Retrieval of GlyTouCan Accessions directly from GlyTouCan

[jeet-vora]

@jonathancrabtree @nsuvarnaiari @mgiglio99 @ReneRanzinger

For every release, we would provide a list of GlyTouCan (GTC) Ids from GlyGen. This list would then be used by the submission prep tool to validate the provided GlyTouCan Ids. It would be better to retrieve the GlyTouCan accessions directly from GlyTouCan and use their list for our validation. GlyGen would only have a subset of their Ids in its submission.

There are two GTC web services that can be used for the retrieval of GTC accessions and can be added in the compound.tsv CV reference file.

https://sparqlist.glycosmos.org/sparqlist/api/glytoucan-data
Provides a JSON “dump” of glycans in GlyTouCan. For each glycan the GlyTouCan accession (AccessionNumber) and the sequence (Sequence) is provided.

https://api.glytoucan.org/swagger-ui.html#!/glycan-controller/listGlycansUsingGET
A swagger documented webservice that allows to get a subset of GlyTouCan Ids (using limit and offset). Only provides GlyTouCan Accessions as response.

glygener/glygen.cfde.generator#18

[nsuvarnaiari]

Hi @jeet-vora ,

We like the idea of retrieving the GlyTouCan accessions directly from GlyTouCan and wanted to implement that before the June submission. But, we realized that involves some complexities and we will need some time to work around them. So, we have postponed it for now but will be our priority for the round of submissions after June.
We request you to send us the list of ids that you plan to submit in the June submission. Sorry about that.

Thanks,
Suvvi

@jonathancrabtree @mgiglio99 @RLC-DCPPC

[jeet-vora]

Hi @nsuvarnaiari,

Sure, no problem and sound good. Will send you the GlyGen glycan masterlist in couple of days.

@jonathancrabtree @mgiglio99 @RLC-DCPPC @ReneRanzinger

[jeet-vora]

Hi @nsuvarnaiari

Here is the GlyGen Glycan Masterlist - https://data.glygen.org/ln2data/releases/data/current/reviewed/glycan_masterlist.csv

From this file you will need the GlyTouCan accessions present in the glytoucan_ac filed. (current 45192 accessions)

Here is also the Glycan PubChem Xref Status - https://data.glygen.org/ln2data/releases/data/current/reviewed/glycan_pubchem_status.csv
This file will provide you with the GlyTouCan AC to PubChem Compound ID mapping.
Please note that you will have to select the PubChem CID ac as the file contains both PubChem SID and CID and not all GlyTouCan accession have PubChem CID mappings.

[nsuvarnaiari]

Thanks Jeet!

Suvvi
@jonathancrabtree @mgiglio99 @RLC-DCPPC