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NCBI’s Virus Discovery Codeathon: Building “FIVE” —The Federated Index of Viral Experiments API Index

Viruses represent important test cases for data federation due to their genome size and the rapid increase in sequence data in publicly available databases. However, some consequences of previously decentralized (unfederated) data are lack of consensus or comparisons between feature annotations. Uni...

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Autores principales: Martí-Carreras, Joan, Gener, Alejandro Rafael, Miller, Sierra D., Brito, Anderson F., Camacho, Christiam E., Connor, Ryan, Deboutte, Ward, Glickman, Cody, Kristensen, David M., Meyer, Wynn K., Modha, Sejal, Norris, Alexis L., Saha, Surya, Belford, Anna K., Biederstedt, Evan, Brister, James Rodney, Buchmann, Jan P., Cooley, Nicholas P., Edwards, Robert A., Javkar, Kiran, Muchow, Michael, Muralidharan, Harihara Subrahmaniam, Pepe-Ranney, Charles, Shah, Nidhi, Shakya, Migun, Tisza, Michael J., Tully, Benjamin J., Vanmechelen, Bert, Virta, Valerie C., Weissman, JL, Zalunin, Vadim, Efremov, Alexandre, Busby, Ben
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7764237/
https://www.ncbi.nlm.nih.gov/pubmed/33322070
http://dx.doi.org/10.3390/v12121424
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author Martí-Carreras, Joan
Gener, Alejandro Rafael
Miller, Sierra D.
Brito, Anderson F.
Camacho, Christiam E.
Connor, Ryan
Deboutte, Ward
Glickman, Cody
Kristensen, David M.
Meyer, Wynn K.
Modha, Sejal
Norris, Alexis L.
Saha, Surya
Belford, Anna K.
Biederstedt, Evan
Brister, James Rodney
Buchmann, Jan P.
Cooley, Nicholas P.
Edwards, Robert A.
Javkar, Kiran
Muchow, Michael
Muralidharan, Harihara Subrahmaniam
Pepe-Ranney, Charles
Shah, Nidhi
Shakya, Migun
Tisza, Michael J.
Tully, Benjamin J.
Vanmechelen, Bert
Virta, Valerie C.
Weissman, JL
Zalunin, Vadim
Efremov, Alexandre
Busby, Ben
author_facet Martí-Carreras, Joan
Gener, Alejandro Rafael
Miller, Sierra D.
Brito, Anderson F.
Camacho, Christiam E.
Connor, Ryan
Deboutte, Ward
Glickman, Cody
Kristensen, David M.
Meyer, Wynn K.
Modha, Sejal
Norris, Alexis L.
Saha, Surya
Belford, Anna K.
Biederstedt, Evan
Brister, James Rodney
Buchmann, Jan P.
Cooley, Nicholas P.
Edwards, Robert A.
Javkar, Kiran
Muchow, Michael
Muralidharan, Harihara Subrahmaniam
Pepe-Ranney, Charles
Shah, Nidhi
Shakya, Migun
Tisza, Michael J.
Tully, Benjamin J.
Vanmechelen, Bert
Virta, Valerie C.
Weissman, JL
Zalunin, Vadim
Efremov, Alexandre
Busby, Ben
author_sort Martí-Carreras, Joan
collection PubMed
description Viruses represent important test cases for data federation due to their genome size and the rapid increase in sequence data in publicly available databases. However, some consequences of previously decentralized (unfederated) data are lack of consensus or comparisons between feature annotations. Unifying or displaying alternative annotations should be a priority both for communities with robust entry representation and for nascent communities with burgeoning data sources. To this end, during this three-day continuation of the Virus Hunting Toolkit codeathon series (VHT-2), a new integrated and federated viral index was elaborated. This Federated Index of Viral Experiments (FIVE) integrates pre-existing and novel functional and taxonomy annotations and virus–host pairings. Variability in the context of viral genomic diversity is often overlooked in virus databases. As a proof-of-concept, FIVE was the first attempt to include viral genome variation for HIV, the most well-studied human pathogen, through viral genome diversity graphs. As per the publication of this manuscript, FIVE is the first implementation of a virus-specific federated index of such scope. FIVE is coded in BigQuery for optimal access of large quantities of data and is publicly accessible. Many projects of database or index federation fail to provide easier alternatives to access or query information. To this end, a Python API query system was developed to enhance the accessibility of FIVE.
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spelling pubmed-77642372020-12-27 NCBI’s Virus Discovery Codeathon: Building “FIVE” —The Federated Index of Viral Experiments API Index Martí-Carreras, Joan Gener, Alejandro Rafael Miller, Sierra D. Brito, Anderson F. Camacho, Christiam E. Connor, Ryan Deboutte, Ward Glickman, Cody Kristensen, David M. Meyer, Wynn K. Modha, Sejal Norris, Alexis L. Saha, Surya Belford, Anna K. Biederstedt, Evan Brister, James Rodney Buchmann, Jan P. Cooley, Nicholas P. Edwards, Robert A. Javkar, Kiran Muchow, Michael Muralidharan, Harihara Subrahmaniam Pepe-Ranney, Charles Shah, Nidhi Shakya, Migun Tisza, Michael J. Tully, Benjamin J. Vanmechelen, Bert Virta, Valerie C. Weissman, JL Zalunin, Vadim Efremov, Alexandre Busby, Ben Viruses Article Viruses represent important test cases for data federation due to their genome size and the rapid increase in sequence data in publicly available databases. However, some consequences of previously decentralized (unfederated) data are lack of consensus or comparisons between feature annotations. Unifying or displaying alternative annotations should be a priority both for communities with robust entry representation and for nascent communities with burgeoning data sources. To this end, during this three-day continuation of the Virus Hunting Toolkit codeathon series (VHT-2), a new integrated and federated viral index was elaborated. This Federated Index of Viral Experiments (FIVE) integrates pre-existing and novel functional and taxonomy annotations and virus–host pairings. Variability in the context of viral genomic diversity is often overlooked in virus databases. As a proof-of-concept, FIVE was the first attempt to include viral genome variation for HIV, the most well-studied human pathogen, through viral genome diversity graphs. As per the publication of this manuscript, FIVE is the first implementation of a virus-specific federated index of such scope. FIVE is coded in BigQuery for optimal access of large quantities of data and is publicly accessible. Many projects of database or index federation fail to provide easier alternatives to access or query information. To this end, a Python API query system was developed to enhance the accessibility of FIVE. MDPI 2020-12-10 /pmc/articles/PMC7764237/ /pubmed/33322070 http://dx.doi.org/10.3390/v12121424 Text en © 2020 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) ).
spellingShingle Article
Martí-Carreras, Joan
Gener, Alejandro Rafael
Miller, Sierra D.
Brito, Anderson F.
Camacho, Christiam E.
Connor, Ryan
Deboutte, Ward
Glickman, Cody
Kristensen, David M.
Meyer, Wynn K.
Modha, Sejal
Norris, Alexis L.
Saha, Surya
Belford, Anna K.
Biederstedt, Evan
Brister, James Rodney
Buchmann, Jan P.
Cooley, Nicholas P.
Edwards, Robert A.
Javkar, Kiran
Muchow, Michael
Muralidharan, Harihara Subrahmaniam
Pepe-Ranney, Charles
Shah, Nidhi
Shakya, Migun
Tisza, Michael J.
Tully, Benjamin J.
Vanmechelen, Bert
Virta, Valerie C.
Weissman, JL
Zalunin, Vadim
Efremov, Alexandre
Busby, Ben
NCBI’s Virus Discovery Codeathon: Building “FIVE” —The Federated Index of Viral Experiments API Index
title NCBI’s Virus Discovery Codeathon: Building “FIVE” —The Federated Index of Viral Experiments API Index
title_full NCBI’s Virus Discovery Codeathon: Building “FIVE” —The Federated Index of Viral Experiments API Index
title_fullStr NCBI’s Virus Discovery Codeathon: Building “FIVE” —The Federated Index of Viral Experiments API Index
title_full_unstemmed NCBI’s Virus Discovery Codeathon: Building “FIVE” —The Federated Index of Viral Experiments API Index
title_short NCBI’s Virus Discovery Codeathon: Building “FIVE” —The Federated Index of Viral Experiments API Index
title_sort ncbi’s virus discovery codeathon: building “five” —the federated index of viral experiments api index
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7764237/
https://www.ncbi.nlm.nih.gov/pubmed/33322070
http://dx.doi.org/10.3390/v12121424
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