Addition of "GlyTouCan ID" and "protein glycosylation site" as data terms

[jeet-vora]

From Dan to OWG Michelle

Could we request addition of "GlyTouCan ID" and "protein glycosylation site" through Interlex as data_type terms for use in our consistency guidelines?

[ReneRanzinger]

Hi Michelle,

Many thanks for your response.

Please add the new InterLex term ‘GlyTouCan ID’ under parent ‘Carbohydrate accession’ data:2900. In the meanwhile, we will temporarily use the term ‘Carbohydrate accession’ and replace it later with ‘GlyTouCan ID’ when available.

Please add the new term ‘protein glycosylation site’ (a sequence position/coordinate) under parent ‘Protein features’ data:1277. Presumably, in the meanwhile, we will temporarily use the term ‘Protein features’ and replace it later with ‘protein glycosylation site’ when available.

Thanks again.

Please let me know if you have any questions.

Best,
Dan

[ReneRanzinger]

@jeet-vora lets try using ‘Carbohydrate accession’ data:2900 and ‘Protein features’ data:1277 for the next submission and see how the prep and submit tool react.

[danlymangw]

Hi Daniel,

Ok, sounds good.

We will make these terms and get them into the vocabularies in c2m2. That won’t be completed until after the break as everyone is going to be out for the next two weeks.

Also, if you could provide definitions for the new terms that would be great. We can always come up with something but you know these terms the best.

Happy Holidays,

Michelle

[ReneRanzinger]

Hi Daniel,

We have created the two new terms – “GlyTouCan accession” and “Protein glycosylation site” in Interlex. You can start using the following Interlex ids in your next data submission to CFDE portal.

Term: GlyTouCan accession
Interlex Id: ILX:0793824
Definition: A globally unique accession assigned to identify or refer to a glycan structure reported in the GlyTouCan repository.

Term: Protein glycosylation site
Interlex Id: ILX:0793825
Definition: The specific amino acid position in a protein or peptide sequence designating a potential or actual covalent attachment of a monosaccharide, oligosaccharide, or polysaccharide/glycan to: 1) a nitrogen atom, usually of asparagine (N-linked); 2) an oxygen atom of a serine, threonine, hydroxyproline or hydroxylysine residue (O-linked); 3) a carbon atom of a tryptophan residue (C-linked); or 4) a sulfur atom of cysteine (S-linked) to perform a structural and/or functional role in the resulting glycoconjugate.

[ReneRanzinger]

@jeet-vora lets update this in the configuration file and see if it fails in the next submission.