Evidence map›Paper›PMID 24163125›Full record

ArticleDatabase : the journal of biological databases and curation2013

Tripal v1.1: a standards-based toolkit for construction of online genetic and genomic databases.

Lacey-Anne Sanderson, Stephen P Ficklin, Chun-Huai Cheng, Sook Jung, Frank A Feltus, Kirstin E Bett, Dorrie Main

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Database : the journal of biological databases and curation, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.

0numbers the graph read from it
0cells of the map it votes in
43citing 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

43 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. FoPGDB: a pangenome database of Fusarium oxysporum, a cross-kingdom fungal pathogen.Database : the journal of biological databases and curation · 2024
    Article
  5. PearMODB: a multiomics database for pear (Pyrus) genomics, genetics and breeding study.Database : the journal of biological databases and curation · 2023
    Article
  6. Article
  7. Article
  8. Article
  9. Article
  10. Article
  11. Article
  12. Review
  13. Tripal MegaSearch: a tool for interactive and customizable query and download of big data.Database : the journal of biological databases and curation · 2021
    Article
  14. CamRegBase: a gene regulation database for the biofuel crop, Camelina sativa.Database : the journal of biological databases and curation · 2020
    Article
  15. Article
  16. Article
  17. Article
  18. Tripal and Galaxy: supporting reproducible scientific workflows for community biological databases.Database : the journal of biological databases and curation · 2020
    Article
  19. Article
  20. 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

7 authors.

Lacey-Anne SandersonDepartment of Plant Sciences, University of Saskatchewan. Saskatoon, SK Canada, Department of Horticulture, Washington State University. Pullman, WA, USA and Department of Genetics and Biochemistry, Clemson University. Clemson, SC, USA.
Stephen P Ficklin
Chun-Huai Cheng
Sook Jung
Frank A Feltus
Kirstin E Bett
Dorrie Main

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Tripal is an open-source freely available toolkit for construction of online genomic and genetic databases. It aims to facilitate development of community-driven biological websites by integrating the GMOD Chado database schema with Drupal, a popular website creation and content management software. Tripal provides a suite of tools for interaction with a Chado database and display of content therein. The tools are designed to be generic to support the various ways in which data may be stored in Chado. Previous releases of Tripal have supported organisms, genomic libraries, biological stocks, stock collections and genomic features, their alignments and annotations. Also, Tripal and its extension modules provided loaders for commonly used file formats such as FASTA, GFF, OBO, GAF, BLAST XML, KEGG heir files and InterProScan XML. Default generic templates were provided for common views of biological data, which could be customized using an open Application Programming Interface to change the way data are displayed. Here, we report additional tools and functionality that are part of release v1.1 of Tripal. These include (i) a new bulk loader that allows a site curator to import data stored in a custom tab delimited format; (ii) full support of every Chado table for Drupal Views (a powerful tool allowing site developers to construct novel displays and search pages); (iii) new modules including 'Feature Map', 'Genetic', 'Publication', 'Project', 'Contact' and the 'Natural Diversity' modules. Tutorials, mailing lists, download and set-up instructions, extension modules and other documentation can be found at the Tripal website located at http://tripal.info. DATABASE URL: http://tripal.info/.

Indexed as

Databases, GeneticInternetSoftwareGenetic VariationGenomeGenomicsGenotypePlantsPublicationsReference StandardsSeedsUser-Computer Interface

Identifiers

PMID24163125
PMCPMC3808541

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.