Evidence map›Paper›PMID 25243218›Full record

ArticleTheScientificWorldJournal2014

VibrioBase: a model for next-generation genome and annotation database development.

Siew Woh Choo, Hamed Heydari, Tze King Tan, Cheuk Chuen Siow, Ching Yew Beh, Wei Yee Wee, Naresh V R Mutha, Guat Jah Wong, Mia Yang Ang, Amir Hessam Yazdi

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in TheScientificWorldJournal, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing 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

4 citing papers in PubMed.

  1. Article
  2. Article
  3. Databases for Microbiologists.Journal of bacteriology · 2015
    Review
  4. 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.

Siew Woh ChooDepartment of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, Malaysia ; Genome Informatics Research Laboratory, HIR Building, University of Malaya, 50603 Kuala Lumpur, Malaysia.
Hamed HeydariGenome Informatics Research Laboratory, HIR Building, University of Malaya, 50603 Kuala Lumpur, Malaysia ; Department of Software Engineering, Faculty of Computer Science and Information Technology, University of Malaya, 50603 Kuala Lumpur, Malaysia.ORCID 0000-0001-6708-9116
Tze King TanDepartment of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, Malaysia ; Genome Informatics Research Laboratory, HIR Building, University of Malaya, 50603 Kuala Lumpur, Malaysia.
Cheuk Chuen SiowGenome Informatics Research Laboratory, HIR Building, University of Malaya, 50603 Kuala Lumpur, Malaysia.ORCID 0000-0001-8336-7059
Ching Yew BehDepartment of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, Malaysia.ORCID 0000-0002-3737-401X
Wei Yee WeeDepartment of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, Malaysia ; Genome Informatics Research Laboratory, HIR Building, University of Malaya, 50603 Kuala Lumpur, Malaysia.ORCID 0000-0001-8965-0680
Naresh V R MuthaGenome Informatics Research Laboratory, HIR Building, University of Malaya, 50603 Kuala Lumpur, Malaysia.
Guat Jah WongDepartment of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, Malaysia ; Genome Informatics Research Laboratory, HIR Building, University of Malaya, 50603 Kuala Lumpur, Malaysia.
Mia Yang AngDepartment of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, Malaysia ; Genome Informatics Research Laboratory, HIR Building, University of Malaya, 50603 Kuala Lumpur, Malaysia.ORCID 0000-0003-2709-6754
Amir Hessam YazdiDepartment of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, Malaysia ; Department of Computer System & Technology, Faculty of Computer Science and Information Technology, University of Malaya, 50603 Kuala Lumpur, Malaysia.ORCID 0000-0001-5685-9568

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

To facilitate the ongoing research of Vibrio spp., a dedicated platform for the Vibrio research community is needed to host the fast-growing amount of genomic data and facilitate the analysis of these data. We present VibrioBase, a useful resource platform, providing all basic features of a sequence database with the addition of unique analysis tools which could be valuable for the Vibrio research community. VibrioBase currently houses a total of 252 Vibrio genomes developed in a user-friendly manner and useful to enable the analysis of these genomic data, particularly in the field of comparative genomics. Besides general data browsing features, VibrioBase offers analysis tools such as BLAST interfaces and JBrowse genome browser. Other important features of this platform include our newly developed in-house tools, the pairwise genome comparison (PGC) tool, and pathogenomics profiling tool (PathoProT). The PGC tool is useful in the identification and comparative analysis of two genomes, whereas PathoProT is designed for comparative pathogenomics analysis of Vibrio strains. Both of these tools will enable researchers with little experience in bioinformatics to get meaningful information from Vibrio genomes with ease. We have tested the validity and suitability of these tools and features for use in the next-generation database development.

Indexed as

Databases, GeneticData CurationGenome, BacterialPhylogenyVibrio

Identifiers

PMID25243218
PMCPMC4138799

What OpenQuestion holds

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Registered trials

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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.