A minified bioinformatics dataset for seeding Tripal sites
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README.md

README.md

DOI Documentation Status

The DevSeed loader User Guide is available here

Tripal DevSeed logo

Tripal DevSeed is a project for getting data loaded into Chado for your Tripal site quickly and easily. It comes with a 200-gene dataset for Fraxinus excelsior, located in /Fexcel_mini. Additionally, it includes the scripts used to download, minify, and annotate this dataset, located in create_seed. Use these scripts to quickly re-create the F. excelsior dataset, or to create your own.

See the description and credits for the full dataset on Hardwoods Genomics Project.

Loading Data Guide

The full guide for loading DevSeed is available on ReadTheDocs!.

File description

sequences

landmark (scaffold), mRNA, and protein FASTA files. An aligned Newick format tree of the mRNA (mrna_mini.fasta.tree)

gff/

Format: Contig0 FRAEX38873_v2 gene 16315 44054 . + . ID=FRAEX38873_v2_000000010;Name=FRAEX38873_v2_000000010;biotype=protein_coding

blast/

BLAST annotation of mRNA against the SWISSPROT and TrEMBL databases.

ips/

Interproscan annotations using the protein files, in tsv and xml format.

biomaterials/

20 biomaterials (biosamples) randomly generated with the python script generate_biomaterials.py.

expression/

Expression data corresponding to the above biosamples. Included as matrix format files. Created with the python script generate_expression.py.

kegg_annotations

KEGG annotations generated using the KEGG BLAST KOALA web tool.

Annotation Software

The DevSeed dataset was generated using the following software and versions.

License and Contributing

This project is open source and provided under the GPL-3.0 license. It was created by Bradford Condon and Meg Staton from the University of Tennessee Knoxville. If you would like to make a contribution, simply fork the repo and make a pull request from there.

The project "logo" is derived from the collectible card game Hearthstone, copyright © Blizzard Entertainment, Inc. Hearthstone® is a registered trademark of Blizzard Entertainment, Inc. Tripal Alchemist is not affiliated or associated with or endorsed by Hearthstone® or Blizzard Entertainment, Inc.