New term request: "4C-seq"

[anjaf]

For new term requests, please provide the following information:

Preferred term label

4C-seq

Synonyms

Textual definition

Circular chromosome conformation capture combined with high-throughput sequencing PMID: 22961246 (https://doi.org/10.1038/nmeth.2173)

Suggested parent term

http://www.ebi.ac.uk/efo/EFO_0003740 http://www.ebi.ac.uk/efo/EFO_0009967

[paolaroncaglia]

@anjaf The new term is EFO_0030037 (4C-seq).

[anjaf]

Thanks a lot @paolaroncaglia! That was quick. :)

[anjaf]

Sorry to be opening this back up. I can't find the term "4C-seq" in EFO and the quoted accession doesn't seem to be the right one. (EFO_0030037 leads to "T cell activation assay"). Maybe something got mixed up?

[paolaroncaglia]

@anjaf

Sorry to be opening this back up. I can't find the term "4C-seq" in EFO and the quoted accession doesn't seem to be the right one. (EFO_0030037 leads to "T cell activation assay"). Maybe something got mixed up?

Thank you for pointing this out. This pull request shows that in mid-October I added and committed EFO_0030037 as '4C-seq'. However, as you noticed, EFO:0030037 now points to 'T cell activation assay', and there is no '4C-seq' in EFO. Let me dig a bit deeper to figure out what went wrong and suggest a course of action.

[paolaroncaglia]

@anjaf In mid-November I indeed added EFO_0030037 as 'T cell activation assay', as shown in this pull request. My Protege is set up so as to remember the last ID used, but apparently EFO_0030037 was still available. I could have somehow unconsciously scrambled the Protege set-up to allow that, or my mid-October commit might have been reverted for some reason - let me check the full commit log. Then I'll see what's best to do, possibly add 4C-seq again... I might need to ask for assistance as I no longer work at EBI, but I'll see that this is addressed soon. Not sure what went wrong but apologies for whatever that was!

[anjaf]

No problem and thank you for looking into it @paolaroncaglia. As I wasn't sure you would see the message here I also opened a new issue: https://github.com/EBISPOT/efo/issues/1635

[paolaroncaglia]

@anjaf It looks like this commit never went through. To fix:

• [ ] A new term should be created for 4C-seq as detailed here;
• [ ] "RIP-Chip by array" should be made a subclass of the additional parent "assay by array".

I'll see that this is all done in time for the mid-July EFO release.

[paolaroncaglia]

@dosumis @zoependlington @bvarner-ebi Tagging all 3 of you as I know that at least 2 of you are away. I somehow lost sight of an EFO commit I made in mid-October, see thread above. I suppose that's what happens to ontologists when they get old. I'd like to re-do the edits in a fresh EFO branch unless you have any objections, I think I still have privileges? Is there anything I should be aware of - any changes in the EFO pipeline since the last time I committed in mid-May? Thanks.

[paolaroncaglia]

P.S. Yes, I checked, and that was the only pull request of mine in the open PR queue ;-)

[zoependlington]

@paolaroncaglia No changes! Please feel free. If you run into any issues, let me know!

[paolaroncaglia]

@anjaf FYI, Zoë will do the edits listed above for me, in time for the July 18th EFO release. Thank you both!

[zoependlington]

@anjaf I have added 4C-seq as EFO_0021526 and completed Paola's other changes that were missing. These will be available after the July release (18th).