دورية أكاديمية
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FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation.

التفاصيل البيبلوغرافية
العنوان: FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation.
المؤلفون: Bolleman JT; Swiss-Prot group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel, Servet, Geneva 4, 1211, Switzerland. jerven.bolleman@sib.swiss., Mungall CJ; Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, 94720, CA, US., Strozzi F; CeRSA, Parco Tecnologico Padano, Lodi, 26900, Italy., Baran J; CODAMONO, 5-121 Marion Street, Toronto, M6R 1E6, Ontario, Canada., Dumontier M; Stanford Center for Biomedical Informatics Research, 1265 Welch Road, Room X223, Stanford, 94305-5479, CA, US., Bonnal RJ; Integrative Biology Program, Istituto Nazionale Genetica Molecolare, Milan, Italy., Buels R; University of California, Berkeley, Berkeley, CA, USA., Hoehndorf R; Department of Computer Science, Aberystwyth, SY23 3DB, UK., Fujisawa T; Center for Information Biology, National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Shizuoka, 411-08540, Japan., Katayama T; Database Center for Life Science, Research Organization of Information and Systems, 2-11-16, Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan., Cock PJ; The James Hutton Institute, Dundee, DD2 5DA, UK.
المصدر: Journal of biomedical semantics [J Biomed Semantics] 2016 Jun 13; Vol. 7, pp. 39. Date of Electronic Publication: 2016 Jun 13.
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: Biomed Central Country of Publication: England NLM ID: 101531992 Publication Model: Electronic Cited Medium: Internet ISSN: 2041-1480 (Electronic) NLM ISO Abbreviation: J Biomed Semantics Subsets: MEDLINE
أسماء مطبوعة: Original Publication: [London] : Biomed Central
مواضيع طبية MeSH: Biological Ontologies* , Semantics*, Molecular Sequence Annotation/*standards , Nucleotides/*genetics , Nucleotides/*metabolism , Proteins/*chemistry , Proteins/*metabolism, Databases, Genetic ; Databases, Protein ; Fuzzy Logic ; Humans ; Reference Books
مستخلص: Background: Nucleotide and protein sequence feature annotations are essential to understand biology on the genomic, transcriptomic, and proteomic level. Using Semantic Web technologies to query biological annotations, there was no standard that described this potentially complex location information as subject-predicate-object triples.
Description: We have developed an ontology, the Feature Annotation Location Description Ontology (FALDO), to describe the positions of annotated features on linear and circular sequences. FALDO can be used to describe nucleotide features in sequence records, protein annotations, and glycan binding sites, among other features in coordinate systems of the aforementioned "omics" areas. Using the same data format to represent sequence positions that are independent of file formats allows us to integrate sequence data from multiple sources and data types. The genome browser JBrowse is used to demonstrate accessing multiple SPARQL endpoints to display genomic feature annotations, as well as protein annotations from UniProt mapped to genomic locations.
Conclusions: Our ontology allows users to uniformly describe - and potentially merge - sequence annotations from multiple sources. Data sources using FALDO can prospectively be retrieved using federalised SPARQL queries against public SPARQL endpoints and/or local private triple stores.
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معلومات مُعتمدة: R24 OD011883 United States OD NIH HHS
فهرسة مساهمة: Keywords: Annotation; Data integration; RDF; SPARQL; Semantic Web; Sequence feature; Sequence ontology; Standardisation
المشرفين على المادة: 0 (Nucleotides)
0 (Proteins)
تواريخ الأحداث: Date Created: 20160615 Date Completed: 20171107 Latest Revision: 20240528
رمز التحديث: 20240528
مُعرف محوري في PubMed: PMC4907002
DOI: 10.1186/s13326-016-0067-z
PMID: 27296299
قاعدة البيانات: MEDLINE
الوصف
تدمد:2041-1480
DOI:10.1186/s13326-016-0067-z