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chembl / IDG

Issue tracker for the IDG interface
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Question about loaded data #50

Closed Anneli15 closed 9 years ago

Anneli15 commented 9 years ago

I was wondering, the data that you loaded recently for me (ion channel active compounds) doesn't seem to have any details like structure, references, mechanism etc. Is there a reason for why this hasn't loaded? `The compounds are in the molecule dictionary but no other tabs seem have any data.

Also, there seem to be a default "YES" for prodrug and "NO" for black box warning. If there is no information about this status, could the default be "unknown" please?

revajk commented 9 years ago

Yes Anneli, Not all the data are loaded yet. I will let you know once they are loaded. I think the data has got some special characters in there and the script keeps dying I will let you know once they are fully loaded.

Reva.

On 15 Sep 2015, at 10:11, Anneli15 notifications@github.com wrote:

I was wondering, the data that you loaded recently for me (ion channel active compounds) doesn't seem to have any details like structure, references, mechanism etc. Is there a reason for why this hasn't loaded? `The compounds are in the molecule dictionary but no other tabs seem have any data.

Also, there seem to be a default "YES" for prodrug and "NO" for black box warning. If there is no information about this status, could the default be "unknown" please?

— Reply to this email directly or view it on GitHub https://github.com/chembl/IDG/issues/50.

Anneli15 commented 9 years ago

OK, thanks. What about the default choices for prodrug and black box?

revajk commented 9 years ago

I have changed them now. You should see them once I deploy them to the servers.

On 15 Sep 2015, at 10:34, Anneli15 notifications@github.com wrote:

OK, thanks. What about the default choices for prodrug and black box?

— Reply to this email directly or view it on GitHub https://github.com/chembl/IDG/issues/50#issuecomment-140337107.

mnowotka commented 9 years ago

Hi, is this completed?

revajk commented 9 years ago

Yes all the ion channels are now loaded.

mnowotka commented 9 years ago

Thanks Reva. @Anneli15, if this satisfies your requirements, please close this issue.

Anneli15 commented 9 years ago

I can't see all the data in my version, only the compounds. Still missing structure, references, mechanism etc.

revajk commented 9 years ago

I am deploying now I will let you know once I finish them

mnowotka commented 9 years ago

OK. Please keep in mind that my definition of 'completed' is tested and deployed to production.

Anneli15 commented 9 years ago

Was adding some details to loaded compounds and noticed that the details of the ion channel compounds are still missing ( except name and Chembl ID etc = "first page" in Molecular dictionary). No targets, references etc. Actually, also true for some kinase inhibitors, seems that this problem concerns compounds loaded in September (02/09 and 07/09) as Aug 25th is OK? Only compound info in the database on September loaded molecules is the data manually added by me. Have re-opened this issue.

Anneli15 commented 9 years ago

The pro-drug and black box issue is still unresolved too ie all compounds seem to be prodrugs, should be made either unknown or preferrably "No". Have changed some manually but too many of them....

revajk commented 9 years ago

Okie! Let me make this clear. This should be the case of a trial process this morning as I took a dump from production and loaded on to the local and made recent changes and deployed again. I have missed to reload the ion_channels. I will replied them now.

Reva.

On 22 Sep 2015, at 14:46, Anneli15 notifications@github.com wrote:

Was adding some details to loaded compounds and noticed that the details of the ion channel compounds are still missing ( except name and Chembl ID etc = "first page" in Molecular dictionary). No targets, references etc. Actually, also true for some kinase inhibitors, seems that this problem concerns compounds loaded in September (02/09 and 07/09) as Aug 25th is OK? Only compound info in the database on September loaded molecules is the data manually added by me. Have re-opened this issue.

— Reply to this email directly or view it on GitHub https://github.com/chembl/IDG/issues/50#issuecomment-142293796.

revajk commented 9 years ago

@Anneli15 , Ion channels are now loaded. and I had add few target dictionaries manually as the complex where not there(eg.CHRNA3/CHRNB4). I haven't updated any other details other than name. CHEMBL lookup prodrug/blackbox should be fixed now.

Anneli15 commented 9 years ago

Ok, thanks. Will have a look in a minute if the system is ready.

revajk commented 9 years ago

Yes the system is ready. Should be able to view the data.

On 22 Sep 2015, at 16:38, Anneli15 notifications@github.com wrote:

Ok, thanks. Will have a look in a minute if the system is ready.

— Reply to this email directly or view it on GitHub https://github.com/chembl/IDG/issues/50#issuecomment-142326963.

Anneli15 commented 9 years ago

Looks good, thanks Reva.

revajk commented 9 years ago

In the excel sheet, for a compound if the prodrug column is empty - does that mean it is Not a prodrug or is it Unknown?

Anneli15 commented 9 years ago

It means it's not a prodrug.

revajk commented 9 years ago

Thanks ! you still working :-)

On 22 Sep 2015, at 16:41, Anneli15 notifications@github.com wrote:

Looks good, thanks Reva.

— Reply to this email directly or view it on GitHub https://github.com/chembl/IDG/issues/50#issuecomment-142327804.

Anneli15 commented 9 years ago

:-) I check my mails, bad habit not to switch off....