Empty gene names in the xml version

SysBioChalmers / Mouse-GEM

Genome-scale model for Mus musculus

Creative Commons Attribution 4.0 International

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Empty gene names in the xml version #10

Closed OmarAshkar closed 1 year ago

OmarAshkar commented 2 years ago

Description of the issue:

When I read the model I got an error and I cannot find any gene names. I am still trying the model so maybe there are other issues followed.

Expected feature/value/output:

Gene names

Current feature/value/output:

empty string

Reproducing these results:

model = read_sbml_model('data/Mouse-GEM.xml')
## '' is not a valid SBML 'SId'.
## https://identifiers.org/taxonomy/ does not conform to 'http(s)://identifiers.org/collection/id' ## or'http(s)://identifiers.org/COLLECTION:id

I hereby confirm that I have:

[x] Tested my code with all requirements for running the model
[x] Done this analysis in the master branch of the repository
[x] Checked that a similar issue does not exist already
[x] If needed, asked first in the Gitter chat room about the issue

haowang-bioinfo commented 2 years ago

@OAshkar can you try command load_yaml_model for loading instead, see if it helps.

OmarAshkar commented 2 years ago

unfortunately. this does not work at all with the following message

ScannerError: mapping values are not allowed here
  in "data/Mouse-GEM.xml", line 15750, column 110

haowang-bioinfo commented 2 years ago

@OAshkar what I suggested was to load the yml model file as such:

model = load_yaml_model('data/Mouse-GEM.yml')

Sorry for the misunderstanding.

OmarAshkar commented 2 years ago

Alright! I imported the model without errors but still no gene names. For example

model.genes.Adh1.name

haowang-bioinfo commented 2 years ago

The Mouse-GEM is developed by RAVEN and in compliance with its model structure, which has only mandatory field genes for gene ids. We haven't include other alternative gene names (e.g. geneShortNames).

Can you please let us know why do you need gene names? if the information of gene ids is not enough?

OmarAshkar commented 2 years ago

It just makes it easier to interactively find gene names. But it's ok. Thank you for your time.

haowang-bioinfo commented 2 years ago

@OAshkar you probably is suggesting to provide multiple sets of gene ids (Ensembl, NCBI, symbol) in Mouse-GEM?

OmarAshkar commented 2 years ago

I think Ensembl ID would be useful for sure

haowang-bioinfo commented 2 years ago

yes, this will be added in the next release

mihai-sysbio commented 2 years ago

Is there a timeline for the next release?

haowang-bioinfo commented 2 years ago

Is there a timeline for the next release?

aim to have the next in this month

mihai-sysbio commented 2 years ago

@haowang-bioinfo pinging about this in case it may be planned for the next release

haowang-bioinfo commented 1 year ago

fixed in v1.5.0