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/met...
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Autor*in:	Cheung, Kei-Hoi [verfasserIn] 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.

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2016

Schlagwörter:	Ontology Extracellular RNA Extracellular vesicle Metadata Faceted search Atlas

Anmerkung:	© Cheung et al. 2016

Übergeordnetes Werk:	Enthalten in: Journal of biomedical semantics - London : BioMed Central, 2010, 7(2016), 1 vom: 12. Apr.
Übergeordnetes Werk:	volume:7 ; year:2016 ; number:1 ; day:12 ; month:04

Links:	Volltext

DOI / URN:	10.1186/s13326-016-0061-5

Katalog-ID:	SPR031355838

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520			\|a 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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700	1		\|a Laurent, Louise C. \|4 aut
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allfields	10.1186/s13326-016-0061-5 doi (DE-627)SPR031355838 (SPR)s13326-016-0061-5-e DE-627 ger DE-627 rakwb eng Cheung, Kei-Hoi verfasserin aut Extending gene ontology in the context of extracellular RNA and vesicle communication 2016 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Cheung et al. 2016 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. Ontology (dpeaa)DE-He213 Extracellular RNA (dpeaa)DE-He213 Extracellular vesicle (dpeaa)DE-He213 Metadata (dpeaa)DE-He213 Faceted search (dpeaa)DE-He213 Atlas (dpeaa)DE-He213 Keerthikumar, Shivakumar aut Roncaglia, Paola aut Subramanian, Sai Lakshmi aut Roth, Matthew E. aut Samuel, Monisha aut Anand, Sushma aut Gangoda, Lahiru aut Gould, Stephen aut Alexander, Roger aut Galas, David aut Gerstein, Mark B. aut Hill, Andrew F. aut Kitchen, Robert R. aut Lötvall, Jan aut Patel, Tushar aut Procaccini, Dena C. aut Quesenberry, Peter aut Rozowsky, Joel aut Raffai, Robert L. aut Shypitsyna, Aleksandra aut Su, Andrew I. aut Théry, Clotilde aut Vickers, Kasey aut Wauben, Marca H.M. aut Mathivanan, Suresh aut Milosavljevic, Aleksandar aut Laurent, Louise C. aut Enthalten in Journal of biomedical semantics London : BioMed Central, 2010 7(2016), 1 vom: 12. Apr. (DE-627)624250865 (DE-600)2548651-2 2041-1480 nnns volume:7 year:2016 number:1 day:12 month:04 https://dx.doi.org/10.1186/s13326-016-0061-5 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 7 2016 1 12 04
spelling	10.1186/s13326-016-0061-5 doi (DE-627)SPR031355838 (SPR)s13326-016-0061-5-e DE-627 ger DE-627 rakwb eng Cheung, Kei-Hoi verfasserin aut Extending gene ontology in the context of extracellular RNA and vesicle communication 2016 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Cheung et al. 2016 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. Ontology (dpeaa)DE-He213 Extracellular RNA (dpeaa)DE-He213 Extracellular vesicle (dpeaa)DE-He213 Metadata (dpeaa)DE-He213 Faceted search (dpeaa)DE-He213 Atlas (dpeaa)DE-He213 Keerthikumar, Shivakumar aut Roncaglia, Paola aut Subramanian, Sai Lakshmi aut Roth, Matthew E. aut Samuel, Monisha aut Anand, Sushma aut Gangoda, Lahiru aut Gould, Stephen aut Alexander, Roger aut Galas, David aut Gerstein, Mark B. aut Hill, Andrew F. aut Kitchen, Robert R. aut Lötvall, Jan aut Patel, Tushar aut Procaccini, Dena C. aut Quesenberry, Peter aut Rozowsky, Joel aut Raffai, Robert L. aut Shypitsyna, Aleksandra aut Su, Andrew I. aut Théry, Clotilde aut Vickers, Kasey aut Wauben, Marca H.M. aut Mathivanan, Suresh aut Milosavljevic, Aleksandar aut Laurent, Louise C. aut Enthalten in Journal of biomedical semantics London : BioMed Central, 2010 7(2016), 1 vom: 12. Apr. (DE-627)624250865 (DE-600)2548651-2 2041-1480 nnns volume:7 year:2016 number:1 day:12 month:04 https://dx.doi.org/10.1186/s13326-016-0061-5 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 7 2016 1 12 04
allfields_unstemmed	10.1186/s13326-016-0061-5 doi (DE-627)SPR031355838 (SPR)s13326-016-0061-5-e DE-627 ger DE-627 rakwb eng Cheung, Kei-Hoi verfasserin aut Extending gene ontology in the context of extracellular RNA and vesicle communication 2016 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Cheung et al. 2016 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. Ontology (dpeaa)DE-He213 Extracellular RNA (dpeaa)DE-He213 Extracellular vesicle (dpeaa)DE-He213 Metadata (dpeaa)DE-He213 Faceted search (dpeaa)DE-He213 Atlas (dpeaa)DE-He213 Keerthikumar, Shivakumar aut Roncaglia, Paola aut Subramanian, Sai Lakshmi aut Roth, Matthew E. aut Samuel, Monisha aut Anand, Sushma aut Gangoda, Lahiru aut Gould, Stephen aut Alexander, Roger aut Galas, David aut Gerstein, Mark B. aut Hill, Andrew F. aut Kitchen, Robert R. aut Lötvall, Jan aut Patel, Tushar aut Procaccini, Dena C. aut Quesenberry, Peter aut Rozowsky, Joel aut Raffai, Robert L. aut Shypitsyna, Aleksandra aut Su, Andrew I. aut Théry, Clotilde aut Vickers, Kasey aut Wauben, Marca H.M. aut Mathivanan, Suresh aut Milosavljevic, Aleksandar aut Laurent, Louise C. aut Enthalten in Journal of biomedical semantics London : BioMed Central, 2010 7(2016), 1 vom: 12. Apr. (DE-627)624250865 (DE-600)2548651-2 2041-1480 nnns volume:7 year:2016 number:1 day:12 month:04 https://dx.doi.org/10.1186/s13326-016-0061-5 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 7 2016 1 12 04
allfieldsGer	10.1186/s13326-016-0061-5 doi (DE-627)SPR031355838 (SPR)s13326-016-0061-5-e DE-627 ger DE-627 rakwb eng Cheung, Kei-Hoi verfasserin aut Extending gene ontology in the context of extracellular RNA and vesicle communication 2016 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Cheung et al. 2016 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. Ontology (dpeaa)DE-He213 Extracellular RNA (dpeaa)DE-He213 Extracellular vesicle (dpeaa)DE-He213 Metadata (dpeaa)DE-He213 Faceted search (dpeaa)DE-He213 Atlas (dpeaa)DE-He213 Keerthikumar, Shivakumar aut Roncaglia, Paola aut Subramanian, Sai Lakshmi aut Roth, Matthew E. aut Samuel, Monisha aut Anand, Sushma aut Gangoda, Lahiru aut Gould, Stephen aut Alexander, Roger aut Galas, David aut Gerstein, Mark B. aut Hill, Andrew F. aut Kitchen, Robert R. aut Lötvall, Jan aut Patel, Tushar aut Procaccini, Dena C. aut Quesenberry, Peter aut Rozowsky, Joel aut Raffai, Robert L. aut Shypitsyna, Aleksandra aut Su, Andrew I. aut Théry, Clotilde aut Vickers, Kasey aut Wauben, Marca H.M. aut Mathivanan, Suresh aut Milosavljevic, Aleksandar aut Laurent, Louise C. aut Enthalten in Journal of biomedical semantics London : BioMed Central, 2010 7(2016), 1 vom: 12. Apr. (DE-627)624250865 (DE-600)2548651-2 2041-1480 nnns volume:7 year:2016 number:1 day:12 month:04 https://dx.doi.org/10.1186/s13326-016-0061-5 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 7 2016 1 12 04
allfieldsSound	10.1186/s13326-016-0061-5 doi (DE-627)SPR031355838 (SPR)s13326-016-0061-5-e DE-627 ger DE-627 rakwb eng Cheung, Kei-Hoi verfasserin aut Extending gene ontology in the context of extracellular RNA and vesicle communication 2016 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Cheung et al. 2016 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. Ontology (dpeaa)DE-He213 Extracellular RNA (dpeaa)DE-He213 Extracellular vesicle (dpeaa)DE-He213 Metadata (dpeaa)DE-He213 Faceted search (dpeaa)DE-He213 Atlas (dpeaa)DE-He213 Keerthikumar, Shivakumar aut Roncaglia, Paola aut Subramanian, Sai Lakshmi aut Roth, Matthew E. aut Samuel, Monisha aut Anand, Sushma aut Gangoda, Lahiru aut Gould, Stephen aut Alexander, Roger aut Galas, David aut Gerstein, Mark B. aut Hill, Andrew F. aut Kitchen, Robert R. aut Lötvall, Jan aut Patel, Tushar aut Procaccini, Dena C. aut Quesenberry, Peter aut Rozowsky, Joel aut Raffai, Robert L. aut Shypitsyna, Aleksandra aut Su, Andrew I. aut Théry, Clotilde aut Vickers, Kasey aut Wauben, Marca H.M. aut Mathivanan, Suresh aut Milosavljevic, Aleksandar aut Laurent, Louise C. aut Enthalten in Journal of biomedical semantics London : BioMed Central, 2010 7(2016), 1 vom: 12. Apr. (DE-627)624250865 (DE-600)2548651-2 2041-1480 nnns volume:7 year:2016 number:1 day:12 month:04 https://dx.doi.org/10.1186/s13326-016-0061-5 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 7 2016 1 12 04
language	English
source	Enthalten in Journal of biomedical semantics 7(2016), 1 vom: 12. Apr. volume:7 year:2016 number:1 day:12 month:04
sourceStr	Enthalten in Journal of biomedical semantics 7(2016), 1 vom: 12. Apr. volume:7 year:2016 number:1 day:12 month:04
format_phy_str_mv	Article
institution	findex.gbv.de
topic_facet	Ontology Extracellular RNA Extracellular vesicle Metadata Faceted search Atlas
isfreeaccess_bool	true
container_title	Journal of biomedical semantics
authorswithroles_txt_mv	Cheung, Kei-Hoi @@aut@@ Keerthikumar, Shivakumar @@aut@@ Roncaglia, Paola @@aut@@ Subramanian, Sai Lakshmi @@aut@@ Roth, Matthew E. @@aut@@ Samuel, Monisha @@aut@@ Anand, Sushma @@aut@@ Gangoda, Lahiru @@aut@@ Gould, Stephen @@aut@@ Alexander, Roger @@aut@@ Galas, David @@aut@@ Gerstein, Mark B. @@aut@@ Hill, Andrew F. @@aut@@ Kitchen, Robert R. @@aut@@ Lötvall, Jan @@aut@@ Patel, Tushar @@aut@@ Procaccini, Dena C. @@aut@@ Quesenberry, Peter @@aut@@ Rozowsky, Joel @@aut@@ Raffai, Robert L. @@aut@@ Shypitsyna, Aleksandra @@aut@@ Su, Andrew I. @@aut@@ Théry, Clotilde @@aut@@ Vickers, Kasey @@aut@@ Wauben, Marca H.M. @@aut@@ Mathivanan, Suresh @@aut@@ Milosavljevic, Aleksandar @@aut@@ Laurent, Louise C. @@aut@@
publishDateDaySort_date	2016-04-12T00:00:00Z
hierarchy_top_id	624250865
id	SPR031355838
language_de	englisch
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author	Cheung, Kei-Hoi
spellingShingle	Cheung, Kei-Hoi misc Ontology misc Extracellular RNA misc Extracellular vesicle misc Metadata misc Faceted search misc Atlas Extending gene ontology in the context of extracellular RNA and vesicle communication
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topic_title	Extending gene ontology in the context of extracellular RNA and vesicle communication Ontology (dpeaa)DE-He213 Extracellular RNA (dpeaa)DE-He213 Extracellular vesicle (dpeaa)DE-He213 Metadata (dpeaa)DE-He213 Faceted search (dpeaa)DE-He213 Atlas (dpeaa)DE-He213
topic	misc Ontology misc Extracellular RNA misc Extracellular vesicle misc Metadata misc Faceted search misc Atlas
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title	Extending gene ontology in the context of extracellular RNA and vesicle communication
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title_full	Extending gene ontology in the context of extracellular RNA and vesicle communication
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author_browse	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.
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title_sort	extending gene ontology in the context of extracellular rna and vesicle communication
title_auth	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. © Cheung et al. 2016
abstractGer	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. © Cheung et al. 2016
abstract_unstemmed	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. © Cheung et al. 2016
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title_short	Extending gene ontology in the context of extracellular RNA and vesicle communication
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author2	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.
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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. 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Extending gene ontology in the context of extracellular RNA and vesicle communication

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