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[bioontology-support] New version of Bioportal comments & questions

Twigger, Simon (MCW) simont at
Thu May 14 10:49:52 PDT 2009

Observations as I use the new version. I was originally looking for  
some specific info related to the rat strain ontology, then thought  
I'd explore more and give feedback on the whole thing. :) hopefully  
its useful!

I like the new look and feel, hard to go wrong with Blue.

The home page dumps you right into the thick of things - this is going  
to be very off putting for new/naive users who need to get their  
bearings first - or even for me coming to the new version trying to  
figure out where to go now things have changed. Add links to help/ 
introl material, the demo video (which is now out of date - the  
downside of video tutorials!), etc. How about a 'What are you trying  
to do...? section or drop down, that might direct people to the  
appropriate tool/page depending on their needs. Tracking something  
like this would also help you know your audience better as they would  
be telling you why they were here, rather than you having to guess  
their intentions from the google stats.

Are there any ontologies that you dont have that people might expect  
to find? Snomed, etc. comes to mind - might be worth mentioning these,  
saying why they arent there and helping people move on to resources  
that might be able to help them if they are interested in these vocabs.

Consider having examples for the various searches that you have at the  
top so people can try something that will return a good hit, rather  
than forcing them to guess what goes in there. Autocompletion of the  
ontology name is good (Find an Ontology) but it only works from the  
start of the ontology name - if I put in Mouse it finds the three  
Mouse ontologies that start with the word Mouse, if I put in 'anatomy'  
it doesnt find any ontology containing the word anatomy which would be  
more useful. Consider making this look for the occurrence of the text  
anywhere in the ontology name, not just at the start (simple regex  
change needed when it does the db lookup?)
The other two searches (search all ontologies and search resources)  
dont seem to have autocompletion - it would be nice if they did.

To be obnoxious I tried search all ontologies with 'a' as the search  
term. It passed me off to the flash search but this still had a  
previous search term in there, it didnt do the search for 'a'.  
Ultimately found out it needs to be 2 chars or longer to run - might  
be worth having this notification on the original form, though  
probably other people wont be trying to break things like I was....

Projects Tab

Needs more categorization and intro material - what is on this page,  
what is a project. Organize this so its useful - try not to become  
like the GO tools page used to be,  a long list of things that had  
little or no info to help a new user figure out what they were and why  
they might invest time looking at them.

Should "Chris's project - Visit the website for a description, I'm too  
lazy to type in stuff here, although I guess I am typeing in stuff  
anyways. Doh...." be one of the first things people see? Doesn't give  
a great impression of quality control to me - are submissions to this  
page reviewed before they go public?

Annotate Tab

Flash came up, no instructions or info about what this page is at the  
top of the page. Clicked help question mark, the help drawer slid out  
from the right but not the whole way - I cant read it. Tried  
reloading, scrolled down a bit and found scroll bar at the bottom of  
the window, my window wasnt big enough to see this before. Might be  
worth having the help panel overlap the form when it appears or make  
the standard flash size a bit smaller. tried annotating a short  
sentence with default settings - it timed out. Consider having a  
working example that will show people what this thing can do, rather  
than leaving new users to guess what should go in and likely giving  
them a timed out result.

Search Tab

Not sure if I like the flash/flex UI vs an ajax/html version but it  
works pretty well. I was very pleasantly surprised when I did a  
search, visited an ontology page and hit the back button to get back  
to the search results - it loaded the original search results again as  
I hoped - nice job not breaking the Back button! This makes me like  
the flash more though I did have to wait for the entire thing to load  
up again rather than it being cached by the browser.

Ok - on to why I was really visiting the site....

Im looking at the rat strain ontology - I like that the terms are now  
in alphabetical order when I get to the Rat Strain ontology via the  
home page's 'Find an Ontology', though when I followed a search (used  
flash search on the Search tab to find a specific strain symbol) to a  
rat strain term, the strains were no longer in alphabetical order.

Resources associated with the Rat Strain ontology - Im here to find  
out how you have managed to link the rat strain terms to these  
external resources. Clicking on an individual resource brings up a  
list of ... hits (?), presumably these are records in the external  
resource that have some association with this term. Clicking on  
'Description Holder' because its the only clickable thing there (very  
unintuitive name btw - what does this mean?) brings up an empty window  
(Firefox 3 on the mac). What does the score mean - Im not sure this  
number adds anything to the user's knowledge at this point, can you  
translate to a word (strong/highly relevant association, weak  
association, etc. that might convey the meaning of the score to a  
general user?

The ID field looks more like it should be the link to the parent  
resource, can you make this clickable? It would be nice to have some  
more context/info about how and why this record is associated with the  
particular ontology (is this what might appear in the description  
holder window?).

Where did the GEO results go?

Hope the feedback/comments were useful - any thoughts on these last  
few questions (finding resources annotated to rat strains, where are  
the GEO results) would be great!



Simon N. Twigger, Ph.D.
Assistant Professor, Department of Physiology
Medical College of Wisconsin
8701 Watertown Plank Road,
Milwaukee, WI, USA
tel: 414-456-8802
fax: 414-456-6516
AIM/iChat: simontatmcw

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