{"id":"https://openalex.org/W2511894380","doi":"https://doi.org/10.1093/database/baw106","title":"BioC viewer: a web-based tool for displaying and merging annotations in BioC","display_name":"BioC viewer: a web-based tool for displaying and merging annotations in BioC","publication_year":2016,"publication_date":"2016-01-01","ids":{"openalex":"https://openalex.org/W2511894380","doi":"https://doi.org/10.1093/database/baw106","mag":"2511894380","pmid":"https://pubmed.ncbi.nlm.nih.gov/27515823"},"language":"en","primary_location":{"id":"doi:10.1093/database/baw106","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baw106","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/baw106/8224952/baw106.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Database","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/baw106/8224952/baw106.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5009019474","display_name":"Soo-Yong Shin","orcid":"https://orcid.org/0000-0002-2410-6120"},"institutions":[{"id":"https://openalex.org/I2801680663","display_name":"Asan Medical Center","ror":"https://ror.org/03s5q0090","country_code":"KR","type":"healthcare","lineage":["https://openalex.org/I2801680663","https://openalex.org/I4210167194"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Soo-Yong Shin","raw_affiliation_strings":["Department of Biomedical Informatics, Asan Medical Center, Seoul 05505, Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Asan Medical Center, Seoul 05505, Korea","institution_ids":["https://openalex.org/I2801680663"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100460452","display_name":"Sun Kim","orcid":"https://orcid.org/0000-0003-3072-6649"},"institutions":[{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sun Kim","raw_affiliation_strings":["National Center for Biotechnology Information, National Library of Medicine, National Institute of Health, Bethesda, MD 20894, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Center for Biotechnology Information, National Library of Medicine, National Institute of Health, Bethesda, MD 20894, USA","institution_ids":["https://openalex.org/I4210109390"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111895206","display_name":"W. John Wilbur","orcid":null},"institutions":[{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"W. John Wilbur","raw_affiliation_strings":["National Center for Biotechnology Information, National Library of Medicine, National Institute of Health, Bethesda, MD 20894, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Center for Biotechnology Information, National Library of Medicine, National Institute of Health, Bethesda, MD 20894, USA","institution_ids":["https://openalex.org/I4210109390"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5091215067","display_name":"Dongseop Kwon","orcid":null},"institutions":[{"id":"https://openalex.org/I89440247","display_name":"Myongji University","ror":"https://ror.org/00s9dpb54","country_code":"KR","type":"education","lineage":["https://openalex.org/I89440247"]}],"countries":["KR"],"is_corresponding":true,"raw_author_name":"Dongseop Kwon","raw_affiliation_strings":["Deptartment of Computer Engineering, Myongji University, Yongin, Gyeonggi-do 17058, Korea dongseop@mju.ac.kr","Deptartment of Computer Engineering, Myongji University, Yongin, Gyeonggi-do 17058, Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Deptartment of Computer Engineering, Myongji University, Yongin, Gyeonggi-do 17058, Korea dongseop@mju.ac.kr","institution_ids":["https://openalex.org/I89440247"]},{"raw_affiliation_string":"Deptartment of Computer Engineering, Myongji University, Yongin, Gyeonggi-do 17058, Korea","institution_ids":["https://openalex.org/I89440247"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5091215067"],"corresponding_institution_ids":["https://openalex.org/I89440247"],"apc_list":{"value":1415,"currency":"GBP","value_usd":1735},"apc_paid":{"value":1415,"currency":"GBP","value_usd":1735},"fwci":0.8016,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.74803547,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"2016","issue":null,"first_page":"baw106","last_page":"baw106"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9958000183105469,"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":0.9958000183105469,"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":0.9733999967575073,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9629999995231628,"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/computer-science","display_name":"Computer science","score":0.7525221109390259},{"id":"https://openalex.org/keywords/upload","display_name":"Upload","score":0.5981748700141907},{"id":"https://openalex.org/keywords/usability","display_name":"Usability","score":0.5935710668563843},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.5475866794586182},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.4921035170555115},{"id":"https://openalex.org/keywords/unicode","display_name":"Unicode","score":0.4722278118133545},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4416287839412689},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.42718270421028137},{"id":"https://openalex.org/keywords/human\u2013computer-interaction","display_name":"Human\u2013computer interaction","score":0.30306845903396606},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.28929638862609863},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2557651400566101}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7525221109390259},{"id":"https://openalex.org/C71901391","wikidata":"https://www.wikidata.org/wiki/Q7126699","display_name":"Upload","level":2,"score":0.5981748700141907},{"id":"https://openalex.org/C170130773","wikidata":"https://www.wikidata.org/wiki/Q216378","display_name":"Usability","level":2,"score":0.5935710668563843},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.5475866794586182},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.4921035170555115},{"id":"https://openalex.org/C500551929","wikidata":"https://www.wikidata.org/wiki/Q8819","display_name":"Unicode","level":2,"score":0.4722278118133545},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4416287839412689},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.42718270421028137},{"id":"https://openalex.org/C107457646","wikidata":"https://www.wikidata.org/wiki/Q207434","display_name":"Human\u2013computer interaction","level":1,"score":0.30306845903396606},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.28929638862609863},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2557651400566101},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","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":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","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":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D066289","descriptor_name":"Data Curation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D066289","descriptor_name":"Data Curation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D066289","descriptor_name":"Data Curation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/database/baw106","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baw106","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/baw106/8224952/baw106.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Database","raw_type":"journal-article"},{"id":"pmid:27515823","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27515823","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":"Database : the journal of biological databases and curation","raw_type":null},{"id":"pmh:oai:open-archive.highwire.org:databa:2016/0/baw106","is_oa":false,"landing_page_url":"http://database.oxfordjournals.org/cgi/content/short/2016/0/baw106","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"},{"id":"pmh:oai:pubmedcentral.nih.gov:4980568","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4980568","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":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Database (Oxford)","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/database/baw106","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baw106","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/baw106/8224952/baw106.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Database","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320320671","display_name":"National Research Foundation","ror":"https://ror.org/05s0g1g46"},{"id":"https://openalex.org/F4320321279","display_name":"Myongji University","ror":"https://ror.org/00s9dpb54"},{"id":"https://openalex.org/F4320322030","display_name":"Ministry of Science, ICT and Future Planning","ror":"https://ror.org/032e49973"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2511894380.pdf","grobid_xml":"https://content.openalex.org/works/W2511894380.grobid-xml"},"referenced_works_count":12,"referenced_works":["https://openalex.org/W2020357318","https://openalex.org/W2098068971","https://openalex.org/W2104148262","https://openalex.org/W2105939244","https://openalex.org/W2106279837","https://openalex.org/W2121157913","https://openalex.org/W2149852578","https://openalex.org/W2169425537","https://openalex.org/W2251971570","https://openalex.org/W2252278859","https://openalex.org/W2509885322","https://openalex.org/W2915975108"],"related_works":["https://openalex.org/W1953677193","https://openalex.org/W3113362864","https://openalex.org/W2404000518","https://openalex.org/W589182691","https://openalex.org/W2039041919","https://openalex.org/W1993328117","https://openalex.org/W2358376734","https://openalex.org/W2160673483","https://openalex.org/W4288900686","https://openalex.org/W2046833766"],"abstract_inverted_index":{"BioC":[0,20,46,77,90,98,101,119,129,142,146,149,175,187],"is":[1,25,152,165],"an":[2,169],"XML-based":[3],"format":[4,24],"designed":[5],"to":[6,26,63,79,127,136,180],"provide":[7],"interoperability":[8],"for":[9,212,217],"text":[10,53],"mining":[11],"tools":[12],"and":[13,54,107,172,220],"manual":[14],"curation":[15],"results.":[16],"A":[17],"challenge":[18],"of":[19,86,141],"as":[21,83,122,124],"a":[22,37,84,148,166,190,200],"standard":[23],"align":[27,182],"annotations":[28,55],"from":[29,158,206],"multiple":[30],"systems.":[31],"Ideally,":[32],"this":[33],"should":[34],"not":[35],"be":[36,197],"major":[38],"problem":[39],"if":[40],"users":[41],"follow":[42],"guidelines":[43],"given":[44],"by":[45],"key":[47],"files.":[48],"Nevertheless,":[49],"the":[50,76,87,97,100,118,128,132,138,159,174,178,184,213],"misalignment":[51,139],"between":[52,168],"happens":[56],"quite":[57],"often":[58],"because":[59],"different":[60,65],"systems":[61],"tend":[62],"use":[64],"software":[66],"development":[67],"environments,":[68],"e.g.":[69],"ASCII":[70],"vs.":[71],"Unicode.":[72],"We":[73],"first":[74],"implemented":[75],"Viewer":[78,102,120,130,176,188],"assist":[80],"BioGRID":[81,207],"curators":[82,208],"part":[85],"BioCreative":[88,133],"V":[89,134],"track":[91],"(Collaborative":[92],"Biocurator":[93],"Assistant":[94],"Task).":[95],"For":[96],"track,":[99],"helped":[103],"curate":[104],"protein-protein":[105],"interaction":[106,109],"genetic":[108],"pairs":[110],"appearing":[111],"in":[112],"full-text":[113,161],"articles.":[114],"Here,":[115],"we":[116],"describe":[117],"itself":[121],"well":[123],"improvements":[125],"made":[126],"since":[131],"Workshop":[135],"address":[137],"issue":[140],"annotations.":[143],"While":[144],"uploading":[145],"files,":[147],"merge":[150],"process":[151],"offered":[153],"when":[154],"there":[155,164],"are":[156],"files":[157],"same":[160],"article.":[162],"If":[163],"mismatch":[167],"annotated":[170],"offset":[171,179],"text,":[173],"adjusts":[177],"correctly":[181],"with":[183],"text.":[185],"The":[186,204],"has":[189,209],"user-friendly":[191],"interface,":[192,215],"where":[193],"most":[194],"operations":[195],"can":[196],"performed":[198],"within":[199],"few":[201],"mouse":[202],"clicks.":[203],"feedback":[205],"been":[210],"positive":[211],"web":[214],"particularly":[216],"its":[218],"usability":[219],"learnability.Database":[221],"URL:":[222],"http://viewer.bioqrator.org.":[223]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2016,"cited_by_count":3}],"updated_date":"2026-08-02T14:50:37.381335","created_date":"2025-10-10T00:00:00"}
