Document the workflow for refreshing DOSDP patterns where CHEBI and PRO are involved

[matentzn]

CHEBI, NCBITAXON and PRO are too large to be managed easily as standard imports. To mitigate this situation, we have decided to manage these as slims which are located here:

• NCBITAXON: https://github.com/obophenotype/ncbitaxon/tree/master/subsets
• PRO: https://github.com/obophenotype/pro_obo_slim
• CHEBI: https://github.com/obophenotype/chebi_obo_slim

Sometimes, a new term you are using in a DOSDP pattern is not yet in a slim. So you will have to refresh the slim first. NCBITaxon is too complicated, so for now, you have to request a refresh on the issue tracker.

Refresh PRO Slim:

Note: you will need at least 32 GB RAM for this

git clone https://github.com/obophenotype/pro_obo_slim
cd pro_obo_slim
git checkout refresh20230312 -b
# Add your terms to seed.txt, and then SORT THE FILE
sh odk.sh make all
git commit -a -m "refresh slim after adding terms for OBA"
git push --set-upstream origin refresh20230312

When this is done, make a PR. Feel free to merge it yourself (no need to ask for a review).

Refresh CHEBI Slim

git clone https://github.com/obophenotype/chebi_obo_slim
cd chebi_obo_slim
# Follow the instructions for the PRO slim from here

The full process of refreshing the DOSDP patterns:

1. Check if new PRO / Chebi terms are not in SLIM, if they are not, add them as described above.
2. Run sh run.sh make IMP=false MIR=false ../patterns/definitions.owl to generate a new pattern ontology component
3. Run sh run.sh make refresh-merged to import the new terms
4. Run sh run.sh make IMP=false MIR=false ../patterns/definitions.owl again to generate the labels correctly where new terms are concerned.

@ar-ibrahim

• Please add a nicely readable version of the above to https://github.com/obophenotype/bio-attribute-ontology/blob/master/docs/editors-guide.md and test it so that we are sure you understand it. (note for Added new 'growth factor' terms #227 I have already refreshed the pro slim).