Checklist for BEL Resource Update

1. Run gp_baseline.py to generate .belns (namespace) and .beleq (equivalence) files, as well as pickled data objects.
   • Check .belns and .beleq files using ns_check.py. This should provide some idea of the quality of the equivalence generation, but pass thresholds still need to be determined.
2. Generate change log for namespaces using change_log.py
   • Requires pickled data objects from gp_baseline run (1) and the previous release gp_baseline run.
   • Need to determine pass thresholds for numbers of unresolved values per namespace. The more frequent the update, the fewer unresolved values should be found.
3. Generate .belanno (annotation) files using belanno.py
4. Run gene_scaffolding.py to generate gene scaffolding resource document
   • Requires HGNC, MGI, and RGD .belns files from gp_baseline run (1)
   • Output file header points to testing namespaces in header
   • Generate .xbel version from output using BEL Framework Document Converter - File is too large to commit to GitHub!
5. Run orthology.py to generate gene-orthology.bel document
   • requires pickled data objects from gp_baseline run (1)
6. Upgrade named-complexes.bel
   • use change_log.json (2) and bel.rb upgrade to update existing .bel document to new namespace version
   • Generate .xbel version from output using BEL Framework Document Converter
7. Upgrade protein-families.bel
   • use change_log.json (2) and bel.rb upgrade to update existing .bel document to new namespace version
   • Generate .xbel version from output using BEL Framework Document Converter
8. Upgrade all sample knowledge
   • use change_log.json (2) and bel.rb upgrade to update existing .bel document to new namespace version
   • Generate .xbel version for the small and large corpuses using BEL Framework Document Converter
9. Update the bel framework index as needed
10. Push all updated files to testing branch, mirror
11. Check compilation of upgraded sample knowledge with new resources
12. Update testing to latest-release
13. Create release notes (new namespaces, any other significant changes), publicize on openbel-discuss