{"id":"https://openalex.org/W2906432481","doi":"https://doi.org/10.1186/s13321-018-0317-4","title":"Configurable web-services for biomedical document annotation","display_name":"Configurable web-services for biomedical document annotation","publication_year":2018,"publication_date":"2018-12-01","ids":{"openalex":"https://openalex.org/W2906432481","doi":"https://doi.org/10.1186/s13321-018-0317-4","mag":"2906432481","pmid":"https://pubmed.ncbi.nlm.nih.gov/30578450"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-018-0317-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-018-0317-4","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-018-0317-4","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"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":"Journal of Cheminformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-018-0317-4","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5073280030","display_name":"S\u00e9rgio Matos","orcid":"https://orcid.org/0000-0003-1941-3983"},"institutions":[{"id":"https://openalex.org/I60858718","display_name":"University of Aveiro","ror":"https://ror.org/00nt41z93","country_code":"PT","type":"education","lineage":["https://openalex.org/I60858718"]}],"countries":["PT"],"is_corresponding":true,"raw_author_name":"S\u00e9rgio Matos","raw_affiliation_strings":["DETI/IEETA, University of Aveiro, Campus Universit\u00e1rio de Santiago, Aveiro, Portugal. aleixomatos@ua.pt","DETI/IEETA, University of Aveiro, Campus Universit\u00e1rio de Santiago, Aveiro, Portugal"],"raw_orcid":"https://orcid.org/0000-0003-1941-3983","affiliations":[{"raw_affiliation_string":"DETI/IEETA, University of Aveiro, Campus Universit\u00e1rio de Santiago, Aveiro, Portugal. aleixomatos@ua.pt","institution_ids":["https://openalex.org/I60858718"]},{"raw_affiliation_string":"DETI/IEETA, University of Aveiro, Campus Universit\u00e1rio de Santiago, Aveiro, Portugal","institution_ids":["https://openalex.org/I60858718"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5073280030"],"corresponding_institution_ids":["https://openalex.org/I60858718"],"apc_list":{"value":1290,"currency":"GBP","value_usd":2190},"apc_paid":{"value":1290,"currency":"GBP","value_usd":2190},"fwci":0.6592,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.67768322,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"10","issue":"1","first_page":"68","last_page":"68"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9998000264167786,"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":0.9998000264167786,"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/T10215","display_name":"Semantic Web and Ontologies","score":0.9965999722480774,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"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/T11986","display_name":"Scientific Computing and Data Management","score":0.9526000022888184,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.8197900652885437},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8189785480499268},{"id":"https://openalex.org/keywords/interoperability","display_name":"Interoperability","score":0.6384573578834534},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.6087678074836731},{"id":"https://openalex.org/keywords/flexibility","display_name":"Flexibility (engineering)","score":0.5517065525054932},{"id":"https://openalex.org/keywords/adaptation","display_name":"Adaptation (eye)","score":0.5438687205314636},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.5425989031791687},{"id":"https://openalex.org/keywords/web-service","display_name":"Web service","score":0.5222266912460327},{"id":"https://openalex.org/keywords/modular-design","display_name":"Modular design","score":0.4917280972003937},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.37396669387817383},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.12662941217422485}],"concepts":[{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.8197900652885437},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8189785480499268},{"id":"https://openalex.org/C20136886","wikidata":"https://www.wikidata.org/wiki/Q749647","display_name":"Interoperability","level":2,"score":0.6384573578834534},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.6087678074836731},{"id":"https://openalex.org/C2780598303","wikidata":"https://www.wikidata.org/wiki/Q65921492","display_name":"Flexibility (engineering)","level":2,"score":0.5517065525054932},{"id":"https://openalex.org/C139807058","wikidata":"https://www.wikidata.org/wiki/Q352374","display_name":"Adaptation (eye)","level":2,"score":0.5438687205314636},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5425989031791687},{"id":"https://openalex.org/C35578498","wikidata":"https://www.wikidata.org/wiki/Q193424","display_name":"Web service","level":2,"score":0.5222266912460327},{"id":"https://openalex.org/C101468663","wikidata":"https://www.wikidata.org/wiki/Q1620158","display_name":"Modular design","level":2,"score":0.4917280972003937},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.37396669387817383},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.12662941217422485},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13321-018-0317-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-018-0317-4","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-018-0317-4","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"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":"Journal of Cheminformatics","raw_type":"journal-article"},{"id":"pmid:30578450","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30578450","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 cheminformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:bde28c9e2f9d4188a5fccc752a7c917d","is_oa":true,"landing_page_url":"https://doaj.org/article/bde28c9e2f9d4188a5fccc752a7c917d","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":"Journal of Cheminformatics, Vol 10, Iss 1, Pp 1-9 (2018)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:6755557","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6755557","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":"J Cheminform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13321-018-0317-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-018-0317-4","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-018-0317-4","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"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":"Journal of Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9","score":0.5600000023841858}],"awards":[{"id":"https://openalex.org/G1167214205","display_name":null,"funder_award_id":"COMPETE","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G121659266","display_name":null,"funder_award_id":"Portugal 2020","funder_id":"https://openalex.org/F4320328601","funder_display_name":"Programa Operacional Regional do Centro"},{"id":"https://openalex.org/G1516346500","display_name":null,"funder_award_id":"01-0145","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"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/G1890519118","display_name":null,"funder_award_id":"PTDC/EEI-ESS/6815/2014","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G1909434394","display_name":null,"funder_award_id":"CENTRO-01-0145-FEDER-000010","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G2311831501","display_name":"Recupera\u00e7\u00e3o de Informa\u00e7\u00e3o Multimodal em Reposit\u00f3rios de Imagem M\u00e9dica","funder_award_id":"PTDC/EEI-ESS/6815/2014","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G2792627247","display_name":null,"funder_award_id":"co-funded by Centro 2020","funder_id":"https://openalex.org/F4320328601","funder_display_name":"Programa Operacional Regional do Centro"},{"id":"https://openalex.org/G3491971210","display_name":null,"funder_award_id":"COMPETE 2020","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G4176497637","display_name":null,"funder_award_id":"COMPETE 2020","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G4481679138","display_name":null,"funder_award_id":"CENTRO-01-0145-FEDER-000010","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G469328782","display_name":null,"funder_award_id":"01-0145-FEDER-000010","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G8387861140","display_name":null,"funder_award_id":"CENTRO-01-0145-FEDER-000010","funder_id":"https://openalex.org/F4320328601","funder_display_name":"Programa Operacional Regional do Centro"}],"funders":[{"id":"https://openalex.org/F4320321033","display_name":"Svenska Forskningsr\u00e5det Formas","ror":"https://ror.org/03pjs1y45"},{"id":"https://openalex.org/F4320328601","display_name":"Programa Operacional Regional do Centro","ror":null},{"id":"https://openalex.org/F4320334779","display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","ror":"https://ror.org/00snfqn58"},{"id":"https://openalex.org/F4320335322","display_name":"European Regional Development Fund","ror":"https://ror.org/00k4n6c32"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2906432481.pdf","grobid_xml":"https://content.openalex.org/works/W2906432481.grobid-xml"},"referenced_works_count":26,"referenced_works":["https://openalex.org/W1528012351","https://openalex.org/W1859283887","https://openalex.org/W1964670939","https://openalex.org/W1976097579","https://openalex.org/W1991811854","https://openalex.org/W1992593537","https://openalex.org/W2040298461","https://openalex.org/W2054118996","https://openalex.org/W2055032581","https://openalex.org/W2065963191","https://openalex.org/W2071038402","https://openalex.org/W2096777607","https://openalex.org/W2097106271","https://openalex.org/W2100627415","https://openalex.org/W2126276057","https://openalex.org/W2147880316","https://openalex.org/W2149369282","https://openalex.org/W2154142897","https://openalex.org/W2160091014","https://openalex.org/W2166240318","https://openalex.org/W2168990503","https://openalex.org/W2169099542","https://openalex.org/W2171374484","https://openalex.org/W2414319702","https://openalex.org/W2775645290","https://openalex.org/W2952769172"],"related_works":["https://openalex.org/W2361861616","https://openalex.org/W2263699433","https://openalex.org/W2377979023","https://openalex.org/W2093262417","https://openalex.org/W2218034408","https://openalex.org/W2392921965","https://openalex.org/W4312626803","https://openalex.org/W2123131699","https://openalex.org/W2358755282","https://openalex.org/W650116260"],"abstract_inverted_index":{"The":[0,69,95],"need":[1],"to":[2,16,76],"efficiently":[3],"find":[4],"and":[5,29,48,66,71,91,106,119],"extract":[6],"information":[7],"from":[8],"the":[9,17,56,81,98,103,117],"continuously":[10],"growing":[11],"biomedical":[12],"literature":[13],"has":[14],"led":[15],"development":[18],"of":[19,27,32,59,97,108,112,121],"various":[20],"annotation":[21,67,78,100,109],"tools":[22,34,90],"aimed":[23],"at":[24],"identifying":[25],"mentions":[26],"entities":[28],"relations.":[30],"Many":[31],"these":[33],"have":[35],"been":[36],"integrated":[37],"in":[38,88],"user-friendly":[39],"applications":[40],"facilitating":[41],"their":[42],"use":[43],"by":[44],"non-expert":[45],"text":[46,64,92],"miners":[47],"database":[49],"curators.":[50],"In":[51],"this":[52,122],"paper":[53],"we":[54],"describe":[55],"latest":[57],"version":[58],"Neji,":[60],"a":[61],"web-services":[62],"ready":[63],"processing":[65],"framework.":[68,123],"modular":[70],"flexible":[72],"architecture":[73],"facilitates":[74],"adaptation":[75],"different":[77],"requirements,":[79],"while":[80],"built-in":[82],"web":[83,99],"services":[84],"allow":[85],"its":[86],"integration":[87],"external":[89],"mining":[93],"pipelines.":[94],"evaluation":[96],"server":[101],"on":[102],"technical":[104],"interoperability":[105],"performance":[107],"servers":[110],"track":[111],"BioCreative":[113],"V.5":[114],"further":[115],"illustrates":[116],"flexibility":[118],"applicability":[120]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":2}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
