W2559537906","https://openalex.org/W2582743722","https://openalex.org/W2765285487","https://openalex.org/W2775233218","https://openalex.org/W2809263752","https://openalex.org/W2978232173","https://openalex.org/W3136918052","https://openalex.org/W4206037526","https://openalex.org/W4245532735"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W3160690796","https://openalex.org/W2945781956","https://openalex.org/W2966875286","https://openalex.org/W2900692317","https://openalex.org/W3003405015","https://openalex.org/W2082860237","https://openalex.org/W4383176220","https://openalex.org/W2749889710","https://openalex.org/W2922162671"],"abstract_inverted_index":{"<ns4:p>":[0,36,117,235],"<ns4:bold>Background:</ns4:bold>":[1],"ELIXIR":[2,40,64,191,204,237],"is":[3,205,238],"an":[4,42],"intergovernmental":[5],"organization,":[6],"primarily":[7],"based":[8],"around":[9],"European":[10],"countries,":[11],"established":[12],"to":[13,78,165],"host":[14],"life":[15],"science":[16],"resources,":[17],"including":[18,103],"databases,":[19],"software":[20],"tools,":[21],"training":[22],"material":[23],"and":[24,50,54,75,82,86,94,98,113,125,133,168,218,229,249],"cloud":[25],"storage":[26],"for":[27,52,96,106,253],"the":[28,46,60,80,84,123,183,200,213,225,245],"scientific":[29,184,227],"community":[30,185],"under":[31],"a":[32,89,126,143,155,174,239],"single":[33],"infrastructure.":[34],"</ns4:p>":[35,116,234,258],"<ns4:bold>Methods:</ns4:bold>":[37],"In":[38,208],"2018,":[39],"commissioned":[41],"international":[43],"survey":[44,68,124,180],"on":[45,152,171],"usage":[47,85],"of":[48,62,88,92,128,148,154,173,215,231],"databases":[49,93],"tools":[51,95],"annotating":[53,97],"curating":[55,99],"human":[56,100],"genomic":[57,101],"variants":[58],"with":[59],"aim":[61],"improving":[63],"resources.":[65,233],"The":[66,179],"27-question":[67],"was":[69],"made":[70],"available":[71],"on-line":[72],"between":[73],"September":[74],"December":[76],"2018":[77],"rank":[79],"importance":[81,214],"explore":[83],"limitations":[87],"wide":[90],"range":[91],"variants,":[102],"resources":[104,188,252],"specific":[105],"next":[107],"generation":[108],"sequencing,":[109],"research":[110,144,157,256],"into":[111],"mitochondria":[112],"protein":[114],"structure.":[115],"<ns4:bold>Results:</ns4:bold>":[118],"Eighteen":[119],"countries":[120],"participated":[121],"in":[122,163],"total":[127],"92":[129],"questionnaires":[130],"were":[131,139],"collected":[132],"analysed.":[134],"Most":[135],"respondents":[136,149,211],"(89%,":[137],"n=82)":[138],"from":[140],"academia":[141],"or":[142,193],"environment.":[145],"51%":[146],"(n=47)":[147],"gave":[150],"answers":[151],"behalf":[153,172],"small":[156],"group":[158,176],"(&lt;10":[159],"people),":[160],"33%":[161],"(n=30)":[162],"relation":[164],"individual":[166],"work":[167,201],"16%":[169],"(n=15)":[170],"large":[175],"(&gt;10":[177],"people).":[178],"showed":[181,198],"that":[182,199,241],"considers":[186],"several":[187],"supported":[189],"by":[190,203,221],"crucial":[192],"very":[194],"important.":[195],"Moreover,":[196],"it":[197],"done":[202],"greatly":[206],"valued.":[207],"particular,":[209],"most":[210,246],"acknowledged":[212],"key":[216],"features":[217],"benefits":[219],"promoted":[220],"ELIXIR,":[222],"such":[223],"as":[224],"verified":[226],"quality":[228],"maintenance":[230],"ELIXIR-approved":[232],"<ns4:bold>Conclusions</ns4:bold>":[236],"\u201cone-stop-shop\u201d":[240],"helps":[242],"researchers":[243],"identify":[244],"suitable,":[247],"robust":[248],"well-maintained":[250],"bioinformatics":[251],"delivering":[254],"their":[255],"tasks.":[257]},"counts_by_year":[{"year":2023,"cited_by_count":1}],"updated_date":"2026-07-15T18:14:33.161393","created_date":"2020-10-15T00:00:00"}
