Talk:AmiGO: Mock-ups

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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?


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!


AmiGO makeover

  1. On the front page, I am thinking we should have two pull-downs (may be more):
    • one like in OBO-edit to allow for specific searches like GO term, gene name, GOID, exact name, contains etc..
    • one for each ontology. This can be a checkbox also.
  2. We should list software that accesses the database separately on the top (GOst, map2slim) and keep search options on the bottom or something like that.
  3. In the Advanced search option, we should provide a list of Reference genomes separately and for the rest, provide a taxonomy browser like the NCBI one. We should group organisms by the kingdom.

Term Detail Page

I like the menu at the top.

Keeping the huge volume of annotations in mind, in our last conference call, we all liked the idea of providing a summary table of number of annotations for each species and provide two options for each species- View annotation, Download annotations, all on the term details page. We may want to add two sub-options for the Annotations option on the menu on the top: View annotations, Download annotations.

We have some room on the page. We can expand the Evidence codes and offer a taxonomy browser to filter.

Term Search Results Page

Here are my comments on the mock up:

  • I am not very fond of the green color for highlighting the matches.
  • We might want to provide on the top the exact match for the query.
  • We should provide the number of annotations for each match in parenthesis or something like that.
  • On the left hand corner, should we just use + to denote that the node can be opened and get rid of that tree icon?
  • I am thinking that clicking on the + should just go to the term tree view page for that term.
  • We should have a download button to download the pages.


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

General Amigo comments:

  1. 'browse GO option'
    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. I was wondering recently (since obsolete GO annotations are not visible, whether it is worth showing the greyed out obsolete terms on the front page. is this useful?
  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. 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?

Mock up specific comments:

  1. The 'browse GO' and search by sequence link doesn't work from the term detail view (main bar)
  2. On the entry point, would it be possible to make it clearer which radio box belongs to which option. The first couple of tests I checked 'gene symbols or name's when I wanted 'terms'


  • 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 much 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!