Lessons learned from troubleshooting ROBOT¶
- Review tutorial on Ontology pipelines with ROBOT and SPARQL
Learn common mistakes when using ROBOT and how to troubleshoot and fix them.
Copying-pasting (especially in google docs) can introduce unexpected format changes in row 2 of the template:¶
- Note that these format changes are not always visible.
- The most common typos are:
- introduction of space in cells
- single quotes are changed into apostrophes
- These errors are most commonly reported as "MANCHESTER PARSE ERROR"
Restrictions for the first 2 rows of a ROBOT template:¶
- In the same column, it is OK to have a header string (row #1) with no template string (row #2).
- the information in the column is useful to curators (e.g. term labels) but will be ignored by ROBOT.
- In the same column, if there is a template string (row #2), there MUST be a header string (row #1)
- if the row #1 is missing, the error will be reported as: COLUMN MISMATCH ERROR the template string in column 1 must have a corresponding header in table "tmp/merge_template.tsv”
The content of the template break some OBO or Protege rules¶
- for example, Protege only allows one comment on a class. If you are adding new comments to terms via ROBOT, you will get an error if a comment already exists on a term.
- error will be reported as: OBO STRUCTURE ERROR Ontology does not conform to OBO structure rules: multiple comment tags not allowed.
- Note: If you run ROBOT and get an error, it may create a blank file. You need to discard the changes and/or open a new branch. The error with the optional “null” is when the mondo-edit file is empty.
Optional.get() cannot be called on an absent value
Use the -vvv option to show the stack trace.
Use the --help option to see usage information
make: *** [mondo.Makefile:454: merge_template] Error 1
New ID prefix:¶
- ROBOT template can be used to add axioms containing terms (and IDs) from other ontologies which were recently imported
- The ID prefix is not recognized by ROBOT, and the error is reported as MANCHESTER PARSE ERROR
- Resolution: the ontology Makefile should be updated to include the prefix in the merge_template.
- Note: If you run ROBOT and get an error, it may create a blank file. You need to discard the changes and/or open a new branch.