The ontoparse CLI

xrefs

Extract cross-references (xrefs) from ontologies. Currenly supports OBO format-version 1.2.

ontoparse xref <FILE> --to <PREFIX> [--from <PREFIX>] [--separator <SEP>]

• Arguments

  • <FILE>: An ontology OBO file.

• Required options

  • --to <PREFIX>: An anchor prefix to map from (e.g, MESH).

• Optional arguments

  • --from <PREFIX>: An anchor prefix to map from (e.g., UBERON). Must contain term entries in the file. Defaults to the most frequent prefix in the file.
  • --separator <SEP>: Delimiter of the output table. Defaults to \t.

Examples

From the primary prefix (i.e., UBERON):

ontoparse xref uberon.obo --to MESH

Or you can specify:

ontoparse xref uberon.obo --to MESH --from UBERON

You can also map from other prefixes if they exist:

ontoparse xref uberon.obo --to MESH --from CL

Write the output to tsv:

ontoparse xref uberon.obo --to MESH > uberon_to_mesh.tsv

You may also change the separator:

ontoparse xref uberon.obo --to MESH --separator "," > uberon_to_mesh.csv