{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,4]],"date-time":"2025-11-04T23:02:58Z","timestamp":1762297378302},"reference-count":32,"publisher":"Oxford University Press (OUP)","issue":"16","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,8,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: One important area of clinical genomics research involves the elucidation of molecular mechanisms underlying (complex) disorders which eventually may lead to new diagnostic or drug targets. To further advance this area of clinical genomics one of the main challenges is the acquisition and integration of data, information and expert knowledge for specific biomedical domains and diseases. Currently the required information is not very well organized but scattered over biological and biomedical databases, basic text books, scientific literature and experts\u2019 minds and may be highly specific, heterogeneous, complex and voluminous.<\/jats:p>\n               <jats:p>Results: We present a new framework to construct knowledge bases with concept maps for presentation of information and the web ontology language OWL for the representation of information. We demonstrate this framework through the construction of a peroxisomal knowledge base, which focuses on four key peroxisomal pathways and several related genetic disorders. All 155 concept maps in our knowledge base are linked to at least one other concept map, which allows the visualization of one big network of related pieces of information.<\/jats:p>\n               <jats:p>Availability: The peroxisome knowledge base is available from www.bioinformaticslaboratory.nl (Support \u2192 Web applications).<\/jats:p>\n               <jats:p>Contact: \u00a0a.h.vankampen@amc.uva.nl<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn274","type":"journal-article","created":{"date-parts":[[2008,8,9]],"date-time":"2008-08-09T13:08:02Z","timestamp":1218287282000},"page":"i21-i27","source":"Crossref","is-referenced-by-count":6,"title":["Organization and integration of biomedical knowledge with concept maps for key peroxisomal pathways"],"prefix":"10.1093","volume":"24","author":[{"given":"A.M.","family":"Willemsen","sequence":"first","affiliation":[{"name":"1 Bioinformatics Laboratory, Clinical Epidemiology, Biostatistics and Bioinformatics, 2Laboratory Genetic Metabolic Disease, Department of Clinical Chemistry and Pediatrics, Academic Medical Center, University of Amsterdam, Meibergdreef 9 1105 AZ Amsterdam, The Netherlands and 3Biosystems Data Analysis, Swammerdam Institute for Life Science, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands"}]},{"given":"G.A.","family":"Jansen","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Laboratory, Clinical Epidemiology, Biostatistics and Bioinformatics, 2Laboratory Genetic Metabolic Disease, Department of Clinical Chemistry and Pediatrics, Academic Medical Center, University of Amsterdam, Meibergdreef 9 1105 AZ Amsterdam, The Netherlands and 3Biosystems Data Analysis, Swammerdam Institute for Life Science, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands"}]},{"given":"J.C.","family":"Komen","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Laboratory, Clinical Epidemiology, Biostatistics and Bioinformatics, 2Laboratory Genetic Metabolic Disease, Department of Clinical Chemistry and Pediatrics, Academic Medical Center, University of Amsterdam, Meibergdreef 9 1105 AZ Amsterdam, The Netherlands and 3Biosystems Data Analysis, Swammerdam Institute for Life Science, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands"}]},{"given":"S.","family":"van Hooff","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Laboratory, Clinical Epidemiology, Biostatistics and Bioinformatics, 2Laboratory Genetic Metabolic Disease, Department of Clinical Chemistry and Pediatrics, Academic Medical Center, University of Amsterdam, Meibergdreef 9 1105 AZ Amsterdam, The Netherlands and 3Biosystems Data Analysis, Swammerdam Institute for Life Science, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands"}]},{"given":"H.R.","family":"Waterham","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Laboratory, Clinical Epidemiology, Biostatistics and Bioinformatics, 2Laboratory Genetic Metabolic Disease, Department of Clinical Chemistry and Pediatrics, Academic Medical Center, University of Amsterdam, Meibergdreef 9 1105 AZ Amsterdam, The Netherlands and 3Biosystems Data Analysis, Swammerdam Institute for Life Science, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands"}]},{"given":"P.M.T.","family":"Brites","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Laboratory, Clinical Epidemiology, Biostatistics and Bioinformatics, 2Laboratory Genetic Metabolic Disease, Department of Clinical Chemistry and Pediatrics, Academic Medical Center, University of Amsterdam, Meibergdreef 9 1105 AZ Amsterdam, The Netherlands and 3Biosystems Data Analysis, Swammerdam Institute for Life Science, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands"}]},{"given":"R.J.A.","family":"Wanders","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Laboratory, Clinical Epidemiology, Biostatistics and Bioinformatics, 2Laboratory Genetic Metabolic Disease, Department of Clinical Chemistry and Pediatrics, Academic Medical Center, University of Amsterdam, Meibergdreef 9 1105 AZ Amsterdam, The Netherlands and 3Biosystems Data Analysis, Swammerdam Institute for Life Science, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands"}]},{"given":"A.H.C.","family":"van Kampen","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Laboratory, Clinical Epidemiology, Biostatistics and Bioinformatics, 2Laboratory Genetic Metabolic Disease, Department of Clinical Chemistry and Pediatrics, Academic Medical Center, University of Amsterdam, Meibergdreef 9 1105 AZ Amsterdam, The Netherlands and 3Biosystems Data Analysis, Swammerdam Institute for Life Science, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands"},{"name":"1 Bioinformatics Laboratory, Clinical Epidemiology, Biostatistics and Bioinformatics, 2Laboratory Genetic Metabolic Disease, Department of Clinical Chemistry and Pediatrics, Academic Medical Center, University of Amsterdam, Meibergdreef 9 1105 AZ Amsterdam, The Netherlands and 3Biosystems Data Analysis, Swammerdam Institute for Life Science, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands"}]}],"member":"286","published-online":{"date-parts":[[2008,8,9]]},"reference":[{"key":"2023020210501743800_B1","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1177\/1460458206061202","article-title":"Personalizing web information for patients: linking patient medical data with the web via a patient personal knowledge base","volume":"12","author":"Al-Busaidi","year":"2006","journal-title":"Health Informatics J"},{"key":"2023020210501743800_B2","doi-asserted-by":"crossref","first-page":"3581","DOI":"10.1093\/nar\/gkh681","article-title":"New strategy for the representation and the integration of biomolecular knowledge at a cellular scale","volume":"32","author":"Barriot","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"2023020210501743800_B3","doi-asserted-by":"crossref","first-page":"D511","DOI":"10.1093\/nar\/gkl972","article-title":"BRENDA, AMENDA and FRENDA: the enzyme information system in 2007","volume":"35","author":"Barthelmes","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"2023020210501743800_B4","doi-asserted-by":"crossref","first-page":"D267","DOI":"10.1093\/nar\/gkh061","article-title":"The unified medical language system (UMLS): integrating biomedical terminology","volume":"32","author":"Bodenreider","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"2023020210501743800_B5","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1016\/j.jbi.2005.09.002","article-title":"Desiderata for domain reference ontologies in biomedicine","volume":"39","author":"Burgun","year":"2006","journal-title":"J. Biomed. Inform"},{"key":"2023020210501743800_B6","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1007\/11510154_11","article-title":"Concept maps: integrating knowledge and information visualization","volume-title":"Knowledge and Information Visualization Searching for Synergies.","author":"Ca\u00f1as","year":"2005"},{"key":"2023020210501743800_B7","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1186\/1471-2105-7-267","article-title":"The use of concept maps during knowledge elicitation in ontology development processes\u2013the nutrigenomics use case","volume":"7","author":"Castro","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"2023020210501743800_B8","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1186\/1471-2105-7-97","article-title":"The ontology lookup service, a lightweight cross-platform tool for controlled vocabulary queries","volume":"7","author":"Cote","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"2023020210501743800_B9","doi-asserted-by":"crossref","first-page":"D258","DOI":"10.1093\/nar\/gkh036","article-title":"The Gene Ontology (GO) database and informatics resource","volume":"32","author":"Harris","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"2023020210501743800_B10","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1186\/1746-4811-2-5","article-title":"A flexible representation of omic knowledge for thorough analysis of microarray data","volume":"2","author":"Hasegawa","year":"2006","journal-title":"Plant Methods"},{"key":"2023020210501743800_B11","first-page":"99","volume-title":"Collaborative Knowledge Capture in Ontologies.","author":"Hayes","year":"2005"},{"key":"2023020210501743800_B12","doi-asserted-by":"crossref","first-page":"D595","DOI":"10.1093\/nar\/gkl1012","article-title":"Hedgehog Signaling Pathway Database: a repository of current annotation efforts and resources for the Hh research community","volume":"35","author":"Hervold","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"2023020210501743800_B13","doi-asserted-by":"crossref","first-page":"524","DOI":"10.1093\/bioinformatics\/btg015","article-title":"The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models","volume":"19","author":"Hucka","year":"2003","journal-title":"Bioinformatics"},{"key":"2023020210501743800_B14","volume-title":"OWL: Representing information using the web ontology language.","author":"Lacy","year":"2005"},{"key":"2023020210501743800_B15","first-page":"234","article-title":"Knowledge representation model for systems-level analysis of signal transduction networks","volume":"15","author":"Lee","year":"2004","journal-title":"Genome Inform"},{"key":"2023020210501743800_B16","doi-asserted-by":"crossref","first-page":"S3","DOI":"10.1186\/1471-2105-8-S3-S3","article-title":"e-Science and biological pathway semantics","volume":"8","author":"Luciano","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"2023020210501743800_B17","doi-asserted-by":"crossref","DOI":"10.1017\/CBO9781139173469","volume-title":"Learning How to Learn.","author":"Novak","year":"1984"},{"key":"2023020210501743800_B18","first-page":"PMC1480139","article-title":"Protege-2000: an open-source ontology-development and knowledge-acquisition environment","volume":"953","author":"Noy","year":"2003","journal-title":"AMIA Annu. Symp. Proc"},{"key":"2023020210501743800_B19","doi-asserted-by":"crossref","first-page":"582","DOI":"10.1016\/j.jbi.2007.03.005","article-title":"Conceptual knowledge acquisition in biomedicine: a methodological review","volume":"40","author":"Payne","year":"2007","journal-title":"J. Biomed. Inform"},{"key":"2023020210501743800_B20","doi-asserted-by":"crossref","first-page":"478","DOI":"10.1016\/j.jbi.2003.11.007","article-title":"A reference ontology for biomedical informatics: the foundational model of anatomy","volume":"36","author":"Rosse","year":"2003","journal-title":"J. Biomed. Inform"},{"key":"2023020210501743800_B21","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1093\/bib\/bbm059","article-title":"Biomedical ontologies: a functional perspective","volume":"9","author":"Rubin","year":"2008","journal-title":"Brief. Bioinform"},{"key":"2023020210501743800_B22","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1186\/1745-7580-3-6","article-title":"IDR knowledge base for primary immunodeficiencies","volume":"3","author":"Samarghitean","year":"2007","journal-title":"Immunome. Res"},{"key":"2023020210501743800_B23","doi-asserted-by":"crossref","first-page":"D815","DOI":"10.1093\/nar\/gkl935","article-title":"PeroxisomeDB: a database for the peroxisomal proteome, functional genomics and disease","volume":"35","author":"Schluter","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"2023020210501743800_B24","doi-asserted-by":"crossref","first-page":"D265","DOI":"10.1093\/nar\/gkl866","article-title":"Defensins knowledgebase: a manually curated database and information source focused on the defensins family of antimicrobial peptides","volume":"35","author":"Seebah","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"2023020210501743800_B25","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1007\/s10877-005-0673-2","article-title":"A grid-based HIV expert system","volume":"19","author":"Sloot","year":"2005","journal-title":"J. Clin. Monit. Comput"},{"key":"2023020210501743800_B26","doi-asserted-by":"crossref","first-page":"1251","DOI":"10.1038\/nbt1346","article-title":"The OBO foundry: coordinated evolution of ontologies to support biomedical data integration","volume":"25","author":"Smith","year":"2007","journal-title":"Nat. Biotechnol"},{"key":"2023020210501743800_B27","doi-asserted-by":"crossref","first-page":"1733","DOI":"10.1016\/j.bbamcr.2006.09.010","article-title":"Peroxisome biogenesis disorders","volume":"1763","author":"Steinberg","year":"2006","journal-title":"Biochim. Biophys. Acta"},{"key":"2023020210501743800_B28","doi-asserted-by":"crossref","first-page":"R39","DOI":"10.1186\/gb-2007-8-3-r39","article-title":"Reactome: a knowledge base of biologic pathways and processes","volume":"8","author":"Vastrik","year":"2007","journal-title":"Genome Biol"},{"key":"2023020210501743800_B29","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1111\/j.1399-0004.2004.00329.x","article-title":"Peroxisomal disorders I: biochemistry and genetics of peroxisome biogenesis disorders","volume":"67","author":"Wanders","year":"2005","journal-title":"Clin. Genet"},{"key":"2023020210501743800_B30","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1146\/annurev.biochem.74.082803.133329","article-title":"Biochemistry of mammalian peroxisomes revisited","volume":"75","author":"Wanders","year":"2006","journal-title":"Annu. Rev. Biochem"},{"key":"2023020210501743800_B31","doi-asserted-by":"crossref","first-page":"1707","DOI":"10.1016\/j.bbamcr.2006.08.010","article-title":"Peroxisomal disorders: the single peroxisomal enzyme deficiencies","volume":"1763","author":"Wanders","year":"2006","journal-title":"Biochim. Biophys. Acta"},{"key":"2023020210501743800_B32","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1089\/omi.2006.10.199","article-title":"Development of FuGO: an ontology for functional genomics investigations","volume":"10","author":"Whetzel","year":"2006","journal-title":"OMICS"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/24\/16\/i21\/49053178\/bioinformatics_24_16_i21.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/24\/16\/i21\/49053178\/bioinformatics_24_16_i21.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T12:49:31Z","timestamp":1675342171000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/24\/16\/i21\/199986"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,8,9]]},"references-count":32,"journal-issue":{"issue":"16","published-print":{"date-parts":[[2008,8,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btn274","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2008,8,15]]},"published":{"date-parts":[[2008,8,9]]}}}