- In mondo-ingest GitHub, navigate to src/ontology/slurp
- Open slurp tsv file in google docs, such as https://github.com/monarch-initiative/mondo-ingest/blob/main/src/ontology/slurp/ordo.tsv.
- Open file in google docs as a google spreadsheet
- 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.
- 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)
- 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.)
- When the spreadsheet is ready, merge the terms into Mondo using the ROBOT merge template workflow.
See example spreadsheet here.
- Google doc
The google doc will be automatically uploaded to this TSV file via a pipeline.
- Review mappings
- Go to https://github.com/monarch-initiative/mondo-ingest/blob/main/src/ontology/lexmatch/README.md
- Review all tables named
- Process tables as usually
- Migrate terms
- go to link: https://github.com/monarch-initiative/mondo-ingest/tree/main/src/ontology/slurp
- 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.
- Mapping reconcilliation
- In process, Nico and Harshad are working on this