{"id":"https://openalex.org/W2128365672","doi":"https://doi.org/10.1186/2041-1480-4-18","title":"The mouse pathology ontology, MPATH; structure and applications","display_name":"The mouse pathology ontology, MPATH; structure and applications","publication_year":2013,"publication_date":"2013-01-01","ids":{"openalex":"https://openalex.org/W2128365672","doi":"https://doi.org/10.1186/2041-1480-4-18","mag":"2128365672","pmid":"https://pubmed.ncbi.nlm.nih.gov/24033988"},"language":"en","primary_location":{"id":"doi:10.1186/2041-1480-4-18","is_oa":true,"landing_page_url":"https://doi.org/10.1186/2041-1480-4-18","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/2041-1480-4-18","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/10.1186/2041-1480-4-18","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5059588755","display_name":"Paul N. Schofield","orcid":"https://orcid.org/0000-0002-5111-7263"},"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":true,"raw_author_name":"Paul N Schofield","raw_affiliation_strings":["Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, CB2 3EG, Cambridge, UK. ps@mole.bio.cam.ac.uk","Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, CB2 3EG, Cambridge, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, CB2 3EG, Cambridge, UK. ps@mole.bio.cam.ac.uk","institution_ids":[]},{"raw_affiliation_string":"Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, CB2 3EG, Cambridge, UK","institution_ids":["https://openalex.org/I241749"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031368365","display_name":"John P. Sundberg","orcid":"https://orcid.org/0000-0002-1523-5430"},"institutions":[{"id":"https://openalex.org/I4210115256","display_name":"Jackson Laboratory","ror":"https://ror.org/021sy4w91","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210115256"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"John P Sundberg","raw_affiliation_strings":["The Jackson Laboratory, 600, Main Street, Bar Harbor, ME, 04609-1500, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Jackson Laboratory, 600, Main Street, Bar Harbor, ME, 04609-1500, USA","institution_ids":["https://openalex.org/I4210115256"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061955580","display_name":"Beth A. Sundberg","orcid":"https://orcid.org/0000-0002-4261-0750"},"institutions":[{"id":"https://openalex.org/I4210115256","display_name":"Jackson Laboratory","ror":"https://ror.org/021sy4w91","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210115256"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Beth A Sundberg","raw_affiliation_strings":["The Jackson Laboratory, 600, Main Street, Bar Harbor, ME, 04609-1500, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Jackson Laboratory, 600, Main Street, Bar Harbor, ME, 04609-1500, USA","institution_ids":["https://openalex.org/I4210115256"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075162277","display_name":"Colin McKerlie","orcid":"https://orcid.org/0000-0002-2232-0967"},"institutions":[{"id":"https://openalex.org/I2801317318","display_name":"Hospital for Sick Children","ror":"https://ror.org/057q4rt57","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I2801317318"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Colin McKerlie","raw_affiliation_strings":["Physiology and Experimental Medicine Research Program, The Hospital for Sick Children, M5G 1X8, Toronto, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Physiology and Experimental Medicine Research Program, The Hospital for Sick Children, M5G 1X8, Toronto, Canada","institution_ids":["https://openalex.org/I2801317318"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5089900113","display_name":"Georgios V. Gkoutos","orcid":"https://orcid.org/0000-0002-2061-091X"},"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":"Georgios V Gkoutos","raw_affiliation_strings":["Department of Computer Science, University of Aberystwyth, Old College, King Street, SY23 2AX, Ceredigion, Wales"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Aberystwyth, Old College, King Street, SY23 2AX, Ceredigion, Wales","institution_ids":["https://openalex.org/I16038530"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5059588755"],"corresponding_institution_ids":["https://openalex.org/I241749"],"apc_list":{"value":1190,"currency":"GBP","value_usd":1459},"apc_paid":{"value":1190,"currency":"GBP","value_usd":1459},"fwci":1.9445,"has_fulltext":true,"cited_by_count":41,"citation_normalized_percentile":{"value":0.86235138,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"4","issue":"1","first_page":"18","last_page":"18"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9426000118255615,"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":0.9426000118255615,"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/T14072","display_name":"Immunotoxicology and immune responses","score":0.0357000008225441,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.003800000064074993,"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":0.8161286115646362},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.5392460227012634},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.4529487192630768},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.44012919068336487}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8161286115646362},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.5392460227012634},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.4529487192630768},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.44012919068336487},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[],"locations_count":7,"locations":[{"id":"doi:10.1186/2041-1480-4-18","is_oa":true,"landing_page_url":"https://doi.org/10.1186/2041-1480-4-18","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/2041-1480-4-18","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:24033988","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24033988","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:aber.ac.uk:publications/e3b34e4b-b5f7-46bc-881a-3816e9ae8029","is_oa":true,"landing_page_url":null,"pdf_url":"http://hdl.handle.net/2160/12517","source":{"id":"https://openalex.org/S4306401660","display_name":"Aberystwyth Research portal (Aberystwyth University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I16038530","host_organization_name":"Aberystwyth University","host_organization_lineage":["https://openalex.org/I16038530"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":""},{"id":"pmh:oai:europepmc.org:2837955","is_oa":true,"landing_page_url":"http://europepmc.org/articles/PMC3851164","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":"","raw_type":"Text"},{"id":"pmh:oai:mouseion.jax.org:stfb2013-1141","is_oa":false,"landing_page_url":"https://mouseion.jax.org/stfb2013/142","pdf_url":null,"source":{"id":"https://openalex.org/S4377196421","display_name":"The Mouseion at the JAXlibrary (Jackson Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210115256","host_organization_name":"Jackson Laboratory","host_organization_lineage":["https://openalex.org/I4210115256"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Faculty Research 2013","raw_type":"text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3851164","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3851164","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/5c98175e-e08d-44f2-ba02-d477358b45bc","is_oa":false,"landing_page_url":"https://research.birmingham.ac.uk/en/publications/5c98175e-e08d-44f2-ba02-d477358b45bc","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Schofield, P N, Sundberg, J P, Sundberg, B A, McKerlie, C & Gkoutos, G V 2013, 'The mouse pathology ontology, MPATH; structure and applications', J Biomed Semantics, vol. 4, no. 1, pp. 18.","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/2041-1480-4-18","is_oa":true,"landing_page_url":"https://doi.org/10.1186/2041-1480-4-18","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/2041-1480-4-18","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":[{"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land","score":0.4099999964237213}],"awards":[],"funders":[{"id":"https://openalex.org/F4320306135","display_name":"Ellison Medical Foundation","ror":"https://ror.org/01pqy3846"},{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2128365672.pdf","grobid_xml":"https://content.openalex.org/works/W2128365672.grobid-xml"},"referenced_works_count":44,"referenced_works":["https://openalex.org/W581031595","https://openalex.org/W604715870","https://openalex.org/W1236321187","https://openalex.org/W1560820255","https://openalex.org/W1757909678","https://openalex.org/W1966108849","https://openalex.org/W1977220356","https://openalex.org/W2002523358","https://openalex.org/W2006917435","https://openalex.org/W2007117925","https://openalex.org/W2022451103","https://openalex.org/W2024551053","https://openalex.org/W2044257395","https://openalex.org/W2048024098","https://openalex.org/W2048495389","https://openalex.org/W2055961987","https://openalex.org/W2095687577","https://openalex.org/W2100462409","https://openalex.org/W2100482380","https://openalex.org/W2101225650","https://openalex.org/W2111299816","https://openalex.org/W2111707517","https://openalex.org/W2124580184","https://openalex.org/W2135140530","https://openalex.org/W2138443244","https://openalex.org/W2144047630","https://openalex.org/W2144245114","https://openalex.org/W2145088924","https://openalex.org/W2146495783","https://openalex.org/W2150838562","https://openalex.org/W2151049342","https://openalex.org/W2155520494","https://openalex.org/W2157217189","https://openalex.org/W2159092541","https://openalex.org/W2163670493","https://openalex.org/W2163685645","https://openalex.org/W2167780877","https://openalex.org/W2168005921","https://openalex.org/W2168372732","https://openalex.org/W2169640462","https://openalex.org/W2178026535","https://openalex.org/W2299444859","https://openalex.org/W2465336579","https://openalex.org/W4253515801"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655","https://openalex.org/W2359140296"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,52],"capture":[2],"and":[3,15,24,48,79,83,89,104,150,193,199,201,210,231,235,262,297],"use":[4,216,267,285],"of":[5,63,68,81,144,175,191,205,217,228,252,283],"disease-related":[6],"anatomic":[7,253],"pathology":[8,131,299],"data":[9,32,85,195,300,303],"for":[10,65,77,86,172,208,249],"both":[11,197],"model":[12],"organism":[13],"phenotyping":[14,241],"human":[16],"clinical":[17],"practice":[18],"requires":[19],"a":[20,61,226,245,281],"relatively":[21],"simple":[22],"nomenclature":[23],"coding":[25,78],"system":[26],"that":[27],"can":[28,256],"be":[29,122,257],"integrated":[30],"into":[31,97],"collection":[33],"platforms":[34],"(such":[35],"as":[36,124,153,155,306],"computerized":[37],"medical":[38],"record-keeping":[39],"systems)":[40],"to":[41,45,115,158,219,238,259,276,288],"enable":[42],"the":[43,66,145,162,173,189,203,215,229,250,290],"pathologist":[44],"rapidly":[46],"screen":[47],"accurately":[49],"record":[50],"observations.":[51],"MPATH":[53,94,168,218,243],"ontology":[54,248],"was":[55,169],"originally":[56,170],"constructed":[57],"in":[58,133,188,202,268,294],"2,000":[59],"by":[60],"committee":[62],"pathologists":[64],"annotation":[67,174],"rodent":[69],"histopathology":[70],"images,":[71],"but":[72,180],"is":[73,95,181,263],"now":[74,182,264],"widely":[75,187],"used":[76,184],"analysis":[80,287],"disease":[82,125,211],"phenotype":[84,209],"rodents,":[87],"humans":[88],"zebrafish.":[90],"CONSTRUCTION":[91],"AND":[92,166],"CONTENT:":[93],"divided":[96],"two":[98],"main":[99],"branches":[100],"describing":[101],"pathological":[102],"processes":[103],"structures":[105],"based":[106],"on":[107],"traditional":[108],"histopathological":[109,176],"principles.":[110],"It":[111,127,273],"does":[112],"not":[113],"aim":[114],"include":[116],"definitive":[117],"diagnoses,":[118],"which":[119,255],"would":[120],"generally":[121],"regarded":[123],"concepts.":[126],"contains":[128],"888":[129],"core":[130],"terms":[132,146],"an":[134],"almost":[135],"exclusively":[136],"is_a":[137],"hierarchy":[138],"nine":[139],"layers":[140],"deep.":[141],"Currently,":[142],"86%":[143],"have":[147],"textual":[148],"definitions":[149,207],"contain":[151],"relationships":[152],"well":[154],"logical":[156,206],"axioms":[157],"other":[159,270,302],"ontologies":[160],"such":[161,305],"Gene":[163],"Ontology.":[164],"APPLICATION":[165],"UTILITY:":[167],"devised":[171],"images":[177],"from":[178,196,225],"mice":[179,198],"being":[183],"much":[185],"more":[186],"recording":[190],"diagnostic":[192],"phenotypic":[194],"humans,":[200],"construction":[204],"ontologies.":[212],"We":[213],"discuss":[214],"generate":[220],"cross-products":[221],"with":[222,301],"qualifiers":[223],"derived":[224],"subset":[227],"Phenotype":[230],"Trait":[232],"Ontology":[233],"(PATO)":[234],"its":[236],"application":[237],"large-scale":[239],"high-throughput":[240],"studies.":[242],"provides":[244],"largely":[246],"species-agnostic":[247],"descriptions":[251],"pathology,":[254],"applied":[258],"most":[260],"amniotes":[261],"finding":[265],"extensive":[266],"species":[269,296],"than":[271],"mice.":[272],"enables":[274],"investigators":[275],"interrogate":[277],"large":[278],"datasets":[279],"at":[280],"variety":[282],"depths,":[284],"semantic":[286],"identify":[289],"relations":[291],"between":[292],"diseases":[293],"different":[295],"integrate":[298],"types,":[304],"pharmacogenomics.":[307]},"counts_by_year":[{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":3},{"year":2021,"cited_by_count":5},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":7},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":5},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":2}],"updated_date":"2026-04-29T09:16:38.111599","created_date":"2025-10-10T00:00:00"}