Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.
We've been trying to run quantms pipelines today and it seems like the ms ontology is inaccessible from the OLS4 api at the moment. For example, this ms api endpoint currently returns no terms:
The missing ontology results in a an error during the SAMPLESHEET_CHECK process using an SDRF file:
...
{row: 95, column: "comment[instrument]"}: "ac=ms:1003231;nt=timstof scp" the term name or title can't be found in the ontology -- ms
{row: 95, column: "comment[cleavage agent details]"}: "ac=ms:1001251;nt=trypsin" the term name or title can't be found in the ontology -- ms
There were validation errors!
It looks like there is currently no way to disable the validation of ms ontology terms or all ontology terms (which could be useful for offline workflow execution).
I propose adding a parameter disable one or both of these checks. I'm also happy to put in a PR.
Description of the bug
We've been trying to run quantms pipelines today and it seems like the
msontology is inaccessible from the OLS4 api at the moment. For example, thismsapi endpoint currently returns no terms:Whereas the
unimodapi endpoint on OLS4 is working:The missing ontology results in a an error during the
SAMPLESHEET_CHECKprocess using an SDRF file:It looks like there is currently no way to disable the validation of
msontology terms or all ontology terms (which could be useful for offline workflow execution).I propose adding a parameter disable one or both of these checks. I'm also happy to put in a PR.
Command used and terminal output
No response
Relevant files
No response
System information
No response