OAK obsoletes command

This notebook is intended as a supplement to the main OAK CLI docs.

This notebook provides examples for the obsoletes command, which shows all obsolete entities in an ontology, plus associated metadata

Help Option

You can get help on any OAK command using --help

!runoak obsoletes --help

Usage: runoak obsoletes [OPTIONS] [TERMS]...

  Shows all obsolete entities.

  Example:

      runoak -i obolibrary:go.obo obsoletes

  To exclude *merged terms*, use the ``--no-include-merged`` flag

  Example:

      runoak -i obolibrary:go.obo obsoletes --no-include-merged

  To show migration relationships, use the ``--show-migration-relationships``
  flag

  Example:

      runoak -i obolibrary:go.obo obsoletes --show-migration-relationships

  You can also specify terms to show obsoletes for:

  Example:

      runoak -i obolibrary:go.obo obsoletes --show-migration-relationships
      GO:0000187 GO:0000188

Options:
  --include-merged / --no-include-merged
                                  Include merged terms in output  [default:
                                  include-merged]
  --show-migration-relationships / --no-show-migration-relationships
                                  Show migration relationships (e.g.
                                  replaced_by, consider)  [default: no-show-
                                  migration-relationships]
  -O, --output-type [obo|obojson|ofn|rdf|json|yaml|fhirjson|csv|nl]
                                  Desired output type
  -o, --output FILENAME           Output file, e.g. obo file
  --help                          Show this message and exit.

alias cl runoak -i sqlite:obo:cl

cl obsoletes > output/cl-obsoletes.tsv

!head output/cl-obsoletes.tsv

cl obsoletes --show-migration-relationships > output/cl-obsoletes-full.tsv

!head output/cl-obsoletes-full.tsv