? about searching on AMIGO ATTN SHuly

[katica at acoma.Stanford.EDU]

Hi Mary,

I hope I can provide some help regarding serches in AmiGO. Please see 
below:

On Fri, 28 Oct 2005, Mary (MaizeGDB) wrote:

> Shuly,
> If, as a user, I want to  look at all the structural terms for a body part,
> e.g. root, can I use AMIGO?

Of course, that's why AmiGO is made for searches and queries.
If you type in 'root' and choose 'exact match' only one term will show up, 
that is, 'root'.

To view the ontology tree, you need to click on the little tree icon next 
to the term name (it is blue icon, while the term name itself is green).
Whan shows up is exactly what you described, ontology lineage for the term 
'root' all the way up to the very top node. The children terms of the root 
would not show up at this point. If you want to further expand the tree, 
and view all the children terms under the node of your interest, you need 
to click on the 'plus sign' that is displeyed next to the term name of the 
node you want to expand. Then, keep clicking till you see all 
granular terms under the node(s) you have chosen.


> I am unable to figure out easily how to do this.
> I typed in 'root', with exact match and was able to get the few terms above
> the node when I click on the 'show tree' button. What I really wanted was to
> explore the terms in the root node.
Ontology tutorials that Leonore created are very helpful for tricks on how
to navigate through the PO.

Ontology tutorials that Leonore created and we put up on the POC web 
site are very helpful for 'tricks' on how to navigate through the PO.

> Second question, if I simply wish to look at all the terms in the anatomy
> module that have a match to 'root', can I do this? Currently it seems that
> we access all 3 modules at once. If indeed it is not just that I am spastic,
> and we can't filter for ontology module, is this an easy filter to aad?

We had discussion about improving the searches in AmiGO last summer, and 
again this fall, and a few suggestions for improvements came from me (I 
believe) - I did suggest filtering the search options by Ontology 
aspect, that is, search in 'structure ontology', growth stages, or 
developmental stages'. Shuly is in contact with GO people who are in 
charge of AmiGO maintenence, since we decided to work with them on these 
improvements.

I hope this helps.

Best,

Katica

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Katica Ilic             		katica at acoma.stanford.edu
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