Evidence map›Paper›PMID 32537769›Full record

ArticleAnimal genetics2020

Using online tools at the Bovine Genome Database to manually annotate genes in the new reference genome.

D A Triant, J J Le Tourneau, C M Diesh, D R Unni, M Shamimuzzaman, A T Walsh, J Gardiner, A K Goldkamp, Y Li, H N Nguyen and 11 more

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

Article in Animal genetics, 2020. 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
0.3field-weighted citation impact, top 46% 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

4 citing papers in PubMed, 5 citations in OpenAlex.

  1. Article
  2. International journal of molecular sciences · 2025
    Article
  3. AgAnimalGenomes: browsers for viewing and manually annotating farm animal genomes.Mammalian genome : official journal of the International Mammalian Genome Society · 2023
    Article
  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

21 authors at 8 institutions in 1 country.

D A TriantDivision of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA.
J J Le TourneauDivision of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA.
C M DieshDepartment of Bioengineering, University of California, Berkeley, Berkeley, CA, 94720, USA.
D R UnniDivision of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, 94608, USA.
M ShamimuzzamanDivision of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA.
A T WalshDivision of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA.
J GardinerDivision of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA.
A K GoldkampDepartment of Animal and Food Sciences, Oklahoma State University, Stillwater, OK, 74078, USA.
Y LiDivision of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA.ORCID https://orcid.org/0000-0003-3062-4626
H N NguyenDivision of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA.ORCID https://orcid.org/0000-0003-1084-3725
C RobertsDivision of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA.
Z ZhaoDivision of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA.ORCID https://orcid.org/0000-0002-3627-5503
L J AlexanderUSDA-ARS-PA-Livestock & Range Research Lab, Miles City, MT, 59301, USA.
J E DeckerDivision of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA.
R D SchnabelDivision of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA.ORCID http://orcid.org/0000-0001-5018-7641
S G SchroederUSDA-ARS Animal Genomics and Improvement Lab, Beltsville, MD, 20705, USA.
T S SonstegardAcceligen, Eagan, MN, 55121, USA.
J F TaylorDivision of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA.ORCID http://orcid.org/0000-0002-6997-7245
R M RiveraDivision of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA.ORCID https://orcid.org/0000-0002-9832-9618
D E HagenDepartment of Animal and Food Sciences, Oklahoma State University, Stillwater, OK, 74078, USA.ORCID https://orcid.org/0000-0001-8295-020X
C G ElsikDivision of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA.ORCID https://orcid.org/0000-0002-4248-7713
University of Missouri · USUniversity of Missouri Health System · USOklahoma State University · USAACC International · USAgricultural Research Service · USFort Keogh Livestock and Range Research Laboratory · USLawrence Berkeley National Laboratory · USUniversity of California, Berkeley · US

Funding

European Union's Seventh Framework Programme 613689United States Department of Agriculture Agricultural Research Service 1265-31000-104United States Department of Agriculture National Institute of Food and Agriculture 2013-67015-21202
6 · The paper itself

Abstract

With the availability of a new highly contiguous Bos taurus reference genome assembly (ARS-UCD1.2), it is the opportune time to upgrade the bovine gene set by seeking input from researchers. Furthermore, advances in graphical genome annotation tools now make it possible for researchers to leverage sequence data generated with the latest technologies to collaboratively curate genes. For many years the Bovine Genome Database (BGD) has provided tools such as the Apollo genome annotation editor to support manual bovine gene curation. The goal of this paper is to explain the reasoning behind the decisions made in the manual gene curation process while providing examples using the existing BGD tools. We will describe the sources of gene annotation evidence provided at the BGD, including RNA-seq and Iso-Seq data. We will also explain how to interpret various data visualizations when curating gene models, and will demonstrate the value of manual gene annotation. The process described here can be applied to manual gene curation for other species with similar tools. With a better understanding of manual gene annotation, researchers will be encouraged to edit gene models and contribute to the enhancement of livestock gene sets.

Indexed as

Databases, GeneticGenomeMolecular Sequence AnnotationOnline SystemsAnimalsCattleBos taurusgene predictiongenome annotationgenome annotation toolsRNA-seq

Identifiers

PMID32537769
PMCPMC7540445
OpenAlexW3035735807

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.