Evidence map›Paper›PMID 28545254›Full record

ArticleViruses2017

Bacterial Virus Ontology; Coordinating across Databases.

Chantal Hulo, Patrick Masson, Ariane Toussaint, David Osumi-Sutherland, Edouard de Castro, Andrea H Auchincloss, Sylvain Poux, Lydie Bougueleret, Ioannis Xenarios, Philippe Le Mercier

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Viruses, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

3 citing papers in PubMed.

  1. Article
  2. Viruses of Microbes.Viruses · 2017
    Article
  3. Prion-Like Domains in Phagobiota.Frontiers in microbiology · 2017
    Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors.

Chantal HuloSwiss-Prot group, SIB Swiss Institute of Bioinformatics, CMU, University of Geneva Medical School, 1211 Geneva, Switzerland. Chantal.Hulo@sib.swiss.
Patrick MassonSwiss-Prot group, SIB Swiss Institute of Bioinformatics, CMU, University of Geneva Medical School, 1211 Geneva, Switzerland. Patrick.Masson@sib.swiss.
Ariane ToussaintUniversity Libre de Bruxelles, Génétique et Physiologie Bactérienne (LGPB), 12 rue des Professeurs Jeener et Brachet, 6041 Charleroi, Belgium. ariane.toussaint@ulb.ac.be.
David Osumi-SutherlandEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK. davidos@ebi.ac.uk.
Edouard de CastroSwiss-Prot group, SIB Swiss Institute of Bioinformatics, CMU, University of Geneva Medical School, 1211 Geneva, Switzerland. edouard.decastro@sib.swiss.
Andrea H AuchinclossSwiss-Prot group, SIB Swiss Institute of Bioinformatics, CMU, University of Geneva Medical School, 1211 Geneva, Switzerland. Andrea.Auchincloss@sib.swiss.
Sylvain PouxSwiss-Prot group, SIB Swiss Institute of Bioinformatics, CMU, University of Geneva Medical School, 1211 Geneva, Switzerland. Sylvain.Poux@sib.swiss.
Lydie BougueleretSwiss-Prot group, SIB Swiss Institute of Bioinformatics, CMU, University of Geneva Medical School, 1211 Geneva, Switzerland. Lydie.Bougueleret@sib.swiss.
Ioannis XenariosSwiss-Prot group, SIB Swiss Institute of Bioinformatics, CMU, University of Geneva Medical School, 1211 Geneva, Switzerland. ioannis.xenarios@sib.swiss.
Philippe Le MercierSwiss-Prot group, SIB Swiss Institute of Bioinformatics, CMU, University of Geneva Medical School, 1211 Geneva, Switzerland. philippe.lemercier@sib.swiss.

Funding

UniProt: A centralized protein sequence and function resourceU41HG007822 · NHGRI · EUROPEAN MOLECULAR BIOLOGY LABORATORY · PI BATEMAN, ALEX · 2014 to 2017
$21.9M
NHGRI NIH HHS U41 HG007822
6 · The paper itself

Abstract

Bacterial viruses, also called bacteriophages, display a great genetic diversity and utilize unique processes for infecting and reproducing within a host cell. All these processes were investigated and indexed in the ViralZone knowledge base. To facilitate standardizing data, a simple ontology of viral life-cycle terms was developed to provide a common vocabulary for annotating data sets. New terminology was developed to address unique viral replication cycle processes, and existing terminology was modified and adapted. Classically, the viral life-cycle is described by schematic pictures. Using this ontology, it can be represented by a combination of successive events: entry, latency, transcription/replication, host-virus interactions and virus release. Each of these parts is broken down into discrete steps. For example enterobacteria phage lambda entry is broken down in: viral attachment to host adhesion receptor, viral attachment to host entry receptor, viral genome ejection and viral genome circularization. To demonstrate the utility of a standard ontology for virus biology, this work was completed by annotating virus data in the ViralZone, UniProtKB and Gene Ontology databases.

Indexed as

Biological OntologiesBacteriophagesDatabases, FactualHost-Pathogen InteractionsTerminology as Topiclife-cycleontologyphage

Identifiers

PMID28545254
PMCPMC5490803

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.