merge GPRs to devel #12
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Apply the changes in GPRs branch to modelIntegration
Convert Recon3D grRules to be compatible with HMR, by replacing with Ensembl ids and converging multiple suffix versions into one in the field. The fields genes and rxnGeneMat are also updated.
Upload associated reaction pairs between HMR2 and Recon3D that are detected from the merged model of the two, in which the Recon3D model was modified into RAVEN format with applying comprehensive association to HMR metabolites.
There are some Recon3D mets are found as duplicates after associating with HMR2 mets. This script aims to remove the duplicate mets according to met ids.
This model structure has updated met relevant fields. The S matrix was also updated by converging multiple rows of duplicate mets into one.
In HMR2, metabolite m00196 refers to 'general protein'. It was directly taken by Recon3D and adopted as 'M00196'. However, Recon3D includes another 'general protein' metabolite as 'protein_c'. Here the two mets are associated together to m00196 in HMR2.
To assist convenient model integration, this script aims to generate a data structure (metAssoc) with one-to-one met assocation between HMR2 and Recon3D from the manually curated data structure metAssocHMR2Recon3.mat.
Split the script by moving the metAssoc.mat generating section out and turn it into a separate script.
Change metNames for 'phacgly_s' and 'phacgly_c' from 'Phenylacetylglycine' to Phenylacetylglycine_phacgly' to avoid duplication
Function is currently hard-coded to work with HMR, iHsa, and Recon3D models, but can be generalized to any models in future versions.
- Removal of confirmed pseudogenes - Replace some Ensembl IDs - Update gene-related fields to the model - Rename the model from HMR to humanGEM
haowang-bioinfo
added a commit
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Mar 28, 2022
- This is to fix the issue reported in Mouse-GEM issue #12
haowang-bioinfo
added a commit
that referenced
this pull request
Mar 28, 2022
- This is to fix the issue reported in Mouse-GEM issue #12
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