{"id":"https://openalex.org/W2117293134","doi":"https://doi.org/10.1186/s13326-015-0001-9","title":"Similarity-based search of model organism, disease and drug effect phenotypes","display_name":"Similarity-based search of model organism, disease and drug effect phenotypes","publication_year":2015,"publication_date":"2015-01-01","ids":{"openalex":"https://openalex.org/W2117293134","doi":"https://doi.org/10.1186/s13326-015-0001-9","mag":"2117293134","pmid":"https://pubmed.ncbi.nlm.nih.gov/25763178"},"language":"en","primary_location":{"id":"doi:10.1186/s13326-015-0001-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13326-015-0001-9","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/s13326-015-0001-9","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/s13326-015-0001-9","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5043808311","display_name":"Robert Hoehndorf","orcid":"https://orcid.org/0000-0001-8149-5890"},"institutions":[{"id":"https://openalex.org/I71920554","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38","country_code":"SA","type":"education","lineage":["https://openalex.org/I71920554"]}],"countries":["SA"],"is_corresponding":true,"raw_author_name":"Robert Hoehndorf","raw_affiliation_strings":["Computational Bioscience Research Center, King Abdullah University of Science and Technology, 4700 KAUST, Thuwal, 23955-6900 Saudi Arabia ; Computer, Electrical and Mathematical Sciences & Engineering Division, King Abdullah University of Science and Technology, 4700 KAUST, Thuwal, 23955-6900 Saudi Arabia","Computational Bioscience Research Center, King Abdullah University of Science and Technology, 4700 KAUST, Thuwal, 23955-6900, Saudi Arabia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Bioscience Research Center, King Abdullah University of Science and Technology, 4700 KAUST, Thuwal, 23955-6900 Saudi Arabia ; Computer, Electrical and Mathematical Sciences & Engineering Division, King Abdullah University of Science and Technology, 4700 KAUST, Thuwal, 23955-6900 Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]},{"raw_affiliation_string":"Computational Bioscience Research Center, King Abdullah University of Science and Technology, 4700 KAUST, Thuwal, 23955-6900, Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053424760","display_name":"Michael Gruenberger","orcid":"https://orcid.org/0000-0002-2112-6791"},"institutions":[{"id":"https://openalex.org/I16038530","display_name":"Aberystwyth University","ror":"https://ror.org/015m2p889","country_code":"GB","type":"education","lineage":["https://openalex.org/I16038530"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Michael Gruenberger","raw_affiliation_strings":["Department of Computer Science, Aberystwyth University, Llandinam Building, Aberystwyth, SY23 3DB UK","Department of Computer Science, Aberystwyth University, Llandinam Building, Aberystwyth, SY23 3DB, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Aberystwyth University, Llandinam Building, Aberystwyth, SY23 3DB UK","institution_ids":["https://openalex.org/I16038530"]},{"raw_affiliation_string":"Department of Computer Science, Aberystwyth University, Llandinam Building, Aberystwyth, SY23 3DB, UK","institution_ids":["https://openalex.org/I16038530"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089900113","display_name":"Georgios V. Gkoutos","orcid":"https://orcid.org/0000-0002-2061-091X"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Georgios V Gkoutos","raw_affiliation_strings":["Department of Physiology, Development & Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3EG UK","Department of Physiology, Development & Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3EG, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Physiology, Development & Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3EG UK","institution_ids":["https://openalex.org/I241749"]},{"raw_affiliation_string":"Department of Physiology, Development & Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3EG, UK","institution_ids":["https://openalex.org/I241749"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5059588755","display_name":"Paul N. Schofield","orcid":"https://orcid.org/0000-0002-5111-7263"},"institutions":[{"id":"https://openalex.org/I16038530","display_name":"Aberystwyth University","ror":"https://ror.org/015m2p889","country_code":"GB","type":"education","lineage":["https://openalex.org/I16038530"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Paul N Schofield","raw_affiliation_strings":["Department of Computer Science, Aberystwyth University, Llandinam Building, Aberystwyth, SY23 3DB UK","Department of Computer Science, Aberystwyth University, Llandinam Building, Aberystwyth, SY23 3DB, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Aberystwyth University, Llandinam Building, Aberystwyth, SY23 3DB UK","institution_ids":["https://openalex.org/I16038530"]},{"raw_affiliation_string":"Department of Computer Science, Aberystwyth University, Llandinam Building, Aberystwyth, SY23 3DB, UK","institution_ids":["https://openalex.org/I16038530"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5043808311"],"corresponding_institution_ids":["https://openalex.org/I71920554"],"apc_list":{"value":1340,"currency":"USD","value_usd":1340},"apc_paid":{"value":1340,"currency":"USD","value_usd":1340},"fwci":1.1025,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.7689824,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"6","issue":"1","first_page":"6","last_page":"6"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9422000050544739,"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":0.9422000050544739,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.023600000888109207,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.010099999606609344,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/phenotype","display_name":"Phenotype","score":0.8103766441345215},{"id":"https://openalex.org/keywords/organism","display_name":"Organism","score":0.8012672662734985},{"id":"https://openalex.org/keywords/model-organism","display_name":"Model organism","score":0.7448760271072388},{"id":"https://openalex.org/keywords/druggability","display_name":"Druggability","score":0.6924273371696472},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6439017057418823},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.64222651720047},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.5288375616073608},{"id":"https://openalex.org/keywords/semantic-similarity","display_name":"Semantic similarity","score":0.46072912216186523},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.454125314950943},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4077273905277252},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3745619058609009},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3338730037212372},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.23419755697250366},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.16472628712654114},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.11572268605232239}],"concepts":[{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.8103766441345215},{"id":"https://openalex.org/C137858568","wikidata":"https://www.wikidata.org/wiki/Q7239","display_name":"Organism","level":2,"score":0.8012672662734985},{"id":"https://openalex.org/C19843653","wikidata":"https://www.wikidata.org/wiki/Q213907","display_name":"Model organism","level":3,"score":0.7448760271072388},{"id":"https://openalex.org/C10679952","wikidata":"https://www.wikidata.org/wiki/Q5308937","display_name":"Druggability","level":3,"score":0.6924273371696472},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6439017057418823},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.64222651720047},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.5288375616073608},{"id":"https://openalex.org/C130318100","wikidata":"https://www.wikidata.org/wiki/Q2268914","display_name":"Semantic similarity","level":2,"score":0.46072912216186523},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.454125314950943},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4077273905277252},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3745619058609009},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3338730037212372},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.23419755697250366},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.16472628712654114},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.11572268605232239},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1186/s13326-015-0001-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13326-015-0001-9","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/s13326-015-0001-9","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:25763178","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25763178","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:repository.kaust.edu.sa:10754/346698","is_oa":true,"landing_page_url":"http://hdl.handle.net/10754/346698","pdf_url":"http://hdl.handle.net/10754/346698","source":{"id":"https://openalex.org/S4306401596","display_name":"King Abdullah University of Science and Technology Repository (King Abdullah University of Science and Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I71920554","host_organization_name":"King Abdullah University of Science and Technology","host_organization_lineage":["https://openalex.org/I71920554"],"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":"Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:4355138","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4355138","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 Biomed Semantics","raw_type":"Text"},{"id":"pmh:oai:pure.atira.dk:openaire_cris_publications/a9ff3d63-0add-458f-9657-754331225b5c","is_oa":true,"landing_page_url":"https://research.birmingham.ac.uk/en/publications/a9ff3d63-0add-458f-9657-754331225b5c","pdf_url":null,"source":{"id":"https://openalex.org/S4306402634","display_name":"University of Birmingham Research Portal (University of Birmingham)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I79619799","host_organization_name":"University of Birmingham","host_organization_lineage":["https://openalex.org/I79619799"],"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":"Hoehndorf, R, Gruenberger, M, Gkoutos, G V & Schofield, P N 2015, 'Similarity-based search of model organism, disease and drug effect phenotypes', J Biomed Semantics, vol. 6, 6. https://doi.org/10.1186/s13326-015-0001-9","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s13326-015-0001-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13326-015-0001-9","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/s13326-015-0001-9","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":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2117293134.pdf","grobid_xml":"https://content.openalex.org/works/W2117293134.grobid-xml"},"referenced_works_count":38,"referenced_works":["https://openalex.org/W55962619","https://openalex.org/W124940209","https://openalex.org/W1871852719","https://openalex.org/W1975138006","https://openalex.org/W1978196155","https://openalex.org/W1980948656","https://openalex.org/W1994612493","https://openalex.org/W2006719549","https://openalex.org/W2012361142","https://openalex.org/W2022451103","https://openalex.org/W2024097840","https://openalex.org/W2049625541","https://openalex.org/W2059313072","https://openalex.org/W2081619597","https://openalex.org/W2084168100","https://openalex.org/W2097057598","https://openalex.org/W2098440497","https://openalex.org/W2103017472","https://openalex.org/W2111707517","https://openalex.org/W2112466127","https://openalex.org/W2116034137","https://openalex.org/W2117243134","https://openalex.org/W2119943416","https://openalex.org/W2124991490","https://openalex.org/W2136265964","https://openalex.org/W2136410628","https://openalex.org/W2142572836","https://openalex.org/W2145547964","https://openalex.org/W2146495783","https://openalex.org/W2157079123","https://openalex.org/W2157217189","https://openalex.org/W2158698691","https://openalex.org/W2162361752","https://openalex.org/W2162891889","https://openalex.org/W2163670493","https://openalex.org/W2163685645","https://openalex.org/W2164290176","https://openalex.org/W2405275595"],"related_works":["https://openalex.org/W4223896405","https://openalex.org/W1969888071","https://openalex.org/W2035422779","https://openalex.org/W2059629050","https://openalex.org/W2258998699","https://openalex.org/W4389227606","https://openalex.org/W2925167008","https://openalex.org/W3013644380","https://openalex.org/W2036884070","https://openalex.org/W2074740504"],"abstract_inverted_index":{"BACKGROUND:":[0],"Semantic":[1],"similarity":[2,135],"measures":[3],"over":[4,53],"phenotype":[5],"ontologies":[6],"have":[7,43],"been":[8],"demonstrated":[9],"to":[10,65,75,83,94,140],"provide":[11,114],"a":[12,47,54,99,115,145],"powerful":[13,116],"approach":[14],"for":[15,118],"the":[16,22,95,119],"analysis":[17],"of":[18,24,27,39,57,68,123,148],"model":[19,69,84,102],"organism":[20,85],"phenotypes,":[21,86],"discovery":[23,120],"animal":[25],"models":[26],"human":[28,76],"disease,":[29],"novel":[30],"pathways,":[31],"gene":[32],"functions,":[33],"druggable":[34],"therapeutic":[35],"targets,":[36],"and":[37,121,137,151],"determination":[38],"pathogenicity.":[40],"RESULTS:":[41],"We":[42],"developed":[44],"PhenomeNET":[45,104,131],"2,":[46],"system":[48],"that":[49,71,79,91],"enables":[50],"similarity-based":[51],"searches":[52,112,136],"large":[55,146],"repository":[56,147],"phenotypes":[58,96],"in":[59,98],"real-time.":[60],"It":[61],"can":[62,113],"be":[63],"used":[64],"identify":[66],"strains":[67],"organisms":[70],"are":[72,80,92],"phenotypically":[73,81],"similar":[74,82,93],"patients,":[77],"diseases":[78],"or":[87,101],"drug":[88],"effect":[89],"profiles":[90],"observed":[97,128],"patient":[100],"organism.":[103],"2":[105,132],"is":[106],"available":[107],"at":[108],"http://aber-owl.net/phenomenet.":[109],"CONCLUSIONS:":[110],"Phenotype-similarity":[111],"tool":[117],"investigation":[122],"molecular":[124],"mechanisms":[125],"underlying":[126],"an":[127],"phenotypic":[129],"manifestation.":[130],"facilitates":[133],"user-defined":[134],"allows":[138],"researchers":[139],"analyze":[141],"their":[142],"data":[143],"within":[144],"human,":[149],"mouse":[150],"rat":[152],"phenotypes.":[153]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":4}],"updated_date":"2026-07-29T09:40:50.615796","created_date":"2025-10-10T00:00:00"}
