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NCATSTranslator / Feedback

A repo for tracking gaps in Translator data and finding ways to fill them.
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Which KP can provide metabolic pathway data for Translator? #64

Open karafecho opened 1 year ago

karafecho commented 1 year ago

The QotM identified PharmGKB, RaMP DB, Rhea-DB, and KEGG Pathway DB as potential sources of metabolic pathway data.

marcdubybroad commented 1 year ago

@karafecho The Genetics KP team is in the process of promoting new data through our stack that has KEGG and WIKIPATHWAYS data. It's currently in our dev stack. We've only loaded disease/pathway association data where the p-value is less than 0.05. The p-values are calculated from the Magma process aggregation of the genes' p-values in the pathway for that disease/phenotype. Example query for our dev server (https://translator.broadinstitute.org/genetics_provider/trapi/v1.3/query)

{
    "message": {
      "query_graph": {
        "nodes": {
          "n0": {
            "ids": ["KEGG:hsa05322"]
          },
          "n1": {
            "categories": ["biolink:NamedThing"]
          }
        },
        "edges": {
          "e01": {
            "subject": "n0",
            "object": "n1"
          }
        }
      }
    }
  }

returns:

                        {
                            "attribute_type_id": "biolink:p_value",
                            "original_attribute_name": "pValue",
                            "value": 0.0019390149921821016
                        }
                    ],
                    "object": "EFO:0004308",
                    "predicate": "biolink:genetic_association",
                    "subject": "KEGG:hsa05322"
                }
karafecho commented 1 year ago

Thanks, Mark! This type of query could be very useful for Translator.

sstemann commented 1 year ago

@sierra-moxon @karafecho NCATS will be creating an RaMP DB KP over the summer

karafecho commented 1 year ago

Wow! Thanks for the update, Sarah.

andrewsu commented 1 year ago

@sstemann Can you put us in touch with the developers of the RaMP API? Since the API already exists, it's possible we can annotate/register it in SmartAPI and have it accessible through BTE without any further development. We were about to get on that, but have one detail we'd like to follow up on first.

sandrine-m commented 11 months ago

This is linked with https://github.com/NCATSTranslator/Feedback/issues/2

sierra-moxon commented 3 months ago

@andrewsu @sstemann - did either of these resources get incorporated into a Translator resource or should we keep this ticket open for further work?

andrewsu commented 3 months ago

Service Provider provides access to a rhea API -- more info in https://github.com/biothings/mychem.info/issues/37

RaMP is ongoing -- linking the currently open issue at https://github.com/biothings/biothings_explorer/issues/705

codewarrior2000 commented 3 months ago

MolePro is in the process of assimilating the Reactome DB, which is "an open-source, open access, manually curated and peer-reviewed pathway database".

In Reactome, the metabolic pathways are grouped under Metabolism, which has the Reactome identifier R-HSA-1430728.

sstemann commented 1 month ago

we deferred to BTEs RaMP integration. If any of these are targeted for this funding phase of the program can folks please add a release (guppy, hammerhead, etc) to the label? @codewarrior2000 @andrewsu

andrewsu commented 1 day ago

Given the recent emphasis on eliminating redundant ingestion of resources into Translator, I'm rethinking how we approach RaMP. TLDR: I don't think we should ingest RaMP directly, but rather focus on Lipid Maps, the only resource that isn't otherwise already present in Translator. More details below...

According to https://rampdb.nih.gov/about, RAMP is an aggregator of the following resources:

HMDB v5.0 (2021-11-17) Reactome v87 (Dec 2023) WikiPathways v20240210 (2024-02-10) KEGG from HMDB (v5.0) (2021-11-17) ChEBI Release 231 (2024-03-01) Lipid Maps Release 2024-03-06 Rhea Release 131 (2024-01-)

My analysis of each one of those resources:

HMDB

Reactome

Wikipathways

KEGG

ChEBI

Lipid Maps

Rhea

Bottom line, the only one that isn't currently ingested into Translator is Lipid Maps. Unless there are objections, I think we should:

There also is the issue of whether the resources above have been captured as completely in the sources above as they have been in RaMP, but barring a drastic difference in completeness/accuracy, I think we should focus on improving the existing resources over adding new ones.