zhanglab / psamm-model-collection Goto Github PK

In the master branch, some models imported from SBML have invalid compartment specifications. This means that the models cannot be loaded correctly by PSAMM and trying to do so will result in error like

psamm.datasource.native.ParseError: Invalid compartment periplasm referenced by compartment Cytosol, Extra_organism

This error stems from an error in the original SBML file where the compartments are referenced using an invalid ID. However, this issue should be fixed so that psamm-import ignores the error in the original SBML files and the models can be used with PSAMM.

While reading .yaml files for indexing with Elasticsearch, I found syntax errors in genes fields of 8 models similar to the following errors:

iSyn731/reactions.yaml:
-  genes: (sll1102 and sll1103and sll1104)
+  genes: (sll1102 and sll1103 and sll1104)
iRS1597/reactions.yaml:
-  genes: AT2G28850 or AT2G28860 or or AT2G34490 or AT2G34500
+  genes: AT2G28850 or AT2G28860 or AT2G34490 or AT2G34500

git-diff for my modifications produces more than 200 lines, I can copy-paste them here or make a pull request but I'm not sure with many of my changes, for example whether the following added operator should be and or or:

iCB925/reactions.yaml:
-  genes: ( Cbei_0661 Cbei_2182 )
+  genes: ( Cbei_0661 or Cbei_2182 )

I also have noticed that all models do not have unique names defined. e.g. name SBML is used in about a dozen of models.