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chembl / GLaDOS

Web Interface for ChEMBL @ EMBL-EBI
https://www.ebi.ac.uk/chembl/
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Missing information when downloading items #1105

Closed nbosc closed 5 years ago

nbosc commented 5 years ago

If you compare the fields you get when you download the drugs between the old interface (https://www.ebi.ac.uk/chembl/old/drugstore) and the new one (https://www.ebi.ac.uk/chembl/g/#browse/drugs/filter/_metadata.compound_records.src_id%3A13), you will see some important ones are missing (canonical_smiles, drug_type...)

nbosc commented 5 years ago

related to #942

nclopezo commented 5 years ago

I am creating this spreadsheet: https://docs.google.com/spreadsheets/d/10GKleHwMfKK2VczSLttQU2ZPrFDtTz7xyZO5v8Zp8U8/edit?usp=sharing

Here we can discuss the current download columns. Log in as chemblgroup@googlemail.com to edit it

nclopezo commented 5 years ago

@nbosc I am doing some changes to the downloads in https://github.com/chembl/GLaDOS/pull/1159. Please see the following file: CHEMBL25-chembl_molecule-bRQyb5FDXEzS6DmEpWMlc4_K_I9oBFDbFkHNcnolUdA=.csv.gz It is a csv file with all the drugs, let me know if this is as expected. It will be generated like that after the pull request is merged.

nbosc commented 5 years ago

To me it’s look good, but the more I think about this, the more I believe that the download file should contain the column filtered. Because every user has different usage.

On 1 Jul 2019, at 17:08, David Mendez notifications@github.com wrote:

@nbosc https://github.com/nbosc I am doing some changes to the downloads in #1159 https://github.com/chembl/GLaDOS/pull/1159. Please see the following file: CHEMBL25-chembl_molecule-bRQyb5FDXEzS6DmEpWMlc4_K_I9oBFDbFkHNcnolUdA=.csv.gz https://github.com/chembl/GLaDOS/files/3346493/CHEMBL25-chembl_molecule-bRQyb5FDXEzS6DmEpWMlc4_K_I9oBFDbFkHNcnolUdA.csv.gz It is a csv file with all the drugs, let me know if this is as expected. It will be generated like that after the pull request is merged.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/chembl/GLaDOS/issues/1105?email_source=notifications&email_token=AGIQJKYTHNP3W6NJMRHRCBDP5ITWDA5CNFSM4HHZFS4KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODY6TSDY#issuecomment-507328783, or mute the thread https://github.com/notifications/unsubscribe-auth/AGIQJK7TEEDRMVYQJWU6OC3P5ITWDANCNFSM4HHZFS4A.

nclopezo commented 5 years ago

Do you mean that the user can select the columns to include in the file?

nbosc commented 5 years ago

Yes

On 1 Jul 2019, at 18:18, David Mendez notifications@github.com wrote:

Do you mean that the user can select the columns to include in the file?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/chembl/GLaDOS/issues/1105?email_source=notifications&email_token=AGIQJKYIIJWHKKTDOC6L5V3P5I4AHA5CNFSM4HHZFS4KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODY6ZIUQ#issuecomment-507352146, or mute the thread https://github.com/notifications/unsubscribe-auth/AGIQJKYEYDWLV54XBE3NWWTP5I4AHANCNFSM4HHZFS4A.

nclopezo commented 5 years ago

All the downloads from all the entities have been reviewed, the downloads package has been refactored, and now this should be fixed, you can try downloading the drugs again. https://www.ebi.ac.uk/chembl/g/#browse/drugs/filter/_metadata.compound_records.src_id%3A13