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MetabolicAtlas / data-files

Source data files used when deploying Metabolic Atlas

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feat: more models #4

Closed mihai-sysbio closed 3 years ago

mihai-sysbio commented 3 years ago

This PR contains all the new models added to Met Atlas, with some map listing curation as well. @nanjiangshu the new annotation files have been added, they have been renamed to contain -new. The .plain extension used so that these files will not be stored with Git LFS, but with normal versioning.

To do:

[ ] remove old annotation files
[ ] update annotation files for all models (not just Human-GEM)
[ ] update all models

nanjiangshu commented 3 years ago

Hi @mihai-sysbio, I could not find any new annotation files for all models except Human-GEM at https://github.com/SysBioChalmers. Should be wait for the modellers to generate them or are there any available scripts that can we can generate them from the raw data?

For yeast-GEM at https://github.com/SysBioChalmers/yeast-GEM, there is not even a subfolder model. Or is this repo the wrong one?

mihai-sysbio commented 3 years ago

Yeast-GEM is a bit special, not yet following the same setup as Human-GEM and the rest. Work has started in this direction, but for now it seems easiest to ignore Yeast-GEM. The annotations for all models except Yeast-GEM will be mostly the same, so for now it is good enough if the same annotation files are used for these models. @Hao-Chalmers is there any forecast regarding annotations in the new format for all the models derived from Human-GEM?

haowang-bioinfo commented 3 years ago

@mihai-sysbio for now the annotation information unique to animal GEMs are also in tsv files (e.g. mouseSpecificMets.tsv) and deposited in corresponding repos. In the future, these files might be merged together and placed in a centralized repo.

mihai-sysbio commented 3 years ago

@Hao-Chalmers, to be more specific, regarding these tsv files in the different repos at the moment:

the model-specific annotation files do not sit in the /model folder, but in the /data folder instead.
the model-specific annotation files do not have the same headers as the original in Human-GEM.

What I meant in the question above

annotations in the new format for all the models derived from Human-GEM?

was if you have any plans for obtaining annotation files for these models that are identical in path and structure to the ones in Human-GEM?

haowang-bioinfo commented 3 years ago

was if you have any plans for obtaining annotation files for these models that are identical in path and structure to the ones in Human-GEM?

there is no plans for this yet, let me know if you any ideas.

mihai-sysbio commented 3 years ago

@Hao-Chalmers Metabolic Atlas will use this new annotation format from Human-GEM as default, so for the annotation to be picked up for the rest of the models equivalent files will be needed.

haowang-bioinfo commented 3 years ago

@mihai-sysbio sounds good, let's move toward this direction

mihai-sysbio commented 3 years ago

This PR is closed in favour of #8.