Evolution of the Sequence Ontology terms and relationships

By C. Mungall, Colin R. Batchelor, Karen Eilbeck. 2010

110 citations recorded by the source corpus.

The Sequence Ontology is an established ontology, with a large user community, for the purpose of genomic annotation. We are reforming the ontology to provide better terms and relationships to describe the features of biological sequence, for both genomic and derived sequence. The SO is working within the guidelines of the OBO Foundry to provide interoperability between SO and the other related OBO ontologies. Here we report changes and improvements made to SO including new relationships to better define the mereological, spatial and temporal aspects of biological sequence.

Subfields: Molecular Biology

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Citations in the corpus

The Gene Ontology Resource: 20 years and still GOing strong (2018, background): “GO imports subsets of these external ontologies that include information about anatomical structures, cell types, chemicals and taxonomic groupings: Uberon (14), Protein Ontology (15), Plant Ontology (16), ChEBI (17), Relations Ontology (18), NCBI Taxonomy (19), Sequence Ontology (20), Ontology of B”
ClinVar: public archive of relationships among sequence variation and human phenotype (2013, neutral): “Evidence Effect of sequence change based on NCBI annotation MolecularConsequence Cross-referenced to Sequence Ontology Observations ObservedData, Co-OccurrenceSet Types of evidence to request and maintain for interpretation are in development Experimental results FunctionalConsequence From published”
Ontological realism: A methodology for coordinated evolution of scientific ontologies (2010, unknown): “…the Protein Ontology Consortium (Arighi et al., 2009); Colin Batchelor, Karen Eilbeck, Janna Hastings and Neocles Leontis in the Sequence Ontology (Mungall et al., 2010), CHEBI ontology of small molecules (de Matos et al., 2010) and RNA Ontology Consortia (Batchelor et al., 2009); Ramona Walls,…”
ClinVar: public archive of interpretations of clinically relevant variants (2015, methodology): “ClinVar also uses terms from Sequence Ontology (SO) (12) and Variation Ontology (VariO) (13) to characterize variant type, molecular consequence and functional consequence.”
Open Targets: a platform for therapeutic target identification and validation (2016, background): “EFO, ECO, GO) or functional consequence terms from SO (44) required to integrate and serve the data.”
The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species (2016, background): “org/ (27) Uberon Uber-anatomy ontology http://uberon.”
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 subontologies…”
ClinVar: improving access to variant interpretations and supporting evidence (2017, unknown): “(vii) A new INFO tag, MC, report the molecular consequence of the variant predicted by NCBI based on the sequence change, including the Sequence Ontology (9) identifier and the molecular consequence term.”