This is a short version of the full information found at http://midasfieldguide.org
The publically available databases are an invaluable resource for the scientific community. However, the curation of a taxonomy over all Bacteria and Archaea is a collosal undertaking we found that many new names were missing from the taxonomy and many of the clades of importance in activated sludge were poorly classified.
The ambition of the MIDAS database is to deliver the best and most updated taxonomy of organisms found in activated sludge ecosystem. The taxonomy strings used are derived from and compatible with the widely-used Greengenes database but is curated mostly at the lower taxonomic levels to improve classification at family and genus level.
The stable releases of the database can be downloaded from the release page.
Initially, the MIDAS taxonomy supports a taxfile for the RDP classifier which we use in the Qiime pipeline.
Simply use midas_taxonomy.txt found in the tax folder as the taxonomy file for running the RDP classifier in place of the standard taxfile
in conjuction with the gg_97_otus_4feb2011.fasta refseq file from Greengenes Feb 2011 release
.
The original database came from the Greengenes Feb 2011 release
A 16S rRNA gene library was made using V1-V3 primers and sequenced with 454 FLX the 400 bp products analysed with Qiime and the the PyNAST aligned 97% OTU representative sequences imported into the ARB database. The sequences were inserted into the reference tree using parsimony insertion. The placement of the short reads was used as a guide for the manual curation of the taxonomy.
Details of the curations are in changelog.txt (in preparation...)
The curated taxonomy was exported from ARB using NDS export of the MSA_id (arb "name" field) and taxonomy fields. The file was reformated to comply with the formatting of the RDP classifier, using the check_rdp_taxfile.py script.
MIDAS: field guide to the microbes of activated sludge by Aaron Saunders, Mads Albertsen, Per Nielsen is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License.
Based on a work at http://greengenes.secondgenome.com/.
