Comments (5)
caufieldjh
commented on September 15, 2024
A very similar error happens when relaxing BERO (Biological and Environmental Research Ontology).
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caufieldjh
commented on September 15, 2024
Same for PR, oddly enough (because that hasn't posed an issue in the past, besides #68 ).
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caufieldjh
commented on September 15, 2024
Also NCBITAXON but that could be a memory issue?
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caufieldjh
commented on September 15, 2024
There was a similar issue before (#15) but that was pretty explicitly due to null values in comment strings.
It's pretty clear that something isn't converting to OBO graph cleanly, and one possibility is that a more recent version of ROBOT handles the remove command differently now so the previously defined process for attempting to fix this no longer works as expected.
This does not work, however (same input ontology as the first example above, for CCO):
robot remove --input /tmp/tmpxpybbnaf --select annotation-properties --exclude-term rdfs:label --exclude-term IAO:0000115 --output transformed/ontologies/CCO/CCO_6_fixed.json -vvv
It still yields the following:
DEBUG Saving ontology as OboGraphs JSON Syntax with to IRI file:/home/harry/BioPortal-to-KGX/transformed/ontologies/CCO/CCO_6_fixed.json
OBO GRAPH ERROR Could not convert ontology to OBO Graph (see https://github.com/geneontology/obographs)
For details see: http://robot.obolibrary.org/errors#obo-graph-error
java.io.IOException: errors#OBO GRAPH ERROR Could not convert ontology to OBO Graph (see https://github.com/geneontology/obographs)
at org.obolibrary.robot.IOHelper.saveOntologyFile(IOHelper.java:1722)
at org.obolibrary.robot.IOHelper.saveOntology(IOHelper.java:846)
at org.obolibrary.robot.CommandLineHelper.maybeSaveOutput(CommandLineHelper.java:667)
at org.obolibrary.robot.RemoveCommand.execute(RemoveCommand.java:202)
at org.obolibrary.robot.CommandManager.executeCommand(CommandManager.java:244)
at org.obolibrary.robot.CommandManager.execute(CommandManager.java:188)
at org.obolibrary.robot.CommandManager.main(CommandManager.java:135)
at org.obolibrary.robot.CommandLineInterface.main(CommandLineInterface.java:61)
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caufieldjh
commented on September 15, 2024
My suspicion is now that this is caused by malformed metadata. Performing the transform from scratch (i.e., removing the temp file and running the following) leads to a successful CCO transform.
$ python run.py --input ~/Bioportal/4store-export-2022-07-20/data/ --kgx_validate --get_bioportal_metadata --ncbo_key [key] --write_curies --include_only fbb225ff0f97d7737e854fd2d48d
Looking for records in /home/harry/Bioportal/4store-export-2022-07-20/data/
Will only include the specified 1 file(s).
1 files found.
Setting up ROBOT...
ROBOT path: /home/harry/BioPortal-to-KGX/robot
ROBOT evironment variables: -Xmx12g -XX:+UseG1GC
Transforming all...
Starting on /home/harry/Bioportal/4store-export-2022-07-20/data/f0/ff/fbb225ff0f97d7737e854fd2d48d
BioPortal metadata not found for CCO_6 - will retrieve.
Accessing https://data.bioontology.org/ontologies/CCO/...
<Response [200]>
Accessing https://data.bioontology.org/ontologies/CCO/latest_submission...
<Response [200]>
Retrieved metadata for CCO (Cell Cycle Ontology)
ROBOT: relax CCO_6
Relaxing /tmp/tmp1pm8qzp3 to transformed/ontologies/CCO/CCO_6_relaxed.json...
Complete.
KGX transform CCO_6
...
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Related Issues (20)
- Aim 2.3.a. Evaluate extent of expected integration between BioPortal ontologies.
- Omit biolink:OntologyClass when assigning new node category
- ValueError: mapping_justification must be supplied HOT 1
- Transform for `ISSVA` fails HOT 1
- Transform for `RDL` fails HOT 4
- General transformation failures for the July 20 2022 data HOT 3
- HGNC type maps incorrect
- UMLS semantic types not being applied HOT 1
- Some prefixes need updates as of Jul 20 2022 BP dump
- Missing IRIs and metadata from many transforms HOT 7
- Convert prefix conversion to use `curies` package HOT 2
- Fix prefixes for OBO:[external resource] HOT 1
- Collision between ATO and ATOL, potentially others of similar names HOT 1
- Produce stats yaml with status and node/edge count of each ontology source HOT 1
- Find alternate solution to SSSOM maps for adding Biolink categories HOT 1
- validate() got an unexpected keyword argument 'stream'
- UnboundLocalError: local variable 'nodecount' referenced before assignment
- Transform from most recent BioPortal data
- Source metadata is missing in new transforms
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