#314 SOM term requests


I would like to annotate some tRNA modifications and possibly features and Midori Harris suggested that we (PomBase) could use the SOM ontology developed by Colin Batchelor.

I'd therefore like to request a few new terms for this ontology, I'm also referencing the SO ID for the modifications:
1. pseudouridine (SO:0001229)
2. 2-methylguanosine (SO:0001325)
3. dihydrouridine (SO:0001228)
4. N6-threonylcarbamoyladenosine (SO:0001305)
5. 7-methylguanosine (SO:0001326)
6. 5-methylcytidine (SO:0001282)
7. 1-methyladenosine (SO:0001295)
8. Grp (SO:0001331)
9. methionine anticodon (child of SOM:0001174 anticodon) 5' CAU 3'
10. anticodon stem
11. D stem
12. T stem
13. acceptor stem


  • Antonia Lock

    Antonia Lock - 2012-09-19
    • assigned_to: eilbeck --> nobody
  • Karen Eilbeck

    Karen Eilbeck - 2012-09-25

    Hi Antonia,
    Mike Bada is the current person who is working with a molecular version of SO.
    I have sent him an email with the link the this request.

    Could you use the SO terms that are currently available as a place holder for the SOM. or MSO terms?


  • Antonia Lock

    Antonia Lock - 2012-09-25

    Thanks for the response Karen. There's no immediate rush - we are a bit unsure how to number the tRNA nucleotides as there is a convention to give certain nucleotides certain numbers - which we worry will lead to computational problems. We are therefore unsure of how to deal with this. I emailed Rfam to see if they have any suggestions but haven't heard back from them yet.

  • Mike Bada

    Mike Bada - 2012-10-01

    Hi Antonia,

    As Karen said, I'm working with Karen on a restructuring of the SO. I envision eventually that the RNA Ontology (another OBO) will be the main resource for RNA-specific terms and will properly link up to the SO. However, there's lots of work to be done before that, so we can plan to add the terms to the SO at least for now. Just let us know when you might need them.



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