AE doc on GO site

[ValWood]

We are currently deploying a new version of Canto which improves curation of annotation extensions by prompting for allowed extensions on specific terms (this goes further than allowed domain and range, because it also restricts to specific ontology subsets).

Whilst deploying Kim has linked to http://geneontology.org/page/annotation-extension I read this and I barely understood it even though I'm familiar with extensions.

It should tell the user briefly what an annotation extension is before explaining a current GO term. It doesn't explain clearly why we use them. Maybe a couple of real examples would be helpful. A link to the AE paper?

[ValWood]

You can assign this to me if you like. I'll draft something and get @rachhuntley to check/revise

[selewis]

That would be fantastic if you would step up to do this Val. Very much appreciated.

-S

On Tue, Mar 15, 2016 at 10:04 PM, Val Wood notifications@github.com wrote:

You can assign this to me if you like. I'll draft something and get @rachhuntley https://github.com/rachhuntley to check/revise

— You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub https://github.com/geneontology/go-site/issues/170#issuecomment-197154723

[ValWood]

I suggest something more like this for the general user: It probably needs refining but there is now more detail but less jargon. I excluded anything about why the terms aren't just precomposed, I don't know if we need to but a link to the paper can probably satisfy the more curious.

A GO annotation is an association between a gene product and a term from the GO ontology. However, to obtain a more completes description of a gene products biological role, the context in which it acts such as, the proteins it modifies, the subcellular location of the activity, the distribution in cell or tissue types, must be described. An “Annotation Extension” is a mechanism to increase the specificity of a GO annotation and provide this additional detail.

For Example, figure 1 fig1 legend: Graphical representation of Nep1 gene product annotations using (a) the core GO annotation model and (b) the extended GO annotation model to represent target genes of the Nedd8 protease.

An extended annotation is an annotation to a GO term followed by one or more relational expressions (extensions). Each relational expression is written as Relation(Entity), where Relation is a label denoting a relationship type, and Entity is an identifier for a database object or ontology term. For example, the Entity identifier for ‘keratinocyte’ (CL:0000312) from the Cell Type Ontology (CL) can be combined with the Relation ‘part_of’ to create the expression “part_of(CL:0000312)”, and when combined with the GO term ‘nucleus’ (GO:0005634) now describes a gene product that localizes to the nucleus of a keratinocyte.

When curators choose to use an Annotation Extension, they are effectively creating on-the-fly (post-composed) ontology terms. The combinatorial term created by a GO term + Annotation Extension is not added to the ontology (pre-composed), but the annotations are included in the GO database. For annotation extension representation in annotation files see . For annotation extension curation guidelines see on the GO Wiki.

Further information about Annotation Extensions and their potential applications see the Any related items in the FAQ to link to? Extensions in AmiGO etc?

@rachhuntley @cmungall

[ValWood]

fig would be

[ValWood]

Also I couldn't find this in the website by browsing. I only knew about it from the link Kim added to the message

Which menu is it under?

[monicacecilia]

@ValWood

Here is how you can currently find this page - and all other pages:

• If you look for the words extension or annotation extension in the search box
• then you get a list of pages that contain these words: I checked

Also, I just added items to top-level menus:

• The menu item 'Annotation Extension' is now available under 'Documentation:
• and it is also available from the menu at the bottom of the 'Introduction' page for the 'Documentation' menu.

However, here is the mystery:

• I can see the new menus when I am logged in, but cannot see it when I am logged out. So I'm passing this last bit to @kltm so he can see if there is any trouble with my 'editing' powers.

[rachhuntley]

Hi Val,

I think this sounds great and much improved on the last content. A link to the AmiGO display of the Nep1 annotations would be good as well. I don't see any FAQs for extensions, but it would be good to have a general one, e.g. "What are annotation extensions/extended annotations?" that points to this documentation and pointing to the paper would also be good.

Just a couple of typos; "However, to obtain a more completes description of a gene products biological role..." change to; "However, to obtain a more complete description of a gene product's biological role..."

Thanks for doing this. Rachael.

[kltm]

@monicacecilia unless you flush the cache, the menus and pages will persist for around a day until they self-purge. This goes for any page edited while logged in.

[monicacecilia]

@kltm I cleaned caches, used incognito windows and three different browsers... but you know how my computer behaves differently than others. grrr... Good thing is, I see all the menus now! :bowtie:

@ValWood are you planning on updating this content yourself? (I hope :wink:).

[ValWood]

Hi Moni, Sorry no, I can't remember how to.... Plus I'm on reduced hours and doing far more GO stuff than I should be, so editing web pages is out of scope. I don't mind contributing content. Val