OpenSourceMalaria / OSM_To_Do_List

Action Items in the Open Source Malaria Consortium
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9) Restart discussions with Chembl about automatic import of SD file #127

Closed alintheopen closed 10 years ago

alintheopen commented 10 years ago

The SD file needs to be continually updated and ideally be part of a Knime workflow that automatically updates to ChEMBL. We need to consult with @madgpap about the best way to implement this tool.

mattodd commented 10 years ago

Telecon with ChEMBL set for Jan 22nd. Will post on the discussion afterwards. Context: http://malaria.ourexperiment.org/osddmalaria_meeting_/8407 Essential point: we'd like to maintain one SD file for all compounds in OSM and have the data automatically imported to ChEMBL rather than doing batch uploads. The question is whether this is possible, and if so, how should the project data be maintained within the SD file?

On 8 January 2014 23:14, alintheopen notifications@github.com wrote:

The SD file needs to be continually updated and ideally be part of a Knime workflow that automatically updates to ChEMBL. We need to consult with @madgpap https://github.com/madgpap about the best way to implement this tool.

— Reply to this email directly or view it on GitHubhttps://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/127 .

MATTHEW TODD | Associate Professor School of Chemistry | Faculty of Science

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mattodd commented 10 years ago

Previous general discussion on visualisation: https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/112 and https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/99

mattodd commented 10 years ago

This phone call between Mat Todd, Alice Williamson and George Papadatos (Chembl @madgpap ) took place on Jan 22nd 2014. Upshot: George happy to scrape data from OSM's SD file that would populate the new open drug discovery page in Chembl (https://www.ebi.ac.uk/chembl/malaria/source) with a table of data of the newest compounds, to allow browsing the data, but these data would not be part of the Chembl database proper. During Chembl's periodic import of data into the full Chembl database, the data would then be included. This would be a good stopgap measure to allow visualisation of the newest compounds quickly. It would also be possible to include a link for each compound to the relevant compound's summary page in the "Experimental Procedures" part of the lab notebook. Action: Start new Issue that trials this functionality, requiring there to be an update of e.g. 5 new compounds which can then be imported automatically. Closing.