ArticleJournal of biomedical semantics2016
FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation.
Article in Journal of biomedical semantics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
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- Generic and queryable data integration schema for transcriptomics and epigenomics studies.Computational and structural biotechnology journal · 2024Article
- A scalable tool for analyzing genomic variants of humans using knowledge graphs and graph machine learning.Frontiers in big data · 2024Article
- Explainable AI for Estimating Pathogenicity of Genetic Variants Using Large-Scale Knowledge Graphs.Cancers · 2023Article
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- The Empusa code generator and its application to GBOL, an extendable ontology for genome annotation.Scientific data · 2019Article
- TogoGenome/TogoStanza: modularized Semantic Web genome database.Database : the journal of biological databases and curation · 2019Article
- SAPP: functional genome annotation and analysis through a semantic framework using FAIR principles.Bioinformatics (Oxford, England) · 2018Article
- NBDC RDF portal: a comprehensive repository for semantic data in life sciences.Database : the journal of biological databases and curation · 2018Article
- YummyData: providing high-quality open life science data.Database : the journal of biological databases and curation · 2018Article
- Spfy: an integrated graph database for real-time prediction of bacterial phenotypes and downstream comparative analyses.Database : the journal of biological databases and curation · 2018Article
- The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species.Nucleic acids research · 2017Article
- DNA Data Bank of Japan.Nucleic acids research · 2017Article
- Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures.Nucleic acids research · 2017Article
- WikiGenomes: an open web application for community consumption and curation of gene annotation data in Wikidata.Database : the journal of biological databases and curation · 2017Article
- Article
- BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains.Journal of biomedical semantics · 2014Article
- Preserving sequence annotations across reference sequences.Journal of biomedical semantics · 2014Article
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11 authors.
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Abstract
backgroundNucleotide 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.
conclusionsOur 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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