{"id":"https://openalex.org/W2108010925","doi":"https://doi.org/10.1186/1471-2105-10-233","title":"A realistic assessment of methods for extracting gene/protein interactions from free text","display_name":"A realistic assessment of methods for extracting gene/protein interactions from free text","publication_year":2009,"publication_date":"2009-07-28","ids":{"openalex":"https://openalex.org/W2108010925","doi":"https://doi.org/10.1186/1471-2105-10-233","mag":"2108010925","pmid":"https://pubmed.ncbi.nlm.nih.gov/19635172"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-10-233","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-233","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-233","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/10.1186/1471-2105-10-233","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5028349382","display_name":"Renata Kabiljo","orcid":"https://orcid.org/0000-0002-5183-4844"},"institutions":[{"id":"https://openalex.org/I98259816","display_name":"Birkbeck, University of London","ror":"https://ror.org/02mb95055","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I98259816"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Renata Kabiljo","raw_affiliation_strings":["School of Crystallography and Institute of Structural and Molecular Biology, Birkbeck College, University of London, Malet Street, London WC1E 7HX UK. r.kabiljo@mail.cryst.bbk.ac.uk","School of Crystallography and Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, UK"],"affiliations":[{"raw_affiliation_string":"School of Crystallography and Institute of Structural and Molecular Biology, Birkbeck College, University of London, Malet Street, London WC1E 7HX UK. r.kabiljo@mail.cryst.bbk.ac.uk","institution_ids":["https://openalex.org/I98259816"]},{"raw_affiliation_string":"School of Crystallography and Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, UK","institution_ids":["https://openalex.org/I98259816"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041774922","display_name":"Andrew B. Clegg","orcid":null},"institutions":[{"id":"https://openalex.org/I4210157240","display_name":"Institute of Structural and Molecular Biology","ror":"https://ror.org/05wsetc54","country_code":"GB","type":"facility","lineage":["https://openalex.org/I124357947","https://openalex.org/I124357947","https://openalex.org/I4210157240","https://openalex.org/I45129253","https://openalex.org/I98259816"]},{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Andrew B Clegg","raw_affiliation_strings":["Research Department of Structural and Molecular Biology and Institute of Structural and Molecular Biology, University College London, Gower St, London, WC1E 6BT, UK","Research Department of Structural and Molecular Biology and Institute of Structural and Molecular Biology, University College London, London, UK"],"affiliations":[{"raw_affiliation_string":"Research Department of Structural and Molecular Biology and Institute of Structural and Molecular Biology, University College London, Gower St, London, WC1E 6BT, UK","institution_ids":["https://openalex.org/I4210157240","https://openalex.org/I45129253"]},{"raw_affiliation_string":"Research Department of Structural and Molecular Biology and Institute of Structural and Molecular Biology, University College London, London, UK","institution_ids":["https://openalex.org/I45129253"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5021137505","display_name":"Adrian J. Shepherd","orcid":"https://orcid.org/0000-0003-0194-8613"},"institutions":[{"id":"https://openalex.org/I4210157240","display_name":"Institute of Structural and Molecular Biology","ror":"https://ror.org/05wsetc54","country_code":"GB","type":"facility","lineage":["https://openalex.org/I124357947","https://openalex.org/I124357947","https://openalex.org/I4210157240","https://openalex.org/I45129253","https://openalex.org/I98259816"]},{"id":"https://openalex.org/I98259816","display_name":"Birkbeck, University of London","ror":"https://ror.org/02mb95055","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I98259816"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Adrian J Shepherd","raw_affiliation_strings":["School of Crystallography and Institute of Structural and Molecular Biology, Birkbeck College, University of London, Malet Street, London, WC1E 7HX, UK","School of Crystallography and Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, UK"],"affiliations":[{"raw_affiliation_string":"School of Crystallography and Institute of Structural and Molecular Biology, Birkbeck College, University of London, Malet Street, London, WC1E 7HX, UK","institution_ids":["https://openalex.org/I98259816","https://openalex.org/I4210157240"]},{"raw_affiliation_string":"School of Crystallography and Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, UK","institution_ids":["https://openalex.org/I98259816"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5028349382"],"corresponding_institution_ids":["https://openalex.org/I98259816"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":3.6392,"has_fulltext":true,"cited_by_count":67,"citation_normalized_percentile":{"value":0.93670129,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"10","issue":"1","first_page":"233","last_page":"233"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9843000173568726,"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":0.9172999858856201,"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":0.7813771963119507},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.6564724445343018},{"id":"https://openalex.org/keywords/biomedical-text-mining","display_name":"Biomedical text mining","score":0.6397325396537781},{"id":"https://openalex.org/keywords/text-messaging","display_name":"Text messaging","score":0.500593900680542},{"id":"https://openalex.org/keywords/f1-score","display_name":"F1 score","score":0.4590936601161957},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.45239630341529846},{"id":"https://openalex.org/keywords/text-mining","display_name":"Text mining","score":0.43620359897613525},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4209236204624176},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.32106658816337585},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.16914957761764526}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7813771963119507},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.6564724445343018},{"id":"https://openalex.org/C165141518","wikidata":"https://www.wikidata.org/wiki/Q4915126","display_name":"Biomedical text mining","level":3,"score":0.6397325396537781},{"id":"https://openalex.org/C3018949938","wikidata":"https://www.wikidata.org/wiki/Q17166101","display_name":"Text messaging","level":2,"score":0.500593900680542},{"id":"https://openalex.org/C148524875","wikidata":"https://www.wikidata.org/wiki/Q6975395","display_name":"F1 score","level":2,"score":0.4590936601161957},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.45239630341529846},{"id":"https://openalex.org/C71472368","wikidata":"https://www.wikidata.org/wiki/Q676880","display_name":"Text mining","level":2,"score":0.43620359897613525},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4209236204624176},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.32106658816337585},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.16914957761764526},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1186/1471-2105-10-233","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-233","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-233","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:19635172","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19635172","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:eprints.bbk.ac.uk.oai2:1091","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306400466","display_name":"BIROn (Birkbeck, University of London)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I98259816","host_organization_name":"Birkbeck, University of London","host_organization_lineage":["https://openalex.org/I98259816"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"PeerReviewed"},{"id":"pmh:oai:doaj.org/article:4a4c7b5b216e4f6891b6333aeeed9778","is_oa":true,"landing_page_url":"https://doaj.org/article/4a4c7b5b216e4f6891b6333aeeed9778","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 10, Iss 1, p 233 (2009)","raw_type":"article"},{"id":"pmh:oai:eprints.ucl.ac.uk.OAI2:118373","is_oa":false,"landing_page_url":"https://discovery.ucl.ac.uk/id/eprint/118373/","pdf_url":null,"source":{"id":"https://openalex.org/S4306400024","display_name":"UCL Discovery (University College London)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I45129253","host_organization_name":"University College London","host_organization_lineage":["https://openalex.org/I45129253"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"   BMC BIOINFORMATICS , 10     , Article 233. (2009)      ","raw_type":"Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2723093","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2723093","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"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:10.1186/1471-2105-10-233","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-233","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-233","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":[{"id":"https://metadata.un.org/sdg/4","score":0.4699999988079071,"display_name":"Quality Education"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2108010925.pdf","grobid_xml":"https://content.openalex.org/works/W2108010925.grobid-xml"},"referenced_works_count":31,"referenced_works":["https://openalex.org/W151685798","https://openalex.org/W859881883","https://openalex.org/W1487177365","https://openalex.org/W1850865022","https://openalex.org/W1963925644","https://openalex.org/W2018874418","https://openalex.org/W2044514479","https://openalex.org/W2058856481","https://openalex.org/W2062163602","https://openalex.org/W2064030835","https://openalex.org/W2097960255","https://openalex.org/W2103612359","https://openalex.org/W2104088268","https://openalex.org/W2107005506","https://openalex.org/W2116786260","https://openalex.org/W2120253533","https://openalex.org/W2121844933","https://openalex.org/W2124772738","https://openalex.org/W2142741334","https://openalex.org/W2149803936","https://openalex.org/W2158796363","https://openalex.org/W2163107094","https://openalex.org/W2164881856","https://openalex.org/W2166474856","https://openalex.org/W2168905447","https://openalex.org/W2169918010","https://openalex.org/W2169974160","https://openalex.org/W2399295001","https://openalex.org/W3154566661","https://openalex.org/W4285719527","https://openalex.org/W4300022934"],"related_works":["https://openalex.org/W3185751515","https://openalex.org/W1479703980","https://openalex.org/W3179963059","https://openalex.org/W2749535755","https://openalex.org/W1553529581","https://openalex.org/W4206039273","https://openalex.org/W4232119327","https://openalex.org/W2911489562","https://openalex.org/W2134429551","https://openalex.org/W4308171175"],"abstract_inverted_index":{"In":[0],"terms":[1],"of":[2,5,36,51],"availability,":[3],"ease":[4],"use":[6],"and":[7,31,44,46],"performance,":[8],"the":[9,61],"potential":[10],"non-specialist":[11],"user":[12],"community":[13],"interested":[14],"in":[15],"automatically":[16],"extracting":[17],"gene":[18],"and/or":[19],"protein":[20],"interactions":[21],"from":[22],"free":[23],"text":[24,63],"is":[25],"poorly":[26],"served":[27],"by":[28,60],"current":[29],"tools":[30,38],"systems.":[32],"The":[33],"public":[34],"release":[35],"extraction":[37],"that":[39,47],"are":[40],"easy":[41],"to":[42],"install":[43],"use,":[45],"achieve":[48],"state-of-art":[49],"levels":[50],"performance":[52],"should":[53],"be":[54],"treated":[55],"as":[56],"a":[57],"high":[58],"priority":[59],"biomedical":[62],"mining":[64],"community.":[65]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":11},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":11},{"year":2012,"cited_by_count":6}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
