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ModelSEED / Model-SEED-core

The Model SEED is a tool for building, curating, and analyzing gonome-scale metabolic models. Visit the Model SEED homepage for installation instructions and full feature documentation.
http://bionet.mcs.anl.gov/index.php/Model_SEED_Homepage
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Using private biochemistry databases #22

Closed samseaver closed 12 years ago

samseaver commented 12 years ago

So, I've installed the KEGG and MetaCyc databases as models, with their own private databases. However, when I install MetaCyc, I use the KEGG private database thus:

bash ModelDriver.sh importmodel?MetaCyc?83333.1?seaver?/Users/seaver/Documents/Projects/Model_Import_Files/?1?/Users/seaver/Software/Model-SEED-core/models/seaver/KEGGimport.2/0/biochemistry/

This runs and completes. However, an analysis of the output shows that the process for MetaCyc didn't completely use the KEGG database.

1) When KEGG installed, it found new compounds and reactions thus:

New:cpd80000 for C06816 New:rxn80000 for R00001

When MetaCyc installed, it found new compounds and reactions thus:

New:cpd80000 for 28-Homocastasterone-Sulfates New:rxn80000 for CHONDROITIN-4-SULFOTRANSFERASE-RXN

Given that it's using the KEGG private metabolic database and we're working towards the reconcilation of metabolic models, the first temporary compound and reaction id for the MetaCyc database should be the last one for the KEGG database, plus one.

2) The installation process for MetaCyc did not find any compounds that were in the new KEGG database, and were not already in the initial biochemistry database. In other words, it did not find any new compounds with a temporary id. There's a chance that this is not a bug, but given the size of the two databases, I doubt it.

However, it did find reactions with a temporary id from the new KEGG database. ie:

Found:rxn80428 for RXN-12014

samseaver commented 12 years ago

I fully tested the private biochemistry database, and the use of provenance from other models is now working as expected.