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Web Interface for ChEMBL @ EMBL-EBI
https://www.ebi.ac.uk/chembl/
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Add withdrawn class on compound report card #787

Closed nclopezo closed 5 years ago

nclopezo commented 6 years ago

As in https://github.com/chembl/chembl_interface/issues/31

FionaEBI commented 5 years ago

Dear David, I note that there's as yet no 'withdrawn_class' for approved drugs on the new interface. Please can you include this field? Here's the set of withdrawn drugs - https://www.ebi.ac.uk/chembl/beta/g/#browse/drugs/filter/withdrawn_flag:1%20AND%20max_phase:4 but for e.g. https://www.ebi.ac.uk/chembl/beta/compound_report_card/CHEMBL865/, I can only see the withdrawn_country, withdrawn_year and withdrawn_reason, but not withdrawn_class:

screenshot 2019-01-29 at 09 54 11

Many thanks for your help! Fiona

nclopezo commented 5 years ago

@FionaEBI The field is now there: https://www.ebi.ac.uk/chembl/beta/compound_report_card/CHEMBL865/ 44d3fd0e1cf9eb38740fb953d3604d99d69287d2

FionaEBI commented 5 years ago

Dear David, Excellent - that’s very nice to see! And timely too because we are discussing updates to the withdrawn drugs information with a collaborator at the University of Oxford next week, so I'm happy that I can show him the withdrawn_class annotation in the web interface. Many thanks, Fiona

On 13 Feb 2019, at 15:36, David Mendez notifications@github.com wrote:

@FionaEBI https://github.com/FionaEBI The field is now there: https://www.ebi.ac.uk/chembl/beta/compound_report_card/CHEMBL865/ https://www.ebi.ac.uk/chembl/beta/compound_report_card/CHEMBL865/ 44d3fd0 https://github.com/chembl/GLaDOS/commit/44d3fd0e1cf9eb38740fb953d3604d99d69287d2 — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/chembl/GLaDOS/issues/787#issuecomment-463245646, or mute the thread https://github.com/notifications/unsubscribe-auth/AfXzWpuGJkAbZAKLQdn5cAHQ6vKnK-p7ks5vNDEHgaJpZM4T7FW2.

Dr Fiona M I Hunter CChem MRSC Chemogenomics Group European Bioinformatics Institute (EMBL-EBI) Wellcome Genome Campus Hinxton Cambridge CB10 1SD United Kingdom

01223 494317 fiona.hunter@ebi.ac.uk mailto:fiona.hunter@ebi.ac.uk

FionaEBI commented 5 years ago

Hi David, I’ve noticed today that the withdrawn_class is also missing from the downloadable information. e.g. using the url https://www.ebi.ac.uk/chembl/beta/g/#browse/drugs/filter/withdrawn_flag:1%20AND%20max_phase:4 <https://www.ebi.ac.uk/chembl/beta/g/#browse/drugs/filter/withdrawn_flag:1 AND max_phase:4> gives a downloadable csv file with only withdrawn_year, withdrawn_reason and withdrawn_country.

Would you mind including it, please? Fiona

On 13 Feb 2019, at 15:48, David Mendez notifications@github.com wrote:

Closed #787 https://github.com/chembl/GLaDOS/issues/787.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/chembl/GLaDOS/issues/787#event-2137116153, or mute the thread https://github.com/notifications/unsubscribe-auth/AfXzWtCDeanI1mDavevA4iNna9TCdFILks5vNDPKgaJpZM4T7FW2.

Dr Fiona M I Hunter CChem MRSC Chemogenomics Group European Bioinformatics Institute (EMBL-EBI) Wellcome Genome Campus Hinxton Cambridge CB10 1SD United Kingdom

01223 494317 fiona.hunter@ebi.ac.uk mailto:fiona.hunter@ebi.ac.uk

nclopezo commented 5 years ago

Hi Fiona,

The withdrawn class is now added, it was also added to the additional columns in the table. You can try again now.

FionaEBI commented 5 years ago

Dear David, Many thanks - that works! It’s a really good example of demonstrating the usefulness of the database to our users - my queries have arisen as a result of questions through the TransQST project.

However, I’m confused why only some columns are included within the downloadable information. I would have expected that all the fields that are available in the ‘filters’ button on the left hand side should appear in the downloadable data?

Also, there is a ‘Withdrawn_Flag' in the ‘Filters’ setting but no other information on Withdrawn status - can you include Withdrawn_year, withdrawn_country, withdrawn_reason and withdrawn_class in these (optional) filters too?

Maybe I am missing something, or it is work that you already have planned, but the current filter options / downloadable data don't yet make good logical sense to me, sorry...

Thanks for your help! Fiona

On 12 Mar 2019, at 14:23, Fiona Hunter fmih@ebi.ac.uk wrote:

Hi David, I’ve noticed today that the withdrawn_class is also missing from the downloadable information. e.g. using the url https://www.ebi.ac.uk/chembl/beta/g/#browse/drugs/filter/withdrawn_flag:1%20AND%20max_phase:4 <https://www.ebi.ac.uk/chembl/beta/g/#browse/drugs/filter/withdrawn_flag:1 AND max_phase:4> gives a downloadable csv file with only withdrawn_year, withdrawn_reason and withdrawn_country.

Would you mind including it, please? Fiona > On 13 Feb 2019, at 15:48, David Mendez > wrote: > > Closed #787 . > > — > You are receiving this because you were mentioned. > Reply to this email directly, view it on GitHub , or mute the thread . > *************************** Dr Fiona M I Hunter CChem MRSC Chemogenomics Group European Bioinformatics Institute (EMBL-EBI) Wellcome Genome Campus Hinxton Cambridge CB10 1SD United Kingdom 01223 494317 fiona.hunter@ebi.ac.uk ***************************

Dr Fiona M I Hunter CChem MRSC Chemogenomics Group European Bioinformatics Institute (EMBL-EBI) Wellcome Genome Campus Hinxton Cambridge CB10 1SD United Kingdom

01223 494317 fiona.hunter@ebi.ac.uk mailto:fiona.hunter@ebi.ac.uk

nclopezo commented 5 years ago

Dear David, Many thanks - that works! It’s a really good example of demonstrating the usefulness of the database to our users - my queries have arisen as a result of questions through the TransQST project. However, I’m confused why only some columns are included within the downloadable information. I would have expected that all the fields that are available in the ‘filters’ button on the left hand side should appear in the downloadable data?

From all the possible properties that a drug (or any item) can have, one subset is the filtering properties, which all need to be 'aggregatable' by elasticsearch. Also, there is a list of properties that people will see in the downloads, this doesn't include many of the other properties that we use for other cases. We have a lot of other properties available such as 'parent_molecule._metadata.drug.drug_data.withdrawn_class', or 'parent_molecule._metadata.target_predictions.in_training'. The properties used depend on the context and we choose which ones to show by configuration files.

So they are different subsets of all the available properties. We can improve this in the future, by for example allowing the user to choose which properties to include in the csv file. But for now it's simpler as it is.

Also, there is a ‘Withdrawn_Flag' in the ‘Filters’ setting but no other information on Withdrawn status - can you include Withdrawn_year, withdrawn_country, withdrawn_reason and withdrawn_class in these (optional) filters too? Maybe I am missing something, or it is work that you already have planned, but the current filter options / downloadable data don't yet make good logical sense to me, sorry... Thanks for your help! Fiona On 12 Mar 2019, at 14:23, Fiona Hunter @.> wrote: Hi David, I’ve noticed today that the withdrawn_class is also missing from the downloadable information. e.g. using the url https://www.ebi.ac.uk/chembl/beta/g/#browse/drugs/filter/withdrawn_flag:1%20AND%20max_phase:4 <https://www.ebi.ac.uk/chembl/beta/g/#browse/drugs/filter/withdrawn_flag:1 AND max_phase:4> gives a downloadable csv file with only withdrawn_year, withdrawn_reason and withdrawn_country. Would you mind including it, please? Fiona > On 13 Feb 2019, at 15:48, David Mendez @. @.*>> wrote: > > Closed #787 <#787>. > > — > You are receiving this because you were mentioned. > Reply to this email directly, view it on GitHub <#787 (comment)>, or mute the thread https://github.com/notifications/unsubscribe-auth/AfXzWtCDeanI1mDavevA4iNna9TCdFILks5vNDPKgaJpZM4T7FW2. > ***** Dr Fiona M I Hunter CChem MRSC Chemogenomics Group European Bioinformatics Institute (EMBL-EBI) Wellcome Genome Campus Hinxton Cambridge CB10 1SD United Kingdom 01223 494317 @. @.> Dr Fiona M I Hunter CChem MRSC Chemogenomics Group European Bioinformatics Institute (EMBL-EBI) Wellcome Genome Campus Hinxton Cambridge CB10 1SD United Kingdom 01223 494317 fiona.hunter@ebi.ac.uk mailto:fiona.hunter@ebi.ac.uk ***

I just added the new filters for withdrawn class here: https://github.com/chembl/GLaDOS/pull/1054. @chembl-bot is testing it.

nclopezo commented 5 years ago

The filters are now ready: https://www.ebi.ac.uk/chembl/beta/g/#browse/drugs