Is it possible to convert Gene Symbol to Ensembl ID?

General
1

AFAIK Open Target needs ID in ensembl-gene format. What is the most convenient way to convert gene-symbol like HGNC to Ensembl preferably within Open Target?

Currently i am using https://www.genetolist.com/ which is great but requires manual upload and downstream parsing…

2

Hi @animesh, and welcome to the Open Targets Community! :tada:

You can search the Platform’s web application using the gene symbol, rather than the Ensembl ID. For example, I would search for NOD to rather than ENSG00000167207.

The Platform also handles synonyms of the gene, so if I were to search for CLR16.3, it would bring up NOD2 as the relevant target.

Screenshot 2022-06-27 at 15.43.09
Screenshot 2022-06-27 at 15.43.092564×608 137 KB

Does this answer your question?

3

Thanks :slight_smile: Is there a way to do this via the API. i.e. using the Gene/Symbol not Ensembl ID?

4

Hi @animesh ,

If you are planning to do a larger scale analysis on our data, I would highly recommend using our target index accessible via ftp as JSON or parquet format. The data is extremely rich, but has the ensembl identifier as id and HGNC gene symbol as approvedSymbol . It worth exploring.

If you are fetching data via GraphQL API requests, it is possible to retrieve data based on search query, where you specify that you are looking for a target and then expand the result on the associated diseases:

query assocs {
  search(queryString: "HER3", entityNames:"target") {
		hits {
      id,
      name,
    	entity,
      object {
        ... on Target {
          associatedDiseases {
            rows {
              score
              datatypeScores{
                id
              	score
              }
              disease {
                id
                name
              }
            }
          }
        }
      }
    }
  }
}

Please let us know if this answer did not cover your question.

2 Likes
5

Thanks @dsuveges , this worked like charm! Solved another of the problem i was facing as well Overall association score via graphql/API !!