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EBISPOT / efo

Github repo for the Experimental Factor Ontology (EFO)
https://www.ebi.ac.uk/efo/
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Write EFO paper #432

Open paolaroncaglia opened 5 years ago

paolaroncaglia commented 5 years ago

This is a reminder of our plan for an EFO general paper. There is some material already that we might link later on.

zoependlington commented 4 years ago

Update: Nico, Paola and myself to meet on 25/11/19 to work on paper.

matentzn commented 4 years ago

@zoependlington , can you create me a simple tree that makes sense for EFO major categories:

Something like:

And so on.. Aiming for someting like 4-5 major categories (like in your presentation) and at most 4 sub categories, ideally two or three). Merci bien!

paolaroncaglia commented 4 years ago

Update re EFO paper: in progress; Nico worked on it; Paola is looking into details of gathering info from internal and possibly external users; Zoe is addressing a few tasks; Paola and Zoe will generally try to work on draft before the holidays, but unsure how much will get done due to other pressing tasks; will surely reconvene after the holidays to discuss progress and pending matters.

matentzn commented 4 years ago

@zoependlington dont forget my comment above! :) I would love to generate the figures tomorrow before I leave, so I can feel you have something to work with to write text.

matentzn commented 4 years ago

The data I won't generate (@zoependlington and @paolaroncaglia, if you happen to get additional data from survey of top of your head, fine, if not, just work with the open targets sources):

Less important, only if easy:

zoependlington commented 4 years ago

Sorry @matentzn, skipped my mind. Here you go! @paolaroncaglia please feel free to add or remove any you don't agree with!

paolaroncaglia commented 4 years ago

@zoependlington and @matentzn Thanks Zoe for drawing the category tree. EFO also has quite a few protocols, so how about replacing the 'Measurements' category with 'Measurements and protocols' and adding 'protocol' (OBI:0000272) beneath it? That's a relevant area for some of our resources. But maybe not vital, I agree.

paolaroncaglia commented 4 years ago

and CL:0000010 'cultured cell' (aka cell lines) under the Anatomy cat please :-)

helenp commented 4 years ago

The protocols are likely to be rather old and were originally created for annotation of MAGE-TAB files for gene expression data. I don't know if therefore if this is a current use case for ArrayExpress or any other resource. No objection to the merge.

paolaroncaglia commented 4 years ago

Would EFO:0000548 'instrument' be useful? Not sure if those terms are old/currently used.

matentzn commented 4 years ago

Zoe and I have worked out a good grouping I think:

image

This shows the distribution of entities into five domains: Diseases, Traits and Phenotypes (DTP), Biological processes (BP), Measurement, assays and compounds (MAC), Anatomy, Development and Cells (ADC) and Other (O) .

I dont have now time to change it before going on holidays, but lets see whether this works..

paolaroncaglia commented 4 years ago

Is there a historical reason why we're using OBI_0100026 for 'organism' instead of NCBITaxon:1 'root', and should we change? Sure, the OBI label is better.

helenp commented 4 years ago

Because NCBITaxonomy isn't an ontology, it's a taxonomy and has no commitment to be an ontology. Would we do this with a MeSH term?

paolaroncaglia commented 4 years ago

@helenp No, of course not :-) but all children of OBI_0100026 'organism' in EFO are NCBITaxon terms, hence my question. Thanks.

paolaroncaglia commented 4 years ago

( @matentzn and @zoependlington thanks for adding biological process, that would have been my last "request".)

zoependlington commented 4 years ago

Sorry! Meant to update my suggested groupings after a chat with Nico earlier to include cultured cell and biological process. These are the new groupings:

matentzn commented 4 years ago

Alright @zoependlington @paolaroncaglia I posted some data all across the paper and tagged you for some tasks.. I will stop working now, but feel free to continue tagging me; I will add any more data that you need in the end of the year. I send Zoe a html dump of the current jupyter notebook; I will clean all that up and add it to the supplementary materials when I am back! Good luck for now :)

paolaroncaglia commented 4 years ago

Making a note of some items for future discussion:

paolaroncaglia commented 2 years ago

@zoependlington I'll remove all assignees except for you and me (but feel free to add back if you disagree). I linked this ticket to the "old" EFO paper draft, but I'd suggest to review this thread and move material to the new draft instead. You'll let me know how I can help when the new draft is ready, no rush. Thanks.

paolaroncaglia commented 2 years ago

@zoependlington FYI, I'm removing my assignment as I'm sorting out my EFO ticket queue. Of course, I'm available for any discussion on the EFO paper - you'll let me know if there are any tasks that I can address this month. Thank you!