Divoli Presentation at EBI Apr2011 Usability Part

European Bioinformatics Institute 13 - Apr - 2011

Human factors in computational biology:

from mathematical models to user interfaces

Anna Divoli

Outline

Human factors: expert opinions & usability studies

1. BioText Usability Studies

1. HCI principles

2. Studies

2. Expert Opinions

Interviews

Analysis

Results

motivation [usability studies…] [expert opinions…] acknowledgments

BioText Search Engine

Marti A. Hearst, Anna Divoli, Harendra Guturu, Alex Ksikes, Preslav Nakov, Michael A. Wooldridge and Jerry Ye (2007) “BioText Search Engine: beyond abstract search” Bioinformatics, 23: 2196-2197

motivation BioText HCI Usability Studies: one, two, three Conclusions [expert opinions…] acknowledgments

Tools for:

machines…

workflows…

end users!


• Design for the user, not for the designers or the system

• Needs assessment: who users arewhat their goals arewhat tasks they need to perform

• Task analysis: characterize what steps users need to takecreate scenarios of actual usedecide which users and tasks to support

• Iterate between: designing & evaluating Design

PrototypeEvaluate

HCI principles


• Make use of cognitive principles where available

Important guidelines: Reduce memory loadSpeak the user’s languageProvide helpful feedbackRespect perceptual principles

• Prototypes: Get feedback on the design fasterExperiment with alternative designsFix problems before code is writtenKeep the design centered on the user

HCI principles


Three Usability Studies for BioText: Study 1

1. Pilot study before releasing BioText to the public

Hearst, M.A., Divoli, A., Ye, J. and Wooldridge, M.A. (2007) "Exploring the Efficacy of Caption Search for Bioscience Journal Search Interfaces", BioNLP Workshop at ACL 2007

Primary Goal: Determine whether biological researchers would find the idea

of caption search and figure display to be useful or not.

Secondary Goal: Should caption search and figure display be useful, how best to support these features in the interface.

- 8 participants, in person, via campus recruitment

- three views, order of presentation was varied, used their own queries

- we remained objective, evaluation via open-ended discussions & questionnaires


• 7 out of 8 said they would want to use one of the caption search interfaces in their bioscience journal article searches

• Many participants noted that caption search would be better for some tasks than others

• Best to show all the thumbnails that correspond to a given article after full text search

• Best to show only the figure that corresponds to the caption in the caption search view

• All four participants who saw the Grid view liked it, but noted that the metadata shown was insufficient: wanted to see title and other bibliographic data

Study 1: Results



2. Study that explored whether or not to show term-extracted entity information to users

Divoli, A., Hearst, M.A. and Wooldridge, M.A. (2008) "Evidence for Showing Gene/Protein Name Suggestions in Bioscience Literature Search", PSB 2008

First Goal: Determine whether or not bioscience literature searchers wish to

see related term suggestions (gene and protein names)

Second Goal: Determine how to display to users term expansions

- online surveys: 38 & 19 participants


Related Information Type Avg rating # selecting 1 or 2

Gene’s Synonyms 4.4 2 Gene’s Synonyms refined by organism 4.0 2 Gene’s Homologs 3.7 5 Genes from same family: parents 3.4 7 Genes from same family: children 3.6 4 Genes from same family: siblings 3.2 9

Genes this gene interacts with 3.7 4 Diseases this gene is associated with 3.4 6 Chemicals/drugs this gene is associated with 3.2 8 Localization information for this gene 3.7 3

1 2 3 4 5

(Do NOT want this) (Neutral) (REALLY want this)

Study 2a: Results

Design 1: baseline


Design 2: links


Design 3: checkboxes


Design 4: categories


Design Participants who rated design 1st or 2nd

Average rating

(1=low, 4=high)

# %

3: checkboxes 15 79 3.3

4: categories 10 53 2.6

2: links 9 47 2.5

1: baseline 0 0 1.6

Study 2b: Results


• Strong desire for the search system to suggest information closely related to gene/protein names.

• Some interest in less closely related information.

• All participants want to see organism names in conjunction with gene names.

• A majority of participants prefer to see term suggestions grouped by type (synonyms, homologs, etc).

• Split in preference between single-click hyperlink interaction (categories or single terms) and checkbox-style interaction.

• The majority of participants prefers to have the option to chose either individual names or whole groups with one click.

• Split in preference between the system suggesting only names that it is highly confident are related and include names that it is less confident about under a “show more” link.

Study 2: More Results


3. Final study once the project was completed

Divoli, A., Hearst, M.A. and Wooldridge, M.A. (2010) "Full Text and Figure Display Improves Bioscience Literature Search”, PLoS ONE 5(4): e9619

Four Hypotheses:

H1: Most participants would have a favorable response to the display of the articles’ figures next to the search results, for most information seeking tasks.

H2: Most participants would have a favorable response to searching over the full text, as opposed to just the abstract and title, for the primary search view.

H3: Some participants would find the grid view with caption search appealing for specialized information seeking tasks.

H4: Some participants would find the table view with table text and caption search appealing for specialized information seeking tasks.



- in person surveys: 20 participants

15/20

10/20 7/20

Text search Figure caption search Table search

Frequently 15 8 6

Sometimes 4 7 4

Rarely 0 4 7

Never 0 0 2

Undecided 1 1 1


Study 3: Results


Study 3: More Results - Favourable features

- Ability to see figure thumbnails.

- Direct links to full paper without going through PubMed.

- Ability to see excerpts and search in captions.

- Good to have two figure view options; grid is good for a quick browse.

- Colors are helpful: easy to keep track what you are looking at.

- The layout, it is easy to navigate.

- Highlighting.

- The expand options don’t require reload so it is fast.

- Clear display/layout. Intuitive/simple. Not distracting despite all the information.

- The caption is viewable without extra work.

- Ability to link to all figures from one paper.

Usability Conclusions


• Biology/bioinformatics are unique.

• Don’t assume you know how users think.

• You have to watch them interact with an interface.

• You can never please everybody.

• Several testing iterations are required.

• We need to be publishing more usability studies’ outcomes in Bioinformatics.

Acknowledgements

Andrey Rzhetsky

Eneida Mendonca

James Evans

Sarah White

Zoe Nyssa

Rzhetsky Lab

LICR

pre-interviews (4)

interviews (28)

focus group (7)

Very grateful to all

the experts/participants!

Funded by:

Marti Hearst

Mike Wooldridge

Preslav Nakov

Jerry Ye

Ariel Schwartz

Harendra Gututru

Alex Ksikes

NSF, Genentech

study 1 (8)

study 2 (48)

study 3 (20)

motivation [usability studies…] [expert opinions…] acknowledgments

Technology

Divoli Presentation at EBI Apr2011 Usability Part