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Reimplement slimmer functionality #144
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Tagged for 2.2 for now, if #69 ends up being nasty, may be kicked to the indefinite future or binned. |
@cmungall may have additional commentary/requests (that may end up being separate issues). |
I think the create-your-own-slim functionality may be best broken into its own ticket - or tagged onto a ticket for a tree browser with gene counts. The basic idea is
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I agree, but let's keep it here for now and break it out once we start work here after #69--we'll have a better idea of performance and consequences at that point. |
From Val:
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Bumping as there was recent interest in this from Helpdesk, spawned from the "Paris" virtual Users Meeting |
@suzialeksander I think this is probably not going to happen in AmiGO. Once the functionality was originally removed, we briefly had it in Galaxy (remember that?) and that never really gained traction. The API covers some of this and this is possibly better tackled via web (Jupyter) notebook or the like. |
But slimmer functionality is not so far removed from the MAtrix tool so why not provide it in the familiar AmiGO environment? |
@ValWood At this point, and with many things that we'd like to do, limited resources and priorities. It may be possible to restart some of this when we start into AmiGO development again, but as it has been for the last few years (last note on ticket five years ago), we are unlikely to meet that need with our current roadmap with the current AmiGO. |
OK. It does feel a little like the public facing and major products of GO (ontology and web tools) are a little deprioritised and starved of resources. But I guess it isn't possible to do everything |
That's certainly something to discuss more. If we are to do more User Meetings, we'll have to improve our APIs and docs indeed. As mentioned in the other ticket, creating a slim is a different task than mapping annotations to a set of higher level terms. The former, I don't see that happening any time soon but the later has been available for some time in the API and is used by the ribbon to create the association tables. |
This isn't something the average biologist could use to slim their own lists though. The slim functionality at PomBase is *really *. popular. We don't have an API, and we've never been asked to provide one (although we should), but the point is most of the GO (potential) user base would not know how to use the API, they will go elsewhere. |
Agreed. I will try to reopen the discussion. Do you have a link to the pombase tool ? Thanks |
The slimmer functionality is embedded into our query tool. https://www.pombase.org/query To try it you can select a list from the commonly used queries (all disease associated genes for example). Click on the list in the results table. very quick, very easy. |
The 'full' slim sets are available from the front page I don't have stats for the query tool, only for the static pages. Slims are really popular for people to orientate themselves with their data. For bench scientists, probably more so than enrichment tools if they are made easily avaiable, and the slim has good coverage. They can see immediately what they are dealing with and plan where to go next. |
There is still interest for online slimming functionality; the goal here is to first implement slimmer functionality with the improvements to the perl backend from #69, then move on to more interesting functionality (like defining your own cutsets using a tree browser).
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