Evidence map›Paper›PMID 28207819›Full record

ArticlePloS one2017

The ins and outs of eukaryotic viruses: Knowledge base and ontology of a viral infection.

Chantal Hulo, Patrick Masson, Edouard de Castro, Andrea H Auchincloss, Rebecca Foulger, Sylvain Poux, Jane Lomax, Lydie Bougueleret, Ioannis Xenarios, Philippe Le Mercier

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in PloS one, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.

0numbers the graph read from it
0cells of the map it votes in
6citing papers in PubMed
0.4field-weighted citation impact, top 38% of its field
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

6 citing papers in PubMed, 11 citations in OpenAlex.

  1. Review
  2. Article
  3. Article
  4. Bacteriophage-Mediated Cancer Gene Therapy.International journal of molecular sciences · 2022
    Review
  5. Review
  6. Review
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 at 2 institutions in 2 countries.

Chantal HuloSIB Swiss Institute of Bioinformatics, CMU, University of Geneva Medical School, Geneva, Switzerland.
Patrick MassonSIB Swiss Institute of Bioinformatics, CMU, University of Geneva Medical School, Geneva, Switzerland.
Edouard de CastroSIB Swiss Institute of Bioinformatics, CMU, University of Geneva Medical School, Geneva, Switzerland.
Andrea H AuchinclossSIB Swiss Institute of Bioinformatics, CMU, University of Geneva Medical School, Geneva, Switzerland.
Rebecca FoulgerEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, United Kingdom.
Sylvain PouxSIB Swiss Institute of Bioinformatics, CMU, University of Geneva Medical School, Geneva, Switzerland.
Jane LomaxEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, United Kingdom.
Lydie BougueleretSIB Swiss Institute of Bioinformatics, CMU, University of Geneva Medical School, Geneva, Switzerland.
Ioannis XenariosSIB Swiss Institute of Bioinformatics, CMU, University of Geneva Medical School, Geneva, Switzerland.
Philippe Le MercierSIB Swiss Institute of Bioinformatics, CMU, University of Geneva Medical School, Geneva, Switzerland.ORCID http://orcid.org/0000-0001-8528-090X
University of Geneva · CHEuropean Bioinformatics Institute · GB

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

Viruses are genetically diverse, infect a wide range of tissues and host cells and follow unique processes for replicating themselves. All these processes were investigated and indexed in 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. The virus life-cycle is classically described by schematic pictures. Using this ontology, it can be represented by a combination of successive terms: "entry", "latency", "transcription", "replication" and "exit". Each of these parts is broken down into discrete steps. For example Zika virus "entry" is broken down in successive steps: "Attachment", "Apoptotic mimicry", "Viral endocytosis/ macropinocytosis", "Fusion with host endosomal membrane", "Viral factory". 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

Terminology as TopicVirus Physiological PhenomenaDatabases, GeneticEukaryotic CellsVirus DiseasesVirusesVirus Replication

Identifiers

PMID28207819
PMCPMC5313201
OpenAlexW2588570952

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.