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HUPO-PSI / psi-mod-CV

Reactivated PSI-MOD ontology for molecular mass modifications
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Light(ish) Ontology Cleanup #42

Closed pmt706 closed 3 years ago

pmt706 commented 3 years ago

There are three major areas of fix here.

  1. Some slight term changes to address N-term/source/etc
  2. Some name changes to fit the rest of the ontology
  3. (and this is the biggest one) I've removed the "Leaf node" characteristics (diff/full formulas/mass) from any polymer-containing entries. These include polyglutamates (where the "N" of glutamyls isn't specified, DNA-RNA based crosslinks, glycans of unspecified size (chondroitin/etc) and poly-ADP Ribose (note that the monoADP-Ribosylations are still in the ontology and intact!)...

The major issue with this is that if you are trying to determine the mass of a protein containing say MOD:00251 which is O-(phospho-5'-DNA)-L-serine, the mass difference isn't 78.989, but that phospho plus an un-knowable mass/composition of DNA, so we shouldn't provide the specificity of the mass/formulae for those specific ontology terms.

I also ran ROBOT to update the OWL with the same changes that were made to the OBO... no need to verify that as it was automatically generated....

ricardblum commented 3 years ago

Many thanks for all the work you are doing. I fully agree with the third point, which is the major one indeed.

Sylvie.

Le 10/12/2020 à 18:23, pmt706 a écrit :

There are three major areas of fix here.

  1. Some slight term changes to address N-term/source/etc
  2. Some name changes to fit the rest of the ontology
  3. (and this is the biggest one) I've removed the "Leaf node" characteristics (diff/full formulas/mass) from any polymer-containing entries. These include polyglutamates (where the "N" of glutamyls isn't specified, DNA-RNA based crosslinks, glycans of unspecified size (chondroitin/etc) and poly-ADP Ribose (note that the monoADP-Ribosylations are still in the ontology and intact!)...

The major issue with this is that if you are trying to determine the mass of a protein containing say MOD:00251 which is O-(phospho-5'-DNA)-L-serine, the mass difference isn't 78.989, but that phospho plus an un-knowable mass/composition of DNA, so we shouldn't provide the specificity of the mass/formulae for those specific ontology terms.

I also ran ROBOT to update the OWL with the same changes that were made to the OBO... no need to verify that as it was automatically generated....

    You can view, comment on, or merge this pull request online at:

https://github.com/HUPO-PSI/psi-mod-CV/pull/42 https://github.com/HUPO-PSI/psi-mod-CV/pull/42

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