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ePlant in 2021: New Species, Viewers, Data Sets, and Widgets

Waese-Perlman, B.; Pasha, A.; Ho, C.; Azhieh, A.; Liu, Y.; Sullivan, A.; Lau, V.; Esteban, E. N.; Waese, J.; Ly, G.; Hooper, C.; Stanton, S. E.; Brereton, N. J. B.; Le, C.; Nelson, R.; Lumba, S.; Goodstein, D. M.; Millar, A. H.; Parkin, I.; Lukens, L. N.; Ehlting, J.; Rieseberg, L.; Pitre, F.; Brown, A.; Provart, N. J.

2021-04-29 bioinformatics
10.1101/2021.04.28.441805 bioRxiv
Show abstract

ePlant was introduced in 2017 for exploring large Arabidopsis thaliana data sets from the kilometre to nanometre scales. In the past four years we have used the ePlant framework to develop ePlants for 15 agronomically-important species: maize, poplar, tomato, Camelina sativa, soybean, potato, barley, Medicago truncatula, eucalyptus, rice, willow, sunflower, Cannabis sativa, wheat and sugarcane. We also updated the interface to improve performance and accessibility, and added two new views to the Arabidopsis ePlant - the Navigator and Pathways viewers. The former shows phylogenetic relationships between homologs in other species and their expression pattern similarities, with links to view data for those genes in the respective ePlants. The latter shows Plant Reactome metabolic reactions. We also describe new Arabidopsis data sets including single cell RNA-seq data from roots, and how to embed ePlant eFP expression pictographs into any web page.

Matching journals

The top 8 journals account for 50% of the predicted probability mass.

1
Bioinformatics
◐ 1204 papers in training set
Top 2%
11.8%
Similar papers in this journal
2
Plant Physiology
◐ 238 papers in training set
Top 0.7%
9.6%
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3
Frontiers in Plant Science
○ 256 papers in training set
Top 1%
7.2%
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4
Plant Direct
○ 95 papers in training set
Top 0.5%
5.4%
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5
Plant Communications
○ 36 papers in training set
Top 0.1%
5.1%
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6
Journal of Open Source Software
● 25 papers in training set
Top 0.1%
4.4%
7
Applications in Plant Sciences
○ 23 papers in training set
Top 0.1%
3.5%
8
Bioinformatics Advances
◐ 203 papers in training set
Top 2%
3.4%
50% of probability mass above
9
GigaScience
◐ 212 papers in training set
Top 1%
3.4%
10
in silico Plants
◐ 27 papers in training set
Top 0.1%
3.2%
11
Methods in Ecology and Evolution
○ 176 papers in training set
Top 0.8%
2.4%
12
PeerJ
◐ 308 papers in training set
Top 4%
2.4%
13
Database
◐ 61 papers in training set
Top 0.4%
1.9%
14
PLOS ONE
● 5266 papers in training set
Top 45%
1.9%
15
Nucleic Acids Research
◐ 1281 papers in training set
Top 8%
1.9%
16
BMC Bioinformatics
○ 457 papers in training set
Top 4%
1.7%
17
The Plant Journal
○ 215 papers in training set
Top 2%
1.7%
18
PLOS Computational Biology
● 1863 papers in training set
Top 15%
1.4%
19
Physiologia Plantarum
○ 39 papers in training set
Top 0.9%
1.4%
20
eLife
● 5828 papers in training set
Top 56%
1.3%
21
Frontiers in Genetics
○ 230 papers in training set
Top 4%
1.1%
22
NAR Genomics and Bioinformatics
◐ 242 papers in training set
Top 3%
1.1%
23
Scientific Data
○ 209 papers in training set
Top 3%
0.8%
24
Frontiers in Bioinformatics
○ 49 papers in training set
Top 1%
0.8%
25
G3: Genes, Genomes, Genetics
◐ 252 papers in training set
Top 4%
0.8%
26
Frontiers in Bioengineering and Biotechnology
○ 98 papers in training set
Top 3%
0.6%
27
Scientific Reports
○ 3612 papers in training set
Top 77%
0.6%
28
Computational and Structural Biotechnology Journal
● 242 papers in training set
Top 8%
0.6%
29
Plant Methods
○ 42 papers in training set
Top 1.0%
0.6%
30
Genome Biology
○ 637 papers in training set
Top 10%
0.6%

"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.