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

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/me...

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Autores principales: Cheung, Kei-Hoi, Keerthikumar, Shivakumar, Roncaglia, Paola, Subramanian, Sai Lakshmi, Roth, Matthew E., Samuel, Monisha, Anand, Sushma, Gangoda, Lahiru, Gould, Stephen, 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.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4830068/
https://www.ncbi.nlm.nih.gov/pubmed/27076901
http://dx.doi.org/10.1186/s13326-016-0061-5
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author Cheung, Kei-Hoi
Keerthikumar, Shivakumar
Roncaglia, Paola
Subramanian, Sai Lakshmi
Roth, Matthew E.
Samuel, Monisha
Anand, Sushma
Gangoda, Lahiru
Gould, Stephen
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.
author_facet Cheung, Kei-Hoi
Keerthikumar, Shivakumar
Roncaglia, Paola
Subramanian, Sai Lakshmi
Roth, Matthew E.
Samuel, Monisha
Anand, Sushma
Gangoda, Lahiru
Gould, Stephen
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.
author_sort Cheung, Kei-Hoi
collection PubMed
description 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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spelling pubmed-48300682016-04-14 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 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. J Biomed Semantics Research 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. BioMed Central 2016-04-12 /pmc/articles/PMC4830068/ /pubmed/27076901 http://dx.doi.org/10.1186/s13326-016-0061-5 Text en © Cheung et al. 2016 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research
Cheung, Kei-Hoi
Keerthikumar, Shivakumar
Roncaglia, Paola
Subramanian, Sai Lakshmi
Roth, Matthew E.
Samuel, Monisha
Anand, Sushma
Gangoda, Lahiru
Gould, Stephen
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
title Extending gene ontology in the context of extracellular RNA and vesicle communication
title_full Extending gene ontology in the context of extracellular RNA and vesicle communication
title_fullStr Extending gene ontology in the context of extracellular RNA and vesicle communication
title_full_unstemmed Extending gene ontology in the context of extracellular RNA and vesicle communication
title_short Extending gene ontology in the context of extracellular RNA and vesicle communication
title_sort extending gene ontology in the context of extracellular rna and vesicle communication
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4830068/
https://www.ncbi.nlm.nih.gov/pubmed/27076901
http://dx.doi.org/10.1186/s13326-016-0061-5
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