{"id":"https://openalex.org/W2135912801","doi":"https://doi.org/10.1186/1471-2105-6-s1-s5","title":"Exploring the boundaries: gene and protein identification in biomedical text","display_name":"Exploring the boundaries: gene and protein identification in biomedical text","publication_year":2005,"publication_date":"2005-05-01","ids":{"openalex":"https://openalex.org/W2135912801","doi":"https://doi.org/10.1186/1471-2105-6-s1-s5","mag":"2135912801","pmid":"https://pubmed.ncbi.nlm.nih.gov/15960839"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-6-s1-s5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-6-s1-s5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-6-S1-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/10.1186/1471-2105-6-S1-S5","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5023694822","display_name":"Jenny Rose Finkel","orcid":null},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jenny Finkel","raw_affiliation_strings":["Department of Computer Science, Stanford University, Stanford, CA 94305-9040, USA. jrfinkel@stanford.edu","Department of Computer Science , Stanford University, Stanford, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Stanford University, Stanford, CA 94305-9040, USA. jrfinkel@stanford.edu","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Department of Computer Science , Stanford University, Stanford, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024785577","display_name":"Shipra Dingare","orcid":null},"institutions":[{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Shipra Dingare","raw_affiliation_strings":["Institute for Communicating and Collaborative Systems, University of Edinburgh, United Kingdom","Institute for Communicating and Collaborative Systems, University of Edinburgh, , United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Communicating and Collaborative Systems, University of Edinburgh, United Kingdom","institution_ids":["https://openalex.org/I98677209"]},{"raw_affiliation_string":"Institute for Communicating and Collaborative Systems, University of Edinburgh, , United Kingdom","institution_ids":["https://openalex.org/I98677209"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046006076","display_name":"Christopher D. Manning","orcid":"https://orcid.org/0000-0001-6155-649X"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Christopher D Manning","raw_affiliation_strings":["Department of Computer Science, Stanford University, Stanford, CA, 94305-9040, USA","Department of Computer Science , Stanford University, Stanford, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Stanford University, Stanford, CA, 94305-9040, USA","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Department of Computer Science , Stanford University, Stanford, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040564747","display_name":"Malvina Nissim","orcid":"https://orcid.org/0000-0001-5289-0971"},"institutions":[{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Malvina Nissim","raw_affiliation_strings":["Institute for Communicating and Collaborative Systems, University of Edinburgh, United Kingdom","Institute for Communicating and Collaborative Systems, University of Edinburgh, , United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Communicating and Collaborative Systems, University of Edinburgh, United Kingdom","institution_ids":["https://openalex.org/I98677209"]},{"raw_affiliation_string":"Institute for Communicating and Collaborative Systems, University of Edinburgh, , United Kingdom","institution_ids":["https://openalex.org/I98677209"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043179000","display_name":"Beatrice Alex","orcid":"https://orcid.org/0000-0002-7279-1476"},"institutions":[{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Beatrice Alex","raw_affiliation_strings":["Institute for Communicating and Collaborative Systems, University of Edinburgh, United Kingdom","Institute for Communicating and Collaborative Systems, University of Edinburgh, , United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Communicating and Collaborative Systems, University of Edinburgh, United Kingdom","institution_ids":["https://openalex.org/I98677209"]},{"raw_affiliation_string":"Institute for Communicating and Collaborative Systems, University of Edinburgh, , United Kingdom","institution_ids":["https://openalex.org/I98677209"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5108653041","display_name":"Claire Grover","orcid":"https://orcid.org/0000-0001-7019-1250"},"institutions":[{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Claire Grover","raw_affiliation_strings":["Institute for Communicating and Collaborative Systems, University of Edinburgh, United Kingdom","Institute for Communicating and Collaborative Systems, University of Edinburgh, , United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Communicating and Collaborative Systems, University of Edinburgh, United Kingdom","institution_ids":["https://openalex.org/I98677209"]},{"raw_affiliation_string":"Institute for Communicating and Collaborative Systems, University of Edinburgh, , United Kingdom","institution_ids":["https://openalex.org/I98677209"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5046006076"],"corresponding_institution_ids":["https://openalex.org/I97018004"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":5.8148,"has_fulltext":true,"cited_by_count":108,"citation_normalized_percentile":{"value":0.97022452,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"6","issue":"S1","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":0.9983000159263611,"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":0.9983000159263611,"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/T10028","display_name":"Topic Modeling","score":0.00039999998989515007,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.00019999999494757503,"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":0.7627577781677246},{"id":"https://openalex.org/keywords/precision-and-recall","display_name":"Precision and recall","score":0.6458215117454529},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.6034405827522278},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5671798586845398},{"id":"https://openalex.org/keywords/biomedical-text-mining","display_name":"Biomedical text mining","score":0.5247576236724854},{"id":"https://openalex.org/keywords/named-entity-recognition","display_name":"Named-entity recognition","score":0.4912378191947937},{"id":"https://openalex.org/keywords/information-extraction","display_name":"Information extraction","score":0.4851594567298889},{"id":"https://openalex.org/keywords/recall","display_name":"Recall","score":0.43313974142074585},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.4265977740287781},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4254530072212219},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.41795897483825684},{"id":"https://openalex.org/keywords/text-mining","display_name":"Text mining","score":0.34213075041770935},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1750946044921875},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.11858507990837097},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09299728274345398}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7627577781677246},{"id":"https://openalex.org/C81669768","wikidata":"https://www.wikidata.org/wiki/Q2359161","display_name":"Precision and recall","level":2,"score":0.6458215117454529},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.6034405827522278},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5671798586845398},{"id":"https://openalex.org/C165141518","wikidata":"https://www.wikidata.org/wiki/Q4915126","display_name":"Biomedical text mining","level":3,"score":0.5247576236724854},{"id":"https://openalex.org/C2779135771","wikidata":"https://www.wikidata.org/wiki/Q403574","display_name":"Named-entity recognition","level":3,"score":0.4912378191947937},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.4851594567298889},{"id":"https://openalex.org/C100660578","wikidata":"https://www.wikidata.org/wiki/Q18733","display_name":"Recall","level":2,"score":0.43313974142074585},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.4265977740287781},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4254530072212219},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.41795897483825684},{"id":"https://openalex.org/C71472368","wikidata":"https://www.wikidata.org/wiki/Q676880","display_name":"Text mining","level":2,"score":0.34213075041770935},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1750946044921875},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.11858507990837097},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09299728274345398},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D005796","descriptor_name":"Genes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005796","descriptor_name":"Genes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005796","descriptor_name":"Genes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008091","descriptor_name":"Literature","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008091","descriptor_name":"Literature","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008091","descriptor_name":"Literature","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000145","qualifier_name":"classification","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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D035843","descriptor_name":"Biomedical Research","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D035843","descriptor_name":"Biomedical Research","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D035843","descriptor_name":"Biomedical Research","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D035843","descriptor_name":"Biomedical Research","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D035843","descriptor_name":"Biomedical Research","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D035843","descriptor_name":"Biomedical Research","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":8,"locations":[{"id":"doi:10.1186/1471-2105-6-s1-s5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-6-s1-s5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-6-S1-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:15960839","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15960839","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:CiteSeerX.psu:10.1.1.135.5386","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.135.5386","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.stanford.edu/~jrfinkel/papers/bmc.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.142.2241","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.142.2241","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.ltg.ed.ac.uk/seer/papers/bmc_BioInf.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.65.5448","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.65.5448","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://nlp.stanford.edu/cmanning/papers/BMC-Bioinformatics-Finkel-2005.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.74.8122","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.74.8122","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://nlp.stanford.edu/cmanning/papers/BMC-Bioinformatics-Finkel-2005.ps","raw_type":"text"},{"id":"pmh:oai:doaj.org/article:dd6064932d02428e8e55575a96b10197","is_oa":false,"landing_page_url":"https://doaj.org/article/dd6064932d02428e8e55575a96b10197","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 6, Iss Suppl 1, p S5 (2005)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:1869019","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1869019","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:10.1186/1471-2105-6-s1-s5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-6-s1-s5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-6-S1-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":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320320332","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2135912801.pdf","grobid_xml":"https://content.openalex.org/works/W2135912801.grobid-xml"},"referenced_works_count":25,"referenced_works":["https://openalex.org/W1482328859","https://openalex.org/W1505083828","https://openalex.org/W1574901103","https://openalex.org/W1773803948","https://openalex.org/W1934019294","https://openalex.org/W1982982698","https://openalex.org/W1988995507","https://openalex.org/W1991154713","https://openalex.org/W2004111828","https://openalex.org/W2004384146","https://openalex.org/W2031868269","https://openalex.org/W2041614298","https://openalex.org/W2083783479","https://openalex.org/W2102667697","https://openalex.org/W2124416056","https://openalex.org/W2130160813","https://openalex.org/W2135843243","https://openalex.org/W2139193890","https://openalex.org/W2144001613","https://openalex.org/W2144087279","https://openalex.org/W2144578941","https://openalex.org/W2147880316","https://openalex.org/W2160842254","https://openalex.org/W2162461580","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W2548624545","https://openalex.org/W2916255597","https://openalex.org/W2017675085","https://openalex.org/W3091569222","https://openalex.org/W3004288456","https://openalex.org/W2134429551","https://openalex.org/W4379379356","https://openalex.org/W1663435917","https://openalex.org/W1496929818","https://openalex.org/W2094989391"],"abstract_inverted_index":{"BACKGROUND:":[0],"Good":[1],"automatic":[2,9],"information":[3],"extraction":[4],"tools":[5],"offer":[6],"hope":[7],"for":[8,25,41],"processing":[10],"of":[11,39,64,68,77,81,93,103,116],"the":[12,56,71,84,97,113],"exploding":[13],"biomedical":[14,48],"literature,":[15],"and":[16,44,60,66,74,79,112,125],"successful":[17],"named":[18],"entity":[19,110],"recognition":[20],"is":[21],"a":[22,31,36,62,75,105],"key":[23],"component":[24],"such":[26],"tools.":[27],"METHODS:":[28],"We":[29],"present":[30],"maximum-entropy":[32],"based":[33],"system":[34,52],"incorporating":[35],"diverse":[37],"set":[38],"features":[40,94],"identifying":[42,109],"gene":[43],"protein":[45],"names":[46],"in":[47,55,70,83],"abstracts.":[49],"RESULTS:":[50],"This":[51],"was":[53],"entered":[54],"BioCreative":[57],"comparative":[58],"evaluation":[59,73],"achieved":[61],"precision":[63,76],"0.83":[65],"recall":[67,80],"0.84":[69],"\"open\"":[72],"0.78":[78],"0.85":[82],"\"closed\"":[85],"evaluation.":[86],"CONCLUSION:":[87],"Central":[88],"contributions":[89],"are":[90],"rich":[91],"use":[92,115],"derived":[95],"from":[96],"training":[98],"data":[99],"at":[100],"multiple":[101],"levels":[102],"granularity,":[104],"focus":[106],"on":[107],"correctly":[108],"boundaries,":[111],"innovative":[114],"several":[117],"external":[118],"knowledge":[119],"sources":[120],"including":[121],"full":[122],"MEDLINE":[123],"abstracts":[124],"web":[126],"searches.":[127]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":6},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":7},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":7},{"year":2012,"cited_by_count":3}],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}
