{"id":"https://openalex.org/W2136345497","doi":"https://doi.org/10.1186/2041-1480-2-3","title":"A shortest-path graph kernel for estimating gene product semantic similarity","display_name":"A shortest-path graph kernel for estimating gene product semantic similarity","publication_year":2011,"publication_date":"2011-07-29","ids":{"openalex":"https://openalex.org/W2136345497","doi":"https://doi.org/10.1186/2041-1480-2-3","mag":"2136345497","pmid":"https://pubmed.ncbi.nlm.nih.gov/21801410"},"language":"en","primary_location":{"id":"doi:10.1186/2041-1480-2-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/2041-1480-2-3","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/2041-1480-2-3","source":{"id":"https://openalex.org/S172276550","display_name":"Journal of Biomedical Semantics","issn_l":"2041-1480","issn":["2041-1480"],"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 Biomedical Semantics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/2041-1480-2-3","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5103559461","display_name":"Marco A. Alvarez","orcid":null},"institutions":[{"id":"https://openalex.org/I121980950","display_name":"Utah State University","ror":"https://ror.org/00h6set76","country_code":"US","type":"education","lineage":["https://openalex.org/I121980950"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Marco A Alvarez","raw_affiliation_strings":["Department of Computer Science, North Dakota State University, Fargo, 58108, USA. changhui.yan@ndsu.edu","Department of Computer Science, Utah State University, Logan, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, North Dakota State University, Fargo, 58108, USA. changhui.yan@ndsu.edu","institution_ids":[]},{"raw_affiliation_string":"Department of Computer Science, Utah State University, Logan, USA","institution_ids":["https://openalex.org/I121980950"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100626347","display_name":"Xiaojun Qi","orcid":"https://orcid.org/0000-0002-4034-8488"},"institutions":[{"id":"https://openalex.org/I121980950","display_name":"Utah State University","ror":"https://ror.org/00h6set76","country_code":"US","type":"education","lineage":["https://openalex.org/I121980950"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xiaojun Qi","raw_affiliation_strings":["Department of Computer Science, Utah State University, Logan, 84322, USA","Department of Computer Science, Utah State University, Logan, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Utah State University, Logan, 84322, USA","institution_ids":["https://openalex.org/I121980950"]},{"raw_affiliation_string":"Department of Computer Science, Utah State University, Logan, USA","institution_ids":["https://openalex.org/I121980950"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100871727","display_name":"Changhui Yan","orcid":"https://orcid.org/0000-0003-3048-8628"},"institutions":[{"id":"https://openalex.org/I57328836","display_name":"North Dakota State University","ror":"https://ror.org/05h1bnb22","country_code":"US","type":"education","lineage":["https://openalex.org/I57328836"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Changhui Yan","raw_affiliation_strings":["Department of Computer Science, North Dakota State University, Fargo, 58108, USA","Department of Computer Science, North Dakota State University Fargo, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, North Dakota State University, Fargo, 58108, USA","institution_ids":["https://openalex.org/I57328836"]},{"raw_affiliation_string":"Department of Computer Science, North Dakota State University Fargo, USA","institution_ids":["https://openalex.org/I57328836"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5103559461"],"corresponding_institution_ids":["https://openalex.org/I121980950"],"apc_list":{"value":1190,"currency":"GBP","value_usd":1459},"apc_paid":{"value":1190,"currency":"GBP","value_usd":1459},"fwci":2.1342,"has_fulltext":true,"cited_by_count":47,"citation_normalized_percentile":{"value":0.87501025,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"2","issue":"1","first_page":"3","last_page":"3"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9997000098228455,"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":0.9997000098228455,"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":0.9901000261306763,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9833999872207642,"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":0.7468154430389404},{"id":"https://openalex.org/keywords/semantic-similarity","display_name":"Semantic similarity","score":0.683647632598877},{"id":"https://openalex.org/keywords/shortest-path-problem","display_name":"Shortest path problem","score":0.6007017493247986},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5221917033195496},{"id":"https://openalex.org/keywords/graph-kernel","display_name":"Graph kernel","score":0.5190352201461792},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.5031744837760925},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5017862319946289},{"id":"https://openalex.org/keywords/kernel","display_name":"Kernel (algebra)","score":0.4788389205932617},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.47490039467811584},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.4338566064834595},{"id":"https://openalex.org/keywords/exploit","display_name":"Exploit","score":0.4174686074256897},{"id":"https://openalex.org/keywords/path","display_name":"Path (computing)","score":0.41151753067970276},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.32227224111557007},{"id":"https://openalex.org/keywords/kernel-method","display_name":"Kernel method","score":0.31587961316108704},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.30665719509124756},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.20462656021118164},{"id":"https://openalex.org/keywords/polynomial-kernel","display_name":"Polynomial kernel","score":0.16535237431526184},{"id":"https://openalex.org/keywords/support-vector-machine","display_name":"Support vector machine","score":0.09262499213218689},{"id":"https://openalex.org/keywords/discrete-mathematics","display_name":"Discrete mathematics","score":0.08287122845649719}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7468154430389404},{"id":"https://openalex.org/C130318100","wikidata":"https://www.wikidata.org/wiki/Q2268914","display_name":"Semantic similarity","level":2,"score":0.683647632598877},{"id":"https://openalex.org/C22590252","wikidata":"https://www.wikidata.org/wiki/Q1058754","display_name":"Shortest path problem","level":3,"score":0.6007017493247986},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5221917033195496},{"id":"https://openalex.org/C100595998","wikidata":"https://www.wikidata.org/wiki/Q11731931","display_name":"Graph kernel","level":5,"score":0.5190352201461792},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.5031744837760925},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5017862319946289},{"id":"https://openalex.org/C74193536","wikidata":"https://www.wikidata.org/wiki/Q574844","display_name":"Kernel (algebra)","level":2,"score":0.4788389205932617},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.47490039467811584},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4338566064834595},{"id":"https://openalex.org/C165696696","wikidata":"https://www.wikidata.org/wiki/Q11287","display_name":"Exploit","level":2,"score":0.4174686074256897},{"id":"https://openalex.org/C2777735758","wikidata":"https://www.wikidata.org/wiki/Q817765","display_name":"Path (computing)","level":2,"score":0.41151753067970276},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.32227224111557007},{"id":"https://openalex.org/C122280245","wikidata":"https://www.wikidata.org/wiki/Q620622","display_name":"Kernel method","level":3,"score":0.31587961316108704},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.30665719509124756},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.20462656021118164},{"id":"https://openalex.org/C160446489","wikidata":"https://www.wikidata.org/wiki/Q7226642","display_name":"Polynomial kernel","level":4,"score":0.16535237431526184},{"id":"https://openalex.org/C12267149","wikidata":"https://www.wikidata.org/wiki/Q282453","display_name":"Support vector machine","level":2,"score":0.09262499213218689},{"id":"https://openalex.org/C118615104","wikidata":"https://www.wikidata.org/wiki/Q121416","display_name":"Discrete mathematics","level":1,"score":0.08287122845649719},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","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/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/2041-1480-2-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/2041-1480-2-3","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/2041-1480-2-3","source":{"id":"https://openalex.org/S172276550","display_name":"Journal of Biomedical Semantics","issn_l":"2041-1480","issn":["2041-1480"],"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 Biomedical Semantics","raw_type":"journal-article"},{"id":"pmid:21801410","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21801410","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 biomedical semantics","raw_type":null},{"id":"pmh:oai:doaj.org/article:5cbf576e647f4e02976e97ed512f053f","is_oa":true,"landing_page_url":"https://doaj.org/article/5cbf576e647f4e02976e97ed512f053f","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":"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 Biomedical Semantics, Vol 2, Iss 1, p 3 (2011)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2165840","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3161911","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:10.1186/2041-1480-2-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/2041-1480-2-3","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/2041-1480-2-3","source":{"id":"https://openalex.org/S172276550","display_name":"Journal of Biomedical Semantics","issn_l":"2041-1480","issn":["2041-1480"],"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 Biomedical Semantics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5143913891","display_name":null,"funder_award_id":"RR0164","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5698253053","display_name":null,"funder_award_id":"P20 RR016471","funder_id":"https://openalex.org/F4320337375","funder_display_name":"National Center for Research Resources"},{"id":"https://openalex.org/G7358404105","display_name":null,"funder_award_id":"P20 RR016471","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320323424","display_name":"Universidade de Lisboa","ror":"https://ror.org/01c27hj86"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337375","display_name":"National Center for Research Resources","ror":"https://ror.org/04pw6fb54"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2136345497.pdf","grobid_xml":"https://content.openalex.org/works/W2136345497.grobid-xml"},"referenced_works_count":30,"referenced_works":["https://openalex.org/W142944101","https://openalex.org/W180620554","https://openalex.org/W1528998781","https://openalex.org/W1647729745","https://openalex.org/W1980948656","https://openalex.org/W1989034333","https://openalex.org/W2006762667","https://openalex.org/W2016343623","https://openalex.org/W2017936606","https://openalex.org/W2055867223","https://openalex.org/W2060948468","https://openalex.org/W2084168100","https://openalex.org/W2096939566","https://openalex.org/W2099438806","https://openalex.org/W2100935296","https://openalex.org/W2103017472","https://openalex.org/W2110595429","https://openalex.org/W2110626682","https://openalex.org/W2117805756","https://openalex.org/W2121343862","https://openalex.org/W2126225210","https://openalex.org/W2127563440","https://openalex.org/W2128049108","https://openalex.org/W2141885858","https://openalex.org/W2149911752","https://openalex.org/W2159348493","https://openalex.org/W2772934464","https://openalex.org/W4210323379","https://openalex.org/W4211208250","https://openalex.org/W4249400168"],"related_works":["https://openalex.org/W2363184354","https://openalex.org/W2179275589","https://openalex.org/W1983263273","https://openalex.org/W3006070568","https://openalex.org/W2189183545","https://openalex.org/W2096302783","https://openalex.org/W2170018389","https://openalex.org/W2974741803","https://openalex.org/W1558903433","https://openalex.org/W2093878082"],"abstract_inverted_index":{"Spgk":[0],"uses":[1],"a":[2],"graph":[3],"kernel":[4],"method":[5],"in":[6],"polynomial":[7],"time":[8],"to":[9,16,27],"exploit":[10],"the":[11,14],"structure":[12],"of":[13],"GO":[15],"calculate":[17],"semantic":[18],"similarity":[19],"between":[20],"gene":[21],"products.":[22],"It":[23],"provides":[24],"an":[25],"alternative":[26],"both":[28],"methods":[29,36],"that":[30],"use":[31],"external":[32],"resources":[33],"and":[34],"\"intrinsic\"":[35],"with":[37],"comparable":[38],"performance.":[39]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":9},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":6},{"year":2014,"cited_by_count":7},{"year":2013,"cited_by_count":5},{"year":2012,"cited_by_count":2}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
