Migration Workflow

1. In mondo-ingest GitHub, navigate to src/ontology/slurp
2. Open slurp tsv file in google docs, such as https://github.com/monarch-initiative/mondo-ingest/blob/main/src/ontology/slurp/ordo.tsv.
3. Open file in google docs as a google spreadsheet
4. View each term to check if it is already in Mondo or if there is something similar - if so, add the source dbxref and add that term to the exclusion list* and delete the row.
5. Add a column in column H for SC_source (G1) and add >A oboInOwl:source SPLIT=| in G2. Add your ORCID as the source (eg https://orcid.org/0000-0001-5208-3432)
6. If it is a term term that should be added, add the ID for the parent in column G (in most cases, we should reclassify the term.)
7. When the spreadsheet is ready, merge the terms into Mondo using the ROBOT merge template workflow.

See example spreadsheet here.

*Exclusion list
- Google doc

Note

The google doc will be automatically uploaded to this TSV file via a pipeline.

Weekly Workflow

1. Review mappings
2. Go to https://github.com/monarch-initiative/mondo-ingest/blob/main/src/ontology/lexmatch/README.md
3. Review all tables named unmapped_%_lex (for example, unmapped_omim_lex) and unmapped_%_lex_exact (for example, unmapped_omim_lex_exact)
4. Process tables as usually
5. Migrate terms
6. go to link: https://github.com/monarch-initiative/mondo-ingest/tree/main/src/ontology/slurp
7. For a ontology X (eg OMIM), if (and only if) there are no unmapped terms according to the previous step, process as usual. IMPORTANT: it is not enough if you have processed all the unmapped terms, the tables need to be empty on GitHub.
8. Mapping reconcilliation
9. In process, Nico and Harshad are working on this