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    October 16, 2023

    CDD Vault Update (October 2023): Keyword Searching, A New Molecule Pop-Up, ELN Summary-Only Export, Structure Searches Return Mixtures, and New API for Handling Files

    Keyword Searching

    When using the Keywords search feature in the main Explore Data > Search tab, there is a new “exact” search option available when you select a specific, non-numeric Molecule or Batch field.

    Helpful hint: the algorithm used when selecting the “has” operator was also updated to no longer wrap the search term in quotes, so your search terms are more likely to return a desirable list of matches. This is especially relevant for IDs with multiple special characters and spaces.

    Updated Molecule Pop-Up

    When clicking on a structure box, the resulting pop-up dialog box has been revamped

    • new Size options are available for downloading SVG and PNG files

    • Molfile and Original options display the file format, with options to Download or Copy

    • A new Identifiers section was added with options to Download or Copy these formats:
      • SMILES
      • CXSMILES
      • InChI
      • InChIKey
      • IUPAC

    ELN Summary-Only Export

    Vault Administrators have always been able to export a set of ELN Entries from the main ELN Index page. A new “Export summary” option has been added to allow Vault Administrators to export a single summary file.

    Helpful Hints:

    • All system ELN metadata fields plus all user-defined ELN Fields are included in the csv Summary file.

    • A new only_summary parameter was added to the GET eln/entries API call to return only this csv Summary file. Simply submit JSON similar to:

    {

       "author":"6021",

       "status":"open",

       "only_summary":true,

       "async":true

    }

    Structure Searches Return Mixtures

    Structure-based queries now return Mixtures which contain components that match the query.

     

    Helpful hints:

    • The mixture components must be registered entities in order to be indexed.
    • Sequence based searches will also return matching mixtures.

    New API for Handling Files

    There is a 2-step API workflow now available to programmatically attach files to Molecule/Batch fields and Protocol readouts.

    The first step involves using thePOST FilesAPI endpoint to send a file to the CDD Vault server. This step returns an internal file id that must be used in a 2nd API call to attach this file to the desired field/readout.

    Step 1

    The 1st API call used is POST /api/v1/vaults/<vault_id>/files which returns JSON containing the internal file id.

    {

       "id": 20167608,

       "name": "FlowCyto.png",

       "expires_at": "2023-10-13"

    }

    Helpful Hint: The JSON includes an “expires_at” date indicating when the file will be removed from the CDD Vault server if it’s not subsequently attached to a field/readout or object.

    Step 2

    The next API call attaches the file to the desired field/readout. This step uses the Molecules, Batches or Readout_Rows endpoints.

    As an example, if the file just POSTed needs to be attached to an existing Batch field, use this API call:

    PUT https://app.collaborativedrug.com/api/v1/vaults/<vault_id>/batches/<batch_id>

    And pass JSON like this:

    {"batch_fields":

       {"DataFile": 20167608}

    }

    As another example, if the file just POSTed needs to be attached to an existing Protocol readout row, use this API call:

    PUT https://app.collaborativedrug.com/api/v1/vaults/<vault_id>/readout_rows/<readout_row_id>

    And pass JSON like this:

    {"readouts":

        {"1146750": {"value": "20167608"}}

    }

    This blog is authored by members of the CDD Vault community. CDD Vault is a hosted drug discovery informatics platform that securely manages both private and external biological and chemical data. It provides core functionality including chemical registrationdata visualization, inventory, and electronic lab notebook capabilities.

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