{"id":"https://openalex.org/W2946102094","doi":"https://doi.org/10.1093/nar/gkz386","title":"Doc2Hpo: a web application for efficient and accurate HPO concept curation","display_name":"Doc2Hpo: a web application for efficient and accurate HPO concept curation","publication_year":2019,"publication_date":"2019-05-01","ids":{"openalex":"https://openalex.org/W2946102094","doi":"https://doi.org/10.1093/nar/gkz386","mag":"2946102094","pmid":"https://pubmed.ncbi.nlm.nih.gov/31106327"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkz386","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkz386","pdf_url":"https://academic.oup.com/nar/article-pdf/47/W1/W566/28879980/gkz386.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/47/W1/W566/28879980/gkz386.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100331534","display_name":"Cong Liu","orcid":"https://orcid.org/0000-0001-6024-3037"},"institutions":[{"id":"https://openalex.org/I78577930","display_name":"Columbia University","ror":"https://ror.org/00hj8s172","country_code":"US","type":"education","lineage":["https://openalex.org/I78577930"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Cong Liu","raw_affiliation_strings":["Department of Biomedical Informatics, Columbia University, New York, NY 10032, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Columbia University, New York, NY 10032, USA","institution_ids":["https://openalex.org/I78577930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079093160","display_name":"Fabr\u00edcio S. P. Kury","orcid":null},"institutions":[{"id":"https://openalex.org/I78577930","display_name":"Columbia University","ror":"https://ror.org/00hj8s172","country_code":"US","type":"education","lineage":["https://openalex.org/I78577930"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Fabricio Sampaio Peres\u00a0Kury","raw_affiliation_strings":["Department of Biomedical Informatics, Columbia University, New York, NY 10032, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Columbia University, New York, NY 10032, USA","institution_ids":["https://openalex.org/I78577930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101820102","display_name":"Ziran Li","orcid":"https://orcid.org/0009-0007-0620-3561"},"institutions":[{"id":"https://openalex.org/I78577930","display_name":"Columbia University","ror":"https://ror.org/00hj8s172","country_code":"US","type":"education","lineage":["https://openalex.org/I78577930"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ziran Li","raw_affiliation_strings":["Department of Biomedical Informatics, Columbia University, New York, NY 10032, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Columbia University, New York, NY 10032, USA","institution_ids":["https://openalex.org/I78577930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051450267","display_name":"Casey Ta","orcid":"https://orcid.org/0000-0002-4679-805X"},"institutions":[{"id":"https://openalex.org/I78577930","display_name":"Columbia University","ror":"https://ror.org/00hj8s172","country_code":"US","type":"education","lineage":["https://openalex.org/I78577930"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Casey Ta","raw_affiliation_strings":["Department of Biomedical Informatics, Columbia University, New York, NY 10032, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Columbia University, New York, NY 10032, USA","institution_ids":["https://openalex.org/I78577930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100437036","display_name":"Kai Wang","orcid":"https://orcid.org/0000-0002-6170-4744"},"institutions":[{"id":"https://openalex.org/I1335321130","display_name":"Children's Hospital of Philadelphia","ror":"https://ror.org/01z7r7q48","country_code":"US","type":"funder","lineage":["https://openalex.org/I1335321130"]},{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Kai Wang","raw_affiliation_strings":["Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA","Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA"],"affiliations":[{"raw_affiliation_string":"Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA","institution_ids":["https://openalex.org/I1335321130"]},{"raw_affiliation_string":"Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA","institution_ids":["https://openalex.org/I79576946"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5009604048","display_name":"Chunhua Weng","orcid":"https://orcid.org/0000-0002-9624-0214"},"institutions":[{"id":"https://openalex.org/I78577930","display_name":"Columbia University","ror":"https://ror.org/00hj8s172","country_code":"US","type":"education","lineage":["https://openalex.org/I78577930"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Chunhua Weng","raw_affiliation_strings":["Department of Biomedical Informatics, Columbia University, New York, NY 10032, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Columbia University, New York, NY 10032, USA","institution_ids":["https://openalex.org/I78577930"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5009604048","https://openalex.org/A5100437036"],"corresponding_institution_ids":["https://openalex.org/I1335321130","https://openalex.org/I78577930","https://openalex.org/I79576946"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":3.5212,"has_fulltext":true,"cited_by_count":79,"citation_normalized_percentile":{"value":0.93724658,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"47","issue":"W1","first_page":"W566","last_page":"W570"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9995999932289124,"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":0.9995999932289124,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9929999709129333,"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":0.9925000071525574,"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/data-curation","display_name":"Data curation","score":0.7107257843017578},{"id":"https://openalex.org/keywords/normalization","display_name":"Normalization (sociology)","score":0.6355054378509521},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5401020050048828},{"id":"https://openalex.org/keywords/prioritization","display_name":"Prioritization","score":0.5353624820709229},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.48830699920654297},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.43613603711128235},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.4190952777862549},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3344075083732605},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.29832684993743896},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.12479400634765625}],"concepts":[{"id":"https://openalex.org/C91632574","wikidata":"https://www.wikidata.org/wiki/Q15088675","display_name":"Data curation","level":2,"score":0.7107257843017578},{"id":"https://openalex.org/C136886441","wikidata":"https://www.wikidata.org/wiki/Q926129","display_name":"Normalization (sociology)","level":2,"score":0.6355054378509521},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5401020050048828},{"id":"https://openalex.org/C2777615720","wikidata":"https://www.wikidata.org/wiki/Q11888847","display_name":"Prioritization","level":2,"score":0.5353624820709229},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.48830699920654297},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.43613603711128235},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4190952777862549},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3344075083732605},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.29832684993743896},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.12479400634765625},{"id":"https://openalex.org/C539667460","wikidata":"https://www.wikidata.org/wiki/Q2414942","display_name":"Management science","level":1,"score":0.0},{"id":"https://openalex.org/C19165224","wikidata":"https://www.wikidata.org/wiki/Q23404","display_name":"Anthropology","level":1,"score":0.0},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D005796","descriptor_name":"Genes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005796","descriptor_name":"Genes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005796","descriptor_name":"Genes","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D066289","descriptor_name":"Data Curation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D066289","descriptor_name":"Data Curation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D066289","descriptor_name":"Data Curation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/nar/gkz386","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkz386","pdf_url":"https://academic.oup.com/nar/article-pdf/47/W1/W566/28879980/gkz386.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:31106327","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31106327","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:europepmc.org:5577283","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6602487","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:10.1093/nar/gkz386","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkz386","pdf_url":"https://academic.oup.com/nar/article-pdf/47/W1/W566/28879980/gkz386.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1998495554","display_name":null,"funder_award_id":"LM012895","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3497591915","display_name":null,"funder_award_id":"(NIH)","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3660065486","display_name":null,"funder_award_id":"R01LM012895-01","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G608050891","display_name":null,"funder_award_id":"R01LM012895","funder_id":"https://openalex.org/F4320337372","funder_display_name":"U.S. National Library of Medicine"},{"id":"https://openalex.org/G895422422","display_name":null,"funder_award_id":"LM012895","funder_id":"https://openalex.org/F4320337372","funder_display_name":"U.S. National Library of Medicine"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2946102094.pdf","grobid_xml":"https://content.openalex.org/works/W2946102094.grobid-xml"},"referenced_works_count":29,"referenced_works":["https://openalex.org/W954754213","https://openalex.org/W1550258693","https://openalex.org/W1971192989","https://openalex.org/W1976316416","https://openalex.org/W2012361142","https://openalex.org/W2055032581","https://openalex.org/W2058490165","https://openalex.org/W2091834108","https://openalex.org/W2096951189","https://openalex.org/W2099964107","https://openalex.org/W2104008606","https://openalex.org/W2119412782","https://openalex.org/W2119613819","https://openalex.org/W2127006085","https://openalex.org/W2138162199","https://openalex.org/W2139865360","https://openalex.org/W2143749588","https://openalex.org/W2146089916","https://openalex.org/W2250522125","https://openalex.org/W2263904841","https://openalex.org/W2529518929","https://openalex.org/W2558643140","https://openalex.org/W2582146834","https://openalex.org/W2783547086","https://openalex.org/W2809721358","https://openalex.org/W2901332105","https://openalex.org/W2951146425","https://openalex.org/W2951328784","https://openalex.org/W6632766574"],"related_works":["https://openalex.org/W2506292322","https://openalex.org/W4283209547","https://openalex.org/W2591697403","https://openalex.org/W4367627632","https://openalex.org/W2944728705","https://openalex.org/W2701062589","https://openalex.org/W2904022177","https://openalex.org/W2359348847","https://openalex.org/W4308914582","https://openalex.org/W3011538607"],"abstract_inverted_index":{"We":[0],"present":[1],"Doc2Hpo,":[2],"an":[3],"interactive":[4,9],"web":[5],"application":[6],"that":[7,54],"enables":[8],"and":[10,41],"efficient":[11],"phenotype":[12],"concept":[13,20,66],"curation":[14],"from":[15],"clinical":[16],"text":[17],"with":[18],"automated":[19],"normalization":[21],"using":[22],"the":[23,31,43],"Human":[24],"Phenotype":[25],"Ontology":[26],"(HPO).":[27],"Users":[28],"can":[29],"edit":[30],"HPO":[32,45,65],"concepts":[33,46],"automatically":[34],"extracted":[35,44],"by":[36],"Doc2Hpo":[37,55,68],"in":[38,64],"real":[39],"time,":[40],"export":[42],"into":[47],"gene":[48],"prioritization":[49],"tools.":[50],"Our":[51],"evaluation":[52],"showed":[53],"significantly":[56],"reduced":[57],"manual":[58],"effort":[59],"while":[60],"achieving":[61],"high":[62],"accuracy":[63],"curation.":[67],"is":[69,77],"freely":[70],"available":[71,78],"at":[72,79],"https://impact2.dbmi.columbia.edu/doc2hpo/.":[73],"The":[74],"source":[75],"code":[76],"https://github.com/stormliucong/doc2hpo":[80],"for":[81,84],"local":[82],"installation":[83],"protected":[85],"health":[86],"data.":[87]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":10},{"year":2024,"cited_by_count":15},{"year":2023,"cited_by_count":9},{"year":2022,"cited_by_count":17},{"year":2021,"cited_by_count":18},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":3}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
