{"id":"https://openalex.org/W2771692618","doi":"https://doi.org/10.1186/s12859-018-2211-5","title":"FamPlex: a resource for entity recognition and relationship resolution of human protein families and complexes in biomedical text mining","display_name":"FamPlex: a resource for entity recognition and relationship resolution of human protein families and complexes in biomedical text mining","publication_year":2018,"publication_date":"2018-06-28","ids":{"openalex":"https://openalex.org/W2771692618","doi":"https://doi.org/10.1186/s12859-018-2211-5","mag":"2771692618","pmid":"https://pubmed.ncbi.nlm.nih.gov/29954318"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-018-2211-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-018-2211-5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2211-5","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","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/track/pdf/10.1186/s12859-018-2211-5","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5016902970","display_name":"John A. Bachman","orcid":"https://orcid.org/0000-0001-6095-2466"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I4210155419","display_name":"Center for Systems Biology","ror":"https://ror.org/05r3dyn47","country_code":"US","type":"facility","lineage":["https://openalex.org/I136199984","https://openalex.org/I4210087915","https://openalex.org/I4210155419","https://openalex.org/I48633490"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"John A. Bachman","raw_affiliation_strings":["Laboratory of Systems Pharmacology, Harvard Medical School, 200 Longwood Ave, Boston, MA, 02115, USA"],"affiliations":[{"raw_affiliation_string":"Laboratory of Systems Pharmacology, Harvard Medical School, 200 Longwood Ave, Boston, MA, 02115, USA","institution_ids":["https://openalex.org/I4210155419","https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022188333","display_name":"Benjamin M. Gyori","orcid":"https://orcid.org/0000-0001-9439-5346"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I4210155419","display_name":"Center for Systems Biology","ror":"https://ror.org/05r3dyn47","country_code":"US","type":"facility","lineage":["https://openalex.org/I136199984","https://openalex.org/I4210087915","https://openalex.org/I4210155419","https://openalex.org/I48633490"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Benjamin M. Gyori","raw_affiliation_strings":["Laboratory of Systems Pharmacology, Harvard Medical School, 200 Longwood Ave, Boston, MA, 02115, USA"],"affiliations":[{"raw_affiliation_string":"Laboratory of Systems Pharmacology, Harvard Medical School, 200 Longwood Ave, Boston, MA, 02115, USA","institution_ids":["https://openalex.org/I4210155419","https://openalex.org/I136199984"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5063426870","display_name":"Peter K. Sorger","orcid":"https://orcid.org/0000-0002-3364-1838"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I4210155419","display_name":"Center for Systems Biology","ror":"https://ror.org/05r3dyn47","country_code":"US","type":"facility","lineage":["https://openalex.org/I136199984","https://openalex.org/I4210087915","https://openalex.org/I4210155419","https://openalex.org/I48633490"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Peter K. Sorger","raw_affiliation_strings":["Laboratory of Systems Pharmacology, Harvard Medical School, 200 Longwood Ave, Boston, MA, 02115, USA. peter_sorger@hms.harvard.edu","Laboratory of Systems Pharmacology, Harvard Medical School, 200 Longwood Ave, Boston, MA, 02115, USA"],"affiliations":[{"raw_affiliation_string":"Laboratory of Systems Pharmacology, Harvard Medical School, 200 Longwood Ave, Boston, MA, 02115, USA. peter_sorger@hms.harvard.edu","institution_ids":["https://openalex.org/I136199984"]},{"raw_affiliation_string":"Laboratory of Systems Pharmacology, Harvard Medical School, 200 Longwood Ave, Boston, MA, 02115, USA","institution_ids":["https://openalex.org/I4210155419","https://openalex.org/I136199984"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5016902970"],"corresponding_institution_ids":["https://openalex.org/I136199984","https://openalex.org/I4210155419"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":2.0479,"has_fulltext":true,"cited_by_count":36,"citation_normalized_percentile":{"value":0.87214174,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"19","issue":"1","first_page":"248","last_page":"248"},"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9775000214576721,"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":0.9681000113487244,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/identifier","display_name":"Identifier","score":0.8285375833511353},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7588469982147217},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.552703320980072},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.5388113856315613},{"id":"https://openalex.org/keywords/unique-identifier","display_name":"Unique identifier","score":0.5316425561904907},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.5181359052658081},{"id":"https://openalex.org/keywords/suffix","display_name":"Suffix","score":0.5106032490730286},{"id":"https://openalex.org/keywords/biomedical-text-mining","display_name":"Biomedical text mining","score":0.49713972210884094},{"id":"https://openalex.org/keywords/information-extraction","display_name":"Information extraction","score":0.4834900498390198},{"id":"https://openalex.org/keywords/precision-and-recall","display_name":"Precision and recall","score":0.4806714951992035},{"id":"https://openalex.org/keywords/resource","display_name":"Resource (disambiguation)","score":0.45122188329696655},{"id":"https://openalex.org/keywords/event","display_name":"Event (particle physics)","score":0.44678249955177307},{"id":"https://openalex.org/keywords/reading","display_name":"Reading (process)","score":0.4273591637611389},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4102984070777893},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.39735549688339233},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3812004327774048},{"id":"https://openalex.org/keywords/text-mining","display_name":"Text mining","score":0.27965882420539856}],"concepts":[{"id":"https://openalex.org/C154504017","wikidata":"https://www.wikidata.org/wiki/Q853614","display_name":"Identifier","level":2,"score":0.8285375833511353},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7588469982147217},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.552703320980072},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.5388113856315613},{"id":"https://openalex.org/C119839945","wikidata":"https://www.wikidata.org/wiki/Q6545185","display_name":"Unique identifier","level":3,"score":0.5316425561904907},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.5181359052658081},{"id":"https://openalex.org/C2779804580","wikidata":"https://www.wikidata.org/wiki/Q102047","display_name":"Suffix","level":2,"score":0.5106032490730286},{"id":"https://openalex.org/C165141518","wikidata":"https://www.wikidata.org/wiki/Q4915126","display_name":"Biomedical text mining","level":3,"score":0.49713972210884094},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.4834900498390198},{"id":"https://openalex.org/C81669768","wikidata":"https://www.wikidata.org/wiki/Q2359161","display_name":"Precision and recall","level":2,"score":0.4806714951992035},{"id":"https://openalex.org/C206345919","wikidata":"https://www.wikidata.org/wiki/Q20380951","display_name":"Resource (disambiguation)","level":2,"score":0.45122188329696655},{"id":"https://openalex.org/C2779662365","wikidata":"https://www.wikidata.org/wiki/Q5416694","display_name":"Event (particle physics)","level":2,"score":0.44678249955177307},{"id":"https://openalex.org/C554936623","wikidata":"https://www.wikidata.org/wiki/Q199657","display_name":"Reading (process)","level":2,"score":0.4273591637611389},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4102984070777893},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.39735549688339233},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3812004327774048},{"id":"https://openalex.org/C71472368","wikidata":"https://www.wikidata.org/wiki/Q676880","display_name":"Text mining","level":2,"score":0.27965882420539856},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"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/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"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},{"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/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"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":"Q000378","qualifier_name":"metabolism","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":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-018-2211-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-018-2211-5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2211-5","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:29954318","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29954318","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:doaj.org/article:bd43bb7063734460852317609c109162","is_oa":true,"landing_page_url":"https://doaj.org/article/bd43bb7063734460852317609c109162","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 19, Iss 1, Pp 1-14 (2018)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:4988138","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6022344","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-018-2211-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-018-2211-5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2211-5","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Quality Education","score":0.7099999785423279,"id":"https://metadata.un.org/sdg/4"}],"awards":[{"id":"https://openalex.org/G3048660544","display_name":null,"funder_award_id":"W911NF-14-1-","funder_id":"https://openalex.org/F4320332180","funder_display_name":"Defense Advanced Research Projects Agency"},{"id":"https://openalex.org/G5150008190","display_name":null,"funder_award_id":"W911NF-14-1-0397","funder_id":"https://openalex.org/F4320332180","funder_display_name":"Defense Advanced Research Projects Agency"},{"id":"https://openalex.org/G7544809666","display_name":null,"funder_award_id":"W911NF-15-1-0544","funder_id":"https://openalex.org/F4320332180","funder_display_name":"Defense Advanced Research Projects Agency"}],"funders":[{"id":"https://openalex.org/F4320332180","display_name":"Defense Advanced Research Projects Agency","ror":"https://ror.org/02caytj08"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2771692618.pdf","grobid_xml":"https://content.openalex.org/works/W2771692618.grobid-xml"},"referenced_works_count":37,"referenced_works":["https://openalex.org/W1610821757","https://openalex.org/W1963925644","https://openalex.org/W1969709265","https://openalex.org/W1973646872","https://openalex.org/W1989277387","https://openalex.org/W1991747826","https://openalex.org/W2001496424","https://openalex.org/W2031966872","https://openalex.org/W2054493965","https://openalex.org/W2105440823","https://openalex.org/W2107580398","https://openalex.org/W2113142309","https://openalex.org/W2116944463","https://openalex.org/W2120609672","https://openalex.org/W2123152121","https://openalex.org/W2123442489","https://openalex.org/W2129113459","https://openalex.org/W2134967412","https://openalex.org/W2141811925","https://openalex.org/W2151598682","https://openalex.org/W2164298117","https://openalex.org/W2165372747","https://openalex.org/W2224812643","https://openalex.org/W2251279337","https://openalex.org/W2251392452","https://openalex.org/W2251677685","https://openalex.org/W2291307173","https://openalex.org/W2414378847","https://openalex.org/W2801356492","https://openalex.org/W2894374770","https://openalex.org/W2912915691","https://openalex.org/W2914431807","https://openalex.org/W2952465807","https://openalex.org/W2952755768","https://openalex.org/W4213060373","https://openalex.org/W4249287847","https://openalex.org/W6691708014"],"related_works":["https://openalex.org/W3004288456","https://openalex.org/W4362496998","https://openalex.org/W2184397297","https://openalex.org/W1663435917","https://openalex.org/W2004087619","https://openalex.org/W2539274330","https://openalex.org/W2810079151","https://openalex.org/W2557094866","https://openalex.org/W2616159224","https://openalex.org/W2164881856"],"abstract_inverted_index":{"FamPlex":[0,23],"is":[1,24],"an":[2],"effective":[3],"resource":[4],"for":[5],"improving":[6],"named":[7],"entity":[8],"recognition,":[9],"grounding,":[10],"and":[11,29,42,49],"relationship":[12],"resolution":[13],"in":[14,22,26],"automated":[15],"reading":[16,51],"of":[17],"biomedical":[18],"text.":[19],"The":[20],"content":[21],"available":[25],"both":[27],"tabular":[28],"Open":[30],"Biomedical":[31],"Ontology":[32],"formats":[33],"at":[34],"https://github.com/sorgerlab/famplex":[35],"under":[36],"the":[37,47],"Creative":[38],"Commons":[39],"CC0":[40],"license":[41],"has":[43],"been":[44],"integrated":[45],"into":[46],"TRIPS/DRUM":[48],"REACH":[50],"systems.":[52]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":8},{"year":2021,"cited_by_count":9},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":8},{"year":2018,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
