{"id":"https://openalex.org/W4319082242","doi":"https://doi.org/10.3390/info14020091","title":"A Tissue-Specific and Toxicology-Focused Knowledge Graph","display_name":"A Tissue-Specific and Toxicology-Focused Knowledge Graph","publication_year":2023,"publication_date":"2023-02-03","ids":{"openalex":"https://openalex.org/W4319082242","doi":"https://doi.org/10.3390/info14020091"},"language":"en","primary_location":{"id":"doi:10.3390/info14020091","is_oa":true,"landing_page_url":"https://doi.org/10.3390/info14020091","pdf_url":"https://www.mdpi.com/2078-2489/14/2/91/pdf?version=1675692895","source":{"id":"https://openalex.org/S4210219776","display_name":"Information","issn_l":"2078-2489","issn":["2078-2489"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Information","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.mdpi.com/2078-2489/14/2/91/pdf?version=1675692895","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5018002605","display_name":"Ignacio J. Tripodi","orcid":"https://orcid.org/0000-0003-3066-4273"},"institutions":[{"id":"https://openalex.org/I1309191912","display_name":"Research Triangle Park Foundation","ror":"https://ror.org/03eqttr49","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1309191912"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ignacio J. Tripodi","raw_affiliation_strings":["Sciome, LLC, Research Triangle Park, Durham, NC 27709, USA"],"raw_orcid":"https://orcid.org/0000-0003-3066-4273","affiliations":[{"raw_affiliation_string":"Sciome, LLC, Research Triangle Park, Durham, NC 27709, USA","institution_ids":["https://openalex.org/I1309191912"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064259189","display_name":"Lena Schmidt","orcid":"https://orcid.org/0000-0003-0709-8226"},"institutions":[{"id":"https://openalex.org/I1309191912","display_name":"Research Triangle Park Foundation","ror":"https://ror.org/03eqttr49","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1309191912"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lena Schmidt","raw_affiliation_strings":["Sciome, LLC, Research Triangle Park, Durham, NC 27709, USA"],"raw_orcid":"https://orcid.org/0000-0003-0709-8226","affiliations":[{"raw_affiliation_string":"Sciome, LLC, Research Triangle Park, Durham, NC 27709, USA","institution_ids":["https://openalex.org/I1309191912"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011043085","display_name":"Brian E. Howard","orcid":"https://orcid.org/0000-0002-6123-7090"},"institutions":[{"id":"https://openalex.org/I1309191912","display_name":"Research Triangle Park Foundation","ror":"https://ror.org/03eqttr49","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1309191912"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Brian E. Howard","raw_affiliation_strings":["Sciome, LLC, Research Triangle Park, Durham, NC 27709, USA"],"raw_orcid":"https://orcid.org/0000-0002-6123-7090","affiliations":[{"raw_affiliation_string":"Sciome, LLC, Research Triangle Park, Durham, NC 27709, USA","institution_ids":["https://openalex.org/I1309191912"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085970204","display_name":"Deepak Mav","orcid":"https://orcid.org/0000-0002-4683-7813"},"institutions":[{"id":"https://openalex.org/I1309191912","display_name":"Research Triangle Park Foundation","ror":"https://ror.org/03eqttr49","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1309191912"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Deepak Mav","raw_affiliation_strings":["Sciome, LLC, Research Triangle Park, Durham, NC 27709, USA"],"raw_orcid":"https://orcid.org/0000-0002-4683-7813","affiliations":[{"raw_affiliation_string":"Sciome, LLC, Research Triangle Park, Durham, NC 27709, USA","institution_ids":["https://openalex.org/I1309191912"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5110539185","display_name":"Ruchir Shah","orcid":null},"institutions":[{"id":"https://openalex.org/I1309191912","display_name":"Research Triangle Park Foundation","ror":"https://ror.org/03eqttr49","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1309191912"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ruchir Shah","raw_affiliation_strings":["Sciome, LLC, Research Triangle Park, Durham, NC 27709, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Sciome, LLC, Research Triangle Park, Durham, NC 27709, USA","institution_ids":["https://openalex.org/I1309191912"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5018002605"],"corresponding_institution_ids":["https://openalex.org/I1309191912"],"apc_list":{"value":1400,"currency":"CHF","value_usd":1515},"apc_paid":{"value":1400,"currency":"CHF","value_usd":1515},"fwci":0.4361,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.65107744,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"14","issue":"2","first_page":"91","last_page":"91"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9980999827384949,"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":0.9932000041007996,"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/ontology","display_name":"Ontology","score":0.6454706788063049},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6265808343887329},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.6084538698196411},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5726594924926758},{"id":"https://openalex.org/keywords/knowledge-graph","display_name":"Knowledge graph","score":0.5571604371070862},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.46423545479774475},{"id":"https://openalex.org/keywords/open-biomedical-ontologies","display_name":"Open Biomedical Ontologies","score":0.4419298470020294},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3893544673919678},{"id":"https://openalex.org/keywords/semantic-web","display_name":"Semantic Web","score":0.26642346382141113},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.20978900790214539},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.20061960816383362},{"id":"https://openalex.org/keywords/upper-ontology","display_name":"Upper ontology","score":0.10253676772117615}],"concepts":[{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.6454706788063049},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6265808343887329},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6084538698196411},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5726594924926758},{"id":"https://openalex.org/C2987255567","wikidata":"https://www.wikidata.org/wiki/Q33002955","display_name":"Knowledge graph","level":2,"score":0.5571604371070862},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.46423545479774475},{"id":"https://openalex.org/C137982476","wikidata":"https://www.wikidata.org/wiki/Q7072326","display_name":"Open Biomedical Ontologies","level":5,"score":0.4419298470020294},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3893544673919678},{"id":"https://openalex.org/C2129575","wikidata":"https://www.wikidata.org/wiki/Q54837","display_name":"Semantic Web","level":2,"score":0.26642346382141113},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.20978900790214539},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.20061960816383362},{"id":"https://openalex.org/C78726541","wikidata":"https://www.wikidata.org/wiki/Q3882785","display_name":"Upper ontology","level":3,"score":0.10253676772117615},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","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},{"id":"https://openalex.org/C50971890","wikidata":"https://www.wikidata.org/wiki/Q7635093","display_name":"Suggested Upper Merged Ontology","level":4,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.3390/info14020091","is_oa":true,"landing_page_url":"https://doi.org/10.3390/info14020091","pdf_url":"https://www.mdpi.com/2078-2489/14/2/91/pdf?version=1675692895","source":{"id":"https://openalex.org/S4210219776","display_name":"Information","issn_l":"2078-2489","issn":["2078-2489"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Information","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:05ea7a6461ca43e6bbdc766cb521e807","is_oa":true,"landing_page_url":"https://doaj.org/article/05ea7a6461ca43e6bbdc766cb521e807","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Information, Vol 14, Iss 2, p 91 (2023)","raw_type":"article"},{"id":"pmh:oai:mdpi.com:/2078-2489/14/2/91/","is_oa":true,"landing_page_url":"https://dx.doi.org/10.3390/info14020091","pdf_url":null,"source":{"id":"https://openalex.org/S4306400947","display_name":"MDPI (MDPI AG)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210097602","host_organization_name":"Multidisciplinary Digital Publishing Institute (Switzerland)","host_organization_lineage":["https://openalex.org/I4210097602"],"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":"Information","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.3390/info14020091","is_oa":true,"landing_page_url":"https://doi.org/10.3390/info14020091","pdf_url":"https://www.mdpi.com/2078-2489/14/2/91/pdf?version=1675692895","source":{"id":"https://openalex.org/S4210219776","display_name":"Information","issn_l":"2078-2489","issn":["2078-2489"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Information","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4319082242.pdf"},"referenced_works_count":24,"referenced_works":["https://openalex.org/W1935434993","https://openalex.org/W2000801162","https://openalex.org/W2036595331","https://openalex.org/W2094121461","https://openalex.org/W2102983252","https://openalex.org/W2103017472","https://openalex.org/W2108798001","https://openalex.org/W2123879591","https://openalex.org/W2130410032","https://openalex.org/W2143023112","https://openalex.org/W2462007197","https://openalex.org/W2557399158","https://openalex.org/W2949311246","https://openalex.org/W2990435446","https://openalex.org/W3003265726","https://openalex.org/W3106811464","https://openalex.org/W3107527779","https://openalex.org/W3112600195","https://openalex.org/W3136918052","https://openalex.org/W3211402536","https://openalex.org/W4212919921","https://openalex.org/W4307717106","https://openalex.org/W6787364303","https://openalex.org/W6810311434"],"related_works":["https://openalex.org/W2127299687","https://openalex.org/W1506177826","https://openalex.org/W2532736362","https://openalex.org/W2726617685","https://openalex.org/W1562796463","https://openalex.org/W1530162452","https://openalex.org/W2008629522","https://openalex.org/W2399880385","https://openalex.org/W2370212190","https://openalex.org/W3135477004"],"abstract_inverted_index":{"Molecular":[0],"biology-focused":[1],"knowledge":[2,165],"graphs":[3,7,49,166],"(KGs)":[4],"are":[5,50,83,135,141,186,197,210],"directed":[6],"that":[8,74,122,155,185],"integrate":[9],"information":[10,64],"from":[11,58,103,199],"heterogeneous":[12],"sources":[13],"of":[14,30,62,78,105,146,152,160,176,182,203],"biological":[15],"and":[16,22,33,56,86,100,118],"biomedical":[17],"data,":[18,207],"such":[19],"as":[20,120,169],"ontologies":[21,55],"public":[23,59],"databases.":[24],"They":[25],"provide":[26],"a":[27,79,97,200],"holistic":[28],"view":[29],"biology,":[31,148],"chemistry,":[32],"disease,":[34],"allowing":[35],"users":[36],"to":[37,143,189],"draw":[38],"non-obvious":[39],"connections":[40],"between":[41],"concepts":[42,67],"through":[43],"shared":[44],"associations.":[45],"While":[46],"these":[47,208],"massive":[48],"constructed":[51,112],"using":[52],"carefully":[53],"curated":[54],"annotations":[57,126],"databases,":[60],"much":[61],"the":[63,66,76,84,88,101,125,150,158,180,190,194],"relating":[65],"is":[68],"context":[69],"specific.":[70],"Two":[71],"important":[72],"variables":[73],"determine":[75],"applicability":[77,159],"given":[80],"ontology":[81,129],"annotation":[82],"species":[85],"(especially)":[87],"tissue":[89,153],"type":[90],"in":[91,179,205,215],"which":[92],"it":[93],"takes":[94],"place.":[95],"Using":[96],"data-driven":[98,195],"approach":[99],"results":[102,178],"thousands":[104],"high-quality":[106],"gene":[107],"expression":[108],"samples,":[109],"we":[110],"have":[111],"tissue-specific":[113],"KGs":[114,134,209],"(using":[115],"liver,":[116],"kidney,":[117],"heart":[119],"examples)":[121],"empirically":[123],"validate":[124],"provided":[127],"by":[128],"curators.":[130],"The":[131],"resulting":[132],"human-centered":[133],"designed":[136],"for":[137,172,214],"toxicology":[138,217],"applications":[139],"but":[140],"generalizable":[142],"other":[144,161],"areas":[145],"human":[147,204],"addressing":[149],"issue":[151],"specificity":[154],"often":[156],"limits":[157],"large":[162,201],"KGs.":[163],"These":[164],"can":[167],"serve":[168],"valuable":[170],"tools":[171],"generating":[173],"transparent":[174],"explanations":[175],"experimental":[177],"form":[181],"mechanistic":[183],"hypotheses":[184],"highly":[187],"relevant":[188],"studied":[191],"tissue.":[192],"Because":[193],"relations":[196],"derived":[198],"collection":[202],"vitro":[206,216],"particularly":[211],"well":[212],"suited":[213],"applications.":[218]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
