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Web Interface for ChEMBL @ EMBL-EBI
https://www.ebi.ac.uk/chembl/
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Show in vivo assay classification on the interface #1201

Closed agaulton closed 4 years ago

agaulton commented 4 years ago

We have the in vivo assay classification already in the web services (assay_class, and also nested in the assays), but might not be in elastic yet...

We would like to have the different levels as filters on the browse assays view (and also maybe on the activities view if that's possible).

But it could also be good to have the whole classification as a sunburst that allowed you to retrieve a set of assays (like we have for protein family classification and targets).

Added to ChEMBL_26 milestone, but not critical for switching off old interface since it's a new feature

agaulton commented 4 years ago

Filters look good. Please could we add the three levels as optional columns for the assay table view/exports also?

For the long term, we need to work out what to do with the 'Other' categories in the filters, but we can discuss that separately...

FionaEBI commented 4 years ago

Hi Juan, Many thanks for including the assay classification in the interface. It looks very nice, and I have a few comments, please.

  1. Can you amend the names of the filter to be 'Assay Classification L1', 'Assay Classification L2' and 'Assay Classification L3'. Not the use of the singular 'classification' not 'classificationS'
  2. The default view for the left hand filter should show 'Type' (ideally as 'Assay Type' to match the column name) before the 'Assay Classification L1'. Screenshot 2019-10-30 at 15 26 23
  3. The Assay Classification L2 shows N/A at the top (as well as 'Other Categories), while Assay Classification L1 and Assay Classification L3 do not include N/A. This is confusing, and should be consistent.
  4. I know that David is working on how to deal with the 'Other Categories' so that these can be searchable? So really just a comment that drilling down on 'Other Categories' in the left hand filter would be very useful for the user. Many thanks for doing this! Fiona
nclopezo commented 4 years ago

Hi Fiona,

I just updated the filters as you suggested in 1 and 2. See https://www.ebi.ac.uk/chembl/g/#browse/assays

FionaEBI commented 4 years ago

Thanks David, It all looks fine.

Regarding 3: the inconsistency was between L1, L2 and L3 (not between N/A and Other Categories within e.g. L1) - but I can no longer see the issue, so perhaps it arose as a result of the assay data that I had selected. So no need to look at this further.

In general N/A is not a helpful label until the user understands that only a small fraction of all the assays have been annotated using the L1, L2, L3 annotation, hence the need to have something that obviously shows that ‘Other Categories’ means more annotated assays that have not been shown in the current view.

Best wishes, Fiona

On 5 Nov 2019, at 11:01, David Mendez notifications@github.com wrote:

Hi Fiona,

I just updated the filters as you suggested in 1 and 2. See https://www.ebi.ac.uk/chembl/g/#browse/assays https://www.ebi.ac.uk/chembl/g/#browse/assays Regarding 3: 'N/A' means 'No value set for this property', whereas 'Other Categories' means 'Categories that don't fit on the space given'. I am not sure I understand what is the inconsistency. Could you please paste here an example of it?

Regarding 4: Just to be clear, I plan to work on the 'Other Categories' but is not currently what I am working on.

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nclopezo commented 4 years ago

There is a new visualisation on the visualisations page, it is a sunburst showing the in vivo assay classification: https://www.ebi.ac.uk/chembl/visualise/