{"id":"https://openalex.org/W3087801495","doi":"https://doi.org/10.1186/s13321-020-00461-4","title":"Linking chemical and disease entities to ontologies by integrating PageRank with extracted relations from literature","display_name":"Linking chemical and disease entities to ontologies by integrating PageRank with extracted relations from literature","publication_year":2020,"publication_date":"2020-09-21","ids":{"openalex":"https://openalex.org/W3087801495","doi":"https://doi.org/10.1186/s13321-020-00461-4","mag":"3087801495","pmid":"https://pubmed.ncbi.nlm.nih.gov/33430995"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-020-00461-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-020-00461-4","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-020-00461-4","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/track/pdf/10.1186/s13321-020-00461-4","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5081030878","display_name":"Pedro Ruas","orcid":"https://orcid.org/0000-0002-1293-4199"},"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":"Pedro Ruas","raw_affiliation_strings":["LASIGE, Faculdade de Ci\u00eancias, Universidade de Lisboa, 1749-016, Lisbon, Portugal. psruas@fc.ul.pt","LASIGE, Faculdade de Ci\u00eancias, Universidade de Lisboa, 1749-016, Lisbon, Portugal"],"raw_orcid":"https://orcid.org/0000-0002-1293-4199","affiliations":[{"raw_affiliation_string":"LASIGE, Faculdade de Ci\u00eancias, Universidade de Lisboa, 1749-016, Lisbon, Portugal. psruas@fc.ul.pt","institution_ids":["https://openalex.org/I141596103"]},{"raw_affiliation_string":"LASIGE, Faculdade de Ci\u00eancias, Universidade de Lisboa, 1749-016, Lisbon, Portugal","institution_ids":["https://openalex.org/I141596103"]}]},{"author_position":"middle","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":false,"raw_author_name":"Andre Lamurias","raw_affiliation_strings":["LASIGE, Faculdade de Ci\u00eancias, Universidade de Lisboa, 1749-016, Lisbon, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"LASIGE, Faculdade de Ci\u00eancias, Universidade de Lisboa, 1749-016, Lisbon, 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, Faculdade de Ci\u00eancias, Universidade de Lisboa, 1749-016, Lisbon, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"LASIGE, Faculdade de Ci\u00eancias, Universidade de Lisboa, 1749-016, Lisbon, Portugal","institution_ids":["https://openalex.org/I141596103"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5081030878"],"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":1.1669,"has_fulltext":true,"cited_by_count":20,"citation_normalized_percentile":{"value":0.77977368,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":98},"biblio":{"volume":"12","issue":"1","first_page":"57","last_page":"57"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.7739999890327454,"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":0.7739999890327454,"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":0.12950000166893005,"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/T10215","display_name":"Semantic Web and Ontologies","score":0.02889999933540821,"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/computer-science","display_name":"Computer science","score":0.7539138793945312},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.6082632541656494},{"id":"https://openalex.org/keywords/pagerank","display_name":"PageRank","score":0.6044511198997498},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.5043648481369019},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.35541826486587524}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7539138793945312},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.6082632541656494},{"id":"https://openalex.org/C2779172887","wikidata":"https://www.wikidata.org/wiki/Q184316","display_name":"PageRank","level":2,"score":0.6044511198997498},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.5043648481369019},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.35541826486587524}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13321-020-00461-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-020-00461-4","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-020-00461-4","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:33430995","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33430995","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:doaj.org/article:a2d677fb86d240ed8d56149359214626","is_oa":true,"landing_page_url":"https://doaj.org/article/a2d677fb86d240ed8d56149359214626","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Cheminformatics, Vol 12, Iss 1, Pp 1-11 (2020)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7507273","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7507273","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Cheminform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13321-020-00461-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-020-00461-4","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-020-00461-4","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":[{"id":"https://metadata.un.org/sdg/4","score":0.6299999952316284,"display_name":"Quality Education"}],"awards":[{"id":"https://openalex.org/G2089664753","display_name":"LASIGE - Extreme Computing","funder_award_id":"UIDB/00408/2020","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G4384961418","display_name":null,"funder_award_id":"PTDC/CCI-BIO/28685/2017","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G5454278309","display_name":null,"funder_award_id":"/2017","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"}],"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/W3087801495.pdf","grobid_xml":"https://content.openalex.org/works/W3087801495.grobid-xml"},"referenced_works_count":34,"referenced_works":["https://openalex.org/W1172683740","https://openalex.org/W1548663377","https://openalex.org/W1550457191","https://openalex.org/W1802346448","https://openalex.org/W1854214752","https://openalex.org/W1935434993","https://openalex.org/W2101680936","https://openalex.org/W2119737821","https://openalex.org/W2142016317","https://openalex.org/W2169923787","https://openalex.org/W2170189740","https://openalex.org/W2252174377","https://openalex.org/W2295227292","https://openalex.org/W2346452181","https://openalex.org/W2414378847","https://openalex.org/W2516150684","https://openalex.org/W2594284271","https://openalex.org/W2612773933","https://openalex.org/W2625465398","https://openalex.org/W2745665559","https://openalex.org/W2767205225","https://openalex.org/W2792330846","https://openalex.org/W2807280045","https://openalex.org/W2896457183","https://openalex.org/W2911489562","https://openalex.org/W2916047525","https://openalex.org/W2967690619","https://openalex.org/W2971810142","https://openalex.org/W2982544799","https://openalex.org/W2991788499","https://openalex.org/W3030645549","https://openalex.org/W6600366268","https://openalex.org/W6702248584","https://openalex.org/W6726594951"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2154222238","https://openalex.org/W2106626222","https://openalex.org/W2980866815","https://openalex.org/W1562405179","https://openalex.org/W2125493559","https://openalex.org/W1544909909","https://openalex.org/W2002053721"],"abstract_inverted_index":{"BACKGROUND:":[0],"Named":[1,58,210,233],"Entity":[2,59,67,211,234],"Linking":[3,60,68,212,235],"systems":[4],"are":[5,36,51,88,98,123],"a":[6,57,82],"powerful":[7],"aid":[8],"to":[9,24,75,101,126,227,241,248],"the":[10,25,31,39,48,86,89,93,96,102,106,109,117,128,135,138,143,149,152,159,162,169,174,180,229],"manual":[11],"curation":[12],"of":[13,38,120,137,151,161,232],"digital":[14],"libraries,":[15],"which":[16,108],"is":[17,255],"getting":[18],"increasingly":[19],"costly":[20],"and":[21,95,116,173,192,224,246],"inefficient":[22],"due":[23],"information":[26,118,216],"overload.":[27],"Models":[28],"based":[29],"on":[30,145],"Personalized":[32],"PageRank":[33],"(PPR)":[34],"algorithm":[35,115],"one":[37],"state-of-the-art":[40],"approaches,":[41],"but":[42],"these":[43,195],"have":[44],"low":[45],"performance":[46],"when":[47],"disambiguation":[49,83,139,230],"graphs":[50],"sparse.":[52],"FINDINGS:":[53],"This":[54],"work":[55],"proposes":[56],"framework":[61],"designated":[62],"by":[63,187,213],"Relation":[64],"Extraction":[65],"for":[66,92,130],"(REEL)":[69],"that":[70,133,205],"uses":[71],"automatically":[72],"extracted":[73],"relations":[74,103],"overcome":[76],"this":[77],"limitation.":[78],"Our":[79],"method":[80,110,144],"builds":[81],"graph,":[84],"where":[85],"nodes":[87],"ontology":[90,122,257],"candidates":[91],"entities":[94],"edges":[97],"added":[99],"according":[100],"established":[104],"in":[105,194,218,221],"text,":[107],"extracts":[111],"automatically.":[112],"The":[113,184],"PPR":[114],"content":[119],"each":[121,131],"then":[124],"applied":[125],"choose":[127],"candidate":[129],"entity":[132],"maximises":[134],"coherence":[136],"graph.":[140],"We":[141,203],"evaluated":[142],"three":[146],"gold":[147,196],"standards:":[148],"subset":[150,160,175],"CRAFT":[153],"corpus":[154,164],"with":[155,165,176],"ChEBI":[156],"annotations":[157,167,178],"(CRAFT-ChEBI),":[158],"BC5CDR":[163],"disease":[166],"from":[168,179],"MEDIC":[170],"vocabulary":[171,182],"(BC5CDR-Diseases)":[172],"chemical":[177],"CTD-Chemical":[181],"(BC5CDR-Chemicals).":[183],"F1-Score":[185],"achieved":[186],"REEL":[188,237],"was":[189],"85.8%,":[190],"80.9%":[191],"90.3%":[193],"standards,":[197],"respectively,":[198],"outperforming":[199],"baseline":[200],"approaches.":[201],"CONCLUSIONS:":[202],"demonstrated":[204],"RE":[206],"tools":[207],"can":[208,238],"improve":[209,228],"capturing":[214],"semantic":[215],"expressed":[217],"text":[219,243],"missing":[220],"Knowledge":[222],"Bases":[223],"use":[225],"it":[226],"graph":[231],"models.":[236],"be":[239],"adapted":[240],"any":[242,249],"mining":[244],"pipeline":[245],"potentially":[247],"domain,":[250],"as":[251,253],"long":[252],"there":[254],"an":[256],"or":[258],"other":[259],"knowledge":[260],"Base":[261],"available.":[262]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":3}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
