Research
Print page Print page
Switch language
The Capital Region of Denmark - a part of Copenhagen University Hospital
Published

NCBI's Virus Discovery Codeathon: Building "FIVE" -The Federated Index of Viral Experiments API Index

Research output: Contribution to journalJournal articleResearchpeer-review

DOI

  1. Virus Adaptation and Selection Following Challenge of Animals Vaccinated against Classical Swine Fever Virus

    Research output: Contribution to journalJournal articleResearchpeer-review

  2. A Protocol for Extraction of Infective Viromes Suitable for Metagenomics Sequencing from Low Volume Fecal Samples

    Research output: Contribution to journalJournal articleResearchpeer-review

  3. Protoparvovirus Cell Entry

    Research output: Contribution to journalReviewpeer-review

  4. Mechanisms and factors that influence high frequency retroviral recombination

    Research output: Contribution to journalJournal articleResearchpeer-review

  1. No additive effect of combining sumatriptan and olcegepant in the GTN mouse model of migraine

    Research output: Contribution to journalJournal articleResearchpeer-review

  2. Acetaminophen metabolism revisited using non-targeted analyses: Implications for human biomonitoring

    Research output: Contribution to journalJournal articleResearchpeer-review

  3. Functional gene networks reveal distinct mechanisms segregating in migraine families

    Research output: Contribution to journalJournal articleResearchpeer-review

  4. No central action of CGRP antagonising drugs in the GTN mouse model of migraine

    Research output: Contribution to journalJournal articleResearchpeer-review

  5. Von Frey testing revisited - provision of an online algorithm for improved accuracy of 50% thresholds

    Research output: Contribution to journalJournal articleResearchpeer-review

  • Joan Martí-Carreras
  • Alejandro Rafael Gener
  • Sierra D Miller
  • Anderson F Brito
  • Christiam E Camacho
  • Ryan Connor
  • Ward Deboutte
  • Cody Glickman
  • David M Kristensen
  • Wynn K Meyer
  • Sejal Modha
  • Alexis L Norris
  • Surya Saha
  • Anna K Belford
  • Evan Biederstedt
  • James Rodney Brister
  • Jan P Buchmann
  • Nicholas P Cooley
  • Robert A Edwards
  • Kiran Javkar
  • Michael Muchow
  • Harihara Subrahmaniam Muralidharan
  • Charles Pepe-Ranney
  • Nidhi Shah
  • Migun Shakya
  • Michael J Tisza
  • Benjamin J Tully
  • Bert Vanmechelen
  • Valerie C Virta
  • Jake L Weissman
  • Vadim Zalunin
  • Alexandre Efremov
  • Ben Busby
View graph of relations

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.

Original languageEnglish
JournalViruses
Volume12
Issue number12
Pages (from-to)1424
ISSN1999-4915
DOIs
Publication statusPublished - 2020

    Research areas

  • data federation, CRISPR, protein domain, metagenomics, virus, genome graphs, HIV-1

ID: 61821830