Evidence map›Paper›PMID 32621602›Full record

ArticleDatabase : the journal of biological databases and curation2020

Tripal and Galaxy: supporting reproducible scientific workflows for community biological databases.

Shawna Spoor, Connor Wytko, Brian Soto, Ming Chen, Abdullah Almsaeed, Bradford Condon, Nic Herndon, Heidi Hough, Sook Jung, Meg Staton and 4 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Database : the journal of biological databases and curation, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing 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

2 citing papers in PubMed.

  1. Article
  2. 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

14 authors.

Shawna SpoorDept of Horticulture, Washington State University, 149 Johnson Hall 646414, Pullman, WA 99164-6414, USA.
Connor WytkoDept of Horticulture, Washington State University, 149 Johnson Hall 646414, Pullman, WA 99164-6414, USA.
Brian SotoDept of Horticulture, Washington State University, 149 Johnson Hall 646414, Pullman, WA 99164-6414, USA.
Ming ChenEntomology and Plant Pathology, University of Tennessee, 2505, 370 E J. Chapman Dr Plant Biotechnology Building, Knoxville, TN 37996, USA.
Abdullah AlmsaeedEntomology and Plant Pathology, University of Tennessee, 2505, 370 E J. Chapman Dr Plant Biotechnology Building, Knoxville, TN 37996, USA.
Bradford CondonEntomology and Plant Pathology, University of Tennessee, 2505, 370 E J. Chapman Dr Plant Biotechnology Building, Knoxville, TN 37996, USA.
Nic HerndonDept of Computer Science, East Carolina University, College of Engineering and Technology East 5th Street Greenville, NC 27858-4353, USA.
Heidi HoughDept of Horticulture, Washington State University, 149 Johnson Hall 646414, Pullman, WA 99164-6414, USA.
Sook JungDept of Horticulture, Washington State University, 149 Johnson Hall 646414, Pullman, WA 99164-6414, USA.
Meg StatonEntomology and Plant Pathology, University of Tennessee, 2505, 370 E J. Chapman Dr Plant Biotechnology Building, Knoxville, TN 37996, USA.
Jill WegrzynEcology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, Unit 3043 Storrs, CT 06269-3043, USA.
Dorrie MainDept of Horticulture, Washington State University, 149 Johnson Hall 646414, Pullman, WA 99164-6414, USA.
F Alex FeltusDept of Genetics and Biochemistry, Clemson University, 154 Poole Agricultural Center Clemson, SC 29634, USA.
Stephen P FicklinDept of Horticulture, Washington State University, 149 Johnson Hall 646414, Pullman, WA 99164-6414, USA.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Online biological databases housing genomics, genetic and breeding data can be constructed using the Tripal toolkit. Tripal is an open-source, internationally developed framework that implements FAIR data principles and is meant to ease the burden of constructing such websites for research communities. Use of a common, open framework improves the sustainability and manageability of such as site. Site developers can create extensions for their site and in turn share those extensions with others. One challenge that community databases often face is the need to provide tools for their users that analyze increasingly larger datasets using multiple software tools strung together in a scientific workflow on complicated computational resources. The Tripal Galaxy module, a 'plug-in' for Tripal, meets this need through integration of Tripal with the Galaxy Project workflow management system. Site developers can create workflows appropriate to the needs of their community using Galaxy and then share those for execution on their Tripal sites via automatically constructed, but configurable, web forms or using an application programming interface to power web-based analytical applications. The Tripal Galaxy module helps reduce duplication of effort by allowing site developers to spend time constructing workflows and building their applications rather than rebuilding infrastructure for job management of multi-step applications.

Indexed as

Database Management SystemsDatabases, GeneticInternetSoftwareComputational Biology

Identifiers

PMID32621602
PMCPMC7334887

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.