IS213 Projects Home

Assignment 1

• Problem Statement
• Project Members

Assignment 2

• Personas
• Task Analysis
• Appendices
• Work Distribution

Assignment 3

• Scenarios
• Comparative Analyses
• Initial Design 1
• Initial Design 2
• Initial Design 3
• Work Distribution

Assignment 4

• Introduction
• Low-Fi Prototype
• Methods
• Test Measures
• Results
• Discussion
• Appendices
• Work Distribution

Assignment 5

• Design Revisions
• Revised Scenarios
• 1st Hi-Fi Prototype
• Storyboards
• Instructions for Use
• Slide Presentation
• Work Distribution

Assignment 6

• Heuristic Evaluation
• Work Distribution

Assignment 7

• 2nd Hi-Fi Prototype
• Responses to HEs
• Work Distribution
• Instructions for Use

Assignment 8

• Introduction
• Method
• Test Measures
• Results
• Discussion
• Appendices
• Work Distribution
• Slide Presentation

Final Write-up

• Problem Statement
• Solution Overview
• Final Personas
• Final Scenarios
• Revised Storyboards
• Final Interface Design
• Design Evolution
• Interactive Prototype
• Instructions for Use
• Work Distribution
• Slide Presentation

Session Transcript for User B

Friday, March 3, 2006

Experience with IMG: Very high.
Experience with annotations: Low.

TASK 1: Look at a specific gene's annotation history

Click on gene object ID or Description. "Interesting." One has conversations about the annotation. "That is pretty cool." Batting average: "That's great." He clicks on "V1.0," and get the annotation history

TASK 2: Modify an existing annotation with homologous data

He clicks 'update annotation' and then studies the Modify Annotation window for a bit. He returns to the original browser window, takes the locus tag and performs a BLAST search. The second gene hit looks promising, so he opens up the gene details page to get all his info. He leaves the pre-fill values drop-down box at 'previous annotation' and manually fills in this homologous data. He would like a way to compare the all the differences between the previous gene annotation and the new gene annotation. He is concerned that a message posted to the Modify Annotation discussion window would get washed out, would not be associated with his annotation, and would lose context and have no meaning. He clicks 'Submit.'

TASK 3 : Save a draft of this annotation modification

He clicks 'save draft.' He leaves the 'saved draft' page open when he walks away. On his return, he clicks 'MyAnnotation.' In the drafts list, he wants to double-check his work, so he clicks   on 'edit', then 'preview', then 'submit'.

TASK 4 : Express opposition to someone else's choice of annotation

First User B would like to see what other people have said on this topic. He clicks "more" (after V1.0...) to see the discussion history.   He would return to the Gene Details page, click on I Disagree, and click Discuss to leave a comment about why he disagreed. He would leave orthology information to back up his disagreement. If he felt really passionate about this error, he would go Update Annotation.

TASK 5: Change an annotation by adding a COG group to it

Click on gene malate dehydrogenase. He goes to the COG browser, searches for the function, identifies cluster id 942 in which there are 123 genes. Once he identifies a COG, he verifies that this gene is a member of that COG by doing a BLAST hit. Finally he enters the COG data and clicks 'Submit.'

 

Open Questions

How useful is ranking information?

The most recent annotator name is very useful. He would take the agree/votes with a grain of salt, believing that the majority of people don't know what they're doing anyways.

Other issues?

The pre-fill values drop-down menu does not give enough information about homologues, and User B doesn't really trust homologues anyway.

Would you vote?

Only if he has studied this gene extensively, in which case he believes he would click either I Agree or Disagree equally. In fact, he thinks I Disagree would happen less often, because if the majority of the annotation is correct, he would not want to call out one small error in one field by disagreeing with the entire thing.

On the one hand, as someone who annotates, he has an interest in making sure that that data is correct. On the other, he is a very busy person, like most grad students, post-docs, and professors, so he won't mess with things that he does not have a vested interest in.

Other Comments?

If I make a discussion about multiple genes from the gene cart, is there a way to know, from each gene, that the annotator annotated all the genes in that particular batch of genes? I can see situations arising where a set of genes should be involved in a discussion.

Possible solutions

• On the annotation history page, we could have the Gene ID of all the other genes who have that comment.
• We'd have the option to post comment to the entire group of genes. Perhaps an option/check-box.
• perhaps the top of the modify annotation would get altered on the fly after selecting an option, to say that this is going to this set of genes.

Would you ever be confident enough to annotate all selected genes at once?

Very Occasionally. If I were running through a process that pulled out a list of genes that were all related for some functional. Something like a screen with all the gene IDs in one window, and then an 'annotate all' button. "I think genes should be annotated one at a time, personally."

What do you think of 'fellows'?

"I think that's a fair request of the user base." It's a way to identify people who are fairly serious about annotations. "I like that idea a lot."

Last Comments

User B would like more substantial evidential support in IMG, so that users know what physical data these annotations are based on. Namely, he wants PFAM and UNIPROT data, or even a link to one of Kimmen Sjolander's gene sequence books.  

You should allow hypertext links to more substantial evidence in the discussion page.

"Pre-fill is clever, but dangerous." User B worries about people getting too caught up in it, pulling data from hypothetical proteins, etc. Also how do you deal with propagating corrections to a certain gene through all the genes that were pre-filled based on that gene? "I would not have a problem with not being given [the pre-fill option]."

"I think this is great. Within 30 seconds, I felt like I had a feeling for what was going on on in the page."