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Add new logical definitions to HPO using DOSDPs
Nicole Vasilevsky edited this page Mar 20, 2019
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- If a pattern exists for the logical definition you want to add, go to your local hpo directory/src/patterns/data/default
- If a TSV file for your pattern does not already exist, create a new TSV file, or open the existing file.
- If you create a new TSV file, name it after the pattern name, e.g., abnormalBiologicalProcessInLocation.tsv
- The column headers should be labeled as following:
- A: defined_class = this is the HPO ID (curie)
- B: defined_class_label = this is the HPO label, for your reference onloy
- C: var1 = this should match the var in the pattern, such as biological_process
- D: var1_label = this is for your reference only, for example, biological_process_label
- E: var2 = this should match the var in the pattern, such as location
- F: var1_label = this is for your reference only, for example, location_label
- Fill in the appropriate data in the cells, ie the HPO ID, label, and the curie (or IRI) and labels for the vars
- Save and commit the file
- If you created a new TSV file, open your local hpo directory/src/patterns/dosdp-patterns/external.txt
- Copy and paste the last line
- Update the line to include the pattern name that for which you just created the TSV file (ie http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalBiologiaclProcessInLocation.yaml)
- The logical definition will be incorporated the next time the pipeline is run.