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Include more metadata in the MCP term info payload

Open cmungall opened this issue 1 month ago • 2 comments

We obviously want to avoid the antipattern of MCP servers mimicking APIs and returning enormous payloads, but I think having some way to access really key term metadata such as the mappings for a term

Compare:

  "id": "go+http://purl.obolibrary.org/obo/GO_0019702",
  "title": "GO:0019702 protein arginine N5-methyltransferase activity",
  "text": "Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to the delta-nitrogen atom of peptidyl-arginine residues. The reaction is S-adenosyl-L-methionine + [protein]-L-arginine = S-adenosyl-L-homocysteine + [protein]-N5-methyl-L-arginine.",
  "url": "http://purl.obolibrary.org/obo/GO_0019702",
  "metadata": {
    "type": "class"
  }
}

With

id: GO:0019702
name: protein arginine N5-methyltransferase activity
namespace: molecular_function
def: "Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to the delta-nitrogen atom of peptidyl-arginine residues. The reaction is S-adenosyl-L-methionine + [protein]-L-arginine = S-adenosyl-L-homocysteine + [protein]-N5-methyl-L-arginine." [EC:2.1.1.322, PMID:11856739, PMID:9873020]
comment: This enzyme, characterized from the yeast Saccharomyces cerevisiae, methylates the delta-nitrogen atom of arginine residues within proteins. Among its substrates are R67 of the ribosomal protein L12.
synonym: "protein arginine N5-methylase activity" EXACT []
synonym: "protein-arginine delta-N-methyltransferase activity" EXACT []
synonym: "protein-arginine N5-methyltransferase activity" EXACT []
synonym: "S-adenosyl-L-methionine:[protein]-L-arginine N-methyltransferase ([protein]-N5-methyl-L-arginine-forming)" RELATED [EC:2.1.1.322]
synonym: "type IV PRMT activity" EXACT []
synonym: "type IV protein arginine methyltransferase activity" EXACT []
xref: EC:2.1.1.322
xref: RHEA:48116
is_a: GO:0016274 ! protein-arginine N-methyltransferase activity

arguably the axiom annotations are not so relevant for many mcp use cases, nor even synonyms, and the parents can be fetched by other calls. But mappings are important.

some options are

  1. just include mappings as a default in the object returned
  2. add a new getMappings tool
  3. add a getTermFull tool
  4. paramtetrize the existing tool to allow for progressively more metadata

cmungall avatar Oct 23 '25 00:10 cmungall