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 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 Raffai; Aleksandra Shypitsyna; Andrew I Su; Clotilde Théry; Kasey Vickers; Marca H M Wauben; Suresh Mathivanan; Aleksandar Milosavljevic; Louise C Laurent

doi:10.1186/s13326-016-0061-5

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 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 journal › Article › Academic › peer-review

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 language	English
Article number	19
Journal	Journal of Biomedical Semantics
Volume	7
DOIs	https://doi.org/10.1186/s13326-016-0061-5
Publication status	Published - 2016

Keywords

Ontology
Extracellular RNA
Metadata
Faceted search
Atlas

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Cheung, K.-H., Keerthikumar, S., Roncaglia, P., Subramanian, S. L., Roth, M. E., Samuel, M., Anand, S., Gangoda, L., Gould, S., Alexander, R., Galas, D., Gerstein, M. B., Hill, A. F., Kitchen, R. R., Lötvall, J., Patel, T., Procaccini, D. C., Quesenberry, P., Rozowsky, J., ... Laurent, L. C. (2016). Extending gene ontology in the context of extracellular RNA and vesicle communication. Journal of Biomedical Semantics, 7, Article 19. https://doi.org/10.1186/s13326-016-0061-5

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title = "Extending gene ontology in the context of extracellular RNA and vesicle communication",

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 = "Ontology, Extracellular RNA, Metadata, Faceted search, Atlas",

author = "Kei-Hoi Cheung and Shivakumar Keerthikumar and Paola Roncaglia and Subramanian, {Sai Lakshmi} and Roth, {Matthew E} and Monisha Samuel and Sushma Anand and Lahiru Gangoda and Stephen Gould and Roger Alexander and David Galas and Gerstein, {Mark B} and Hill, {Andrew F} and Kitchen, {Robert R} and Jan L{\"o}tvall and Tushar Patel and Procaccini, {Dena C} and Peter Quesenberry and Joel Rozowsky and Raffai, {Robert L} and Aleksandra Shypitsyna and Su, {Andrew I} and Clotilde Th{\'e}ry and Kasey Vickers and Wauben, {Marca H M} and Suresh Mathivanan and Aleksandar Milosavljevic and Laurent, {Louise C}",

year = "2016",

doi = "10.1186/s13326-016-0061-5",

language = "English",

volume = "7",

journal = "Journal of Biomedical Semantics",

issn = "2041-1480",

publisher = "BioMed Central",

}

Cheung, K-H, Keerthikumar, S, Roncaglia, P, Subramanian, SL, Roth, ME, Samuel, M, Anand, S, Gangoda, L, Gould, S, 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, 19. https://doi.org/10.1186/s13326-016-0061-5

TY - JOUR

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

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

PY - 2016

Y1 - 2016

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.

AB - 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.

KW - Ontology

KW - Extracellular RNA

KW - Metadata

KW - Faceted search

KW - Atlas

U2 - 10.1186/s13326-016-0061-5

DO - 10.1186/s13326-016-0061-5

M3 - Article

C2 - 27076901

SN - 2041-1480

VL - 7

JO - Journal of Biomedical Semantics

JF - Journal of Biomedical Semantics

M1 - 19

ER -

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

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