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Meeting Report

Model Organism Database User Interface Caucus

GMOD Meeting, January 18, 2007, San Diego, CA, USA

Executive Summary

The user interface (UI) is the most visible aspect of a model organism database (MOD), and arguably has the most direct impact on the satisfaction of its users. On the first day of the January 2007 GMOD meeting, we shared experiences, discussed lessons learned, and identified unsolved problems in the field of MOD user interface design. To drive the discussion, representatives of several MODs (including both model and multi-organism databases) presented aspects of their UI that related to a common set of use cases. This brought to light several useful topics that that are not widely known, and that new and old MODs can benefit from.

General lessons learned: Clarity in actions required of users, and clarity and reliability of results of these are important to users. Contextual examples and help links are very useful to users. Appearance is less important to users than functionality and responsiveness. Developing good UIs takes sustained work, including feedback and community testing. Complexity is an inherent problem: MODs deal with rich, complex data that is constantly expanding and changing. A central challenge for a MOD's user interface is to make common tasks easy and complex tasks possible. This problem is addressed through user interface design, engineering of site infrastructure, and user education and documentation. There is a need at many MODs for broader availability of power-user interfaces for complex queries, for uploading and operating on sets of genes in one step, and for flexible configuration of data output formats. Good new ideas in development: Wikipedia provides an excellent example for science community participation that several MODs are adopting. More dynamic web content and graphical summaries can help manage information. Interactive auto-complete of words typed in search boxes gives users immediate feedback. Google can be harnessed to aid, but is not solely sufficient for, searching MOD data. Providing "server snapshots" is a useful mechanism for keeping older database versions available.

Participants and Presentations

This meeting drew together some 60 biologists, bioinformaticians and other interested people, representing more than 25 database projects and organizations. The list of attendees is here. The day included thirteen presentations, and a round table discussion at the end. Slides and text summaries of individual presentations are provided at the MOD Face Talks page.

Detailed Report

Addressing Six MOD Use Cases

Many simple/quick/global searches. Most MODs have some variation of a "search everything" option that is the primary search entry. Simple searches at MODs vary principally in the details of data classes (which were searched and whether or not they needed to be specified) and how terms are matched (exact, partial, phrase and/or wildcard). These types of simple searches must balance ease of use with relevance of results. How results can be handled also varies between MODs. Various MODs allow searches and results to be saved, refined, downloaded and/or exported to other tools. One challenge is how to support user expectations to make "simple" searches that return quality answers. The TAIR presentation details a several-year process to determine best functionality of simple search from user feedback: it takes effort to develop "simple and quick" searches that return what biologists really looking for. We note that "simple" searches present a trade-off between simplicity of specifying the query and simplicity of searching through the returned results. In the case that a keyword entered into a "simple search" box returns only a few results, merely listing the results is sufficient. In the case that such a search returns many results, often of different types, it makes sense to do one of the following 1) structure the returned information by "type", list the types and show the first few of that type, allowing the user to expand/contract those lists by type, 2) permit the user at this point to interact to choose to either further limit the returned results or to page through the results. The threshhold at which one strategy is preferable to another needs to be determined through user studies.

Gene page reports. Most MODs agree that users like short summaries and graphical presentations of data. Individiual MODs vary widely in deciding how much detail is displayed in the default view. Individual MODs struggle with how to direct users, in an obvious manner, toward deeper levels of information.

Advanced/attribute searches. Many MODs allow some sort of advanced search where users can specify search criteria over multiple data types. Some MODs (e.g. NCBI, ApiDB) allowed query histories to be combined, allowing for complex, refined searches and results, and others (FlyMine) provide this functionality through set operations on 'bags' of objects.

User choices in data reports. This is an acknowledged weak aspect at many MODs. Most have yet to develop systems that allow users to fully customize reports. The basic state is that users parse information from a given MOD's defined formats (which tend to vary between MODs). Some MODs (e.g. FlyMine, FlyBase) allow choice of output columns and their order.

UIs for bulk data handling. Many MODs allow some sort of bulk query, although the allowed data types varys. BioMart provides a common UI that is used at several MODs (WormBase, Gramene, DictyBase, DroSpeGe) for bulk data search and retreival, and is in development at others. Some MODs (e.g. FlyMine) provide a more complex query UI that can operate on large lists (e.g. all genes), supporting pre-defined or user-defined data export formats. In addition intermediate results can be saved in 'bags' and these lists combined and/ or used in subsequent queries.

Cross-site facilitation. Some MODs allow searches for IDs and/or names that might be found elsewhere. Many MODs use ontologies (e.g. GO) or orthologies to link to other databases, one at least (NCBI) offers computed relations between databases. A common problem in this is keeping up-to-date across databases. Some MODs (e.g. FlyMine, Wormbase, SGD) maintain lists of orthologues for many species. This allows a set of genes from one species to be imported, and the list of corresponding genes from another, more data rich species, to be derived and then explored.

User Interface Development

Lessons Learned from Experience

  • Clear (better yet, obvious) input actions and requirements are important. For example, "What, exactly, are people expected to type into a 'quick search' box?" and "If the 'log on' box is at the top of the homepage, does that mean I have to register and log on to use the site?". Also, input fields should be prefilled with an example query value to give user an idea of the type of value to be entered (and to permit

easy exploration by novices).

  • Reliable results are important.
  • Fast results are good.
  • What users ask for isn't always what they really want (see the ApiDB presentation).
  • Appearance is less important than functionality.
  • UI components and report sections should be clearly labeled and include tips, sample queries and default values. Results should include brief summaries whenever possible.
  • Use terms the bio-community understands and try to stay away from those that you might want them to learn, but that aren't strictly necessary for usage (e.g. the word "Boolean" at ApiDB )
  • Don't change what works for users; even if you develop a "better" more sophisticated tool, the users might still prefer the one they know how to use (e.g. the Batch Sequences tool at Wormbase). MODs generally thought that we should avoid rapid turnover in UI, but many felt that frequent, small changes and additions can be useful to community (if clearly explaned)

  • Support for User preferences/sessions/configurations (e.g. "MyNCBI", FlyMine's "MyMine")
    • default UI dilemma: simple/dumb for general audience, or sophisticated/complex for focused users
    • variable (low) use of preference options?
    • needs transparency to user (avoid logins/extra effort)

Gathering and Analyzing User Feedback

Using User Feedback to Guide UI Design

Start early. There was broad agreement that usability studies for a user interface should be conducted as early as possible in its development cycle. The more development effort that has already been devoted to a tool, the harder it is to make any suggested changes that may arise from a usability study. Moreover, the existing structure of the interface under test can profoundly influence the shape of suggested changes, possibly stifling perhaps profitable UI design ideas that may otherwise have been free to arise, or giving undue weight to ideas that happen to coincide with the current direction of development.

Users may not know what they need any better than the developers do. UI development should be a creative collaboration between users and developers. Neither party alone should drive the development, but the two should work closely together. In practice, users often have too little opportunity to participate in the UI design process.

Site Logging

A MOD site's server logs can be useful for gathering indirect user feedback. This user feedback mechanism is often overlooked, yet it is relatively easy to work with and can provide very rich data, limited only by the investigator's ingenuity. For example, a MOD might configure its server logs to provide information on user searches, how much time each search took, and the number of results returned by the search. The MOD might then analyze this data to find common instances of "failed" searches that return no results, then identify ways to improve its user interface to make any obscure data more accessible. A MOD might also use server logs to identify the types of data users search for most frequently, and give that data a more prominent place in the site's user interface. Tools for visualizing these logs, named "Ajaxalytics" have been developed by ApiDB personnel and are available through sourceforge. Further work with these tools to cluster and characterize user behavior is underway.

Card Sorting

"Card sorting" is an easy to implement and powerful method of discovering how users naturally group items of data. An investigator gives each user a stack of cards, on each of which is written a word or phrase describing a concept. The user is then asked to sort the cards into piles, and optionally sub-piles, that group the concepts in the way that makes the most "intuitive sense". The users are then asked to label these piles, by writing a category name on a blank card and clipping them together.

At least one MOD in the meeting reported successfully using this method to design easy-to-navigate groupings of menu choices for their site's UI.

Watching Users

Watching users interact with a MOD's user interface can tell an investigator more than user opinions and surveys. ApiDB recounted some of the methods they used for conducting user interface testing. One type of study they did involved pairs of users sitting at computers outfitted with video and keystroke capture devices, as well as audio recording. These pairs of users were asked to perform various tasks using the user interface under test. The video and keystroke capturing provided a comprehensive record of all actions the users performed with the site. Additionally, the audio recording of each pair allowed investigators to hear how the users talked about and explained the site to each other, shedding some light on the way users think about their interactions with the site. ApiDB's presentation also pointed one disdvantage of this approach, which is the difficulty of analyzing the large amount of data collected during the study, since most of it is in the form of many hours of audio and video recordings. Despite the analysis difficulties, ApiDB reported that they had found the data to be quite useful. After the ApiDB presentation, Ceri Van Slyke from ZFIN remarked that ZFIN had conducted similar usability studies, with similar experiences.

Balancing Completeness and Simplicity

Too much information and too many choices can overwhelm users, but restricting choices and hiding data limits the usefulness of a MOD. This dilemma and how best to handle it was a common theme in presentations. Easier to Use versus Does More Things is a good way to express this. Achieving a good balance requires a great deal of thought and user input.

An illustrative example can be found in map displays and reports, where detail sections are hidden, but available through linked pages or dynamic web displays. At SGD, a sidebar of menu choices was found to hide too much from users. It is being replaced with an web page that openly exposes all choices.

A related issue is providing adequate information on what the different choices available actually do, and the provenance of data: what data are present and where they came from.

New Trends in MOD UIs

Community Participation

Wikipedia provides an excellent example of the power of community participation in science documentation. Many new genomics and biology wikis are springing up, running on the reusable software and documentation provided by Wikipedia. Members of this new generation of wikis include: , an outcome of the GMOD meeting , , , , , , , , , , .

This growing list of wikis offer scientists a common, well-documented user interface that is expected to facilitate expanded use, as experience in participation one site carries over to others. The EcoliWiki provides a prototype for gene annotations. Further integration of wiki methods for genome community annotation have been recently proposed [1], [2]. Also at the meeting, SGN presented an experimental community gene curation interface for use by authorized users of the site.

Client-side Scripting (JavaScript)

In recent years, general web development practices have been trending toward increased use of client-side scripts written in JavaScript to provide richer, more responsive user interfaces for web sites. This trend has been driven by the increasing market share of browsers with relatively mature JavaScript implementations (IE 6+, Firefox), and by the high-profile success of several web applications making use of this increased JavaScript support (such as Google Maps).

Most web developers at MODs have a responsibility to ensure broad access to the MOD's data, thus they do not have unlimited freedom to introduce new user interface features that may not be compatible with older versions of browser software. Instead, they must take great care to ensure either a.) that newer UI features "degrade gracefully" when viewed with older browser software, but preserving basic functionality, or b.) that an alternate method of accessing the data is available for users of less functional browsers.

Some examples of gracefully degrading client-side features showcased at this meeting were:

  • dynamic, database-backed automatic completion of entries typed into web search forms (older browsers simply won't see any automatic completion)
  • dynamically expanding or collapsing sections of large data displays
  • drag-and-drop map track reording in GMOD's GBrowse software

Dynamic web page content, user preferences and histories are becoming more widely available at MODs. These are used for showing or hiding contents (aiding the dilemma of supporting both the beginner and advanced user), for map track reordering, retaining history of user queries and answers, and other uses.

  • more graphical summaries of long lists/tables are possible; can be useful
  • improving comparative genomics aspects to aid broader audience
  • include curator/community edits/updates to contents (part of same reading UI) (ZFIN,SGN,)

Using Virtualization for MOD Snapshots

Providing stable "snapshots" of the data in a MOD is important for reproducing results in publications that cite the MOD. Many MODs provide snapshots in the form of large data dumps created at specific time intervals, which could be used to laboriously reconstruct the state of the MOD's data at a given point in time. WormBase takes this idea a step further, using virtualization technology to capture the complete state of the WormBase site for each snapshot. These snapshot images can be accessed via the web in the same manner as the main WormBase site, or can be downloaded for playback on any computer that supports the free VMWare player. This practice greatly facilitates reproduction of results from papers that cite WormBase.

Using Google and Other General Search Engines

A number of MODs represented at the meeting used Google to provide some of the search functionality on their site. It was generally agreed that if an external search engine is allowed to fully index a MOD's pages, it can usually provide very useful full-text search results. However, since generalized search engines do not have specific knowledge of the structure of a MOD's data, it may not be possible to obtain relevant results for very specific searches. For example, it would probably not be possible to use a generalized search engine for searching genes based on their exact physical locations in a genome.

It was briefly mentioned that some standard search engine optimization techniques may be used to improve results with external search engines, particularly providing a "site map" page with deep links to all or most of the pages in your site.

One concern that was raised was that the "crawlers" used by external search engines for indexing web pages sometimes impose unacceptable demands on a MOD's web servers, particularly when crawlers from multiple search engines are indexing a site at once. Some solutions to this were suggested, including carefully tuning your site's robots.txt file to avoid computation-intensive pages, and simply buying more servers and/or optimizing your site's code to better handle the load. Googlebot and perhaps other robots can be told to reduce their hit rate to an acceptable level.

A different strategy pursued by some MODs is to use generalized search software on their own servers, such as Lucene or LuceGene, a Lucene variant customized for indexing many types of biological data. This approach offers more control over the indexing, searching, and result presentation than using an external search engine.

User Interface Conventions

One subject that was raised, but was not fully discussed in the time available, was the idea of developing common user interface conventions among MODs. Attendees notes several cases of "convergent evolution" among the MOD user interfaces:

  • most MODs seem to have some sort of unified search feature for all data in the MOD
  • wide adoption of GMOD's GBrowse software
  • existing tools for bulk data download, movement toward more flexible search and reporting tools such as BioMart and InterMine

Todd Harris proposed developing a convention for common URLs for bulk downloading of genome data, but the subject was not fully discussed. A page outling the common urls can be found at Common Download URL.

Dr. Peter Karp presented a useful list of common elements that every MOD should be sure to include:

  • procedures for citing the MOD in publications
  • "contact us" links
  • facilities for downloading datasets and software
  • community news
  • MOD data cross-referenced to publications
  • summary statistics of data in the MOD
    • if possible, a history of these statistics over time
  • update history (a.k.a. changelog) of MOD
  • central credits list for MOD contributors

General Discussion

  • Steps in developing good MOD Faces
    help links everywhere are useful. Examples on input fields are easy to add, and very useful.
    • Sample values are frequently invaluable near the text input box.
    • There is no one right answer in UI design, there are many right answers. There are also many wrong answers.
    • Never create a link to a location where there's nothing to be found. Indicate, by some means, if there's no information or more information.
  • User community testing, interviews, surveys, HCI principles
    • Differing views on value of types and stages in user testing (Is user testing necessary? What about releasing software as a means to get feedback?)
      • It may be that user testing is most valuable when attempting to solve specific problems, as opposed to "design". User testing is probably most useful in the earliest phase, looking at prototypes or prototypes on paper.
      • Monitoring and logging is important, you must know what occupies the user the most.
  • Dilemma of too much or too little information/choice
    • Consensus: complexity goes with the territory, but you have to make the most common things easy and the hard things possible, and have good user education and documentation.
    • Is it true that complexity should be concealed? How does one strike the balance between providing for the expert and for the novice?
  • Google is your enemy/friend ...
    • Differing views on advantage/disadavantages of Google as adjunct to MOD search systems (No consensus that using Google is advantageous; Techniques for guiding Google/Bots below)
  • Good new ideas
    • More dynamic content, graphics summaries may be good
      • Can we make more use of graphics to replace text? E.g. a generated image replaces expression information.
      • Word or string completion as user asks questions is useful UI technique (see Javascript and AJAX below)
  • Common UIs across MODs?
    Not discussed (sigh :()

Implementation Techniques

  • Easy way to direct Google/Bots to best or full content (e.g. gene pages) is with a site map with links to everything you want to expose.
    • detecting user agent, query referal string, etc., in web query lets report software alter output (e.g. give Google all of report to index, highlight Google user queries)
    • Google offers indexing tips, directions to update or hide specific parts
  • Dynamic content (Javascript/AJAX):
    • Word or string completion using Javascript/AJAX and dedicated, simple databases of words to complete work well (Wormbase, EBI Ontology Lookup Service, others?).
    • use to hide and show sections of pages; reorder tracks in a genome browser;
  • RSS is probably underutilized, but would it be widely used if available?
  • An XML representation of an "entry" makes a "diff" or change easy to assess, and reliable alerts could be constructed.


  1. Salzberg SL. Genome re-annotation: a wiki solution? Genome Biol. 2007 Feb 1;8(1):102; PMID: 17274839
  2. Bradley I. Arshinoff, Garret Suen, Eric M. Just, Sohel M. Merchant, Warren A. Kibbe, Rex L. Chisholm, and Roy D. Welch. Xanthusbase: adapting wikipedia principles to a model organism database. Nucl. Acids Res. 2007 35: D422-D426; doi:10.1093/nar/gkl881