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openphacts / coreGUI

This is the repo for the central GUI API and GUI components code
GNU General Public License v3.0
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Target selection by ontology #7

Open leeharland opened 12 years ago

leeharland commented 12 years ago

[USC Feedback] while target ontology is not yet available should be able to pick by any ontology, can prototype using GO?

askjaer commented 12 years ago

This would be an issue relating to the ConceptWiki API lookup and could perhaps be a feature enhancement to this. I am reassigning this issue to Kees fto get his comment.

leeharland commented 12 years ago

I think this is more a question of data in the cache. Essentially we need to be able to build and navigate protein taxonomies, so i think this is more a get the data, write the query, write the widget issue

askjaer commented 12 years ago

It would be cool if we had data on target taxonomies in the LDC such that we could do a target broswing tool like they have on ChEMBL. Doing the tree and the pie chart stuff is very easy in ExtJS and something we would need. Can we get the target ontology/taxonomy used by ChEMBL?

leeharland commented 12 years ago

There are two answers to this! Firstly, there is a new working group on target ontology that is led by christine which will look to addressing exactly this. The idea to create a full ontology by merging different EFPIA lists. But this will take a long time to deliver. In any case, the functionality we build should be generic. Any tree which has proteins as leaves should be able to be loaded up in the same widget "browse proteins by tree X". So, developing against the GO tree would be the same code as the chembl tree, just a different query. I do like the idea of using the chembl tree BUT i am not sure if its in the RDF we have. We need to check if that data has been RDFised, if not then we cant do this and should choose GO.

leeharland commented 12 years ago

At the TTF the manchester group agreed to look into this, a series of areas to consider:

  1. Is the target tree from chembl available (check with egon)
  2. Can we load GO + GOA into the system to enable queries of the form "give me a list of proteins who are defined by the ontology node X". This of course should include all proteins attached to siblings of that node
  3. with sune/steve, look at tree widgets that could be used in the GUI to select nodes in the first place
leeharland commented 12 years ago

Oh, and 4. decide which order we can do these 2 examples, GO or chembl tree first (or both together)