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

Kei Hoi Cheung, Shivakumar Keerthikumar, Paola Roncaglia, Sai Lakshmi Subramanian, Matthew E. Roth, Monisha Samuel, Sushma Anand, Lahiru Gangoda, Stephen J Gould, Roger Alexander, David Galas, Mark B. Gerstein, Andrew F. Hill, Robert R. Kitchen, Jan Lötvall, Tushar Patel, Dena C. Procaccini, Peter Quesenberry, Joel Rozowsky, Robert L. RaffaiAleksandra Shypitsyna, Andrew I. Su, Clotilde Théry, Kasey Vickers, Marca H M Wauben, Suresh Mathivanan, Aleksandar Milosavljevic, Louise C. Laurent

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Article number19
JournalJournal of Biomedical Semantics
Volume7
Issue number1
DOIs
StatePublished - Apr 12 2016

Fingerprint

Gene Ontology
RNA
Ontology
Genes
Communication
Molecular Sequence Annotation
Metadata
Extracellular Vesicles
Exosomes
Atlases
Terminology
Messenger RNA

Keywords

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

ASJC Scopus subject areas

  • Information Systems
  • Computer Science Applications
  • Health Informatics
  • Computer Networks and Communications

Cite this

Cheung, K. H., Keerthikumar, S., Roncaglia, P., Subramanian, S. L., Roth, M. E., Samuel, M., ... Laurent, L. C. (2016). Extending gene ontology in the context of extracellular RNA and vesicle communication. Journal of Biomedical Semantics, 7(1), [19]. https://doi.org/10.1186/s13326-016-0061-5

Extending gene ontology in the context of extracellular RNA and vesicle communication. / Cheung, Kei Hoi; Keerthikumar, Shivakumar; Roncaglia, Paola; Subramanian, Sai Lakshmi; Roth, Matthew E.; Samuel, Monisha; Anand, Sushma; Gangoda, Lahiru; Gould, Stephen J; Alexander, Roger; Galas, David; Gerstein, Mark B.; Hill, Andrew F.; Kitchen, Robert R.; Lötvall, Jan; Patel, Tushar; Procaccini, Dena C.; Quesenberry, Peter; Rozowsky, Joel; Raffai, Robert L.; Shypitsyna, Aleksandra; Su, Andrew I.; Théry, Clotilde; Vickers, Kasey; Wauben, Marca H M; Mathivanan, Suresh; Milosavljevic, Aleksandar; Laurent, Louise C.

In: Journal of Biomedical Semantics, Vol. 7, No. 1, 19, 12.04.2016.

Research output: Contribution to journalArticle

Cheung, KH, Keerthikumar, S, Roncaglia, P, Subramanian, SL, Roth, ME, Samuel, M, Anand, S, Gangoda, L, Gould, SJ, Alexander, R, Galas, D, Gerstein, MB, Hill, AF, Kitchen, RR, Lötvall, J, Patel, T, Procaccini, DC, Quesenberry, P, Rozowsky, J, Raffai, RL, Shypitsyna, A, Su, AI, Théry, C, Vickers, K, Wauben, MHM, Mathivanan, S, Milosavljevic, A & Laurent, LC 2016, 'Extending gene ontology in the context of extracellular RNA and vesicle communication', Journal of Biomedical Semantics, vol. 7, no. 1, 19. https://doi.org/10.1186/s13326-016-0061-5
Cheung KH, Keerthikumar S, Roncaglia P, Subramanian SL, Roth ME, Samuel M et al. Extending gene ontology in the context of extracellular RNA and vesicle communication. Journal of Biomedical Semantics. 2016 Apr 12;7(1). 19. https://doi.org/10.1186/s13326-016-0061-5
Cheung, Kei Hoi ; Keerthikumar, Shivakumar ; Roncaglia, Paola ; Subramanian, Sai Lakshmi ; Roth, Matthew E. ; Samuel, Monisha ; Anand, Sushma ; Gangoda, Lahiru ; Gould, Stephen J ; Alexander, Roger ; Galas, David ; Gerstein, Mark B. ; Hill, Andrew F. ; Kitchen, Robert R. ; Lötvall, Jan ; Patel, Tushar ; Procaccini, Dena C. ; Quesenberry, Peter ; Rozowsky, Joel ; Raffai, Robert L. ; Shypitsyna, Aleksandra ; Su, Andrew I. ; Théry, Clotilde ; Vickers, Kasey ; Wauben, Marca H M ; Mathivanan, Suresh ; Milosavljevic, Aleksandar ; Laurent, Louise C. / Extending gene ontology in the context of extracellular RNA and vesicle communication. In: Journal of Biomedical Semantics. 2016 ; Vol. 7, No. 1.
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T1 - Extending gene ontology in the context of extracellular RNA and vesicle communication

AU - Cheung, Kei Hoi

AU - Keerthikumar, Shivakumar

AU - Roncaglia, Paola

AU - Subramanian, Sai Lakshmi

AU - Roth, Matthew E.

AU - Samuel, Monisha

AU - Anand, Sushma

AU - Gangoda, Lahiru

AU - Gould, Stephen J

AU - Alexander, Roger

AU - Galas, David

AU - Gerstein, Mark B.

AU - Hill, Andrew F.

AU - Kitchen, Robert R.

AU - Lötvall, Jan

AU - Patel, Tushar

AU - Procaccini, Dena C.

AU - Quesenberry, Peter

AU - Rozowsky, Joel

AU - Raffai, Robert L.

AU - Shypitsyna, Aleksandra

AU - Su, Andrew I.

AU - Théry, Clotilde

AU - Vickers, Kasey

AU - Wauben, Marca H M

AU - Mathivanan, Suresh

AU - Milosavljevic, Aleksandar

AU - Laurent, Louise C.

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N2 - 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.

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KW - Atlas

KW - Extracellular RNA

KW - Extracellular vesicle

KW - Faceted search

KW - Metadata

KW - Ontology

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