'MISSING MIREOT TERMS ERROR' that can't be resolved

[shbrief]

Hi! I have an issue with the extract function on EFO. Here is the script I used:

wget http://www.ebi.ac.uk/efo/efo.obo
robot extract --method MIREOT \
    --input efo.obo \
    --branch-from-term "EFO:0000408" \
    --output cmd_disease_EFO_enums.owl

... and the error message I got:

MISSING MIREOT TERMS ERROR either lower term(s) or branch term(s) must be specified for MIREOT
For details see: http://robot.obolibrary.org/extract#missing-mireot-terms-error
Use the -vvv option to show the stack trace.
Use the --help option to see usage information.

I double-checked that the above efo.obo file contains 'EFO:0000408'. Are there any suggestions on how to resolve this? Thanks!

-Sehyun

[jamesaoverton]

Hmm. Please try using the full IRI for your EFO term, or defining a prefix for EFO: http://robot.obolibrary.org/global#prefixes.

[shbrief]

It works with the full IRI ("http://www.ebi.ac.uk/efo/EFO_0000408"). It turned out obo_context.jsonld doesn't include EFO. Thanks!

[jamesaoverton]

Glad that it worked! Yes, EFO is not an OBO ontology, although it is quite similar and makes wide use of OBO terms and techniques.