Thomas Zajac

Upon a bit of further investigation annotations for some species reference the same entity, but in different organisms and, as the code to retrieve a BiGGId from annotations currently cannot...

Hi @glucksfall and sorry for the very late response, I started a new job, did not get the notification and haven't had that much time to look into this issue,...

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...

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...

Implemented as described above in 2.1. branch. Leaving open to discuss the correct qualifier.

I moved some of the annotation logic from BiGGAnnotation into separate classes, so Species, Reaction, GeneProduct and Compartment all have their respective Annotation class and could theoretically be annotated directly...