Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Complement system proteins from MESH:D003165 not correctly normalized #615

Closed
TranslatorIssueCreator opened this issue Oct 24, 2023 · 5 comments
Assignees

Comments

@TranslatorIssueCreator
Copy link

Type: Bug Report

URL: https://ui.test.transltr.io/main?fm=true

ARS PK: d62dfecf-5b6e-4156-bf08-fc9095dc8666

Steps to reproduce:

MVP1 on MODY
submitted by @sandrine-muller-research

Screenshots:

@sandrine-muller-research
Copy link
Collaborator

MESH:D003165 is shown as a chemical entity and should be a biological entity:
image
Node norm:
Hitting NodeNorm is not found:

{
  "MESH:D0031653": null
}

@cbizon
Copy link
Collaborator

cbizon commented Oct 24, 2023

FWIW, I think that there's an extra 3 on the identifier in the comment above. NN does know about the term, but it also does call it a chemical.

@sandrine-muller-research
Copy link
Collaborator

Oh right! there's a typo in the ID... Here is the returned json from NodeNorm with correct ID:

{
  "MESH:D003165": {
    "id": {
      "identifier": "MESH:D003165",
      "label": "Complement System Proteins"
    },
    "equivalent_identifiers": [
      {
        "identifier": "MESH:D003165",
        "label": "Complement System Proteins"
      },
      {
        "identifier": "UMLS:C0009498",
        "label": "Complement System Proteins"
      }
    ],
    "type": [
      "biolink:ChemicalEntity",
      "biolink:NamedThing",
      "biolink:Entity",
      "biolink:PhysicalEssence",
      "biolink:ChemicalOrDrugOrTreatment",
      "biolink:ChemicalEntityOrGeneOrGeneProduct",
      "biolink:ChemicalEntityOrProteinOrPolypeptide",
      "biolink:PhysicalEssenceOrOccurrent"
    ]
  }
}

@gaurav
Copy link

gaurav commented Jan 23, 2024

Tracking at Babel at TranslatorSRI/Babel#200

@sierra-moxon
Copy link
Member

I retested this morning and no longer see "Complement system proteins" as a result in the MODY type 2 query. Please reopen if this is a different MODY or otherwise still a problem as I did my best to test it and follow the related links and can't see the issue any longer. :)

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
None yet
Development

No branches or pull requests

5 participants