{"id":"https://openalex.org/W3134505048","doi":null,"title":"Foundations for a Realism-Based Ontology of Protein Aggregates.","display_name":"Foundations for a Realism-Based Ontology of Protein Aggregates.","publication_year":2020,"publication_date":"2020-09-01","ids":{"openalex":"https://openalex.org/W3134505048","mag":"3134505048","pmid":"https://pubmed.ncbi.nlm.nih.gov/34707469","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/8547170"},"language":"en","primary_location":{"id":"pmid:34707469","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34707469","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,"listed_in":[],"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":"CEUR workshop proceedings","raw_type":"Journal Article"},"volume":null,"type":"conference-paper","is_traditional":true,"indexed_in":["pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"http://europepmc.org/pmc/articles/PMC8547170","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5010620055","display_name":"Lauren Wishnie","orcid":"https://orcid.org/0000-0002-7245-3450","observed_orcids":["https://orcid.org/0000-0002-7245-3450"]},"institutions":[{"id":"https://openalex.org/I63190737","display_name":"University at Buffalo, State University of New York","ror":"https://ror.org/01y64my43","country_code":"US","type":"education","lineage":["https://openalex.org/I63190737"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lauren Wishnie","raw_affiliation_strings":["Department of Biomedical Informatics, University at Buffalo, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, University at Buffalo, USA","institution_ids":["https://openalex.org/I63190737"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055380655","display_name":"Alexander P. Cox","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I63190737","display_name":"University at Buffalo, State University of New York","ror":"https://ror.org/01y64my43","country_code":"US","type":"education","lineage":["https://openalex.org/I63190737"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alexander P Cox","raw_affiliation_strings":["Department of Biomedical Informatics, University at Buffalo, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, University at Buffalo, USA","institution_ids":["https://openalex.org/I63190737"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084833749","display_name":"Alexander D. Diehl","orcid":"https://orcid.org/0000-0001-9990-8331","observed_orcids":["https://orcid.org/0000-0001-9990-8331"]},"institutions":[{"id":"https://openalex.org/I63190737","display_name":"University at Buffalo, State University of New York","ror":"https://ror.org/01y64my43","country_code":"US","type":"education","lineage":["https://openalex.org/I63190737"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alexander D Diehl","raw_affiliation_strings":["Department of Biomedical Informatics, University at Buffalo, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, University at Buffalo, USA","institution_ids":["https://openalex.org/I63190737"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5007545122","display_name":"Werner M Ceusters","orcid":"https://orcid.org/0000-0002-2676-8689","observed_orcids":["https://orcid.org/0000-0002-2676-8689"]},"institutions":[{"id":"https://openalex.org/I63190737","display_name":"University at Buffalo, State University of New York","ror":"https://ror.org/01y64my43","country_code":"US","type":"education","lineage":["https://openalex.org/I63190737"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Werner Ceusters","raw_affiliation_strings":["Department of Biomedical Informatics, University at Buffalo, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, University at Buffalo, USA","institution_ids":["https://openalex.org/I63190737"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I63190737"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.0,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"2807","issue":null,"first_page":"K1","last_page":"K10"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9848999977111816,"subfield":{"id":"https://openalex.org/subfields/2718","display_name":"Health Informatics"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9848999977111816,"subfield":{"id":"https://openalex.org/subfields/2718","display_name":"Health Informatics"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10215","display_name":"Semantic Web and Ontologies","score":0.0031999999191612005,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10778","display_name":"Philosophy of Biology and Scientific Explanation","score":0.002899999963119626,"subfield":{"id":"https://openalex.org/subfields/1207","display_name":"History and Philosophy of Science"},"field":{"id":"https://openalex.org/fields/12","display_name":"Arts and Humanities"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/protein-aggregates","display_name":"protein aggregates","score":0.9679999947547913},{"id":"https://openalex.org/keywords/ontology-definition","display_name":"ontology definition","score":0.6060000061988831},{"id":"https://openalex.org/keywords/realism","display_name":"realism","score":0.47099998593330383},{"id":"https://openalex.org/keywords/structural-alterations","display_name":"structural alterations","score":0.41999998688697815},{"id":"https://openalex.org/keywords/biomedical-terminology","display_name":"biomedical terminology","score":0.6539999842643738}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6825764179229736},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.6119568943977356},{"id":"https://openalex.org/C4679612","wikidata":"https://www.wikidata.org/wiki/Q866298","display_name":"Aggregate (composite)","level":2,"score":0.5125589370727539},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.43599390983581543},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.37074342370033264},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.352440744638443},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.34644782543182373},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3237451910972595},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.1230018138885498},{"id":"https://openalex.org/C159985019","wikidata":"https://www.wikidata.org/wiki/Q181790","display_name":"Composite material","level":1,"score":0.0},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"pmid:34707469","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34707469","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,"listed_in":[],"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":"CEUR workshop proceedings","raw_type":"Journal Article"},{"id":"pmh:oai:europepmc.org:7437220","doi":null,"is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC8547170","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,"listed_in":[],"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":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:8547170","doi":null,"is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC8547170/","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,"listed_in":[],"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":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"CEUR Workshop Proc","raw_type":"Text"},{"id":"mag:3134505048","doi":null,"is_oa":true,"landing_page_url":"http://ceur-ws.org/Vol-2807/paperK.pdf","pdf_url":null,"source":{"id":"https://openalex.org/S4210204615","display_name":"CEUR Workshop Proceedings","issn_l":"1613-0073","issn":["1613-0073"],"is_oa":true,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","jufo-1","norway-1"],"host_organization":"https://openalex.org/P4310312761","host_organization_name":"Samara National Research University","host_organization_lineage":["https://openalex.org/P4310312761"],"host_organization_lineage_names":["Samara National Research University"],"type":"journal"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":"CEUR Workshop Proceedings","raw_type":null}],"best_oa_location":{"id":"pmh:oai:europepmc.org:7437220","doi":null,"is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC8547170","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,"listed_in":[],"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":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"","raw_type":"Text"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G520438669","display_name":"Institutional Career Development","funder_award_id":"KL2TR001413","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7918204433","display_name":"University of Buffalo Clinical and Translational Science Institute","funder_award_id":"UL1TR001412","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":9,"referenced_works":["https://openalex.org/W51164494","https://openalex.org/W1990619980","https://openalex.org/W2003550891","https://openalex.org/W2028429944","https://openalex.org/W2053727980","https://openalex.org/W2103017472","https://openalex.org/W2141545183","https://openalex.org/W2152495216","https://openalex.org/W2950595506"],"related_works":["https://openalex.org/W3204224695","https://openalex.org/W2061231608","https://openalex.org/W2296435332","https://openalex.org/W6996352272","https://openalex.org/W2107740219","https://openalex.org/W2124103257","https://openalex.org/W7100416494","https://openalex.org/W2106830745","https://openalex.org/W26084547","https://openalex.org/W7097048123"],"abstract_inverted_index":{"The":[0],"objective":[1],"of":[2,24,36,62,84,131,145],"this":[3,42,85],"paper":[4],"is":[5,117],"to":[6,48,70,119,124,148],"propose":[7,88,102],"formal":[8],"definitions":[9,65,72,90],"for":[10,52,73,91],"the":[11,20,46,50,60,68,71,82,92,103,143,146,162],"terms":[12,26,75,93],"'protein":[13,94],"aggregate'":[14,95],"and":[15,22,32,64,96,135],"'protein-containing":[16,97],"complex'":[17],"such":[18,128,153],"that":[19,33,108,137],"descriptions":[21],"usages":[23,63],"these":[25,56],"in":[27,67,77,113,122,142,161],"biomedical":[28],"literature":[29,47,69],"are":[30,38,159],"unified":[31],"those":[34,74],"portions":[35],"reality":[37],"correctly":[39],"represented.":[40],"To":[41],"end,":[43],"we":[44,87,101],"surveyed":[45],"assess":[49],"need":[51],"a":[53,132],"distinction":[54],"between":[55],"entities,":[57],"then":[58],"compared":[59],"features":[61],"found":[66,76],"Bioportal":[78],"ontologies.":[79],"Based":[80],"on":[81],"results":[83],"comparison,":[86],"updated":[89],"complex'.":[98],"Thus":[99],"far,":[100],"following":[104],"distinguishing":[105],"factors:":[106],"first,":[107],"one":[109],"important":[110,139],"difference":[111,140],"lies":[112,141],"whether":[114],"an":[115,138,154],"entity":[116,147],"disposed":[118],"change":[120],"type":[121],"response":[123],"certain":[125],"structural":[126],"alterations,":[127],"as":[129],"dissociation":[130],"continuant":[133],"part,":[134],"second":[136],"ability":[144],"realize":[149],"its":[150],"function":[151],"after":[152],"event":[155],"occurs.":[156],"These":[157],"distinctions":[158],"reflected":[160],"proposed":[163],"definitions.":[164]},"counts_by_year":[],"updated_date":"2026-11-10T11:39:43.021295","created_date":"2021-03-15T00:00:00"}