The AWS RODA Solution isn't working for the `Targets` table

Data Access
1

The AWS RODA solution for fetching Open Targets Platform used to have data for targets in its own table. However, this doesn’t seem to be the case and the s3://aws-roda-hcls-datalake/opentargets_latest/targets/ doesn’t look like it exists anymore. Was this an intentional change and if so, how can I retrieve the same data now?

2

Hi, Welcome to the OpenTargets community. Thank you for reporting this issue! Unfortunately, syncing our data to AWS is entierly managed and overseen by the Open Data team at Amazon. As their documentation says, any issue needs to be reported on their github issues page. Apparently someone else has already opened a relevant ticket (#29) last month, unfortunately no reply since.

We are looking into reaching out some contacts with AWS to prioritize the issue. In the meantime, keep your eyes on the AWS bucket and the github issues for updates, as we might not get update about a successful resolution.

3

It seems like this whole dataset on AWS has been deprecated, according to the first section on this page: https://registry.opendata.aws/opentargets/. This is a shame, as it was a great resource! And it appears there was no response to the issue raised on GitHub, so it has been silently shuttered :disappointed:

Did the OpenTargets team get any further information about it? Thanks in advance.

4

Hi @vcatterson, yes you are right. Unfortunately the Open Targets dataset in the Registry of Open Data on AWS has been deprecated.

There is a thread on GitHub by the AWS team highlighting deprecation of multiple datasets from AWS RODA including Open Targets data. According to the AWS team, "The group responsible for this collection of datasets was no longer able to maintain the dataset and made the resource unavailable. Given those circumstances, we felt it best to delist the resources from the Registry".

The Open Targets team does not have any further information at this time. We will inform the community if this changes in the future.

Also, Open Targets data is now available as an Open Dataset through Microsoft Azure.

1 Like
5

Thank you so much for the further information! I will update my workflow to use one of the other download options.