dosumis
commented
1 year ago Test: Sheet 2 on this table has a list of metabolites measured in a GWAS study. https://static-content.springer.com/esm/art%3A10.1038%2Fs41588-022-01270-1/MediaObjects/41588_2022_1270_MOESM4_ESM.xlsx
The table is very rich in chemical identifiers:
| Metabolites | Compound ID (Metabolon) | CHRO_LIB_ENTRY_ID | COMP_ID | LIB_ID | SUPER_PATHWAY | SUB_PATHWAY | PATHWAY_SORTORDER | TYPE | INCHIKEY | SMILES | CAS | CHEMSPIDER | HMDB | HMDB_curated | KEGG | PUBCHEM | PUBCHEM_curated |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| S-1-pyrroline-5-carboxylate | X35 | 166164 | 42370 | 400 | Amino Acid | Glutamate Metabolism | 62 | NAMED | DWAKNKKXGALPNW-REWHXWOFAV | OC(C1CCC=N1)=O | 2906-39-0 | 10140206 | HMDB0001301 | HMDB0001301 | C04322 | 11966181 | 11966181 |
| spermidine | X50 | 157851 | 485 | 402 | Amino Acid | Polyamine Metabolism | 545 | NAMED | ATHGHQPFGPMSJY-UHFFFAOYAK | NCCCCNCCCN | 124-20-9 | 1071 | HMDB0001257 | HMDB0001257 | C00315 | 1102 | 1102 |
| 1-methylnicotinamide | X55 | 155829 | 27665 | 400 | Cofactors and Vitamins | Nicotinate and Nicotinamide Metabolism | 4316 | NAMED | LDHMAVIPBRSVRG-UHFFFAOYAE | C[N+]1=CC(C([NH-])=O)=CC=C1 | 1005-24-9 | 8305504 | HMDB0000699 | HMDB0000699 | C02918 | 457 | 457 |
Given the identifier mappings extracted from CHEBI & Swisslipids, how many terms from this table can we map to an ontology identifier (=> separate breakdowns for CHEBI & Swisslipids).
If many do not map, I would be interested to discuss with chemi-informatics experts whether there are good strategies for mapping up. I'm hoping it would be enough to have a short discussion on OBO Slack with some examples.
Motivating issue: https://github.com/EBISPOT/efo/issues/1905
Note - Santhi originally requested 415 terms (although the abstract mentions associations for 690 metabolites). Following discussion of identifiers, she has reduced her list to just 28 terms, but I think that is just because we communicated back that IDs are needed and she chose a subset of possible IDs (CAS ID/KEGG ID/PubChem ID), not because the science or needs of the GWAS catalog dictate adding such a small set.
cmungall
Background - The GWAS catalog needs to curate associations between variants and changes in the levels of many metabolites in, for example, blood. Studies often measure large numbers of metabolites and record these using standard chemical identifiers. We need to map these in to chemical ontologies that we can use - this means CHEBI right now, and possibly SwissLipids in the near future. Both of these ontologies are rich sources of ID mappings.
Proposed strategy - ensure that chemical ID mappings from CHEBI & swissslipids are available in OxO (loaded as SSOM) and that they can be used easily for mapping lists of IDs from GWAS curators to CHEBI/SwissLipids. From there we need SOPs/pipelines to get these IDs into TSVs for generation of OBA terms - with the OBA terms added to lists for import to EFO + a mechanism to inform GWAS curators of term availability.
Potential issue: Chemicals not in CHEBI. Can we devise a strategy for mapping up? Worth discussing with experts on CHEBI channel on OBO foundry.
As well as clear SOPs - all involved in mapping and term generation should have a good understanding of the whole process of generation of and use of mappings so that they can take ownership in future.