feat: subsystem annotations

[sulheim]

Description of the issue:

In iKS1317 most of the reactions were annotated with both KEGG pathway and KEGG subsystem (header for KEGG pathways), see https://www.genome.jp/kegg/pathway.html. A new annotation should be performed to cover the reactions added from Sco4 and iAA1259.

Additionally, for the reactions without a KEGG identifier it should be possible to acquire the pathway from biocyc? The pathway names acquired from BioCyc should then be translated into the namespace of KEGG to make the annotations more homogenous.

If BioCyc doesn't provide this, maybe we can use the metanetx identfiers?

Expected feature/value/output:

As many reactions as possible annotated with pathway / subsystem. The annotations are currently given as kegg.susbsytem and kegg.pathway, and I think we should continue with these annotations. If the pathway annotation is translated from a biocyc-name, we can include as biocyc.pathway annotation as well.

To do:

• [x] Rerun KEGG pathway and subsystem annotation script to cover new reactions
• [x] Extract pathway annotation for the reactions without KEGG-ID by either using the BioCyc ot metanetx annotation
• [x] Translate the pathway annotations into the KEGG-pathways namespace

I hereby confirm that:

• [x] This problem persists in the master branch of the repository
• [x] A similar issue does not already exist
• [x] I've considered asking this first in the Gitter chat room

[edkerk]

BioCyc pathways are not as neatly formatted as KEGG's. They are typically smaller (so more different pathways) and can have different instances (slight variations): https://biocyc.org/SCO/class-tree?object=Pathways. While not impossible, it is not that trivial to map these to KEGG pathways / subsystems. MetaNetX doesn't seem to connect reactions to KEGG either?

[sulheim]

Your right about MetaNetX at least, no subsystem or pathway annotation is available. However, I think it is possible to bin the BioCyc pathways into the KEGG pathways by combining some automatic mapping based on name with manual curation. It will take some time though

[sulheim]

This is finished, see PR #72