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Add new logical definitions to HPO using DOSDPs

Nicole Vasilevsky edited this page Mar 20, 2019 · 2 revisions
  1. If a pattern exists for the logical definition you want to add, go to your local hpo directory/src/patterns/data/default
  2. If a TSV file for your pattern does not already exist, create a new TSV file, or open the existing file.
  3. If you create a new TSV file, name it after the pattern name, e.g., abnormalBiologicalProcessInLocation.tsv
  4. 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
  1. Fill in the appropriate data in the cells, ie the HPO ID, label, and the curie (or IRI) and labels for the vars
  2. Save and commit the file
  3. If you created a new TSV file, open your local hpo directory/src/patterns/dosdp-patterns/external.txt
  4. Copy and paste the last line
  5. 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)
  6. The logical definition will be incorporated the next time the pipeline is run.