{"id":"https://openalex.org/W3116099552","doi":"https://doi.org/10.1093/bib/bbaa344","title":"PharmKG: a dedicated knowledge graph benchmark for bomedical data mining","display_name":"PharmKG: a dedicated knowledge graph benchmark for bomedical data mining","publication_year":2020,"publication_date":"2020-12-12","ids":{"openalex":"https://openalex.org/W3116099552","doi":"https://doi.org/10.1093/bib/bbaa344","mag":"3116099552","pmid":"https://pubmed.ncbi.nlm.nih.gov/33341877"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaa344","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbaa344","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"http://hdl.handle.net/10072/407465","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5075817762","display_name":"Shuangjia Zheng","orcid":"https://orcid.org/0000-0001-9747-4285"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Shuangjia Zheng","raw_affiliation_strings":["School of Data and Computer Science at the Sun Yat-Sen University"],"raw_orcid":"https://orcid.org/0000-0001-9747-4285","affiliations":[{"raw_affiliation_string":"School of Data and Computer Science at the Sun Yat-Sen University","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015329746","display_name":"Jiahua Rao","orcid":"https://orcid.org/0000-0002-6840-8198"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jiahua Rao","raw_affiliation_strings":["School of Data and Computer Science at the Sun Yat-Sen University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Data and Computer Science at the Sun Yat-Sen University","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034582116","display_name":"Song Ying","orcid":"https://orcid.org/0009-0005-3744-0362"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ying Song","raw_affiliation_strings":["School of Systems Science and Engineering at the Sun Yat-Sen University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Systems Science and Engineering at the Sun Yat-Sen University","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023108523","display_name":"Jixian Zhang","orcid":"https://orcid.org/0000-0003-3933-2558"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jixian Zhang","raw_affiliation_strings":["Aladdin Healthcare Technologies Ltd"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Aladdin Healthcare Technologies Ltd","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088846231","display_name":"Xianglu Xiao","orcid":"https://orcid.org/0000-0002-8648-6245"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Xianglu Xiao","raw_affiliation_strings":["Aladdin Healthcare Technologies Ltd"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Aladdin Healthcare Technologies Ltd","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048788845","display_name":"Evandro Fei Fang","orcid":"https://orcid.org/0000-0003-0355-7202"},"institutions":[{"id":"https://openalex.org/I184942183","display_name":"University of Oslo","ror":"https://ror.org/01xtthb56","country_code":"NO","type":"education","lineage":["https://openalex.org/I184942183"]},{"id":"https://openalex.org/I2800192669","display_name":"Akershus University Hospital","ror":"https://ror.org/0331wat71","country_code":"NO","type":"healthcare","lineage":["https://openalex.org/I2800192669"]}],"countries":["NO"],"is_corresponding":false,"raw_author_name":"Evandro Fei Fang","raw_affiliation_strings":["Department of Clinical Molecular Biology, University of Oslo and Akershus University Hospital, L\u00f8renskog, Norway"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Clinical Molecular Biology, University of Oslo and Akershus University Hospital, L\u00f8renskog, Norway","institution_ids":["https://openalex.org/I2800192669","https://openalex.org/I184942183"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023539493","display_name":"Yuedong Yang","orcid":"https://orcid.org/0000-0002-6782-2813"},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yuedong Yang","raw_affiliation_strings":["School of Data and Computer Science and the National Super Computer Center at Guangzhou, Sun Yat-sen University, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Data and Computer Science and the National Super Computer Center at Guangzhou, Sun Yat-sen University, China","institution_ids":["https://openalex.org/I157773358"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5023829396","display_name":"Zhangming Niu","orcid":"https://orcid.org/0000-0002-7009-946X"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Zhangming Niu","raw_affiliation_strings":["Aladdin Healthcare Technologies Ltd"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Aladdin Healthcare Technologies Ltd","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5023539493","https://openalex.org/A5023829396"],"corresponding_institution_ids":["https://openalex.org/I157773358"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":6.0014,"has_fulltext":false,"cited_by_count":163,"citation_normalized_percentile":{"value":0.97427093,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"22","issue":"4","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","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/T10887","display_name":"Bioinformatics and Genomic Networks","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/T10885","display_name":"Gene expression and cancer classification","score":0.9962999820709229,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9927999973297119,"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":0.7735368013381958},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.6538119316101074},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.5700763463973999},{"id":"https://openalex.org/keywords/vocabulary","display_name":"Vocabulary","score":0.522648811340332},{"id":"https://openalex.org/keywords/biomedicine","display_name":"Biomedicine","score":0.510466456413269},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.4897894859313965},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4790257513523102},{"id":"https://openalex.org/keywords/knowledge-graph","display_name":"Knowledge graph","score":0.4703643023967743},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.46064454317092896},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4557556211948395},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.41001278162002563},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.4083620309829712},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.395171582698822},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.27409422397613525},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.17067396640777588}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7735368013381958},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.6538119316101074},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.5700763463973999},{"id":"https://openalex.org/C2777601683","wikidata":"https://www.wikidata.org/wiki/Q6499736","display_name":"Vocabulary","level":2,"score":0.522648811340332},{"id":"https://openalex.org/C66782513","wikidata":"https://www.wikidata.org/wiki/Q864601","display_name":"Biomedicine","level":2,"score":0.510466456413269},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.4897894859313965},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4790257513523102},{"id":"https://openalex.org/C2987255567","wikidata":"https://www.wikidata.org/wiki/Q33002955","display_name":"Knowledge graph","level":2,"score":0.4703643023967743},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.46064454317092896},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4557556211948395},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.41001278162002563},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.4083620309829712},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.395171582698822},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.27409422397613525},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.17067396640777588},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","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/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"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":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012660","descriptor_name":"Semantics","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":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D035843","descriptor_name":"Biomedical Research","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D035843","descriptor_name":"Biomedical Research","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D035843","descriptor_name":"Biomedical Research","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbaa344","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbaa344","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:33341877","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33341877","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:research-repository.griffith.edu.au:10072/407465","is_oa":true,"landing_page_url":"http://hdl.handle.net/10072/407465","pdf_url":null,"source":{"id":"https://openalex.org/S4306402548","display_name":"Griffith Research Online (Griffith University, Queensland, Australia)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I11701301","host_organization_name":"Griffith University","host_organization_lineage":["https://openalex.org/I11701301"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Journal article"}],"best_oa_location":{"id":"pmh:oai:research-repository.griffith.edu.au:10072/407465","is_oa":true,"landing_page_url":"http://hdl.handle.net/10072/407465","pdf_url":null,"source":{"id":"https://openalex.org/S4306402548","display_name":"Griffith Research Online (Griffith University, Queensland, Australia)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I11701301","host_organization_name":"Griffith University","host_organization_lineage":["https://openalex.org/I11701301"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Journal article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1129173493","display_name":null,"funder_award_id":"#81971327","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2357475255","display_name":null,"funder_award_id":"#262175","funder_id":"https://openalex.org/F4320323299","funder_display_name":"Norges Forskningsr\u00e5d"},{"id":"https://openalex.org/G2491791631","display_name":null,"funder_award_id":"#277813","funder_id":"https://openalex.org/F4320323299","funder_display_name":"Norges Forskningsr\u00e5d"},{"id":"https://openalex.org/G4021471878","display_name":null,"funder_award_id":"#2017056","funder_id":"https://openalex.org/F4320335102","funder_display_name":"Helse S\u00f8r-\u00d8st RHF"},{"id":"https://openalex.org/G6565700349","display_name":null,"funder_award_id":"#61772566","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7414379287","display_name":null,"funder_award_id":"#62041209","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320310758","display_name":"Kreftforeningen","ror":"https://ror.org/01925vb10"},{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320323299","display_name":"Norges Forskningsr\u00e5d","ror":"https://ror.org/00epmv149"},{"id":"https://openalex.org/F4320335102","display_name":"Helse S\u00f8r-\u00d8st RHF","ror":"https://ror.org/02qx2s478"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":92,"referenced_works":["https://openalex.org/W50244796","https://openalex.org/W90362830","https://openalex.org/W205829674","https://openalex.org/W1529533208","https://openalex.org/W1533230146","https://openalex.org/W1804706545","https://openalex.org/W1985166282","https://openalex.org/W1988037271","https://openalex.org/W1994127362","https://openalex.org/W2000123680","https://openalex.org/W2000595776","https://openalex.org/W2005598989","https://openalex.org/W2019369036","https://openalex.org/W2026375298","https://openalex.org/W2034166503","https://openalex.org/W2034537627","https://openalex.org/W2035761153","https://openalex.org/W2040096338","https://openalex.org/W2040462263","https://openalex.org/W2047710557","https://openalex.org/W2053186076","https://openalex.org/W2054155190","https://openalex.org/W2056823439","https://openalex.org/W2060449537","https://openalex.org/W2064505617","https://openalex.org/W2065990465","https://openalex.org/W2082042799","https://openalex.org/W2084619201","https://openalex.org/W2089468765","https://openalex.org/W2098464936","https://openalex.org/W2109108939","https://openalex.org/W2118482957","https://openalex.org/W2121604817","https://openalex.org/W2127069089","https://openalex.org/W2127795553","https://openalex.org/W2138192231","https://openalex.org/W2145578524","https://openalex.org/W2147353380","https://openalex.org/W2151357092","https://openalex.org/W2163480486","https://openalex.org/W2164791461","https://openalex.org/W2165428180","https://openalex.org/W2184957013","https://openalex.org/W2187089797","https://openalex.org/W2283196293","https://openalex.org/W2464950095","https://openalex.org/W2562531153","https://openalex.org/W2604314403","https://openalex.org/W2605353548","https://openalex.org/W2609069535","https://openalex.org/W2625343706","https://openalex.org/W2753953057","https://openalex.org/W2759136286","https://openalex.org/W2765988449","https://openalex.org/W2766208765","https://openalex.org/W2767891136","https://openalex.org/W2774837955","https://openalex.org/W2781816753","https://openalex.org/W2786016794","https://openalex.org/W2797328566","https://openalex.org/W2899728356","https://openalex.org/W2911248861","https://openalex.org/W2911489562","https://openalex.org/W2911932738","https://openalex.org/W2916047525","https://openalex.org/W2946099214","https://openalex.org/W2949311246","https://openalex.org/W2950595506","https://openalex.org/W2951105272","https://openalex.org/W2951364005","https://openalex.org/W2966787092","https://openalex.org/W2966864197","https://openalex.org/W2977367243","https://openalex.org/W2977393556","https://openalex.org/W2982150041","https://openalex.org/W2993701748","https://openalex.org/W2999407430","https://openalex.org/W3000365198","https://openalex.org/W3011072970","https://openalex.org/W3020759564","https://openalex.org/W3043498388","https://openalex.org/W3087156149","https://openalex.org/W3112755591","https://openalex.org/W4252698039","https://openalex.org/W4297733535","https://openalex.org/W6602046895","https://openalex.org/W6603694148","https://openalex.org/W6631964550","https://openalex.org/W6678830454","https://openalex.org/W6684123488","https://openalex.org/W6747094798","https://openalex.org/W6766976422"],"related_works":["https://openalex.org/W2604454537","https://openalex.org/W4206028705","https://openalex.org/W2808284704","https://openalex.org/W2883748392","https://openalex.org/W2897702399","https://openalex.org/W2757431232","https://openalex.org/W2954554213","https://openalex.org/W3200431764","https://openalex.org/W4288286922","https://openalex.org/W4206547516"],"abstract_inverted_index":{"Biomedical":[0],"knowledge":[1],"graphs":[2],"(KGs),":[3],"which":[4],"can":[5],"help":[6],"with":[7,109,126],"the":[8,42,77,85,145,185,227],"understanding":[9],"of":[10,45,97,116,174,232],"complex":[11,39],"biological":[12,209],"systems":[13],"and":[14,26,34,41,57,63,107,139,147,160,179,211,214,230,243],"pathologies,":[15],"have":[16],"begun":[17],"to":[18,37,83,192,218,236],"play":[19],"a":[20,72,91,114,161,172,220],"critical":[21],"role":[22],"in":[23,31,80,122,222,238],"medical":[24],"practice":[25],"research.":[27],"However,":[28],"challenges":[29],"remain":[30],"their":[32,38,46],"embedding":[33,157,242],"use":[35,219],"due":[36],"nature":[40],"specific":[43],"demands":[44],"construction.":[47],"Existing":[48],"studies":[49],"often":[50],"suffer":[51],"from":[52,131],"problems":[53],"such":[54],"as":[55],"sparse":[56],"noisy":[58],"datasets,":[59],"insufficient":[60],"modeling":[61],"methods":[62],"non-uniform":[64],"evaluation":[65,199],"metrics.":[66,200],"In":[67],"this":[68],"work,":[69],"we":[70,88,152,188,202],"established":[71],"comprehensive":[73],"KG":[74,156,221,240],"system":[75],"for":[76,216],"biomedical":[78,94,148,239],"field":[79],"an":[81],"attempt":[82],"bridge":[84],"gap.":[86],"Here,":[87],"introduced":[89],"PharmKG,":[90],"multi-relational,":[92],"attributed":[93],"KG,":[95],"composed":[96],"more":[98],"than":[99],"500":[100],"000":[101],"individual":[102],"interconnections":[103],"between":[104],"genes,":[105],"drugs":[106],"diseases,":[108],"29":[110],"relation":[111],"types":[112],"over":[113],"vocabulary":[115],"~8000":[117],"disambiguated":[118],"entities.":[119],"Each":[120],"entity":[121],"PharmKG":[123,233],"is":[124],"attached":[125],"heterogeneous,":[127],"domain-specific":[128],"information":[129],"obtained":[130],"multi-omics":[132],"data,":[133],"i.e.":[134],"gene":[135],"expression,":[136],"chemical":[137],"structure":[138,178],"disease":[140],"word":[141],"embedding,":[142],"while":[143],"preserving":[144],"semantic":[146],"features.":[149,182],"For":[150],"baselines,":[151],"offered":[153],"nine":[154],"state-of-the-art":[155],"(KGE)":[158],"approaches":[159],"new":[162],"biological,":[163],"intuitive,":[164],"graph":[165],"neural":[166],"network-based":[167],"KGE":[168,195],"method":[169],"that":[170,226],"uses":[171],"combination":[173],"both":[175],"global":[176],"network":[177],"heterogeneous":[180],"domain":[181],"Based":[183],"on":[184],"proposed":[186],"benchmark,":[187],"conducted":[189],"extensive":[190],"experiments":[191],"assess":[193],"these":[194],"models":[196],"using":[197],"multiple":[198],"Finally,":[201],"discussed":[203],"our":[204],"observations":[205],"across":[206],"various":[207],"downstream":[208],"tasks":[210],"provide":[212],"insights":[213],"guidelines":[215],"how":[217],"biomedicine.":[223],"We":[224],"hope":[225],"unprecedented":[228],"quality":[229],"diversity":[231],"will":[234],"lead":[235],"advances":[237],"construction,":[241],"application.":[244]},"counts_by_year":[{"year":2026,"cited_by_count":10},{"year":2025,"cited_by_count":42},{"year":2024,"cited_by_count":39},{"year":2023,"cited_by_count":37},{"year":2022,"cited_by_count":23},{"year":2021,"cited_by_count":11},{"year":2020,"cited_by_count":1}],"updated_date":"2026-05-27T09:02:27.158192","created_date":"2025-10-10T00:00:00"}
