-
Notifications
You must be signed in to change notification settings - Fork 6
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Annotating models with the genome identifier #96
Comments
There is a ncbi_assembly id column in the genome table of BiGG DB, however, it appears to be empty. Additionally there are accession_type and accession_value columns, where accession_type is currently one of ncbi_accession or ncbi_assembly. From what I've gathered from BiGG, neither these accessions nor the taxon ids appear in any other place, so retrieving RefSeq annotations would likely require to fetch the corresponding entry from GenBank. |
Had another look at the data BiGG provides and this is actually easy to do, albeit with some issues regarding the MIRIAM compliance. Must have been half asleep when looking at the issue last time... All accession starting with NC_ or NZ_ can be converted to MIRIAM compliant URIs.
Edit: Just realized we have a INCLUDE_ANY_URI flag we could use here. |
Implemented as described above in 2.1. branch. |
@Midnighter requests at SBRG/bigg_models#368:
Many models in BiGG are currently annotated with a taxonomic identifier and a reference to the model itself, for example, as shown below.
On the website, BiGG also provides a link to the genome sequence that was used to create the model, see, for example, http://bigg.ucsd.edu/models/iML1515.
Where possible, it would be great to also create MIRIAM compliant annotations of the genome on the model using the identifier from the genome database or RefSeq namespaces as defined at Identifiers.org.
Is this a task for ModelPolisher?
The text was updated successfully, but these errors were encountered: