It is worth exploring whether there are better alternatives to insect KEGG pathway annotation than KOBAS since when we developed the pipeline ~5 years ago.

General considerations:

• have other databases/entities started annotating Refseq proteins with KEGG pathways? (e.g. KEGG itself; uniprot)
  • eggnog is often wrong wrt finding orthologs
• what software programs exist that we could use, instead? Create list with pros and cons.
• should we explore using flybase pathway annotations? (are they free; machine readable?)? Wormbase? Alliance?

Software considerations:

• Is the software maintained?
• Is it already used/adopted by the bioinformatics community?
• Is the pathway annotation transferred directly from the entity that was curated to the new protein, or are there intermediate steps?

Other considerations:

• InterProScan is not adding Reactome data anymore via AgBase; script to add it is broken. (How does Interproscan actually assign the Reactome data to proteins?)