=Paper=
{{Paper
|id=Vol-273/paper-10
|storemode=property
|title=Adding Value to Biodiversity Images Through Community Annotation
|pdfUrl=https://ceur-ws.org/Vol-273/paper_42.pdf
|volume=Vol-273
|dblpUrl=https://dblp.org/rec/conf/www/Riccardi07a
}}
==Adding Value to Biodiversity Images Through Community Annotation==
https://ceur-ws.org/Vol-273/paper_42.pdf
Adding Value to Biodiversity Images through Community
Annotation in the Morphbank System
Greg Riccardi
College of Information
Florida State University
Tallahassee, FL 32306-2100 USA
01-850-644-2869
Riccardi@ci.fsu.edu
Morphbank, an on-line collection of museum-quality biological Discovering and recording ad-hoc data is the most problematic. It
images, is an NSF funded project designed to facilitate the on-line is particularly difficult to find ways that users can record
collaboration of biologists around the world. Our primary goal is associations among objects.
to aid in the collection and management of images that are useful
As long as data is well formatted and constrained to the database
in phylogenetic research.
schema, finding and retrieving it is simple. However, as we’ve
Morphbank users are actively collaborating on the creation of discovered, there is no practical limit to the amount of information
information that represents the associations among images and a scientist may wish to store with a particular specimen. Most of
related biodiversity data objects. This demo will explain the the knowledge is contained in the memory of these scientists or in
Morphbank annotation tool and data models and give examples of hand written notebooks. Although it is recognized that manual
how users create structured information in the system. annotation is expensive and time consuming it is nevertheless still
Schematized annotation provides biologists with a flexible essential in documenting collaborative knowledge in biological
framework to create semantically-rich annotations using their own systems [2]. Translating and storing this knowledge in a
data models. searchable form is the challenge.
The demo will include access to the Morphbank image repository,
image annotation tools and association mapping tools. We will
1.1 Morphbank Objects
Each object in the Morphbank system is uniquely identified and
demonstrate the scientific process that uses the annotation tools to
includes a set of standard fields that assist us in cataloging its
create semantically rich associations. Users will be given access to
location and type, the identification of the user who added the
the full capabilities of the working system.
object, the date and time of creation, an optional description of the
object, and the last time the object was modified. These attributes
1. Morphbank Objects allow anyone accessing Morphbank sufficient information to find
Morphbank is an open Web repository of images that serves the and catalog data and associate related objects. Each object is
biodiversity research community. It is currently being used to externally identified by a Life Science Identifier (LSID) [13].
document specimens in natural history collections, to voucher
DNA sequence data, and to share research results in disciplines 1.2 Morphbank Object Relationships
such as taxonomy, morphometrics, comparative anatomy, and Since each Morphbank object is uniquely identified, any object
phylogenetics. can be the target of a stored reference. A single column within a
Morphbank contains information about organisms. Each image in Morphbank table holding a foreign key may refer to several an
the system is associated with one or more specimens. Each object of any type. Thus a collection object can be heterogeneous.
specimen is a representation of information about an organism. For instance, an annotation object may define an association
Specimens are in turn associated with localities, contributors, among images, specimens, locations, users, or even other
taxonomic concepts annotations.
The initial requirements analysis for the Morphbank system This flexibility allows for the creation of complex collections of
identified several challenges in discovering and creating objects that can be shared with other users of the Morphbank
information about images and their related objects. system. Although there are a series of predefined relationships in
Morphbank, the use of unique identifiers allows users to define an
Finding images and specimens associated with a specific unrestricted set of complex relationships of objects within the
species and genus, confines of the system.
Finding and recording information about that image and its
related objects, and 2. Morphbank Object Annotation
A variety of annotation technologies allow users to add value to
The discovery and recording of ad-hoc associations among images by creating associations between those images, text and
the various objects. other digital objects. Morphbank takes this one step further by
making the associations into first class objects that can themselves
be annotated and associated with other objects. Morphbank also
1
Supported by NSF contract DBI-0446224, 2005-2008 allows associations to take on specific semantic characteristics
WWW 2007, May 8--12, 2007, Banff, Canada. that constrain their meaning and thereby improve searching and
understanding.
3. Biological Annotation Requirements relationships between data objects, and the development of
A problem of biodiversity annotation is that biologists have electronic research records [10]. Users are able to record
increased the number of specimens they can gather but have not associations between digital objects across and among projects.
increased their ability to catalog, identify, and study them. Morphbank seeks to combine these ideas by allowing
Collaborations still include the exchange of physical specimens incorporating an extensible annotation type system and by
and the manual annotations of the images using indexed cards and systematically expanding the scope of associations by including
paper documents. At the functional level, many users have any objects referenced by globally unique IDs (GUID).
developed their own specific but proprietary solution to this
problem. Through the use of Morphbank and a Web based Morphbank was designed to allow users to take advantage of Web
annotation tool, we can solve most if not all of these problems. service products to gain access to the data by conforming to
industry practices and standards but maintain the ontology of the
3.1 Morphbank Object Annotation original data. Users will browse or search the Web site for
A variety of annotation technologies allow users to add value to Morphbank objects using a variety of tools provided through the
images by creating associations between those images, text and Web site.
other digital objects. Morphbank takes this one step further by
making the associations into first class objects that can themselves 4. Demonstrations
be annotated and associated with other objects. Morphbank also The demonstration of the Morphbank system will allow
allows associations to take on specific semantic characteristics participants to collaborate by adding annotations to a collection of
that constrain their meaning and thereby improve searching and images of tropical fish in order to reach consensus on the
understanding. similarity and diversity of their markings and colorings. Each
participant will be able to identify the various features on the fish
Image annotation is available in a variety of image management images.
Web sites. The simplest annotations are found in systems that
support attaching tags to images and other media. Flickr.com and Participants will use the Morphbank tools to compare the image
YouTube.com, e.g., allow users to add text attributes (tags) to annotations. Each person will be able to record their evaluations
images and use those tags to support searching. FotoTagger.com, of these annotations.
among others, goes a step further and allows the tags to be If all goes well, the participants will reach consensus on the
attached to specific locations on images. feature identification. Experts from outside of the workshop will
Blogging is another form of image annotation in which text add their own evaluations.
passages are linked to images, Web pages and other digital
objects. A blog entry creates an associate between its own text and
the linked objects. Full list of Authors:
Greg Riccardi, Andrew Deans, David Gaitros, Neelima
Annotea.org supports the creation of RDF attributes for image Jammingumpula, Corinne Jorgensen, Peter Jorgensen, Austin
tags. These attributes can be used to provide search inference Mast, Karolina Maneva-Jakimoska, Debbie Paul, Fredrik
capabilities for users of image repositories. Ronquist, Katja Seltman, Steven Winner
Another annotation strategy involves the development of College of Information and College of Computational
laboratory notebooks such as those under development at the Science
United States Department of Energy, National Collaboratories
under the guidance of Dr. Jim Myers [11]. These middle-ware Florida State University,riccardi@ci.fsu.edu
products present researchers, applications, problem-solving
environments (PSE), and software agents with a layered set of
application services that provide a finite set of capabilities for the
creation and management of meta-data, the definition of semantic