Evidence map›Paper›PMID 34010390›Full record

ArticleDatabase : the journal of biological databases and curation2021

Integration of 1:1 orthology maps and updated datasets into Echinobase.

Saoirse Foley, Carolyn Ku, Brad Arshinoff, Vaneet Lotay, Kamran Karimi, Peter D Vize, Veronica Hinman

Open access · goldAbstract read
In one paragraph

Article in Database : the journal of biological databases and curation, 2021. 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
2.2field-weighted citation impact, top 13% 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, 10 citations in OpenAlex.

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  6. A nomenclature for echinoderm genes.Database : the journal of biological databases and curation · 2021
    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 at 2 institutions in 2 countries.

Saoirse FoleyDepartment of Biological Sciences, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA.ORCID 0000-0002-1791-2837
Carolyn KuDepartment of Biological Sciences, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA.
Brad ArshinoffDepartment of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta TN2 1N4, Canada.
Vaneet LotayDepartment of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta TN2 1N4, Canada.
Kamran KarimiDepartment of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta TN2 1N4, Canada.
Peter D VizeDepartment of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta TN2 1N4, Canada.
Veronica HinmanDepartment of Biological Sciences, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA.
University of Calgary · CACarnegie Mellon University · US

Funding

Software Development to Enhance EchinobaseP41HD095831 · NICHD · UNIVERSITY OF FLORIDA · PI CHARLES A. ETTENSOHN, Veronica Frances Hinman · 2018 to 2026
$6.5M
NICHD NIH HHS P41 HD095831
6 · The paper itself

Abstract

Echinobase (https://echinobase.org) is a central online platform that generates, manages and hosts genomic data relevant to echinoderm research. While the resource primarily serves the echinoderm research community, the recent release of an excellent quality genome for the frequently studied purple sea urchin (Strongylocentrotus purpuratus genome, v5.0) has provided an opportunity to adapt to the needs of a broader research community across other model systems. To this end, establishing pipelines to identify orthologous genes between echinoderms and other species has become a priority in many contexts including nomenclature, linking to data in other model organisms, and in internal functionality where data gathered in one hosted species can be associated with genes in other hosted echinoderms. This paper describes the orthology pipelines currently employed by Echinobase and how orthology data are processed to yield 1:1 ortholog mappings between a variety of echinoderms and other model taxa. We also describe functions of interest that have recently been included on the resource, including an updated developmental time course for S.purpuratus, and additional tracks for genome browsing. These data enhancements will increase the accessibility of the resource to non-echinoderm researchers and simultaneously expand the data quality and quantity available to core Echinobase users. Database URL: https://echinobase.org.

Indexed as

EchinodermataGenomeAnimalsDatabases, FactualDatabases, GeneticGenomics

Identifiers

PMID34010390
PMCPMC8132956
OpenAlexW3163423203

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.