{"id":"https://openalex.org/W2905553692","doi":"https://doi.org/10.1186/s13321-018-0319-2","title":"SIA: a scalable interoperable annotation server for biomedical named entities","display_name":"SIA: a scalable interoperable annotation server for biomedical named entities","publication_year":2018,"publication_date":"2018-12-01","ids":{"openalex":"https://openalex.org/W2905553692","doi":"https://doi.org/10.1186/s13321-018-0319-2","mag":"2905553692","pmid":"https://pubmed.ncbi.nlm.nih.gov/30552534"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-018-0319-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-018-0319-2","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-018-0319-2","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":["arxiv","crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-018-0319-2","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Johannes Kirschnick","orcid":null},"institutions":[{"id":"https://openalex.org/I33256026","display_name":"German Research Centre for Artificial Intelligence","ror":"https://ror.org/01ayc5b57","country_code":"DE","type":"funder","lineage":["https://openalex.org/I33256026"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Johannes Kirschnick","raw_affiliation_strings":["DFKI Language Technology Lab, Alt-Moabit 91c, Berlin, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"DFKI Language Technology Lab, Alt-Moabit 91c, Berlin, Germany","institution_ids":["https://openalex.org/I33256026"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Philippe Thomas","orcid":null},"institutions":[{"id":"https://openalex.org/I33256026","display_name":"German Research Centre for Artificial Intelligence","ror":"https://ror.org/01ayc5b57","country_code":"DE","type":"funder","lineage":["https://openalex.org/I33256026"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Philippe Thomas","raw_affiliation_strings":["DFKI Language Technology Lab, Alt-Moabit 91c, Berlin, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"DFKI Language Technology Lab, Alt-Moabit 91c, Berlin, Germany","institution_ids":["https://openalex.org/I33256026"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Roland Roller","orcid":null},"institutions":[{"id":"https://openalex.org/I33256026","display_name":"German Research Centre for Artificial Intelligence","ror":"https://ror.org/01ayc5b57","country_code":"DE","type":"funder","lineage":["https://openalex.org/I33256026"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Roland Roller","raw_affiliation_strings":["DFKI Language Technology Lab, Alt-Moabit 91c, Berlin, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"DFKI Language Technology Lab, Alt-Moabit 91c, Berlin, Germany","institution_ids":["https://openalex.org/I33256026"]}]},{"author_position":"last","author":{"id":null,"display_name":"Leonhard Hennig","orcid":"https://orcid.org/0000-0002-9594-2011"},"institutions":[{"id":"https://openalex.org/I33256026","display_name":"German Research Centre for Artificial Intelligence","ror":"https://ror.org/01ayc5b57","country_code":"DE","type":"funder","lineage":["https://openalex.org/I33256026"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Leonhard Hennig","raw_affiliation_strings":["DFKI Language Technology Lab, Alt-Moabit 91c, Berlin, Germany. leonhard.hennig@dfki.de"],"raw_orcid":"https://orcid.org/0000-0002-9594-2011","affiliations":[{"raw_affiliation_string":"DFKI Language Technology Lab, Alt-Moabit 91c, Berlin, Germany. leonhard.hennig@dfki.de","institution_ids":["https://openalex.org/I33256026"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I33256026"],"apc_list":{"value":2190,"currency":"USD","value_usd":2190},"apc_paid":{"value":2190,"currency":"USD","value_usd":2190},"fwci":0.0824,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.44900367,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"10","issue":"1","first_page":"63","last_page":"63"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9879000186920166,"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":0.9879000186920166,"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":0.002400000113993883,"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":0.0008999999845400453,"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":0.7986000180244446},{"id":"https://openalex.org/keywords/interoperability","display_name":"Interoperability","score":0.7742000222206116},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.7044000029563904},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.6848000288009644},{"id":"https://openalex.org/keywords/server","display_name":"Server","score":0.5598999857902527},{"id":"https://openalex.org/keywords/information-extraction","display_name":"Information extraction","score":0.5333999991416931},{"id":"https://openalex.org/keywords/named-entity-recognition","display_name":"Named-entity recognition","score":0.5241000056266785}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8366000056266785},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.7986000180244446},{"id":"https://openalex.org/C20136886","wikidata":"https://www.wikidata.org/wiki/Q749647","display_name":"Interoperability","level":2,"score":0.7742000222206116},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.7044000029563904},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.6848000288009644},{"id":"https://openalex.org/C93996380","wikidata":"https://www.wikidata.org/wiki/Q44127","display_name":"Server","level":2,"score":0.5598999857902527},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.5333999991416931},{"id":"https://openalex.org/C2779135771","wikidata":"https://www.wikidata.org/wiki/Q403574","display_name":"Named-entity recognition","level":3,"score":0.5241000056266785},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.4902999997138977},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4876999855041504},{"id":"https://openalex.org/C2780560020","wikidata":"https://www.wikidata.org/wiki/Q79719","display_name":"License","level":2,"score":0.4569000005722046},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.3831999897956848},{"id":"https://openalex.org/C91632574","wikidata":"https://www.wikidata.org/wiki/Q15088675","display_name":"Data curation","level":2,"score":0.36649999022483826},{"id":"https://openalex.org/C2777889803","wikidata":"https://www.wikidata.org/wiki/Q25047676","display_name":"Named entity","level":2,"score":0.34529998898506165},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.3199000060558319},{"id":"https://openalex.org/C2985727698","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Semantic annotation","level":3,"score":0.3034000098705292},{"id":"https://openalex.org/C165141518","wikidata":"https://www.wikidata.org/wiki/Q4915126","display_name":"Biomedical text mining","level":3,"score":0.29919999837875366},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.29440000653266907},{"id":"https://openalex.org/C72634772","wikidata":"https://www.wikidata.org/wiki/Q386824","display_name":"Data integration","level":2,"score":0.2872999906539917},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.257999986410141}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1186/s13321-018-0319-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-018-0319-2","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-018-0319-2","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:30552534","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30552534","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:arXiv.org:2004.03822","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2004.03822","pdf_url":"https://arxiv.org/pdf/2004.03822","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"pmh:oai:doaj.org/article:8b87272a24044c1985fcb98322a0aada","is_oa":true,"landing_page_url":"https://doaj.org/article/8b87272a24044c1985fcb98322a0aada","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 1-7 (2018)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:6755617","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6755617","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/s13321-018-0319-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-018-0319-2","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-018-0319-2","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":[],"awards":[{"id":"https://openalex.org/G2469576159","display_name":null,"funder_award_id":"01MD16011F","funder_id":"https://openalex.org/F4320323803","funder_display_name":"Bundesministerium f\u00fcr Wirtschaft und Energie"},{"id":"https://openalex.org/G7809013012","display_name":null,"funder_award_id":"01IS14013E","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G7993038824","display_name":null,"funder_award_id":"01IS14013E","funder_id":"https://openalex.org/F4320334604","funder_display_name":"Banting and Best Diabetes Centre, University of Toronto"},{"id":"https://openalex.org/G920034530","display_name":null,"funder_award_id":"01MD15007B","funder_id":"https://openalex.org/F4320323803","funder_display_name":"Bundesministerium f\u00fcr Wirtschaft und Energie"}],"funders":[{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"},{"id":"https://openalex.org/F4320323803","display_name":"Bundesministerium f\u00fcr Wirtschaft und Energie","ror":"https://ror.org/02vgg2808"},{"id":"https://openalex.org/F4320334604","display_name":"Banting and Best Diabetes Centre, University of Toronto","ror":"https://ror.org/03dbr7087"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2905553692.pdf","grobid_xml":"https://content.openalex.org/works/W2905553692.grobid-xml"},"referenced_works_count":12,"referenced_works":["https://openalex.org/W1570445666","https://openalex.org/W1976316416","https://openalex.org/W1983296967","https://openalex.org/W2099964107","https://openalex.org/W2100627415","https://openalex.org/W2101553882","https://openalex.org/W2121810937","https://openalex.org/W2123079914","https://openalex.org/W2142016317","https://openalex.org/W2159583324","https://openalex.org/W2414451196","https://openalex.org/W2425612555"],"related_works":[],"abstract_inverted_index":{"Recent":[0],"years":[1],"showed":[2],"a":[3,67],"strong":[4],"increase":[5,12],"in":[6,13],"biomedical":[7],"sciences":[8],"and":[9,28,45,60,70,88,90],"an":[10],"inherent":[11],"publication":[14],"volume.":[15],"Extraction":[16],"of":[17,35,62],"specific":[18],"information":[19,29],"from":[20],"these":[21],"sources":[22],"requires":[23],"highly":[24],"sophisticated":[25],"text":[26],"mining":[27],"extraction":[30],"tools.":[31],"However,":[32],"the":[33,57],"integration":[34],"freely":[36,92],"available":[37,93],"tools":[38],"into":[39],"customized":[40],"workflows":[41],"is":[42,91],"often":[43],"cumbersome":[44],"difficult.":[46],"We":[47],"describe":[48],"SIA":[49],"(Scalable":[50],"Interoperable":[51],"Annotation":[52],"Server),":[53],"our":[54],"contribution":[55],"to":[56],"BeCalm-Technical":[58],"interoperability":[59],"performance":[61],"annotation":[63,72],"servers":[64],"(BeCalm-TIPS)":[65],"task,":[66],"scalable,":[68],"extensible,":[69],"robust":[71],"service.":[73],"The":[74],"system":[75],"currently":[76],"covers":[77],"six":[78],"named":[79],"entity":[80],"types":[81],"(i.e.,":[82],"chemicals,":[83],"diseases,":[84],"genes,":[85],"miRNA,":[86],"mutations,":[87],"organisms)":[89],"under":[94],"Apache":[95],"2.0":[96],"license":[97],"at":[98],"https://github.com/Erechtheus/sia":[99],".":[100]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2019,"cited_by_count":1}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2018-12-22T00:00:00"}
