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

被引：25

作者：

Cheung, Kei-Hoi ^{[1
,2
]}

Keerthikumar, Shivakumar ^{[3
]}

Roncaglia, Paola ^{[4
]}

Subramanian, Sai Lakshmi ^{[5
]}

Roth, Matthew E. ^{[5
]}

Samuel, Monisha ^{[3
]}

Anand, Sushma ^{[3
]}

Gangoda, Lahiru ^{[3
]}

Gould, Stephen ^{[6
]}

Alexander, Roger ^{[7
]}

Galas, David ^{[7
]}

Gerstein, Mark B. ^{[8
,9
,10
]}

Hill, Andrew F. ^{[3
]}

Kitchen, Robert R. ^{[8
]}

Lotvall, Jan ^{[11
]}

Patel, Tushar ^{[12
]}

Procaccini, Dena C. ^{[13
]}

Quesenberry, Peter ^{[14
]}

Rozowsky, Joel ^{[8
,10
]}

Raffai, Robert L. ^{[15
,16
]}

Shypitsyna, Aleksandra ^{[4
]}

Su, Andrew I. ^{[17
]}

Thery, Clotilde ^{[18
]}

Vickers, Kasey ^{[19
]}

Wauben, Marca H. M. ^{[20
]}

Mathivanan, Suresh ^{[3
]}

Milosavljevic, Aleksandar ^{[5
]}

Laurent, Louise C. ^{[21
]}

机构：

[1] Yale Univ, Sch Med, Dept Emergency Med, Yale Ctr Med Informat, New Haven, CT USA

[2] VA Connecticut Healthcare Syst, West Haven, CT USA

[3] La Trobe Univ, La Trobe Inst Mol Sci, Dept Biochem & Genet, Melbourne, Vic 3086, Australia

[4] European Mol Biol Lab, European Bioinformat Inst EMBL EBI, Wellcome Trust Genome Campus, Cambridge CB10 1SD, England

[5] Baylor Coll Med, Dept Mol & Human Genet, Bioinformat Res Lab, Houston, TX 77030 USA

[6] Johns Hopkins Univ, Sch Med, Dept Biol Chem, Baltimore, MD 21205 USA

[7] Pacific Northwest Diabet Res Inst, Seattle, WA USA

[8] Yale Univ, Dept Mol Biophys & Biochem, New Haven, CT USA

[9] Yale Univ, Dept Comp Sci, POB 2158, New Haven, CT 06520 USA

[10] Yale Univ, Program Computat Biol & Bioinformat, New Haven, CT USA

[11] Univ Gothenburg, Gothenburg, Sweden

[12] Mayo Clin Jacksonville, 4500 San Pablo Rd, Jacksonville, FL 32224 USA

[13] NIDA, Div Neurosci & Behav, Rockville, MD USA

[14] Univ Med Comprehens Canc Ctr, Providence, RI USA

[15] Univ Calif San Francisco, Dept Surg, San Francisco, CA USA

[16] VA Med Ctr, San Francisco, CA USA

[17] Scripps Res Inst, Dept Mol & Expt Med, 10666 N Torrey Pines Rd, La Jolla, CA 92037 USA

[18] PSL Res Univ, Inst Curie, INSERM, U932, Paris, France

[19] Vanderbilt Univ, Sch Med, Dept Med, Nashville, TN 37212 USA

[20] Univ Utrecht, Dept Biochem & Cell Biol, Utrecht, Netherlands

[21] Univ Calif San Diego, Dept Reprod Med, La Jolla, CA 92093 USA

来源：

JOURNAL OF BIOMEDICAL SEMANTICS | 2016年 / 7卷

关键词：

Ontology; Extracellular RNA; Extracellular vesicle; Metadata; Faceted search; Atlas; VIRUS-LIKE PARTICLES; MEDIATED TRANSFER; MICRORNAS; PLASMA; TOOL; IDENTIFICATION; ASSOCIATION; UNIFICATION; PROTEINS; ANATOMY;

D O I：

10.1186/s13326-016-0061-5

中图分类号：

Q [生物科学];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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.

引用

页数：9