Hi!
Thank you for creating this tool, I think it has great potential!
I have been working on a model and decided to use your tool to add cross-references to the metabolites and reactions. Your tool is in general doing a great job, but I have noticed some issues... When I tried to upload the model to BioModels they told me that there were several invalid URIs because they are not written in the correct format according to 'identifiers.org'. I created my model initially with CarveMe, which is based on the syntax of the BiGG database.
Here are some examples and what they should be according to the latest standard:
https://identifiers.org/seedm/- -> https://identifiers.org/seed.compound/-
https://identifiers.org/biggm/- -> https://identifiers.org/bigg.metabolite/-
https://identifiers.org/reactomem/- -> https://identifiers.org/reactome/-
...
Also, for pubchem, it is creating invalid URIs because it doesn't split the elements into two parts:
Example: https://identifiers.org/pubchem.compound/9547068 46891690
Correct: https://identifiers.org/pubchem.compound/9547068 and https://identifiers.org/pubchem.compound/46891690
...
In addition, several exchange reactions have been given metadata for transport reactions and vice-versa:
R_EX_4abut_e
<rdf:li rdf:resource="https://identifiers.org/bigg.reaction/4ABUTth"/> (This is a corrected URI)
For other people who want to add their models to BioModels it would be nice if you could look into these issues. :) I guess it should not be too difficult to fix.
Best regards,
Idun Burgos
Hi!
Thank you for creating this tool, I think it has great potential!
I have been working on a model and decided to use your tool to add cross-references to the metabolites and reactions. Your tool is in general doing a great job, but I have noticed some issues... When I tried to upload the model to BioModels they told me that there were several invalid URIs because they are not written in the correct format according to 'identifiers.org'. I created my model initially with CarveMe, which is based on the syntax of the BiGG database.
Here are some examples and what they should be according to the latest standard:
https://identifiers.org/seedm/- -> https://identifiers.org/seed.compound/-
https://identifiers.org/biggm/- -> https://identifiers.org/bigg.metabolite/-
https://identifiers.org/reactomem/- -> https://identifiers.org/reactome/-
...
Also, for pubchem, it is creating invalid URIs because it doesn't split the elements into two parts:
Example: https://identifiers.org/pubchem.compound/9547068 46891690
Correct: https://identifiers.org/pubchem.compound/9547068 and https://identifiers.org/pubchem.compound/46891690
...
In addition, several exchange reactions have been given metadata for transport reactions and vice-versa:
R_EX_4abut_e
<rdf:li rdf:resource="https://identifiers.org/bigg.reaction/4ABUTth"/> (This is a corrected URI)
For other people who want to add their models to BioModels it would be nice if you could look into these issues. :) I guess it should not be too difficult to fix.
Best regards,
Idun Burgos