User Manual

This manual introduces the basic concepts and functions of Wildbook.

Overview

Wildbook is a cloud-based software application for collaboratively storing and analyzing data about animals in a study population. Its ultimate goal is to make it easy for a wildlife project to quickly go from data collection to analysis and generation of new knowledge. Wildbook allows you to collaborate better and to save time managing data sets.

A single software instance of Wildbook application is deployed into a web server (we use Amazon Web Services Ubuntu servers) and can host one or multiple distinct mark-recapture studies. We will call this distinct instance of the application for a particular study a “Wildbook instance”.

Examples

Here are some examples of Wildbook-based projects:

Data Structure

Wildbook divides its managed mark-recapture data into these distinct types:

MediaAsset

A MediaAsset represents a media object (photo or video) captured in a wildlife study. The corresponding data construct within Wildbook is org.ecocean.media.MediaAsset. A MediaAsset is stored in a MediaAssetStore object. A MediaAssetStore may be a local file system or a remote service, such as Amazon S3.

Figure. A MediaAsset object rendered in Wildbook

Annotation

An Annotation is generally a subset of a MediaAsset in which ecological information has been detected. For example, an Annotation is created when a whale fluke is found within a larger MediaAsset. The Annotation of the fluke can then be passed on to computer vision for identification (i.e., Which whale is this?).

Figure. Multiple Annotations have been found in this MediaAsset. Each Annotation is represented by a box.

Encounter

An Encounter is an individual sighting of a member of a target population of a single species. An encounter report is submitted to the framework via a web interface and may represent (if enough data is present for identification) a “mark” (first sighting) or “recapture” (subsequent re-sighting) of an individual from a study population. Each encounter contains data that represent one individual at one point in time. For example, an Encounter may represent the photographing of a single dolphin at a specific point in time and/or the collection of a tissue sample for genetic identification later. An encounter can be added to a previously identified marked individual in the database, representing a re-sighting of that animal, or it can be allocated as a new marked individual and given a name or tag number (e.g. “A-001”), representing a new animal previously undocumented in the wildbook. The corresponding data construct within Wildbook is org.ecocean.Encounter.

Click here to see an example Encounter displayed in Wildbook.

Marked Individual

A Marked Individual is an uniquely identified member of a population and includes one or more reported encounters. It is up to each library and its research staff to determine the minimum amount of data and procedures required for a unique identification (e.g., a distinct ear tag, a visual photo-identification, digital extraction of spot patterning, a distinct DNA pattern, etc.). As the study acquires more and more encounters for each individual in the wildbook, it will be able to build up robust metrics for population analysis, allowing its research team to better understand population trends. The corresponding data construct within Wildbook is org.ecocean.MarkedIndividual.

Click here to see an example Marked Individual displayed in Wildbook.

Occurrence

An Occurrence represents a observation of multiple individuals together and includes one or more encounters over a short duration of time. The purpose of an occurrence is to provide an hierarchical category to represent groups of individuals and potentially the relationships among them at a point in time and space. For example, an occurrence might represent a pod of baleen whales, which are typically fluid in membership, even over brief periods of observation (e.g., less than an hour), or more stable groups, such as sperm whales, which might remain relatively stable over a longer period of continuous observation (e.g., several hours). The corresponding data construct within Wildbook is org.ecocean.Occurrence.

Biological Sample

A Biological Sample (a.k.a. “Tissue Sample” but not strictly a tissue) represents the retrieval of a small amount of biological material from an animal. For example, this may be a direct biopsy, a fecal sample, a blood sample, or a mucus sample. Because a biological sample is collected at a location and point in time, it is added to an Encounter, representing an additional part of an animal sighting record. Wildbook currently allows you to add data for these types of subsequent analyses upon a Biological Sample:

  • One or more haplotype analyses and determinations
  • One or more genotype analyses (microsatellite markers)
  • One or more genetic sex determinations
  • One or more biological/chemical measurement. For example, you could record a stable isotope determination of “-2.4 ppm for 13C” or record a pollutant measurement detected in the sample.

The corresponding data construct within Wildbook is org.ecocean.genetics.TissueSample.

Relationship

A Relationship (e.g., the mother-calf relationship between a whale and her offspring) represents an observed relationship between two animals in the wild. The corresponding data construct within Wildbook is org.ecocean.social.Relationship.

Social Unit

A Social Unit (e.g., a pack of wolves, a pod of dolphins, etc.) represents a formal grouping of animals linked by a set of observed Relationships, and those relationships exist within the context of a social unit. The corresponding data construct within Wildbook is org.ecocean.social.SocialUnit.

Recorded data

Wherever possible, the data attributes recorded for an Encounter or a Marked Individual are named according to their Darwin Core equivalents. A definition of the Darwin Core can be found on the TDWG web site:

“The Darwin Core is body of standards. It includes a glossary of terms (in other contexts these might be called properties, elements, fields, columns, attributes, or concepts) intended to facilitate the sharing of information about biological diversity by providing reference definitions, examples, and commentaries. The Darwin Core is primarily based on taxa, their occurrence in nature as documented by observations, specimens, and samples, and related information.”

This is not a clean one-to-one mapping (the Darwin Core does not specifically address mark-recapture or its terminology), but our implementation does make it fairly easy to map a TapirLink provider or IPT web application to the Encounter database table if you're using Wildbook Framework with a relational database. This allows mark-recapture data to serve a dual purpose: local population analysis and broader biodiversity analysis in frameworks such as the GBIF and OBIS.

Let's take a look at the fields recorded for Encounter and Marked Individual records. If you're using a relational database (e.g., Wildbook framework ships with an Apache Derby database that is created on first startup), these fields (or “attributes”) map to columns in the appropriately named database tables (i.e., “Encounter” and “MarkedIndividual”).

Encounter

The following attributes are described in the Darwin Core quick reference at: http://rs.tdwg.org/dwc/terms/#dcterms:type

Wherever possible, this class will be extended with Darwin Core attributes for greater adoption of the standard.

  • catalogNumber - “An identifier (preferably unique) for the record within the data set or collection.” In Wildbook, the catalogNumber is the primary key for encounters in the database.
  • otherCatalogNumbers - “A list (concatenated and separated) of previous or alternate fully qualified catalog numbers or other human-used identifiers for the same Occurrence, whether in the current or any other data set or collection.” Often times, researchers will assign an encounter number to a sighting in the field, and that number will differ to the catalogNumber assigned when the sighting is added to the database in Wildbook. This field allows multiple catalog numbers to be recorded to account for this.
  • individualID - “An identifier for an individual or named group of individual organisms represented in the Occurrence. Meant to accommodate resampling of the same individual or group for monitoring purposes. May be a global unique identifier or an identifier specific to a data set.”
  • locationID - “An identifier for the set of location information (data associated with dcterms:Location). May be a global unique identifier or an identifier specific to the data set.”
  • decimalLatitude - “The geographic latitude (in decimal degrees, using the spatial reference system given in geodeticDatum) of the geographic center of a Location. Positive values are north of the Equator, negative values are south of it. Legal values lie between -90 and 90, inclusive.”
  • decimalLongitude - “The geographic longitude (in decimal degrees, using the spatial reference system given in geodeticDatum) of the geographic center of a Location. Positive values are east of the Greenwich Meridian, negative values are west of it. Legal values lie between -180 and 180, inclusive.”
  • verbatimLocality - “The original textual description of the place.”
  • maximumDepthInMeters - “The greater depth of a range of depth below the local surface, in meters.”
  • maximumElevationInMeters - “The upper limit of the range of elevation (altitude, usually above sea level), in meters.”
  • sex - “The sex of the biological individual(s) represented in the Occurrence. Recommended best practice is to use a controlled vocabulary.”
  • day - “The integer day of the month on which the Event occurred.”
  • month - “The ordinal month in which the Event occurred.”
  • year - “The four-digit year in which the Event occurred, according to the Common Era Calendar.”
  • verbatimEventDate - “The verbatim original representation of the date and time information for an Event.”
  • occurrenceRemarks - “Comments or notes about the Occurrence.”
  • modified - “The most recent date-time on which the resource was changed. For Darwin Core, recommended best practice is to use an encoding scheme, such as ISO 8601:2004(E).”
  • occurrenceID - “An identifier for the Occurrence (as opposed to a particular digital record of the occurrence). In the absence of a persistent global unique identifier, construct one from a combination of identifiers in the record that will most closely make the occurrenceID globally unique.”
  • recordedBy - “A list (concatenated and separated) of names of people, groups, or organizations responsible for recording the original Occurrence. The primary collector or observer, especially one who applies a personal identifier (recordNumber), should be listed first.”
  • behavior - “A description of the behavior shown by the subject at the time the Occurrence was recorded. Recommended best practice is to use a controlled vocabulary.”
  • eventID - “An identifier for the set of information associated with an Event (something that occurs at a place and time). May be a global unique identifier or an identifier specific to the data set.”
  • dynamicProperties - “A list (concatenated and separated) of additional measurements, facts, characteristics, or assertions about the record. Meant to provide a mechanism for structured content such as key-value pairs.”
  • identificationRemarks - “Comments or notes about the Identification.”
  • genus - “The full scientific name of the genus in which the taxon is classified.”
  • specificEpithet - “The name of the first or species epithet of the scientificName.”

The following fields are specific to this mark-recapture project and do not have an easy to map Darwin Core equivalent.

  • dwcImageURL - An URL to a thumbnail image representing the encounter.
  • measurements - An array of physical Measurement objects that define point-in-time measurements on the animal (e.g., height, weight, etc.)
  • livingStatus - Defines whether the sighting represents a living or deceased individual. Currently supported values are: “alive” and “dead”.
  • dwcDateAdded - Date the encounter was added to the library.
  • researcherComments - Additional comments added by library users
  • submitterID - Username of the logged in researcher assigned to the encounter.
  • submitterEmail, submitterPhone, submitterAddress - name, email, phone, address of the encounter submitter.
  • informothers - other email addresses to inform of status changes to this encounter (e.g., other members of a tour group reporting this encounter)
  • photographerName, photographerEmail, photographerPhone, photographerAddress - name, email, phone, address of the encounter photographer.
  • additionalImageNames - names and relative paths of the photos submitted for this encounter.
  • interestedResearchers - researcher email addresses to notify when data for this encounter is modified.
  • hour - hour of the sighting
  • minutes - minutes of the sighting
  • patterningCode - an open ended string that allows a type of patterning to be identified. As an example, see the use of color codes at splashcatalog.org, allowing pre-defined fluke patterning types to be used to help narrow the search for a marked individual.
  • images - an array of the SinglePhotoVideo objects that represent individual photos and videos gathered during this encounter.
  • tissueSamples - an array of the TissueSample objects that represent biological samples (biopsies, blood samples, etc.) gathered during this encounter.

Marked Individual

The following data are recorded for marked individuals.

  • individualID - unique identification string of the MarkedIndividual, such as 'A-109. This is the same intended value as Encounter.individualID.
  • alternateid - alternate id for the MarkedIndividual, such as a physical tag number of reference in another database.
  • encounters - an array of the encounters of this marked individual.
  • comments - additional comments added by researchers.
  • sex - overall determined sex of the MarkedIndividual.
  • nickName - nickname for the MarkedIndividual.
  • nickNamer - individual (person) who nicknamed this marked individual.
  • dataFiles - an array of filenames of additional data files added to the MarkedIndividual.
  • interestedResearchers - a list of email addresses to notify when this MarkedIndividual is modified.
  • dateTimeCreated - creation time of this data object.
  • dynamicProperties - from the Darwin Core: “A list (concatenated and separated) of additional measurements, facts, characteristics, or assertions about the record. Meant to provide a mechanism for structured content such as key-value pairs.”
  • patterningCode - an open-ended string that allows a type of patterning to be identified. As an example, see the use of color codes at splashcatalog.org, allowing pre-defined fluke patterning types to be used to help narrow the search for a marked individual.

Occurrence

The following data are recorded for occurrences.

  • encounters - an array of the encounters comprising this encounter.
  • comments - additional comments added by researchers.
  • groupBehavior - description of the aggregate behaviors of the individuals in the group represented by this occurrence.
  • individualCount - estimated number of total individuals in this occurrence, which may be greater than the number “captured” and recorded.

Installation

Installation of Wildbook Framework is relatively simple, but it does involve installation of a web server, which many users may be unfamiliar with.

Prerequisites

To run the framework, you will need a Linux server (recommended) with the following software pre-installed:

  • Java SE 7 (a.k.a, “Java 1.7”). These are available from Oracle. At a minimum, download and install the Java Runtime Environment (JRE); if you wish to develop Java programs, download and install the Java Development Kit (JDK), which includes the JRE. Don't forget to define JAVA_HOME as a system environment variable (settings its value to the file system path to Java on your computer) to allow Java-based applications to use your installed Java version.
  • Tomcat 7 and 8, which is available from the Apache Software Foundation. Download the “binary distribution” that is appropriate for your operating system (e.g., “64-bit Windows zip” for 64-bit Windows machines, or “zip” or “tar.gz” for Linux and Macintosh machines). Tomcat is a “servlet container” that can run Java-based applications under a web server. It can also act as a web server by itself. Jetty, older versions of Tomcat, and other J2EE containers/servers may work but have not been tested. Integration of Tomcat with third party web servers (e.g., Apache 2.2.x) is common, but this topic is well beyond the scope of these instructions. These sample instructions assume that Tomcat has been installed on your local laptop or desktop and is listening on port 8080.
  • ImageMajick - ImageMajick must be available from the command line for image manipulation. Specifically, we use the 'convert' command for image thumbnail generation but may use other commands in the future.
  • PostgreSQL database installed on the server. Wildbook by default tries to connect to a Postgres database on the same server named 'wildbook' on localhost:5432 with username 'wildbook' and password 'wildbook' permissions.
  • sendmail - Wildbook can email data contributors and researchers with data updates. On Linux servers, sendmail is required.

Technically, Wildbook can also be run on Windows and Mac laptops and desktops, but we highly recommend running Wildbook on an Ubuntu Linux virtual machine from Amazon Web Services, which makes the server setup and management process very easy. If you need Mac and Windows support, please contact services@wildme.org.

Installing Tomcat

Installing Tomcat is beyond the scope of this document, but it is very well documented on the web.

We HIGHLY recommend running Wildbook on an Ubuntu Linux web server through Amazon Web Services' EC2 service.

  • Tomcat is very well supported for Linux, but instructions for downloading and installing will vary according to Linux flavor. Consult your Linux distro (you may already have Tomcat) or the Web for Tomcat installation instructions for your Linux platform.
  • For Windows operating systems, Tomcat can be downloaded with Windows installers, making the installation process very easy.
  • For Macintosh hardware, these instructions are excellent. Use Apple's “Terminal” app to type the various “sudo” commands shown in the instructions.

NOTE: Since somewhere around version 7.0.30+ (approximately), Tomcat includes a tomcat7-websockets.jar file that must be removed before Tomcat will load with Wildbook.

Known good configurations

We run Wildbook exclusively on Ubuntu servers on Amazon Web Services (generally an m4.large EC2 instance). We use Java 8 and Tomcat 7/8.

Deploying the WAR file

Wildbook is downloaded and deployed as a web application archive file (.WAR) in Tomcat. To install this file:

  1. Using your web browser, download the latest available WAR file (wildbook.war) from the downloads page.
  2. Place the wildbook.war file in the "webapps" folder of Tomcat. For example:
    • If you installed Tomcat to "/var/lib/tomcat7" on Linux, then you would place the WAR file in the folder "/var/lib/tomcat7/webapps". The folder "/var/lib/tomcat7/webapps/wildbook" will be created when Tomcat is restarted (e.g., 'service tomcat7 restart').
  3. Open a web browser to your server's URL or IP address plus "/wildbook". A default landing page for Wildbook is displayed. This steps assumes a basic Tomcat installation on a web server with Tomcat assigned to use its default port 8080.
  4. Log into the framework using the default 'tomcat' user ID and 'tomcat123' password.

Wildbook is now ready for use. Keep in mind that Tomcat must be running to enable access to Wildbook through your Web browser. If Tomcat is stopped, or your computer is rebooted, Tomcat must be restarted as described above.

Wildbook is a menu-driven interface. The following table lists the menus included by default. You can also customize Wildbook's navigation to include your project-specific information.

Menu Description
Return to your Wildbook main landing page.
Report an Encounter Allows researchers to supply data and images gathered during an encounter with a member of your target species.
Learn -> Learn More about Wildbook Navigate to the main Wildbook web site.
Individuals Menu
Individuals -> View All View a list of Marked Individuals. A Marked Individual a uniquely-identified member of a population and includes one or more reported encounters.
Encounters Menu
View Encounters (By State) Browse a lists of encounters (sightings of individuals) in the database.
View Images Browse images collected during encounters.
Encounter Calendar This option displays all encounters in a calendar format.
Sites Menu
View Encounter data by preconfigured study sites. Specifically, these are configured as locationIDs in commonConfiguration.properties.
Search Menu
Search Encounters Perform a filtered search of encounters (sightings) of your study population(s).
Individual Search Perform a filtered search of marked individuals in your study population(s).
Search Comparison Compare the results of two Individual Searches side-by-side.
Contact Us Information about how web site visitors can contact your organization.
Administer Menu
My Account Information about you. Reset your password. Enable social media login. Upload a profile photo. And more.
General The general administration option allows site administrators to make changes to Wildbook that may affect many or all records in the library. The following options are available from this screen:
  • Restore a deleted encounter.
  • Update Email Address of Submitter or Photographer Across the Entire Library.
  • Swap old location code for new across all encounters.
  • Expose all approved encounters to the Global Biodiversity Information Facility (GBIF). GBIF was established by governments in 2001 to encourage free and open access to biodiversity data through the Internet.
    Global Biodiversity Information Facility Home Page
  • Logs
  • Set Location Codes for all encounters matching a string.
  • Set Inform Others for all encounters matching a string.
Logs Provides links to related Wildbook log files.
Grid Administration
(only for use with spot pattern recognition)
Grid Administration displays active and completed spot pattern comparison jobs, as well as the parameters controlling the grid and the nodes responding. Only users of Wildbook who are working with spotted species would ever use this screen.
Grid Administration includes the following options:
  • Pending scantasks
  • Completed scanTasks
  • gridManager Adjustment
  • gridManager Statistics
  • Creation / Deletion Threads
User Management View, add, and remove Wildbook users.
Photo Keywords Create and manage keywords applied to images in your library. Keywords increase the efficiency of your searches.
Javadoc Javadoc describes all the classes and interfaces in Wildbook Programming Interface. The Wildbook API allows Java programmers to customize, extend and enhance the functions in Wildbook application framework.
Data Import Import data into Wildbook in the SRGD format.

Submitting data

By default, any visitor to your Wildbook site can submit data as an Encounter (a sighting of one animal at a point in time). Login is not required, though this can be configured. Information collected from researchers and other sources are added to your library as unapproved encounters. Unapproved encounters can be reviewed by authorized personnel and approved if they provide enough information to be useful in research.

The most critical information to capture is:

  • Photos of the animal
  • Date
  • Location
  • Contact information
  • Any additional or unique comments.

Wildbook places these fields first in the submission form.

Click here to see an example of a Wildbook Encounter submission page.

Additional encounter data fields

The following additional data fields are also available for data submission if you click: Do you have advanced information?

Fields in this form can be added, removed, and/or required through manual customization.

Menu Description
Measurements A configurable set of measurements for the animal can be entered in customizable units. The measurements and their units are defined in commonConfiguration.properties and localizable (translatable) in commonConfigurationLabels.properties in the appropriate language folder.
Sex Choose Male, Female, or Unknown.
GPS Latitude Longitudes and Latitudes are expressed in decimal degrees notation. A link to a simple converter program (GPS Latitude and Longitude Converter) is included.
GPS Longtitude
Sea floor depth at encounter site Only one of these measurements will apply to any encounter.
Elevation at encounter site
Status Choose Alive or Dead.
Behavior Observed behavior of this animal during this encounter.
Noticeable Scarring Animals that have unusual physical characteristics, such as physical damage or unusual physical structures, can be re-identified later by other researchers using these identifying characteristics. Photographs of the characteristics you describe here are helpful.
Other email addresses to inform of resightings and status Supply email addresses of other interested parties in a comma-delimited list as shown in the following figure.
Species The species observed. This is configured through commonConfiguration.properties. If only one species is configured, Wildbook will default to that species with every Encounter submission.
Life Stage The customizable life stage of the observed animal, such as: juvenile, sub-adult, and adult.
Tags Record satellite, acoustic, physical, and archival metadata here.

Once your submission is complete, click Send encounter report to add your encounter to Wildbook library.

Encounters and Workflow

Encounters entered into a Wildbook can be part of a data processing workflow according to their Encounter.state value. By default, these values are:

  • unapproved - This is the default state for new data in a Wildbook. These encounters have not been reviewed for quality. To view unapproved encounters, choose menu option EncountersView Unapproved Encounters.
  • approved - These encounters contain sufficient information to identify the animal as a marked individual, and a reviewer has specifically changed the Encounter state to approved. To view approved encounters, choose menu option EncountersView Approved Encounters.
  • unidentifiable - These encounters have been reviewed, but insufficient information exists in the encounter record to identify the animal. To view unidentifiable encounters, choose menu option EncountersView Unidentifiable Encounters.

If you choose any of these three options, a table of encounters appears, allowing you to sort by column and filter by text. Like any Encounter Search in Wildbook, you can also view these encounters on a map, on a calendar, as thumbnails, as charts, etc.

Figure. Viewing New, Unapproved Encounters in Wildbook (Encounters → View Unapproved Encounters menu option)

Approving and rejecting encounters

This section describes how to approve or reject a newly submitted encounter. Sometimes encounters are added with incomplete or inaccurate information. It is best to leave these encounters as Unapproved until the submitter has been contacted and the information has been corrected.

Reviewing a new encounter

To review a new, unapproved encounter, follow these steps:

  1. Look at the new encounter in the View Unapproved Encounters view (login required by default) and ensure that the its thumbnail image was correctly rendered. If not, use the Reset thumbnail command on the encounter page to choose a photo to render a new thumbnail from.
  2. Check to make sure that all of the photos submitted contain material appropriate for display on your web site. It is important to be sure that offensive material or photos showing inappropriate interaction with animals are not displayed in the library. If the photos contain appropriate content and have enough information to reasonably expect that the animal can be re-identified now or in the future, proceed to the next step. If the encounter contains offensive material, no photos, or poor quality photos, proceed to Rejecting an Encounter below.
  3. Click on each photo one by one to view it in full detail. Note the presence of any distinguishing characteristics, such as scars, distinct spot patterning, or physical tags, using the pulldown list of keywords above each photo.
  4. Check and edit the data submitted for each encounter as needed. For example, verify that the size estimate is realistic (30 feet versus 30 meters) and that the submitted comments contain appropriate language and correct spelling.
  5. Add the appropriate Location ID to the encounter and check any reported GPS coordinates for accuracy using the displayed Google Map.
  6. If the content of the unapproved encounter is acceptable, click Approve to make the encounter visible to the general public once all of the above steps have been completed.

Editing encounters

TBD

Keywords

You can add, rename and remove keywords from your Shepherd library. Once keywords are established, you can apply them to photos in your library to accelerate searching.

To manage keywords, log in as a site administrator and choose AdministerPhoto Keywords.

Photo Keywords Management

Creating a keyword

To create a keyword, you must supply two pieces of information.

  • A Keyword String Identifier - This string serves as a unique key in the database table that holds the keywords. It must be unique.
  • The Keyword itself.

Once you supply information to both fields, click Add.

Removing a Keyword

To remove an existing keyword, follow these steps:

  1. Choose the keyword you want to delete from the list.
  2. Click Remove.

Renaming a keyword

If you mis-spelled a keyword, or you want to change an existing keyword for any other reason, follow these steps:

  1. Choose the keyword yuu want to rename from the list.
  2. Enter the new string for the keyword.
  3. Click Rename.

Applying keywords to an image

To apply keywords to an image, follow these steps:

  1. Log in to Wildbook as a user with privileges for the image's encounter.
  2. Edit the encounter for which the image was supplied. The image management features are in the right-hand column of the encounter record. The following figure shows an image in an Encounter record with no applied keywords.
  3. Choose a keyword from the list, and click add.

Removing keywords from an image

To apply keywords in your database to an image, follow these steps:

  1. Log in to Wildbook as a user with privileges for the image's encounter.
  2. Edit the encounter for which the photo with the applied keywords was supplied. The following figure shows an image in an Encounter record with two applied keywords.
  3. Click directly on the keyword under the Remove Keywords label. This removed the keyword from the encounter.
    Note:The the keyword still exists in your library and can be applied to other encounter images.

Searching for encounters using keywords

Wildbook includes a powerful search engine that allows you to locate encounter records in your database using many criteria. You can use the Photo Keywords in your library as a search criteria. Follow these steps:

  1. Choose SearchEncounter Search from Wildbook menu.
  2. Click Observation attribute filter header. The following fields appear.
    Observation attribute filters
  3. Click a keyword, use Ctrl-Click to choose more than one keyword, or Shift-Click to choose a group of keywords.

    keywords_selection3 keywords_selection1 keywords_selection2

  4. Click Search Sightings at the bottom of the Encounter Criteria page.

Managing biological samples

Biological samples in Wildbook represent the collection of an amount of tissue, blood, scat, mucus, etc. during an Encounter. These samples may be used for genetic analysis, for toxicology, or for the analysis of diet through stable isotopes. Because you may collect multiple biological samples and/or types of samples during an Encounter with an animal, Wildbook allows for one or more biological samples to be added to each Encounter record. For each biological sample, you can add the following:

  • Sample ID (required) - a unique identifier for the sample. This becomes the primary key for the TISSUESAMPLE table in Wildbook database.
  • A genetic sex determination (e.g., from chemical analysis of blood or analysis of DNA from a tissue sample)
  • A haplotype determination
  • A Microsatellite marker (genotype) analysis in the form of n-number of loci and paired allele lengths
  • n-number of biological measurements, which can be configured to include:
    • Multiple stable isotope markers appropriate for the sample type, species, and study
    • Multiple chemical markers appropriate for the sample type, species, and study
  • Alternate sample ID - an alternate identifier for the sample.
  • Sample type - The biological nature of the sample (e.g., “blood”, “mucus”, “tissue”). These values can be configured for the project in commonConfiguration.properties as tissueType0, tissueType1, etc.
  • Preservation method - The preservation method for the sample.
  • Storage lab ID - The lab storing the biological sample.
  • Sampling Protocol - The protocol used is sample collection.
  • Sampling effort - The effort required for collection.
  • Field sample number - The sample number assigned int he field if different from the primary Sample ID.
  • Field notes - Any notes from the field about the sample and its collection.
  • Remarks - Any general notes and remarks about the sample.
  • Institution ID - Institution responsible fo the sample.
  • Collection ID - The collection housing the sample
  • Collection code - The ID of the sample withing the collection if different from the assigned Sample ID.
  • Dataset ID - The dataset ID to which the sample belongs.
  • Dataset name - The name of the dataset to which the sample belongs.

Configuration options

Wildbook allows for you to configure the types of biological samples your project collects and the types of measurements that might be performed upon them.

Configuring allowed sample types

Your project may collect multiple types of biological samples from an animal. These may include scat, tissue, blood, mucus, and other bodily fluids or secretions. To configure Wildbook to list your types of biological samples:

  1. Open the WEB-INF/classes/bundles/commonConfiguration.properties file with your favorite text editor.
  2. Starting with tissueType0, define each biological sample type you want your project to collect, incrementing the number by 1 with each additional value (e.g., tissueType0, tissueType1, tissueType2). You can easily add or remove values in the future. The properties file notation of Java allows only one entry per line, and the key (e.g., “tissueType0” and the value (e.g., “blood”) must be separated by an equals sign.
  3. Save and exit commonConfiguration.properties.
  4. Restart Tomcat to pick up the change.

Here is an example set of definitions:

#tissue sample types
tissueType0 = Tissue sample
tissueType1 = Fecal sample
tissueType2 = Mucus sample
tissueType3 = Blood sampe
tissueType4 = Parasite sample

Configuring species-specific microsatellite markers (genotype)

Wildbook allows you to configure the following aspects of genotype determination for your species:

  • numLoci - The number of loci used for genotype determination in your project. This value determines the number of loci name entries that appear when you add and search for genotype determinations.
  • numPloids - The number of sets of chromosomes in your species' biological cells. This value determines the number of allele value entries that appear when you add and search for genotype determinations. Most species are diploids, and this value will almost always be 2.
  • alleleRelaxMaxValue - This value is used in conjunction with the Encounter Search and Individual Search functions of Wildbook. This is the maximum value that will appear in the Relax allele length value by: +/- pulldown menu of these search forms. The purpose of this value is to allow for a certain amount of loose matching of allele values if needed.
#genetic parameters
numLoci = 14
numPloids = 2
alleleRelaxMaxValue = 5

Configuring biologiocal measurement types

Whether conducting a toxicology analysis or examining diet with stable isotopes, you can configure Wildbook to store multiple “biological measurements” for each biological sample you add to an Encounter. The configuration for biological measurements is done in the file WEB-INF/classes/bundles/commonConfiguration.properties. The relevant fields in this file are:

  • biologicalMeasurementTypeX - The descriptor of the measurement type. For example, “Methylmercury” for toxicology or “13C” for stable isotope analysis. Replace X with an integer, starting with 0.
  • biologicalMeasurementUnitsX - The units for the corresponding entry of biologicalMeasurementTypeX. Replace X with an integer, starting with 0.
  • biologicalMeasurementSamplingProtocolsX - A possible sampling protocol used for the measurement. Replace X with an integer, starting with 0. This value does NOT necessarily correspond with the corresponding biologicalMeasurementTypeX value, and the number of entries here may NOT match the number of entries for biologicalMeasurementTypeX.

To configure Wildbook to list your types of biological sample measurements:

  1. Open the WEB-INF/classes/bundles/commonConfiguration.properties file with your favorite text editor.
  2. Starting with biologicalMeasurementType0, define each biological sample measurement type you want your project to collect, incrementing the number by 1 with each additional value (e.g., biologicalMeasurementType0, biologicalMeasurementType1, biologicalMeasurementType2). You can easily add or remove values in the future. The properties file notation of Java allows only one entry per line, and the key (e.g., “biologicalMeasurementType0” and the value (e.g., “13C”) must be separated by an equals sign.
  3. Starting with biologicalMeasurementUnits0, define each biological sample measurement type units (e.g., “parts per million”) that you want your project to collect, incrementing the number by 1 with each additional value. The units defined here correspond to the same number of biologicalMeasurementTypeX.
  4. Starting with biologicalMeasurementSamplingProtocols0, define each biological sample measurement protocol (e.g., “lipids extracted”) that you want your project to collect, incrementing the number by 1 with each additional value. This value does NOT necessarily correspond with the corresponding biologicalMeasurementTypeX value, and the number of entries here may NOT match the number of entries for biologicalMeasurementTypeX.
  5. Save and exit commonConfiguration.properties.
  6. Restart Tomcat to pick up the change.

Here is an example set of definitions:

#biological measurement types
biologicalMeasurementType0 = 13C
biologicalMeasurementType1 = 15N
biologicalMeasurementType2 = 34S
biologicalMeasurementType3 = Methylmercury

#corresponding biological measurement units
biologicalMeasurementUnits0 = ppm
biologicalMeasurementUnits1 = ppm
biologicalMeasurementUnits2 = ppm
biologicalMeasurementUnits3 = ppm

#corresponding biological measurement sampling protocols
biologicalMeasurementSamplingProtocols0 = Lipids extracted
biologicalMeasurementSamplingProtocols1 = No lipids extracted, corrected
biologicalMeasurementSamplingProtocols2 = No lipids extracted, uncorrected
biologicalMeasurementSamplingProtocols3 = Extraction
biologicalMeasurementSamplingProtocols4 = Alkaline digestion

Adding a biological sample

After you have configured your project's allowed biological sample types, you can add biological samples to any Encounter in your project. To add a sample to an Encounter page:

  1. Log into your Wildbook.
  2. Navigate to the Encounter page to which you want to add a biological sample.
  3. In the Biological Samples section of the page, click Add biological sample. The Create/update biological sample form for creating the sample appears in the blue bar on the left of the page.
  4. Enter a required Sample ID for the Encounter.
  5. Enter any other relevant fields for the sample.
  6. Click Set to add the biological sample to the Encounter. The sample will then be displayed and summarized in the Biological Samples section of the page.

Figure: Biological Sample Example

Biological sample example in Wildbook

Adding a haplotype analysis

To add a haplotype determination to a biological sample:

  1. Navigate to the Biological samples section of the relevant Encounter page.
  2. In the entry for the biological sample you want to add the haplotype determination to, click Add haplotype.
  3. In the Add/update haplotype form, fill out the following fields as required or needed:
    1. Analysis ID (required) - A unique ID for this analysis.
    2. Haplotype (required) - The determined haplotype value.
    3. Processing lab task ID - The identifier for the analysis performed at the processing lab/
    4. Processing lab name - The name of the lab that made the haplotype determination.
    5. Processing lab contact name - The name of the individual to contact with questions about this analysis as performed at the processing lab
    6. Processing lab contact details - Contact details for more information about this analysis.
  4. Click Set to store the haplotype determination.

Adding microsatellite markers

To add microsatellite markers to a biological sample:

  1. Navigate to the Biological samples section of the relevant Encounter page.
  2. In the entry for the biological sample you want to add the markers to, click Add microsatellite markers.
  3. In the Add/update microsatellite markers form, fill out the following fields as required or needed:
    1. Analysis ID (required) - A unique ID for this analysis.
    2. Processing lab task ID - The identifier for the analysis performed at the processing lab/
    3. Processing lab name - The name of the lab that made the haplotype determination.
    4. Processing lab contact name - The name of the individual to contact with questions about this analysis as performed at the processing lab
    5. Processing lab contact details - Contact details for more information about this analysis.
    6. Locus (multiple) - The name of the locus for which you have allele lengths to record.
    7. Allele (multiple) - The length of the allele as an integer.
  4. Click Set to store this genotype determination.

Adding stable isotope markers

To add a stable isotope determination to a biological sample:

  1. Navigate to the Biological samples section of the relevant Encounter page.
  2. In the entry for the biological sample you want to add the stable isotope determination to, click Add biological/chemical measurement.
  3. In the Add/update biological/chemical measurement form, fill out the following fields as required or needed:
    1. Analysis ID (required) - A unique ID for this analysis.
    2. Type (required) - The type of this measurement.
    3. Value (required) - The value of this stable isotope measurement.
    4. Sampling Protocol - The sampling protocol used for this stable isotope determination.
    5. Processing lab task ID - The identifier for the analysis performed at the processing lab.
    6. Processing lab name - The name of the lab that made the analysis.
    7. Processing lab contact name - The name of the individual to contact with questions about this analysis as performed at the processing lab.
    8. Processing lab contact details - Contact details for more information about this analysis.
  4. Click Set to store the stable isotope value.

Adding a toxicology/chemical measurement

To add a toxicology or chemical measurement determination to a biological sample:

  1. Navigate to the Biological samples section of the relevant Encounter page.
  2. In the entry for the biological sample you want to add the chemical measurement determination to, click Add biological/chemical measurement.
  3. In the Add/update biological/chemical measurement form, fill out the following fields as required or needed:
    1. Analysis ID (required) - A unique ID for this analysis.
    2. Type (required) - The type of this measurement.
    3. Value (required) - The value of this chemical measurement.
    4. Sampling Protocol - The sampling protocol used for this chemical measurement.
    5. Processing lab task ID - The identifier for the analysis performed at the processing lab.
    6. Processing lab name - The name of the lab that made the analysis.
    7. Processing lab contact name - The name of the individual to contact with questions about this analysis as performed at the processing lab.
    8. Processing lab contact details - Contact details for more information about this analysis.
  4. Click Set to store the measurement value.

Editing and deleting biological samples and associated analyses

The Wildbook edit icon icon allows you to edit the fields of a biological sample or one of its associated analyses.

The Wildbook cancel icon icon allows you to delete a biological sample or one of its associated analyses.

Viewing a summary of all samples for a marked individual

The biological samples for a Marked Individual, spanning all of its Encounters, are summarized on its inididivual web page in Wildbook.

Marked individual biological samples summary

Managing marked individuals

Marked individuals are animals in your database for which there is sufficient information to identify them upon recapture. This often means that the encounter record includes photographic evidence that reveals identifying characteristics. For example, WhaleShark.org relies on left side spot pattern recognition to identify unique individuals.

The following figure shows the Marked Individual table that appears when you choose IndividualsView All.

?750

Adding a marked individual

To add a marked individual to the Shepherd library, follow these steps:

  1. Edit an encounter that has sufficient information to qualify as a marked individual.
  2. Click the edit icon on the Identified as: field.
  3. In the Create Marked Individual section of the Manage Identity dialog box, enter a new, unique ID for the Marked Individual.
  4. Click Create.

Adding an Encounter to a Marked Individual

A marked individual may have multiple encounters. If an encounter, upon analysis, matches a marked individual record, follow these steps to add that encounter to the marked individual.

  1. Edit the encounter that you want to include as part of the Marked Individual.
  2. Click the edit icon on the Identified as: field.
  3. In the **Manage Identity** dialog box, look for the **Add to Marked Individual** area and enter the **Individual** to which you want to assign the encounter.
  4. Choose the method of identification in the **Matched by** field. Choose from one of the following analytical methods:
    • Pattern match
    • Visual inspection
    • Unmatched first encounter
  5. Enable the Suppress e-mail/RSS option if you want to prevent interested parties from receiving email and RSS feed notifications about your changes. Leave the option unchecked to notify the interested parties. Emails will be sent to submitters, photographers, and adopters of each and every encounter of the marked individual.
  6. Click Add.

Deleting a Marked Individual

To remove an encounter from a marked individual, follow these steps:

  1. Edit an encounter that has been added to a marked individual.
  2. Click edit on the Identified as: field.
  3. In the Manage Identity dialog box, click Remove.

Managing Group Occurrences

An Occurrence represents a observation of multiple individuals together and includes one or more encounters over a short duration of time. The purpose of an occurrence is to provide an hierarchical category to represent groups of individuals and potentially the relationships among them at a point in time and space. For example, an occurrence might represent a pods of baleen whales, which are typically fluid in membership, even over brief periods of observation (e.g., less than an hour), or more stable groups, such as sperm whales, which might remain relatively stable over a longer period of continuous observation (e.g., several hours).

Click here to see an example occurrence record.

Occurrences are created from a single Encounter, and then more encounters are added to represent the set of related sightings. None, some, or all of the Encounters in an Occurrence may be identified and associated with a Marked Individual. An Occurrence can contain the following information about a group of animals sighted in close proximity:

  • Group behavior (user defined)
  • Number of Marked Individuals sighted together (calculated)
  • Estimated total number of marked individuals in the Occurrence (user defined)
  • Location ID (calculated, should be the same for all Encounters of the Occurrence)
  • Encounters (user added)
  • Thumbnail gallery of images (displayed from the Encounter records)
  • Mapping of added Encounters

Co-participation in an Occurrence defines a social relationship in Wildbook between two marked individuals, as displayed on the page for each Marked Individual.

Figure: A Social Relationship Table for a Marked Individual
Social relationship table for a Marked Individual

Creating an Occurrence

To create an Occurrence:

  1. In Wildbook, go to an Encounter page that represents one of the animal sightings in the Occurrence you want to record.
  2. After logging into Wildbook, click edit next to the Occurrence ID field.
  3. In the Create occurrence form that appears in the blue bar on the left of the Encounter page, enter a New Occurrence ID to uniquely identify the occurrence in the database.
  4. Click Create to create the new Occurrence record in the database of Wildbook.

Adding an Encounter to an Occurrence

To create an Occurrence:

  1. In Wildbook, go to an Encounter page that represents one of the animal sightings in the Occurrence you want to record.
  2. After logging into Wildbook, click edit next to the Occurrence ID field of the Encounter page.
  3. In the Add to occurrence form that appears in the blue bar on the left of the Encounter page, enter an Occurrence ID to identify the Occurrence to ad this Encounter to.
  4. Click Add to finish adding the encounter to the group occurrence record.

Removing an Occurrence

To create an Occurrence:

  1. In Wildbook, go to the page of the Encounter that you want to remove from an Occurrence.
  2. After logging into Wildbook, click edit next to the Occurrence ID field of the Encounter page.
  3. In the Remove from occurrence form that appears in the blue bar on the left of the Encounter page, click Remove to finish removing the encounter from the group occurrence record.

Searching

Wildbook offers extensive search functionality that allows you to quickly locate records in your library based on a large set of filter criteria. The Search menu includes these options:

  • Encounter Search
  • Individual Search
  • Search Comparison
  • Google Search

If you choose SearchEncounter Search, Wildbook searches across sighting reports and displays the following set of configurable filters.

  • Location filter (map) allows you to define a boundary box on a map and initiate a search based on encounters in that location.
  • Location filters (text) allow you to execute a search against location IDs and verbatim location descriptions in your library.
  • Date filters allow you to search by a date range and/or by pre-defined verbatim date(s) (e.g., “Summer sampling 2004”).
  • Observation attribute filters allow you to search by sex, status, length, behavior descriptions or pre-defined keywords.
  • Identity filters allow you to search across encounter by marked individual attributes, such as alternate ID or number of sightings.
  • Tags filters allow you to search on Metal, Acoustic, and Satellite Tag metadata.
  • Biological samples and analyses filters allow you to search on biological samples and their attached measurements and analyses (e.g., haplotype, microsatellite markers, genetic sex, etc.)
  • Metadata filters allow you to search three types of encounters - Approved, Unapproved, and Unidentifiable. You can choose more than one encounter type.
  • Export Options allow you to create a spreadsheet listing encounter records that match your search criteria.

If you specify parameters for more than one filter, Wildbook applies a logical AND to your result sets for each defined filter. For example, if you specify that you are searching for females, and you specify that you are searching encounters that occurred in 2009, your result set will include all females encountered in 2009.

The following sections describe each filter classification.

Location Filter (Map)

The Location Filter Map has several controls that allow you to narrow the geographical focus of your search. Only animals encountered within the geographical boundaries of your search are included in the search results. The following table shows the Map controls.

Field Description
area zoom Area Zoom. This button allows you to draw a rectangle on the map. Your search will be limited to the area you draw.
zoom in Zoom in.
zoom out Zoom out.
arrow up Move the visible area of the map slightly north.
arrow down Move the visible area of the map slightly south.
arrow left and right Move the visible area of the map east or west.

GPS entry fields

Below the map are four fields that display the longitude and latitude of the northeast and southwest corners of the displayed map segment. The following figure shows an example map with these fields populated.

Map longitude and latitude

Location filters (text)

Location Filters (Text) allows you to search encounters by the name of the location or by the Location ID.

Location Text

Date Filters

Date Filters allow you to filter for encounter records by supplying a beginning and end date for your search. All encounters that fall on or between these two dates are included in the search results.

You can also filter records on the verbatim event date field.

Date Filters

Observation Attribute Filters

The Observation Attribute Filters allow you to search for encounters that were observed to have specific physical attributes (e.g., sex, size) and behaviors. This filter set also includes search by applied photo keywords.

Observation Attribute Filters

Identity filters

Identity filters allow you to search identified encounters (i.e., those for which an identification resulted) by Alternate ID or by the number of times they have been encountered.

Observation Attribute Filters

Tags filters

Tag filters allow you to search on physical tagging metadata. You can search on:

  • Metal tags - Search on left and right side physical tag identifiers that were applied to the animal.
  • Acoustic tag - Search on the serial number and ID number of acoustic tags applied to the animal.
  • Satellite tag - Name, serial number, and Argos PTT number of a satellite tag deployed on the animal.

Biological samples and analyses filters

The Biological samples and analyses filters allow you to search on biological samples that were collected during the course of an Encounter and on the resulting analyses of those samples.

The following filters are available:

  • Has biological sample - filters Encounters down to those with added biological samples.
  • Haplotype is - filters Encounters by one or more selected haplotype analysis results that have been performed on a biological sample added to the Encounter.
  • Sex was determined from genetic analysis as - filters Encounters by a sex determination analysis performed on a biological sample added to the Encounter.
  • Has microsatellite marker loci - filters Encounters by microsatellite markers obtained from a biological sample added to the Encounter. You can filter the markers by:
    • Marker - Check the box for each marker name that you want to filter by. Each additional marker is added as a requirement to the search filter. You do not need to specify allele lengths in the provided field blanks, but you can if you require fine-grained filtering. The more complex your filters, the slower your results will be displayed in Wildbook. Some complex microsatellite marker filter choices have taken ten minutes or more to return results.
    • Relax allele length value by - If you filter on allele lengths, you can allow for imprecise length matching (plus or minus) up to the limit you set here.

Metadata Filters

Metadata filters allow you to search by encounter type. Click the check boxes next to the encounter type categories you want to include in your search.

Observation Attribute Filters

Exporting to Excel

To Export your search results to an Excel Spreadsheet, follow these steps:

  1. Choose the Generate an Excel File of the Filtered Results option.
  2. Click Search Sightings. The Search Result screen appears.
  3. Click the Results Table tab. The Excel spreadsheet is available as a download from the link at the top of the encounter table, as shown in the following figure.

    Image Tiles

OBIS Data Export

You can export data from Wildbook as an Excel file that can be delivered to OBIS-SEAMAP. To export data in an easy format for OBIS-SEAMAP to ingest:

  1. Create an Encounter Search in Wildbook.
  2. Click the Encounter Search Export tab.
  3. Click Exported Excel spreadsheet (.xls) file in OBIS format to download the Excel file.

You can optionally click Exported Excel spreadsheet (.xls) file in OBIS format with locale inclusion for unreported GPS instead if you want Wildbook to use the default study site GPS values defined in locationIDGPS.properties for Encounters without explicit latitude and longitude values.

Exporting to KML Format

KML file format is a tag-based markup language usable by Google Earth and Google Maps. For a complete description of the KML file format, and its applications, refer to the following document:

What is KML?

To Export your search results to an KML file, follow these steps:

  1. Set your filter parameters using the options described in this article.
  2. Click Search Sightings. The Search Result screen appears.
  3. Click the Mapped Results tab. The KML file is available as a download from the link below the map, as shown in the following figure.

Exporting to ESRI Shapefile Format

A shapefile stores nontopological geometry and attribute information for the spatial features in a data set. The geometry for a feature is stored as a shape comprising a set of vector coordinates. The following whitepaper describes the ESRI Shapefile format in detail.

ESRI Shapefile Technical Description

Any set of filtered encounter results generates a shapefile data set. Shapefiles are delivered as a zip file, and are available from the Mapped Results tab. (See the figure in the previous section.)

You can view a shapefile dataset by using the ESRI Shapefile viewer at the following link:

ESRI Shapefile Viewer

Browsing Search Results

When you enter search criteria and click Search Sightings at the bottom of the page, Wildbook lists all records in your library that match your criteria. The search results are categorized in four ways:

  • Results Table shows a tabular list of encounters.
  • Matching Images / Videos shows a set of thumbnails of pictures and video stills that match your criteria. The following figure shows an example.

    Image Tiles

  • Mapped Results shows matching encounter records plotted on a map.

    Mapped Results

  • Results Calendar shows matching search results in a calendar format.

Wildbook includes a set of filters designed for searching Marked Individuals in your database. It is important to understand that Individual Search is a composite search. While an Encounter Search requires every Encounter result to match all selected filters, Individual Search matches filters across the Encounters of a Marked Individual. Some matching data points, such as a haplotype, apply to the life history of the animal, while other data points, such as a biological measurement (e.g., a stable isotope measurement), are point in time measurements and must match along with the selected date and time filters.

If you choose SearchIndividual Search, Wildbook displays the following set of configurable filters.

  • Location filter (map) allows you to pinpoint a location on a map, and initiate a search based on that location. This filter has exactly the same fields as the Location Filter (Map) encounter search.
  • Location filters (text) allows you to execute a string search against location codes and descriptions in your library. This filter also allows you to specify one or more location IDs.
  • Date filters allows you to search by date. This filter set is identical to the encounter search date filters.
  • Observation attribute filters allow you to search by these characteristics:
    • sex
    • length
    • photo keywords
    • submitter name
    • photographer name
    • submitter or photographer email address
  • Identity filters allow you to search for a marked individual who has been sighted multiple times by setting the Maximum years between resightings field. You can also search the marked individuals in your database by Alternate ID.
  • Tags filters allow you to search on Metal, Acoustic, and Satellite Tag metadata.
  • Biological samples and analyses filters allow you to search on biological samples and their attached measurements and analyses (e.g., haplotype, microsatellite markers, genetic sex, etc.). See the description of these fields in the Encounter Search section.

If you specify parameters for more than one filter, Wildbook applies a logical AND to your result sets for each defined filter. For example, if you specify that you are searching for females, and you specify individuals encountered after January 1, 2010, your result set will include all females encountered after 1/1/2010.

Search Comparison

TBD

Administration

The Administer menu offers site managers and programmers some additional features and detailed information about the software. Many of the options on this menu are powerful features that affect many records in your database. It is recommended that you limit access to the features to trusted visitors to your site.

The following options appear on the Administer menu.

General Administration

This menu item allows access to the following options.

  • Restore a deleted encounter.
  • Update email address of Submitter or Photographer Across the Entire Library
  • Swap old location code for new across all encounters
  • Expose all approved encounters to the GBIF.
  • Logs
  • Set the location code for all encounters matching a string
  • Set Inform Others for all encounters matching a string

These options are described in the sections that follow.

Restore a deleted encounter

To restore a deleted encounter, follow these steps:

  1. Choose AdministerGeneral.
  2. Enter the ID of a deleted encounter into the Encounter Number field of the Restore a Deleted Encounter option.
    Restore Deleted Encounter
  3. Click Restore.

Update email addresses across Wildbook library

This option allows you to make a library-wide change to an email address of a submitter or photographer. This is useful when individuals change email addresses but still want to be kept updated of animal re-sightings.

Restore Deleted Encounter
  1. Enter the email address to change in the Old Email Address field. Only email addresses exactly matching the entry in this field are modified.
  2. Enter the new email address in the New Email Address field.
  3. Click Update.

Swap old location code for new across all encounters

This option allows you to make a library-wide change to a location code in all encounter records.

Change Location Codes
  1. Enter the location code to change in the Old Location Code. Only location codes exactly matching the entry in this field are modified.
  2. Enter the new location code in the New Location Code field.
  3. Click Update.

Expose all approved encounters to the GBIF

Click Expose to GBIF to expose all approved encounters to the Global Biodiversity Information Facility (GBIF).

Expose to GBIF

The GBIF was established in 2001 to encourage free and open access to biodiversity data through the Internet.

Global Biodiversity Information Facility Home Page

By default, approved encounters are exposed to GBIF if you have properly configured a TapirLink or IPT provider to the database underlying your Wildbook instance.

Logs

Wildbook Logs feature is under development. Site administrators should refer to the logging features of the J2EE container on which they have Wildbook installed. For example, with Tomcat, Shepherd outputs issues to catalina.out. This may be different for other containers.

Set Inform Others for all encounters matching a string

This option lets you set one or more email addresses into the Others to Inform field of an encounter.

Modify Inform Others

Enter a string in the Test String to Match field. Wildbook adds the email addresses in the Inform Others email addresses to assign field to any encounter record that includes the matching string in any of these fields:

  • Submitter Name
  • Submitter email address
  • Photographer Name
  • Photographer email address

Note that this is a fuzzy match, so the string Robert will match with any of these records:

  • Robert James
  • Roberta Muldoon
  • Robin Roberts
  • researcher5@BrobertCorp.com.

Photo Keywords

The option AdministerPhoto Keywords allows you to add, delete, and modify keywords for images in your library. These keywords can be used to search for specific images. The following section describes all of these functions in detail.

Keywords

Adoptions

You can allow visitors to your site to adopt animals identified in your database. By adopting an animal, they can be provided with updates on the animal's status, notifications of additional sightings, and other information.

To enable adoptions on your site, set the allowAdoptions field in commonConfiguration.properties to TRUE.

#whether to display and allow adoptions - set to true for yes and false for no
allowAdoptions = true

When you set the allowAdoptions parameter, to TRUE, Wildbook displays the Adoptions menu under Administration.

View All Adoptions

If you choose AdministrationAdoptionsView All Adoptions, a table of active adoptions displays.

all adoptions

The adoptions table contains the information described in the following table.

Field Description
Thumbnail The first column always shows a thumbnail picture of the creator of the adoption record.
Number The adoption ID. This is a unique ID created when you add the adoption to the library.
Name Name of the user adopting an animal.
Type By default, Wildbook supports three types: promotional, individual adoption, and group adoption, corporate adoption.
Adopted This is a marked individual ID for an animal in your database.
Start Date The starting date of the adoption period.
End Date The ending date of the adoption period. Adoptions can have no end date, which means they are open ended.

Create / Edit Adoption

If you choose Create / Edit Adoption from the Administer menu, you can add an adoption through the Create Adoption form. The following table describes the fields in the Create Adoption form.

Field Description
Name Name of the user adopting an animal.
email A valid email address for the adopter. You can enter multiple emails delimited by commas, as shown in the following figure.
adoption email
image By default, Wildbook supports three types: promotional, individual adoption, and group adoption, corporate adoption.
Adopter quote This is a marked individual ID for an animal in your database.
Marked Individual This is a marked individual ID for an animal in your database.
Encounter This is an encounter ID for an animal in your database.
Adoption Type By default, Wildbook supports these types:< promotional, individual adoption, and group adoption, corporate adoption.
Adoption Manager By default, this is the login user name of the creator of the adoption record.
Adoption Start Date The starting date of the adoption period.
Adoption End Date The ending date of the adoption period. Adoptions can have no end date, which means they are open ended.
Adoption Notes This is any arbitrary information describing this adoption.

Restore a Deleted Adoption

Enter the adoption id of the deleted adoption, then click Submit.

Customizing Wildbook

See Configuring Wildbook for more information about customizing Wildbook for your research.

Get Support

The following support options can help you use Wildbook.