{"id":"https://openalex.org/W2161919540","doi":"https://doi.org/10.1186/1758-2946-7-s1-s13","title":"Improving chemical entity recognition through h-index based semantic similarity","display_name":"Improving chemical entity recognition through h-index based semantic similarity","publication_year":2015,"publication_date":"2015-01-19","ids":{"openalex":"https://openalex.org/W2161919540","doi":"https://doi.org/10.1186/1758-2946-7-s1-s13","mag":"2161919540","pmid":"https://pubmed.ncbi.nlm.nih.gov/25810770"},"language":"en","primary_location":{"id":"doi:10.1186/1758-2946-7-s1-s13","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-7-s1-s13","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-7-S1-S13","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-7-S1-S13","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5024583659","display_name":"Andr\u00e9 Lam\u00farias","orcid":"https://orcid.org/0000-0001-7965-6536"},"institutions":[{"id":"https://openalex.org/I141596103","display_name":"University of Lisbon","ror":"https://ror.org/01c27hj86","country_code":"PT","type":"education","lineage":["https://openalex.org/I141596103"]}],"countries":["PT"],"is_corresponding":true,"raw_author_name":"Andre Lamurias","raw_affiliation_strings":["LaSIGE, Departamento de Inform\u00e1tica, Faculdade de Ci\u00eancias, Universidade de Lisboa, 1749-016 Lisboa, Portugal","LaSIGE, Departamento de Inform\u00e1tica, Faculdade de Ci\u00eancias, Universidade de Lisboa, 1749-016, Lisboa, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"LaSIGE, Departamento de Inform\u00e1tica, Faculdade de Ci\u00eancias, Universidade de Lisboa, 1749-016 Lisboa, Portugal","institution_ids":[]},{"raw_affiliation_string":"LaSIGE, Departamento de Inform\u00e1tica, Faculdade de Ci\u00eancias, Universidade de Lisboa, 1749-016, Lisboa, Portugal","institution_ids":["https://openalex.org/I141596103"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5114374455","display_name":"Jo\u00e3o D. Ferreira","orcid":"https://orcid.org/0000-0002-6900-3168"},"institutions":[{"id":"https://openalex.org/I141596103","display_name":"University of Lisbon","ror":"https://ror.org/01c27hj86","country_code":"PT","type":"education","lineage":["https://openalex.org/I141596103"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Jo\u00e3o D Ferreira","raw_affiliation_strings":["LaSIGE, Departamento de Inform\u00e1tica, Faculdade de Ci\u00eancias, Universidade de Lisboa, 1749-016 Lisboa, Portugal","LaSIGE, Departamento de Inform\u00e1tica, Faculdade de Ci\u00eancias, Universidade de Lisboa, 1749-016, Lisboa, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"LaSIGE, Departamento de Inform\u00e1tica, Faculdade de Ci\u00eancias, Universidade de Lisboa, 1749-016 Lisboa, Portugal","institution_ids":[]},{"raw_affiliation_string":"LaSIGE, Departamento de Inform\u00e1tica, Faculdade de Ci\u00eancias, Universidade de Lisboa, 1749-016, Lisboa, Portugal","institution_ids":["https://openalex.org/I141596103"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5014333753","display_name":"Francisco M. Couto","orcid":"https://orcid.org/0000-0003-0627-1496"},"institutions":[{"id":"https://openalex.org/I141596103","display_name":"University of Lisbon","ror":"https://ror.org/01c27hj86","country_code":"PT","type":"education","lineage":["https://openalex.org/I141596103"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Francisco M Couto","raw_affiliation_strings":["LaSIGE, Departamento de Inform\u00e1tica, Faculdade de Ci\u00eancias, Universidade de Lisboa, 1749-016 Lisboa, Portugal","LaSIGE, Departamento de Inform\u00e1tica, Faculdade de Ci\u00eancias, Universidade de Lisboa, 1749-016, Lisboa, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"LaSIGE, Departamento de Inform\u00e1tica, Faculdade de Ci\u00eancias, Universidade de Lisboa, 1749-016 Lisboa, Portugal","institution_ids":[]},{"raw_affiliation_string":"LaSIGE, Departamento de Inform\u00e1tica, Faculdade de Ci\u00eancias, Universidade de Lisboa, 1749-016, Lisboa, Portugal","institution_ids":["https://openalex.org/I141596103"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5024583659"],"corresponding_institution_ids":["https://openalex.org/I141596103"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":2.8611,"has_fulltext":true,"cited_by_count":30,"citation_normalized_percentile":{"value":0.91264424,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"7","issue":"S1","first_page":"S13","last_page":"S13"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9160000085830688,"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":0.9160000085830688,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.060499999672174454,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.00570000009611249,"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":0.7270742058753967},{"id":"https://openalex.org/keywords/index","display_name":"Index (typography)","score":0.5933952927589417},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.5224789381027222},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.5045915842056274},{"id":"https://openalex.org/keywords/semantic-similarity","display_name":"Semantic similarity","score":0.4975884258747101},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3887999951839447},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.38403376936912537},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.21899950504302979}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7270742058753967},{"id":"https://openalex.org/C2777382242","wikidata":"https://www.wikidata.org/wiki/Q6017816","display_name":"Index (typography)","level":2,"score":0.5933952927589417},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.5224789381027222},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.5045915842056274},{"id":"https://openalex.org/C130318100","wikidata":"https://www.wikidata.org/wiki/Q2268914","display_name":"Semantic similarity","level":2,"score":0.4975884258747101},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3887999951839447},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.38403376936912537},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.21899950504302979},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1186/1758-2946-7-s1-s13","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-7-s1-s13","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-7-S1-S13","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:25810770","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25810770","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:europepmc.org:3334606","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4331689","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:10.1186/1758-2946-7-s1-s13","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-7-s1-s13","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-7-S1-S13","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":[],"funders":[{"id":"https://openalex.org/F4320334779","display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","ror":"https://ror.org/00snfqn58"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2161919540.pdf","grobid_xml":"https://content.openalex.org/works/W2161919540.grobid-xml"},"referenced_works_count":20,"referenced_works":["https://openalex.org/W1495712943","https://openalex.org/W1523838071","https://openalex.org/W1668989518","https://openalex.org/W1964808688","https://openalex.org/W1980885411","https://openalex.org/W2006636719","https://openalex.org/W2046747418","https://openalex.org/W2098173334","https://openalex.org/W2099100406","https://openalex.org/W2117805756","https://openalex.org/W2128438887","https://openalex.org/W2133990480","https://openalex.org/W2140611297","https://openalex.org/W2145870108","https://openalex.org/W2149369282","https://openalex.org/W2165084475","https://openalex.org/W2213189003","https://openalex.org/W2259510613","https://openalex.org/W2403322245","https://openalex.org/W2950225692"],"related_works":["https://openalex.org/W2375480909","https://openalex.org/W2353314428","https://openalex.org/W2012019886","https://openalex.org/W2936184523","https://openalex.org/W2388928357","https://openalex.org/W2380654781","https://openalex.org/W2114797768","https://openalex.org/W2176214140","https://openalex.org/W2516873349","https://openalex.org/W1990601549"],"abstract_inverted_index":{"BACKGROUND:":[0],"Our":[1,38],"approach":[2],"to":[3,30,69,100,152],"the":[4,42,47,65,73,90,94,106,127,131,146,169,198,202,206,232,237,247],"BioCreative":[5],"IV":[6],"challenge":[7],"of":[8,12,22,33,50,75,141,174,186],"recognition":[9],"and":[10,86,88,180,249],"classification":[11],"drug":[13],"names":[14],"(CHEMDNER":[15],"task)":[16],"aimed":[17],"at":[18,218],"achieving":[19],"high":[20,242],"levels":[21],"precision":[23,165,179,195,243],"by":[24,63,119,136,166,240],"applying":[25],"semantic":[26,55,66,123,210],"similarity":[27,67,191,211],"validation":[28,58,155,187],"techniques":[29],"Chemical":[31],"Entities":[32],"Biological":[34],"Interest":[35],"(ChEBI)":[36],"mappings.":[37],"assumption":[39],"is":[40],"that":[41,114,158],"chemical":[43],"entities":[44],"mentioned":[45],"in":[46,82],"same":[48,199],"fragment":[49],"text":[51,220],"should":[52],"share":[53],"some":[54],"relation.":[56],"This":[57],"method":[59,81],"was":[60,215],"further":[61],"improved":[62,126,231],"adapting":[64],"measure":[68,99,212],"take":[70],"into":[71],"account":[72],"h-index":[74,147],"each":[76,97],"ancestor.":[77],"We":[78,177,230],"applied":[79],"this":[80],"two":[83],"measures,":[84,192],"simUI":[85],"simGIC,":[87],"validated":[89],"results":[91,170,222,233],"obtained":[92,129,235],"for":[93,159,183,197,236],"competition,":[95,107],"comparing":[96],"adapted":[98],"its":[101],"original":[102],"version.":[103],"RESULTS:":[104],"For":[105],"we":[108,149,163,213,234],"trained":[109],"a":[110,139,160,171,184],"Random":[111,133],"Forest":[112],"classifier":[113],"uses":[115],"various":[116],"scores":[117],"provided":[118],"our":[120,154],"system,":[121],"including":[122],"similarity,":[124],"which":[125],"F-measure":[128],"with":[130,201],"Conditional":[132],"Fields":[134],"classifiers":[135,226],"4.6%.":[137],"Using":[138],"notion":[140],"concept":[142],"relevance":[143],"based":[144,204],"on":[145,205],"measure,":[148],"were":[150],"able":[151],"enhance":[153],"process":[156],"so":[157],"fixed":[161],"recall,":[162],"increased":[164],"excluding":[167],"from":[168,223],"higher":[172,194],"amount":[173],"false":[175],"positives.":[176],"plotted":[178],"recall":[181,200,248],"values":[182,196,244],"range":[185],"thresholds":[188],"using":[189],"different":[190],"obtaining":[193],"measures":[203],"h-index.":[207],"CONCLUSIONS:":[208],"The":[209],"introduced":[214],"more":[216],"efficient":[217],"validating":[219],"mining":[221],"machine":[224],"learning":[225],"than":[227],"other":[228],"measures.":[229],"CHEMDNER":[238],"task":[239],"maintaining":[241],"while":[245],"improving":[246],"F-measure.":[250]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2021,"cited_by_count":4},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":9},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":4}],"updated_date":"2026-04-29T09:16:38.111599","created_date":"2025-10-10T00:00:00"}
