Talk:AmiGO: Mock-ups: Difference between revisions

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I think that's enough. Great job Amelia!
I think that's enough. Great job Amelia!
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Val
I only have some minor suggestions and these are mostly about general Amigo display issues.
1. General Amigo comment:
'browse GO option'
http://toy.lbl.gov:9006/cgi-bin/amigo/go.cgi?search_constraint=terms&action=replace_tree&session_id=2920b1153155127
It was mentioned at the reference genome meeeting that this page is fairly unintuitive for users to land at, and it was suggested that this would be a good place to provide very basic instructions/details about exactly wht this view is, and
text for example saying 'clicking on the + icon will show child terms' etc. I guess there will be general feedback about this from the meeting.
2. General Amigo comment:
I was wondering recently (since obsolete GO annoptations are not visible, whether it is worth showing the greyed out obsolete terms on the front page/
is this useful?
# open [http://toy.lbl.gov:9006/cgi-bin/amigo/go.cgi?action=plus_node&depth=1&search_constraint=terms&query=obsolete_biological_process&session_id=2920b1153155127 is_a relationship] [http://toy.lbl.gov:9006/cgi-bin/amigo/go.cgi?view=details&search_constraint=terms&depth=0&query=obsolete_biological_process&session_id=2920b1153155127 obsolete_biological_process : obsolete_biological_process  ( 0 )]
# open [http://toy.lbl.gov:9006/cgi-bin/amigo/go.cgi?action=plus_node&depth=1&search_constraint=terms&query=obsolete_cellular_component&session_id=2920b1153155127 is_a relationship] [http://toy.lbl.gov:9006/cgi-bin/amigo/go.cgi?view=details&search_constraint=terms&depth=0&query=obsolete_cellular_component&session_id=2920b1153155127 obsolete_cellular_component : obsolete_cellular_component ( 0 )] 
# open [http://toy.lbl.gov:9006/cgi-bin/amigo/go.cgi?action=plus_node&depth=1&search_constraint=terms&query=obsolete_molecular_function&session_id=2920b1153155127 is_a relationship] [http://toy.lbl.gov:9006/cgi-bin/amigo/go.cgi?view=details&search_constraint=terms&depth=0&query=obsolete_molecular_function&session_id=2920b1153155127 obsolete_molecular_function : obsolete_molecular_function (0)]
3. The text from the search says (for example)
*46* results for gene product rpr in field Gene Symbol
Should this say *46* results for *search string*  (or something similar)  rpr in field Gene Symbol?
4. General Amigo comment:
The query (gene name/symbol) implies the gene name is being searched, but actually the gene name and product/description is being searched. This is a bit confusing, and a bit annoying if you really are searching for a gene name.
For example I wouldn't expect to retrieve things like 'early germ cell ove****rpr****oliferation' if I was searching on genesymbol/name rpr, but this appears to be normal Amigo behaviour?
Should we really be searching descriptions with this option?
5. Mock up specific comment, The 'browse GO' and search by sequence link doesn't work from the term detail view (main bar)
6. Mock up specific comment.
On the entry point, wopuld it be possible to make it clearer which rafio box belongs to which option. The first couple of tests I checked 'gene symbols or name's when I wanted 'terms'

Revision as of 01:53, 27 July 2006

[jane]

I really like the front page mock-up, much cleaner and less confusing. Couple of things resolving weirdly on my browser (FireFox, Linux) though: I can't see the box you type the text into on the front page, and the tree view is a bit distorted, all the filter boxes too big, can't see top of the term names. But I guess these are the sort of things we'd sort out later?

an idea - can we make the tree browser so when you click a term, it opens the branch below, rather than taking you to term details, and at the end of each term, we have a little icon that says (genes) or (details) or something? This should stop people clicking the high level terms so often...?

Another little thing, can we have a mouse-over for the pie chart icons?

[Rachael]

I like this a lot. The design is much cleaner and easier to read than previously. I love that the results open in the same page and not in a smaller new window as before. I'm using Firefox, but the only display problem I see is with the Gene Product Filter boxes extending too far to the right in the left menu bar. On the front search page the 'Query by Sequence' is in bold whereas the 'Browse GO' and 'Advanced Query' are not - is this intentional? I can see that highlighting the search results in blue is less offensive to the eye, but I kind of feel it's too much blue, so the highlights aren't very obvious - maybe another colour to contrast with the blue but not give you a headache - light grey??

[gwg (Amelia)]

  • I've changed the highlight colour to a different shade so it's a bit more visible.
  • I've tried to change the form elements so they display a bit better in FireFox - let me know if they're still outsized.
  • I de-bolded those links Rachael mentioned - I'm not sure why they were in bold, maybe because it's the link to GOst?
  • I like Jane's idea about expanding a node in the treeview by click on either the plus sign or the term name - it would be useful to have the mouseover text say what is going to happen if you click on the term name, rather than telling you the term def... then again, it's also useful to know the def. Hmmm...

Keep the comments coming!

[Pascale]

  • I agree with Val (see email) about the front page issue, ie we need to explain what AmiGO does. The new front page is already mauch better than what we currrently have (that is, going directly to the GO browser). We just need a little blurb. Maybe something similar to the first line of the Users Guide would do? "Browse, query and visualize terms and annotations from the Gene Ontology", just below the AmiGO icon?
  • I would move the links in the footer [GOst and User Guide] up with Browse GO- advanced query - search by sequence. So this would become: Browse GO • Advanced Query • Query By Sequence (GOst) • Users Guide
  • In the footer, I think we should rename "help" to "contact us". When I see "help" I expect the user guide (I might just have a strange expectation here).
  • I quite like the menu bar you have on top of the results pages. How about replacing the options Browse GO • Advanced Query • Query By Sequence (GOst) • Users Guide by that menu on the front page as well?
  • Following up on Val's comment about obsolete terms, I wonder if we could only show them when someone does a keyword search, but not show them in the browser view?
  • It's nice that there is a "Search GO" option on all pages. Could we make it the same everywhere and at the same location? Also, on all the pages (other than the front page) there are two Search boxes, plus sometimes a link to "search". To me that's confusing. My preference is for the way you have it on the "term results" page, with the search box below the menu (but then I would remove "Search" from the menu). Also I am tempted to suggest to remove the search in the upper right hand corner.
  • I am with Rama about the green highlight-- what was wrong with the yellow highlight we currently have?
  • In the "term" results page, I thing "filter results" go below the term name, wth "term information" etc. The other options in that top menu seem more general.

I think that's enough. Great job Amelia!



Val

I only have some minor suggestions and these are mostly about general Amigo display issues.


1. General Amigo comment:

'browse GO option' http://toy.lbl.gov:9006/cgi-bin/amigo/go.cgi?search_constraint=terms&action=replace_tree&session_id=2920b1153155127 It was mentioned at the reference genome meeeting that this page is fairly unintuitive for users to land at, and it was suggested that this would be a good place to provide very basic instructions/details about exactly wht this view is, and text for example saying 'clicking on the + icon will show child terms' etc. I guess there will be general feedback about this from the meeting.


2. General Amigo comment: I was wondering recently (since obsolete GO annoptations are not visible, whether it is worth showing the greyed out obsolete terms on the front page/

is this useful?

  1. open is_a relationship obsolete_biological_process : obsolete_biological_process ( 0 )
  2. open is_a relationship obsolete_cellular_component : obsolete_cellular_component ( 0 )
  3. open is_a relationship obsolete_molecular_function : obsolete_molecular_function (0)

3. The text from the search says (for example)

*46* results for gene product rpr in field Gene Symbol

Should this say *46* results for *search string* (or something similar) rpr in field Gene Symbol?


4. General Amigo comment:

The query (gene name/symbol) implies the gene name is being searched, but actually the gene name and product/description is being searched. This is a bit confusing, and a bit annoying if you really are searching for a gene name.

For example I wouldn't expect to retrieve things like 'early germ cell ove****rpr****oliferation' if I was searching on genesymbol/name rpr, but this appears to be normal Amigo behaviour? Should we really be searching descriptions with this option?


5. Mock up specific comment, The 'browse GO' and search by sequence link doesn't work from the term detail view (main bar)


6. Mock up specific comment. On the entry point, wopuld it be possible to make it clearer which rafio box belongs to which option. The first couple of tests I checked 'gene symbols or name's when I wanted 'terms'