The Sequence Ontology: a tool for the unification of genome annotations

By Karen Eilbeck, Suzanna Lewis, C. Mungall, Mark Yandell, Lincoln D. Stein, Richard Durbin, Michael Ashburner. Genome Biology, 2005

868 citations recorded by the source corpus.

The Sequence Ontology (SO) is a structured controlled vocabulary for the parts of a genomic annotation. SO provides a common set of terms and definitions that will facilitate the exchange, analysis and management of genomic data. Because SO treats part-whole relationships rigorously, data described with it can become substrates for automated reasoning, and instances of sequence features described by the SO can be subjected to a group of logical operations termed extensional mereology operators.

Subfields: Artificial Intelligence, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/f0fb587d99844259fcb73997f5c11616f6250d34

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Citations in the corpus

The druggable genome and support for target identification and validation in drug development (2016, background): “We examined sequence ontology consequence types (42) of disease- and biomarker-associated variants and found most to be noncoding, mainly intronic, presumably altering or marking variants that alter mRNA expression or availability, or marking variants that alter structure or activity of encoded prot”
Concept annotation in the CRAFT corpus (2012, background): “…and protein complexes), the Sequence Ontology (SO, representing biomacromolecular sequences and their associated attributes and operations) [22,23], the entries of the Entrez Gene database (EG, representing genes and other DNA sequences at the species level) [24], and the three…”
The Comprehensive Antibiotic Resistance Database (2013, methodology): “All molecular sequences within the CARD are classified and organized using the Sequence Ontology (18), which is comprised of a set of ontology terms describing the many levels of organization and relationships between different molecular sequences (e.”
Identification of a large set of rare complete human knockouts (2015, background): “5%) contribute to knockout of the 8,041 (1,741) individuals in 1 of the 1,171 (775) genes.”
Rfam: Wikipedia, clans and the “decimal” release (2010, background): “Two efforts of particular relevance to Rfam are the sequence ontology (SO) and the gene ontology (GO) (26,27).”
Gene Ontology Consortium: going forward (2014, background): “A version of the ontology containing all relationships, including information from the Uberon anatomy (or stage) ontology (7), the Chemical Entities of Biological Interest ontology (ChEBI; (8)), the Plant Ontology for plant structure/stage (PO; (9)), the Phenotypic Quality Ontology (PATO; (10)) and ”
A beginner's guide to eukaryotic genome annotation (2012, background): “This is the approach taken by the Sequence Ontology Project to calculate annotation edit distance (AED), which can be used to measure the congruence between an annotation and its supporting evidence 96 .”
g:Profiler—a web server for functional interpretation of gene lists (2016 update) (2016, neutral): “An additional tool g:SNPense maps human single nucleotide polymorphisms (SNP) to gene names, chromosomal locations and variant consequence terms from Sequence Ontology (19,20). g:Profiler regularly synchronises with the Ensembl database for gene annotations and identifiers.”
Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database (2008, background): “The Chado schema is designed to store descriptions of any feature that can be located in a genome.”
Deep whole-genome resequencing sheds light on the distribution and effect of amphioxus SNPs (2022, methodology): “In addition to annotation in VCF format, SnpEff generated the statistics of SNPs’ genomic locations and coding effect defined in SO [52] terms, which were extracted to plot SNP distribution heatmap and other statistic charts (Fig.”
COSMIC: a curated database of somatic variants and clinical data for cancer (2023, neutral): “Genes, variants, and transcripts use external vocabularies and ontologies—HGNC ( 10 ), Sequence Ontology ( 11 ) and HGVS ( 12 ), or Ensembl ( 13 ), respectively .”
Evolution of the Sequence Ontology terms and relationships (2010, methodology): “Here we report changes and improvements made to SO including new relationships to better define the mereological, spatial and temporal aspects of biological sequence.”
FlyBase: updates to the Drosophila genes and genomes database (2024, neutral): “Transgenic alleles now have a “Transgenic product class” field that describes the nature of the encoded gene product using appropriate Sequence Ontology term(s) (Eilbeck et al .”
The Gene Ontology (GO) project in 2006 (2005, background): “Its purpose is to promote the standardization of sequence annotation among different organisms (34).”
Bio-ontologies: current trends and future directions (2006, background): “The two most significant OBO are the GO [12] and the Sequence Ontology [15].”