The Enzyme Portal: a case study in applying user-centred design methods in bioinformatics

User-centred design (UCD) is a type of user interface design in which the needs and desires of users are taken into account at each stage of the design process for a service or product; often for software applications and websites. Its goal is to facilitate the design of software that is both useful and easy to use. To achieve this, you must characterise users’ requirements, design suitable interactions to meet their needs, and test your designs using prototypes and real life scenarios.For bioinformatics, there is little practical information available regarding how to carry out UCD in practice. To address this we describe a complete, multi-stage UCD process used for creating a new bioinformatics resource for integrating enzyme information, called the Enzyme Portal (http://www.ebi.ac.uk/enzymeportal). This freely-available service mines and displays data about proteins with enzymatic activity from public repositories via a single search, and includes biochemical reactions, biological pathways, small molecule chemistry, disease information, 3D protein structures and relevant scientific literature.We employed several UCD techniques, including: persona development, interviews, ‘canvas sort’ card sorting, user workflows, usability testing and others. Our hope is that this case study will motivate the reader to apply similar UCD approaches to their own software design for bioinformatics. Indeed, we found the benefits included more effective decision-making for design ideas and technologies; enhanced team-working and communication; cost effectiveness; and ultimately a service that more closely meets the needs of our target audience.

[1]  M. Sheelagh T. Carpendale,et al.  Sketching User Experiences - The Workbook , 2011 .

[2]  Lincoln Stein,et al.  Reactome: a database of reactions, pathways and biological processes , 2010, Nucleic Acids Res..

[3]  William Hudson,et al.  Reduced empathizing skills increase challenges for user-centered design , 2009, CHI.

[4]  A. Pandey,et al.  Human Protein Reference Database and Human Proteinpedia as resources for phosphoproteome analysis. , 2012, Molecular bioSystems.

[5]  Bill Buxton,et al.  Sketching User Experiences: Getting the Design Right and the Right Design , 2007 .

[6]  S. Baron-Cohen The Essential Difference: Men, Women and the Extreme Male Brain , 2007 .

[7]  Zachary C. Wright,et al.  Heuristic Evaluations of Bioinformatics Tools: A Development Case , 2009, HCI.

[8]  Sameer Velankar,et al.  PDBe: Protein Data Bank in Europe , 2009, Nucleic Acids Res..

[9]  Christoph Steinbeck,et al.  Bioinformatics Meets User-Centred Design: A Perspective , 2012, PLoS Comput. Biol..

[10]  John S. Pruitt,et al.  The Persona Lifecycle: Keeping People in Mind Throughout Product Design , 2006 .

[11]  Jakob Nielsen,et al.  A mathematical model of the finding of usability problems , 1993, INTERCHI.

[12]  Carolyn Snyder,et al.  Paper Prototyping: The Fast and Easy Way to Design and Refine User Interfaces , 2003 .

[13]  Amos Bairoch,et al.  neXtProt: a knowledge platform for human proteins , 2011, Nucleic Acids Res..

[14]  Mike Kuniavsky,et al.  Observing the User Experience: A Practitioner's Guide to User Research (Second Edition) , 2013, IEEE Transactions on Professional Communication.

[15]  Christoph Steinbeck,et al.  Chemical Entities of Biological Interest: an update , 2009, Nucleic Acids Res..

[16]  Rodrigo Lopez,et al.  Fast and efficient searching of biological data resources - using EB-eye , 2010, Briefings Bioinform..

[17]  Eileen Kraemer,et al.  EuPathDB: a portal to eukaryotic pathogen databases. Nucleic acids research , 2009 .

[18]  Barry W. Boehm,et al.  A spiral model of software development and enhancement , 1986, Computer.

[19]  Vito Perrone,et al.  Better bioinformatics through usability analysis , 2009, Bioinform..

[20]  Amos Bairoch,et al.  Review of the selected proceedings of the Fifth International Workshop on Data Integration in the Life Sciences 2008 , 2008, BMC Bioinformatics.

[21]  David A. Wagner,et al.  Analyzing internet voting security , 2004, CACM.

[22]  BMC Bioinformatics , 2005 .

[23]  Liping Wei,et al.  Genes and (Common) Pathways Underlying Drug Addiction , 2007, PLoS Comput. Biol..

[24]  Clare Churcher,et al.  Usability of Navigation Tools for Browsing Genetic Sequences , 2010, AUIC.

[25]  Michele Magrane,et al.  UniProt Knowledgebase: a hub of integrated protein data , 2011, Database J. Biol. Databases Curation.

[26]  Michael Y. Galperin,et al.  The 2012 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection , 2011, Nucleic Acids Res..

[27]  S. Baron-Cohen,et al.  The Empathy Quotient: An Investigation of Adults with Asperger Syndrome or High Functioning Autism, and Normal Sex Differences , 2004, Journal of autism and developmental disorders.

[28]  Anna Zhukova,et al.  Modeling sample variables with an Experimental Factor Ontology , 2010, Bioinform..

[29]  Janet M. Thornton,et al.  The CoFactor database: organic cofactors in enzyme catalysis , 2010, Bioinform..

[30]  Barry Kirwan,et al.  A Guide To Task Analysis: The Task Analysis Working Group , 1992 .

[31]  Ahmed Seffah,et al.  Beyond power: making bioinformatics tools user-centered , 2004, CACM.

[32]  Alan Cooper,et al.  The Inmates are Running the Asylum , 1999, Software-Ergonomie.

[33]  Monica M. C. Schraefel,et al.  Breaking the book: translating the chemistry lab book into a pervasive computing lab environment , 2004, CHI.

[34]  Dave Gray,et al.  Gamestorming: A Playbook for Innovators, Rulebreakers, and Changemakers , 2010 .

[35]  Eileen Kraemer,et al.  EuPathDB: a portal to eukaryotic pathogen databases , 2009, Nucleic Acids Res..

[36]  Hagen Blankenburg,et al.  Integrating biological data – the Distributed Annotation System , 2008, BMC Bioinformatics.

[37]  Mike Kuniavsky,et al.  Observing the User Experience: A Practitioner's Guide to User Research (Morgan Kaufmann Series in Interactive Technologies) (The Morgan Kaufmann Series in Interactive Technologies) , 2003 .

[38]  Alan Cooper,et al.  The Inmates Are Running the Asylum: Why High Tech Products Drive Us Crazy and How to Restore the Sanity (2nd Edition) , 1999 .

[39]  Philip E. Bourne,et al.  Computational Biology Resources Lack Persistence and Usability , 2008, PLoS Comput. Biol..

[40]  Simon Baron-Cohen,et al.  The systemizing quotient: an investigation of adults with Asperger syndrome or high-functioning autism, and normal sex differences. , 2003, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[41]  John P. Overington,et al.  ChEMBL: a large-scale bioactivity database for drug discovery , 2011, Nucleic Acids Res..

[42]  Jacob O. Wobbrock,et al.  Understanding usability practices in complex domains , 2010, CHI.

[43]  David Pinelle,et al.  Heuristic evaluation for games: usability principles for video game design , 2008, CHI.

[44]  Gemma L. Holliday,et al.  MACiE: exploring the diversity of biochemical reactions , 2011, Nucleic Acids Res..

[45]  Indra Neil Sarkar,et al.  The Barcode of Life Data Portal: Bridging the Biodiversity Informatics Divide for DNA Barcoding , 2011, PloS one.

[46]  Songyan Liu,et al.  The IKMC web portal: a central point of entry to data and resources from the International Knockout Mouse Consortium , 2010, Nucleic Acids Res..

[47]  Rolf Apweiler,et al.  IntEnz, the integrated relational enzyme database , 2004, Nucleic Acids Res..

[48]  Venkataraman Ramesh,et al.  Understanding usability in mobile commerce , 2003, CACM.