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We need to extend PTM coverage to include relative clauses (that, when, etc).
Examples (and description of desired behavior):
- "Src tyrosyl phosphorylates Ras that is ubiquitinated."
- `theme` of…
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Hey folks,
not sure as no results yet, but I am a bit confused about the X!Tandem parameter file - but it may be right (couldn't check anymore as I have to leave the lab now and fly to Europe tomorro…
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PSI-MI CVs have number of mod terms see http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI&termId=MI%3A0120&termName=post%20translation%20modification
that should now be obsoleted and user shou…
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We decided in Ghent to get rid of the concept of "final PSM list" and "intermediate list" - only final results are allowed to make reading easier. @germa Please remove this from the mapping file and …
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John G would like to see all the children of 'post-translational protein modification ;GO:0043687' moved up to be direct children of 'protein modification process ; GO:0006464'.
Reasoning: There are …
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otherwise MOD cannot be used for ptms
Reported by: luisa_montecchi
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```
> What steps will reproduce the problem?
loading of data after SearchGUI to peptideshaker
> What is the expected output? What do you see instead?
found less D-scores than PTMs for modification o…
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More terms are requested to annotate the ptms (PMID:22231400).
The suggested new terms should be children of observed-ptm (MI:0925):
1) decreasing-ptm
2) disrupting-ptm
3) increasing-ptm
Reported by…
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this is great that you added PTMs, but it should be a one-letter code, for example "P". I think it is better to change "mgArg" into "R", some features overalp, the shorter the label, less chance they …
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This would be a direct child of the biological feature used
to specify position of the peptide bond cleaved by a protease
See, eg, PMID:20439754
If the term is accepted we should probably also add a…