—- This page was updated on 17 and 21 August 2012 with recommendations from @BMC_series and others. I will make further changes if necessary so please contact me if you have any suggestions —-
When reviewing the recent GARNet workshop Making Data Accessible to All, we thought it was a good idea to collate the important bioscience databases on the web. I set to work and came up with the table below.
GARNet are keen to get an impression of how the plant science community actually use online databases, so please use the form at the end of this post to let us know how you use these types of resources. Do you deposit data in them, use them to guide practical work, or build whole research projects around them?
You’ll notice there are some blank spaces – if you know a resource that can fill it, please let me know. Likewise if you think I’ve got something wrong (I have personally worked with only a handful of these resources!) or missed off your favourite database, please leave a comment, tweet me or use the form below to tell me about it.
|Data type||Main repository||Plant repository||Data standards, minimum information guidelines||General journal requirement||Other repositories|
|Genes and gene nomenclature||Genbank||TAIR||Genbank, TAIR||Submission to Genbank, or TAIR for plant journals|
|Genome sequence||Genbank||TAIR||MIGS (Field et al., 2008)||Submission to Genbank||EMBL|
|DNA barcodes||EMBL||Barcode of Life standards||BOLD|
|RNA sequences||EMBL||BCB RNA-seq||RefSeq|
|Chip sequencing||GEO||Minseq(draft), GEO||Submission to GEO||Sequence read archive, IRC|
|Transcriptomics||GEO||NASC||MIAME||Submission to GEO or Array Express||Array Express, PLEXdb, EFP Browser *|
|Protein structure and sequence||PDB||Plant PDB||Submission to PDB, PIR||Protein, PIR|
|Proteomics||GEO||MASCP-Gator||MIAPE (Taylor et al., 2007)||Submission to GEO, SwissProt||PRIDE, Protein, Plant PDB, EMBL|
|Metabolomics||BMRBiHUB (Ionomics)||PMN||MSI||Submission to BMRB||Metabolome Express|
|Epigenomics||NCBI Epigenomics||MINSEQE(draft), NCBI||Chromatin.csl|
|Interactions||IMEX||TAIR||IntAct||Submission to IMEX||IntAct, Reactome (no Arabidopsis data yet)|
|Mathematical models||Biomodels.net||PlaSMo||Model file: MIRIAM
Model experiment: MAISE
|Pathway information||BioCyc||TAIR: AraCyc||Biogrid
Reactome (no Arabidopsis data yet)
|Synthetic biology||Parts registry||Parts registry||SBOL|
* To add data to EFP Browser, go to the development page.