Please add an "Arabidopsis thaliana" model to the species that are already included in Metaboverse.

[RNiloP]

Is your feature request related to a problem? Please describe. I have used A. thaliana models from the specialized literature, but they do not work with Metaboverse.

Describe the solution you'd like Upload a model from Arabidopsis thaliana, such as the one from Arnold and Nikoloski (Bottom-up metabolic reconstruction of Arabidopsis and its application to determining the metabolic costs of enzyme production. Plant physiology. 2014 Jul 1;165(3):1380-91.), Supplemental Data S2.

[stale[bot]]

Is this still relevant? If so, what is blocking it? Is there anything you can do to help move it forward?

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs.

[j-berg]

Making some progress here -- I was able to get the Arabidopsis model into Metaboverse format. Some things we will need to work on though...

1) It does not appear that this network annotates all proteins, genes, etc. explicitly. It annotates components like "taurine importer" and "serine exporter", but no explicit names/IDs, so only metabolomics data consistently will work. 2) The current id and name synonym matching database does not seem to be able to make matches easily to the chosen names and IDs in this network. You can see an example of these IDs here: name_db.csv. We will need to make sure that your data is able to map to these IDs or names. I tried cleaning up some of the names and sending them through MetaboAnalyst and also having troubles getting good matches. However, if your data uses these same names as the network, or can be manually converted, then we should be able to make some progress.