Annotation consistency: IEA, ISS, IC Usage Discussion
Email exchange
Tanya Berardini, Emily Dimmer, Pascale Gaudet, Chris Mungall, Kimberly VanAuken
Hello,
I am going through the action items for next week's reference genome conference call. At the reference genome meeting we all eagerly volunteered to come up with some guidelines as to how to use ISS, IEA and IC (too much coffee??). Here's the major points I remember:
- IC: came up during the example of a translation initiation factor
annotated to a good function and component but had a root annotation for process. It was suggested maybe that could have got an IC annotation. (gene is mouse Eif2b2)
- related is ISS and IEAs: David pointed out this gene probably had a
goos IEA annotation from interpro. The question was how to address this: dicty and pombe would make this an ISS annotation, to avoid the root annotation. The problem is, InterPro domains and mappings can change so maybe that's not such a good practice after all. However, since IEAs ware not displayed in AmiGO (and perhaps excluded in certain studies are poorly reliable), some valuable information is not used.
Was that your recollection as well? Can we make a plan to discuss that at some point and come up with suggestions? (It doesn't have to be before the call next Tuesday; but I wanted to write down the important discussion points).
Cheers, Pascale
Hi,
My memory of the Reference Genome discussion for IEA was that as many of the IEA methods used have increased in quality over the last 5 years, some groups are becoming more accepting of the data they provide. I thought that Judy's suggestion was that a group should overview these methods and decide which sets of data should be displayed in AmiGO (ie. if an annotation is supported by multiple independent IEA methods).
If that is a true memory it might be handy to draw up a list of the IEA methods that we want to discuss. From the GOA perspective, I would like to include:
- InterPro2GO
- SwissProt Keyword 2GO
- EC2GO
- HAMAP2GO
- UniProt subcellular location 2GO
- Ensembl Compara - projection of annotation from ortholog data.
Cheers, Emily