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Update columns and data returned in CSV download of drugs data table #605

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andrewhercules opened this issue May 20, 2019 · 1 comment

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commented May 20, 2019

Full details TBC pending decision about potential aggregation of drugs evidence for 19.06 release

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commented May 28, 2019

Currently, if a user downloads the current Drugs tab data table, the CSV file is missing identifiers for diseases, targets, and drugs, along with reference links for the mechanism of action and evidence.

Screenshot 2019-05-28 at 11 09 05

This data has been requested by users at Sanofi as they would like to see all of the data that is displayed in the UI and integrate the files into their own pipelines. This is particularly important once Sanofi begins to import its own drug evidence strings - and likely will be a similar request from our other partners.

Can we please update the file that users can download and ensure that it has the following data that is available within each evidence string?

  • disease_id from disease.efo_info.efo_id
  • drug_id from drug.id
  • mechanism_of_action_references from evidence.target2drug.urls
  • target_id from target.gene_info.geneid
  • evidence_url from drug2clinic.urls[0].url

For the mechanism_of_action_references column, please return the entire urls array as it includes both the nice_name and url values.

For the disease_id and drug_id columns, can we please parse the response from the API and extract the identifier? The API currently returns URLs (e.g. http://www.ebi.ac.uk/efo/EFO_0003922 or http://identifiers.org/chembl.compound/CHEMBL135) but computational users would prefer the file download to contain only the id (e.g. EFO_0003922 or CHEMBL135).

For the order of the columns - if possible - can we please have the columns appear in the following order based on the proposed file download format?

  • disease_name
  • disease_id
  • drug_name
  • drug_id
  • phase_numeric
  • status
  • type
  • mechanism_of_action
  • mechanism_of_action_references
  • activity
  • target
  • target_id
  • target_class
  • evidence_source
  • evidence_url

Also - if possible - can we please change the file type from CSV to TSV to accommodate the list of objects (separated by commas) that is returned by the API for the mechanism_of_action_references?

LucaFumis added a commit to opentargets/webapp that referenced this issue Jun 18, 2019

LucaFumis added a commit to opentargets/webapp that referenced this issue Jun 18, 2019

LucaFumis added a commit to opentargets/webapp that referenced this issue Jun 19, 2019

LucaFumis added a commit to opentargets/webapp that referenced this issue Jun 19, 2019

LucaFumis added a commit to opentargets/webapp that referenced this issue Jun 19, 2019

LucaFumis added a commit to opentargets/webapp that referenced this issue Jun 19, 2019

LucaFumis added a commit to opentargets/webapp that referenced this issue Jun 19, 2019

@ElaineMcA ElaineMcA closed this Jul 1, 2019

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