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J Biomed Semantics. 2016 Apr 12;7:19. doi: 10.1186/s13326-016-0061-5. eCollection 2016.

Extending gene ontology in the context of extracellular RNA and vesicle communication.

Author information

1
Department of Emergency Medicine, Yale Center for Medical Informatics, Yale University School of Medicine, New Haven, CT USA ; VA Connecticut Healthcare System, West Haven, CT USA ; Extracellular RNA Communication Consortium (ERCC), ᅟ, ᅟ
2
Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086 Australia ; Extracellular RNA Communication Consortium (ERCC), ᅟ, ᅟ
3
European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD UK ; Gene Ontology Consortium (GOC), ᅟ, ᅟ
4
Bioinformatics Research Laboratory, Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX USA ; Extracellular RNA Communication Consortium (ERCC), ᅟ, ᅟ
5
Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086 Australia.
6
Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD USA ; Extracellular RNA Communication Consortium (ERCC), ᅟ, ᅟ ; American Society for Exosomes and Microvesicles (ASEMV), ᅟ, ᅟ
7
Pacific Northwest Diabetes Research Institute, Seattle, WA USA ; Extracellular RNA Communication Consortium (ERCC), ᅟ, ᅟ
8
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT USA ; Department of Computer Science, Yale University, New Haven, CT USA ; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT USA ; Extracellular RNA Communication Consortium (ERCC), ᅟ, ᅟ
9
Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086 Australia ; International Society for Extracellular Vesicles (ISEV), ᅟ, ᅟ
10
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT USA ; Extracellular RNA Communication Consortium (ERCC), ᅟ, ᅟ
11
University of Gothenburg, Gothenburg, Sweden ; International Society for Extracellular Vesicles (ISEV), ᅟ, ᅟ
12
Mayo Clinic, Jacksonville, FL USA ; Extracellular RNA Communication Consortium (ERCC), ᅟ, ᅟ
13
Division of Neuroscience and Behavior, National Institute on Drug Abuse (NIDA), Rockville, MD USA ; Extracellular RNA Communication Consortium (ERCC), ᅟ, ᅟ
14
University Medicine Comprehensive Cancer Center, Providence, RI USA ; Extracellular RNA Communication Consortium (ERCC), ᅟ, ᅟ ; International Society for Extracellular Vesicles (ISEV), ᅟ, ᅟ
15
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT USA ; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT USA ; Extracellular RNA Communication Consortium (ERCC), ᅟ, ᅟ
16
Department of Surgery, University of California San Francisco and VA Medical Center, San Francisco, CA USA ; Extracellular RNA Communication Consortium (ERCC), ᅟ, ᅟ
17
Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA USA ; Extracellular RNA Communication Consortium (ERCC), ᅟ, ᅟ
18
Institut Curie, PSL Research University, INSERM U932, Paris, France ; International Society for Extracellular Vesicles (ISEV), ᅟ, ᅟ
19
Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN USA ; Extracellular RNA Communication Consortium (ERCC), ᅟ, ᅟ
20
Department of Biochemistry & Cell Biology, Utrecht University, Utrecht, Netherlands ; International Society for Extracellular Vesicles (ISEV), ᅟ, ᅟ
21
Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086 Australia ; Extracellular RNA Communication Consortium (ERCC), ᅟ, ᅟ ; International Society for Extracellular Vesicles (ISEV), ᅟ, ᅟ
22
Department of Reproductive Medicine, University of California, San Diego, La Jolla, CA USA ; Extracellular RNA Communication Consortium (ERCC), ᅟ, ᅟ

Abstract

BACKGROUND:

To address the lack of standard terminology to describe extracellular RNA (exRNA) data/metadata, we have launched an inter-community effort to extend the Gene Ontology (GO) with subcellular structure concepts relevant to the exRNA domain. By extending GO in this manner, the exRNA data/metadata will be more easily annotated and queried because it will be based on a shared set of terms and relationships relevant to extracellular research.

METHODS:

By following a consensus-building process, we have worked with several academic societies/consortia, including ERCC, ISEV, and ASEMV, to identify and approve a set of exRNA and extracellular vesicle-related terms and relationships that have been incorporated into GO. In addition, we have initiated an ongoing process of extractions of gene product annotations associated with these terms from Vesiclepedia and ExoCarta, conversion of the extracted annotations to Gene Association File (GAF) format for batch submission to GO, and curation of the submitted annotations by the GO Consortium. As a use case, we have incorporated some of the GO terms into annotations of samples from the exRNA Atlas and implemented a faceted search interface based on such annotations.

RESULTS:

We have added 7 new terms and modified 9 existing terms (along with their synonyms and relationships) to GO. Additionally, 18,695 unique coding gene products (mRNAs and proteins) and 963 unique non-coding gene products (ncRNAs) which are associated with the terms: "extracellular vesicle", "extracellular exosome", "apoptotic body", and "microvesicle" were extracted from ExoCarta and Vesiclepedia. These annotations are currently being processed for submission to GO.

CONCLUSIONS:

As an inter-community effort, we have made a substantial update to GO in the exRNA context. We have also demonstrated the utility of some of the new GO terms for sample annotation and metadata search.

KEYWORDS:

Atlas; Extracellular RNA; Extracellular vesicle; Faceted search; Metadata; Ontology

PMID:
27076901
PMCID:
PMC4830068
DOI:
10.1186/s13326-016-0061-5
[Indexed for MEDLINE]
Free PMC Article

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