{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T11:46:17Z","timestamp":1753875977297,"version":"3.41.2"},"reference-count":40,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2023,12,2]],"date-time":"2023-12-02T00:00:00Z","timestamp":1701475200000},"content-version":"vor","delay-in-days":335,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010146","name":"Alzheimer Forschung Initiative","doi-asserted-by":"publisher","award":["#18006CB"],"award-info":[{"award-number":["#18006CB"]}],"id":[{"id":"10.13039\/100010146","id-type":"DOI","asserted-by":"publisher"}]},{"name":"eBRAINs-Health project","award":["Project 101058516"],"award-info":[{"award-number":["Project 101058516"]}]},{"DOI":"10.13039\/100010146","name":"Alzheimer Forschung Initiative","doi-asserted-by":"publisher","award":["#18006CB"],"award-info":[{"award-number":["#18006CB"]}],"id":[{"id":"10.13039\/100010146","id-type":"DOI","asserted-by":"publisher"}]},{"name":"eBRAINs-Health project","award":["Project 101058516"],"award-info":[{"award-number":["Project 101058516"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,12,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>As one of the leading causes for dementia in the population, it is imperative that we discern exactly why Alzheimer\u2019s disease (AD) has a strong molecular association with beta-amyloid and tau. Although a clear understanding about etiology and pathogenesis of AD remains unsolved, scientists worldwide have dedicated significant efforts to discovering the molecular interactions linked to the pathological characteristics and potential treatments. Knowledge representations, such as domain ontologies encompassing our current understanding about AD, could greatly assist and contribute to disease research. This paper describes the construction and application of the integrated Alzheimer\u2019s Disease Ontology (ADO), combining selected concepts from the former version of the ADO and the Alzheimer\u2019s Disease Mapping Ontology (ADMO). In addition to the existing entities available from these knowledge models, essential knowledge about AD from public sources, such as newly discovered risk factor genes and novel treatments, was also integrated. The ADO can also be leveraged in text mining scenarios given that it is conceptually enriched with domain-specific knowledge as well as their relations. The integrated ADO consists of 39\u2009855 total axioms. The ontology covers many aspects of the AD domain, including risk factor genes, clinical features, treatments and experimental models. The ontology complies with the Open Biological and Biomedical Ontology principles and was accepted by the foundry. In this paper, we illustrate the role of the presented ontology in extracting textual information from the SCAIView database and key measures in an ADO-based corpus.<\/jats:p>\n               <jats:p>Database URL: \u00a0https:\/\/academic.oup.com\/database<\/jats:p>","DOI":"10.1093\/database\/baad085","type":"journal-article","created":{"date-parts":[[2023,12,2]],"date-time":"2023-12-02T19:43:40Z","timestamp":1701546220000},"source":"Crossref","is-referenced-by-count":0,"title":["Design of\u00a0the formalized and\u00a0integrated Alzheimer\u2019s Disease Ontology and\u00a0its application in\u00a0retrieving textual data via text mining"],"prefix":"10.1093","volume":"2023","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6571-0033","authenticated-orcid":false,"given":"Bide","family":"Zhang","sequence":"first","affiliation":[{"name":"Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI) , Schloss Birlinghoven, Sankt Augustin 53754, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1374-8184","authenticated-orcid":false,"given":"Vanessa","family":"Lage-Rupprecht","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI) , Schloss Birlinghoven, Sankt Augustin 53754, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1159-9269","authenticated-orcid":false,"given":"Philipp","family":"Wegner","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI) , Schloss Birlinghoven, Sankt Augustin 53754, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5860-6369","authenticated-orcid":false,"given":"Astghik","family":"Sargsyan","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI) , Schloss Birlinghoven, Sankt Augustin 53754, Germany"}]},{"given":"Stephan","family":"Gebel","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI) , Schloss Birlinghoven, Sankt Augustin 53754, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4153-3930","authenticated-orcid":false,"given":"Marc","family":"Jacobs","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI) , Schloss Birlinghoven, Sankt Augustin 53754, Germany"}]},{"given":"J\u00fcrgen","family":"Klein","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI) , Schloss Birlinghoven, Sankt Augustin 53754, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9012-6720","authenticated-orcid":false,"given":"Martin","family":"Hofmann-Apitius","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI) , Schloss Birlinghoven, Sankt Augustin 53754, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9896-3531","authenticated-orcid":false,"given":"Alpha","family":"Tom Kodamullil","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI) , Schloss Birlinghoven, Sankt Augustin 53754, Germany"},{"name":"Causality Biomodels, Kinfra Hi-Tech Park , Kalamassery, Cochin, Kerala 683503, India"}]}],"member":"286","published-online":{"date-parts":[[2023,12,2]]},"reference":[{"author":"\u201cDementia\u201d","key":"2023120222033480400_R1","article-title":"World Health Organization"},{"key":"2023120222033480400_R2","article-title":"Alzheimer Disease","volume-title":"StatPearls","author":"Kumar","year":"2022"},{"key":"2023120222033480400_R3","doi-asserted-by":"crossref","DOI":"10.1136\/bmjopen-2016-015746","article-title":"Signs and\u00a0symptoms preceding the diagnosis of\u00a0Alzheimer\u2019s Disease: a systematic scoping review of\u00a0literature from 1937 to 2016","volume":"7","author":"Bature","year":"2017","journal-title":"BMJ Open"},{"key":"2023120222033480400_R4","doi-asserted-by":"crossref","DOI":"10.3390\/molecules25245789","article-title":"Comprehensive review on\u00a0Alzheimer\u2019s Disease: causes and\u00a0treatment","volume":"25","author":"Breijyeh","year":"2020","journal-title":"Molecules"},{"key":"2023120222033480400_R5","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1126\/science.aap8002","article-title":"The molecular basis of\u00a0Alzheimer\u2019s plaques","volume":"358","author":"Pospich","year":"2017","journal-title":"Science"},{"key":"2023120222033480400_R6","doi-asserted-by":"crossref","first-page":"514","DOI":"10.1111\/j.1755-5949.2010.00177.x","article-title":"The role of\u00a0tau in\u00a0Alzheimer\u2019s Disease and\u00a0related disorders","volume":"17","author":"Medeiros","year":"2011","journal-title":"CNS Neurosci. Ther."},{"key":"2023120222033480400_R7","doi-asserted-by":"crossref","first-page":"7552","DOI":"10.1073\/pnas.88.17.7552","article-title":"Senile plaque neurites in\u00a0Alzheimer disease accumulate amyloid precursor protein","volume":"88","author":"Cras","year":"1991","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"volume-title":"Alzheimer\u2019s Disease: Drug Discovery","year":"2020","author":"Sheppard","key":"2023120222033480400_R8"},{"key":"2023120222033480400_R9","article-title":"An ontology-based approach for\u00a0modelling and\u00a0querying Alzheimer\u2019s disease data","volume":"23","author":"Taglino","year":"2023","journal-title":"BMC Med. Inf. Decis. 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