Online resources for sharing and viewing data

by Charis Cook
Categories: methods, synthetic biology, systems biology
Tags: , , ,
Comments: 1 Comment
Published on: August 15, 2012

—-  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

 PLoS one

Molecular Systems Biology

 Biomodels

CellML
Pathway information BioCyc TAIR: AraCyc

Reactome (no Arabidopsis data yet)
Synthetic biology Parts registry Parts registry SBOL

* To add data to EFP Browser, go to the development page.

Your details will not appear on the website.



1 Comment - Leave a comment
  1. quoted on Making Data Accessible to All « « Weeding the GemsWeeding the Gems says:
    October 18, 2012 at 8:19 am

    […] To see the resources and repositories GARNet recommends for sharing different types of data, including plant-specific ones, see this post. […]

    Reply

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