Introducing Wildbook: A Web-based Application for Wildlife Data Management

Wildbook (formerly the “Shepherd Project”) is an open source software framework to support mark-recapture, molecular ecology, and social ecology studies.

The biological and statistical communities already support a number of excellent tools, such as Program MARK,GenAlEx, and SOCPROG for use in analyzing wildlife data. Wildbook is a complementary software application that:

  • provides a scalable and collaborative platform for intelligent wildlife data storage and management, including advanced, consolidated searching
  • provides an easy-to-use software suite of functionality that can be extended to meet the needs of wildlife projects, especially where individual identification is used
  • provides an API to support the easy export of data to cross-disciplinary analysis applications (e.g., GenePop ) and other software (e.g., Google Earth)
  • provides a platform that supports the exposure of data in biodiversity databases (e.g., GBIF and OBIS)
  • provides a platform for animal biometrics that supports easy data access and facilitates matching application deployment for multiple species

Wildbook started as a collaborative software platform for globally-coordinated whale shark (Rhincodon typus ) research as deployed in the Wildbook for Whale Sharks. After many requests to use our software outside of whale shark research, it is now an open source, community-maintained standard for mark-recapture studies.

Who is currently using this software?

People

jason_profile.jpg

Jason Holmberg is the Information Architect for Wildbook. Jon Van Oast is the new primary software developer, bringing a wealth of programming experience to the project.

Dr. Scott Baker of Oregon State University designed the DNA-related components within the software and remains an active adviser on the project.

Demo Site

We are happy to give demos of the software via webinars. We also have a demo site here:

http://www.wildbookdna.org/demo

Please email “jason [at] whaleshark [dot] org” to receive access credentials for the demo site, which refreshes itself periodically, allowing you to run real world tests of Wildbook.

News

2014-04-04

We are pleased to release Wildbook 5.3.0 with the following new fixes and features!

  • FIX: Encounter Search title on haplotype map
  • FIX: Biological samples not showing in encounter.jsp and individuals.jsp
  • NEW: Better stream closing on EXIF data loading for images
  • NEW: Significant performance improvement in image thumbnail display in Encounter Search
  • NEW: Add assigned user filter to Individual Search and set alpha sort order
  • FIX: Encounters menu did not expand on mobile devices
  • NEW: Spot mapping is now performed in the browser!
  • NEW: Support context-based data access through REST data interface

2015-01-29

We released Wildbook 5.2.0 today with the following changes:

  • NEW: Upgrade to DataNucleus 4.0.3
  • FIX: Encounter.dateInMilliseconds off by one hour for Encounters with no date specified, shifting their position in search results back one day
  • FIX: Minor map display zoom and bad data filtering improvements
  • FIX: UUID switch broke reference image comparison in Encounter Search
  • MOD: Improved support to handle valuable but poorly formatted Dates in EncounterForm
  • FIX: Individual new/previous sighting bar chart in Individual Search showing inconsistent values
  • FIX: Date-based search results had variable behavior with results who days exceeded month boundaries
  • FIX: UpdateEmailAddress threw an NPE after a bad merge
  • NEW: 20% speed improvement in Individual Search mapping through gzip compression of GeoJSON results
  • MOD: Allow for null values in Encounter.dateInMilliseconds
  • NEW: Encounter Search filter by date submitted (not date of actual sighting)
  • NEW: Encounter Search Analysis tab: new charts and metrics
    • Bar chart of encounter totals by year submitted
    • Bar chart of total encounters by submission year
    • Pie chart of Encounters by workflow state
    • Additional calculated values (#submitters, # represented marked individuals, etc.)
  • NEW: Encounter Search filter by strings in the Encounter additional comments
  • NEW: REST interface improvements - Part 1 - add new read-only /api REST URL with capability for custom behavior hooks
  • NEW: Convert JSP-based UI to HTML5 and REST/JSON - Part 1
    • NEW: Convert Encounter Search table tab to JSON-based, filterable, sortable JavaScript table
    • NEW: Convert individuals.jsp Encounter list for a marked individual to a sortable table
    • NEW: Convert Individual Search table tab to JSON-based, filterable, sortable JavaScript table
  • FIX: L10N ongoing cleanup of untranslated stragglers

2015-01-25

Happy 2015! Wildbook 5.2 is up on whaleshark.org for testing. All of the code is done, and much of it has already been tested in a production environment. We should have a full release in less than a week!

2014-10-23

We released Wildbook 5.1.0 today with the following changes:

  • FIX: allow data submission if user has cookies disabled
  • MOD: updated the JPEG metadata reader software and centralize the EXIF data reading and display function (done)
    • UPGRADE: XMP and metadata-extractor JAR files need to be added/upgraded
  • MOD: More elegant error handling in resetThumbnail.jsp
  • FIX: support for custom measurement types was lost in the 5.0 upgrade.
  • FIX: “View all sharks” text still appearing in some locations
  • MOD: Switch Encounter.date and Encounter.releaseDate to calendar selector
    • Do not allow future date submissions
    • Preserve existing date value in selector when setting\editing date and release date
  • MOD: Improve file name character filtering
  • FIX: Remove the unused commonConfiguration.properties administration form
  • NEW: Silo security (BETA) (Flukebook)
  • NEW: ImageMajick support for more efficient processing of images outside of the Java JVM
  • MOD: Remove Struts 1 code to reduce risk of DOS attacks
    • UPGRADE: Remove Struts JARs and XML config files in WEB-INF

Past news...

Support

Past development work for Wildbook has been supported by:

Collaboration Model

Wildbook is designed to produce successful, reproducible collaborations between biologists, biostatisticians, computer scientists, and citizen scientists by providing a Web-based software platform for collaboration.

Is Wildbook right for you?

If you answer yes to any of these questions, Wildbook may be a very good choice for your research.

  • Are you trying to track individual animals in a wildlife population using natural markings or genetic identifiers?
  • Are you collecting biological samples from a wildlife population and performing genetic or chemical analyses (e.g., stable isotope measurements, haplotype determination, etc.)?
  • Are you looking to increase wildlife data collection through citizen science?
  • Are you looking to build a collaborative, distributed research network for a species?
  • Are you looking to develop a new animal biometrics solution (e.g., pattern matching from photos) for one or more species?
  • Are you collecting behavioral and/or social data for a wildlife study population?

Screenshots

Features

Using the web-based interface of Wildbook Framework, a research team can:

Encounters (a.k.a. “captures” or “sightings”)

  • Record an encounter (individual animal at a point in time and location) through a standardized data collection form
  • Search a database of standardized encounter data using predefined search criteria
  • Receive automated email updates when encounter reports are assigned to new or previously identified marked individuals
  • Receive RSS feeds of encounter identifications as they are made
  • View all reported encounters
  • View individual encounter reports
  • View thumbnail catalogs of submitted images
  • View adopters of individual encounters (a fundraising tool)
  • Edit encounter data with all changes tracked and permanently logged
  • Assign encounters to new or existing marked individuals
  • Set a list of additional email addresses to be notified with status and sighting updates for submitted encounters
  • View an on-line calendar of whale shark encounter reports
  • Restore accidentally deleted encounters
  • Easily map a TapirLink provider or Integrated Publishing Toolkit (IPT) to the underlying relational database for exposure of mark-recapture data to biodiversity frameworks
  • For species with marked individuals identified by unique spot patterning:
    1. Extract spot patterning from photographs and scan for matches across all patterns in library using two approaches to pattern recognition (I3S and Modified Groth).
    2. Share computing power among globally distributed machines.
    3. View pattern match reports and evaluate matches side-by-side, including direct spot remapping and statistical analysis of results.
  • Record physical, acoustic, and satellite tag data deployed during an encounter
  • Record tissue samples collected with an encounter
  • Record the results of genetic sex, haplotype, microsatellite marker, stable isotope, and contaminant analyses performed on a tissue sample

Marked Individuals

  • View all marked individuals
  • View consolidated capture and sampling history of marked individuals
  • Receive automated email updates when a marked individual is re-sighted
  • Search a global database of marked individuals using predefined search criteria
  • View consolidated mapping of sighting locations an individual
  • View co-occurrence for the individual with other individual (e.g., social grouping)

Photos

  • Define common photo keywords for your species (e.g. scarring types)
  • Add/remove keywords to encounter photos
  • Search across photographs using assigned keywords
  • Search all images\video using encounter data to create customized albums of images
  • View photo metadata (e.g. EXIF data)

General

  • Search all encounters and marked individual data using Google Search (when deployed as a web server)
  • Assign alternate identifiers to encounters and marked individuals
  • View sighting locations with satellite imagery incorporated from Google Maps (encounters, amrked individuals, and Encounter Search results)
  • Export sighting data as a KML file or an Excel spreadsheet for use in Google Earth and other mapping applications (Encounter Search).
  • Create and edit animal adoptions for project fundraising.
  • Review access security logs and track the source of individual logins.
  • Use a variety of relational and non-relational database types to store data. The full list of supported databases in available from the DataNucleus web site (our middleware).

API

The framework is open source and meant for you to extend it for your specific project! If it doesn't have the feature you need, use some simple Java programming and create it. Some things we have used it to do on whaleshark.org are:

  • Quickly generate open and closed capture history files for population modeling in statistical packages, such as U-CARE, CloseTest, and Program MARK
  • Generate statistical reports
  • Rely on spam filters to block spurious data submission

The development of additional functionality is currently underway.

Donation

You can help move Wildbook forward by making a donation! Your donation is tax deductible in the United States.

Feedback

Please send feedback to jason at whaleshark dot org. Your ideas to improve Wildbook are most welcome!

History

Wildbook started as the software behind the Wildbook for Whale Sharks, which is a multiuser, web-based, research application for studying whale sharks (Rhincodon typus). The aim of WIldbook for Whale Sharks is to prevent individual “silos” of whale shark data and to promote a global, cooperative approach to whale shark research using the Web as a communications and research platform. The Library went on-line and began collecting whale shark encounter data from the web in January 2003. In early 2004, the pattern-recognition system that allows the Library to distinguish between individual whale sharks using natural spot patterning was integrated. Since its first line of code, this Wildbook has seen continuous feature additions, bug fixes, and performance enhancements. Our work to maintain and enhance the Library is ongoing and requires knowledge of Java, J2EE, JDO, PHP , Flash/Flex, HTML , XML , RSS , a wee bit of Python, and CSS .

Publications

Design Influences

The following publications have influenced our design and development of Wildbook:

Copyright

Esri and the Esri Logo are licensed trademarks of Environmental Systems Research Institute, Inc.


Personal Tools