Biological Concept Diagram Editor (BCDE)
This is a test version of Biological Concept Diagram Editor. Most of the functions are
working. If you see any bugs please email mcfouzer@umich.edu. The beta release required
Java Run Time Environment 1.6. Please download if you don't have it install on your
computer. If you wish to be added to the BCDE email list please send a subscribe email to
mcfouzer@umich.edu.
What is BCDE:
Biological Concept Diagram Editor (BCDE) is a conceptual relationship
diagramming tool specifically designed for biomedical researchers.
Compared to existing diagramming/drawing tools, BCDE has several
advantages. It allows for efficient knowledge/data capture, fast diagram
creation, easy data retrieval and flexible exporting.
The BCDE application is the main diagramming tool in the system. It is
based on the JHotDraw framework. Through it, users can create, modify,
load, and save BCDE diagrams. The diagrams created with BCDE
application are network oriented. When the diagram is displayed on the
BCDE application’s canvas, it is represented by a network of nodes (figures)
and edges. Each BCDE figure can be annotated using fields from the
BioPAX level II format. In addition, a user can add URL links and
attachments to a BCDE figure. Diagrams generated in BCDE are stored in
the BCDE XML format for better database integration and better data
extraction. The XML files can be saved onto a local hard drive or uploaded
to the BCDE XML database.
BCDE also uses a RDF database to store and retrieve information. We
used Oracle's Spatial Network Data Model (NDM), which is developed on
top of Oracle's relational database, as a foundation. In the RDF database,
each interaction in any biological pathway is stored as a RDF triple with the
format: <subject> <predicate> <object>. Furthermore, each triple can be
viewed as a directed graph with two nodes (<subject> and <object>) and an
edge (<predicate>). Since in RDF database, each element has a URI, By
consistently reusing the same URI for the same concept in the RDF database,
we can essentially create a directed graph of all the information in our
database; thus forming something we call the “pathway-interaction
continuum”. Upon initial look, this might not be very useful. However,
more complex query algorithms can be used to explore concept
relationships. For example, one can query all the concepts adjacent to the
concept “HIV virus”. By looking at those adjacent nodes, a researcher might
be able to form new and innovative hypothesis regarding the HIV virus.
A major design goal of BCDE is to greatly increase efficiency of
capturing data from electronic sources; to this end we develop a transfer
function to allow for drag-and-drop input methods with text, images, and
files. The transfer function, the BCDEBar, is in the style of Google/Yahoo
toolbar. With the help of BCDEBar users are able to select text, images or a
mixture of both from a webpage or a local document they are working on and
simply drag-and-drop the selection atop a designated place on the BCDEBar,
which will automatically transfer the selection to BCDE. In addition to
transferring user selected input, we also include certain metadata such as the
location address (URL) of the page currently displayed and time/date of the
transfer. The actual transfer is dependant on type of the data that was
dropped.
BCDE supports adding attachments to any of the BCDE figures.
Attachments could be text files, pictures, word documents, or other files the
user may have on their computer. In addition to simply storing attachments,
BCDE acts as a data repository where the stored attachments can be accessed
and modified using native handlers provided by the operating system. The
right side of the BCDEBar is designed to make adding attachment from the
internet an easy experience. Just like the left side of the BCDEBar, a user
can drag items or strings from a webpage onto it. But instead of creating a
new icon with every drop, the right side of the BCDEBar stores the selected
data into a special dialog box in BCDE called "attachment dialog". The data
in the attachment dialog box can then be drag onto the canvas. If the data is
dragged onto an empty spot on the canvas, a new BCDE figure would be
created just like the first transfer method of the BCDEBar. However, if the
data is dragged onto a BCDE figure that’s already on the canvas, the new
data would be added as an attachment to that BCDE figure.
Since BioPAX is likely to become the common data exchange format for
biological pathways in future, we implemented support for BioPAX in
BCDE. Currently, BCDE allows the user to import a BioPAX file, up to
BioPAX Level II format, onto the canvas. We use four BCDE figures from
our collection to represent all the physical entities in BioPAX. They are
RNA, Membrane, Small Molecule, and Protein. For interactions, we use the
Process figure to indicate the interaction and edges to link the concepts that
are involved in the interaction.
Because Cytoscape is the most used diagram program in the Biological field, it is
important for BCDE to be able to support Cytoscape’s formats. Currently, we only support
the import of SIF files. However in later releases, we will enable the importations of the
other various formats used by Cytoscape. Our current import function requires a
valid SIF file. Just like Cytoscape, the corresponding node and edge attribute
files are optional. Once the SIF is processed, BCDE uses the information to
generate a diagram similar to the way it generates diagrams from BioPax
files. Then, if any attribute file is included, BCDE will process the attribute
file and assign the attribute to the correct concept.
Diagrams are often used for presentation purposes and it will be
important for users to be able to easily modify diagrams using other popular
presentation programs such as PowerPoint or Visio. One of the problems of
existing diagram editors or knowledge bases is they mostly use proprietary
data formats and can only export diagrams in jpg or bmp format, losing
annotations associated with various objects in diagrams. To overcome this
shortcoming, BCDE currently supports exporting BCDE diagrams to
PowerPoint and Visio. When exporting to Visio and PowerPoint, BCDE will
embed almost all the annotations into the generated documents. Currently,
we do not export attachments for the BCDE figures due to the fact that
PowerPoint and Visio do not support attachments for individual figures.
Although the BCDE is still under development, the unique functions we
already implemented make BCDE distinct among other pathway editors in
terms of knowledge/data capture efficiency and compatibility with other
programs and data formats. We plan to add support for Cytoscape format as
well as the upcoming BioPAX Level III format. Advanced searching,
comparison and merging functions will also be included for knowledge
mining.
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BCDE Demo:
1. How to draw two nodes and a link using BCDE
2. How to annotate a node
3. How to add a URL link to a node
4. How to add an attachment to a node
5. How to load an BioPax file into BCDE
6. How to load an Cytoscape SIF file into BCDE
7. How to export BCDE diagram into PowerPoint Slides
8. How to export BCDE diagram into Visio documents
9. How to use the BCDEBar
10. How to use the annotation query web-service
11. Example of a RDF query
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Download BCDE:
Click here to download the BCDE Evaluation version for Windows XP. (This is only for
evaluation purposes.)
Click here to download the BCDE Evaluation version for MacOS X or Linux or Unix. (Use the
shell program run-UNIX.sh or run-MacOS.sh)
Click here to download Java® from Sun Microsystems®. (Java Runtime Enviroment 6 required)
Click here to download Microsoft Office 2003 Primary InterOp Assembly.
Setup Troubleshooting:
You need to have administrator privilege to install BCDE application and the text transfer function
plug-in on your computer. The Windows XP installer will install both components, the BCDE
application and the BrainArray Toolbar, which contain the text drag-and-drop transfer function. Both
function can be uninstalled using the “Add or Remove Programs” function in the Windows XP Control
Panel.
To correctly add the Toolbar to your Internet Explorer (sorry Firefox users), you need to choose
"BrainArrayBar" under the "View" ==> "Toolbars" ==> "BrainArrayBar". Sometimes the bars are way
off to the side of the window, in that case, make sure "View" ==> "Toolbars" ==> "Lock the Toolbars"
is uncheck. Then you can drag the BrainArray toolbar to the desired location.
If you cannot see a shortcut to BCDE on your desktop, you need to go to the C:\Program Files\BCDE
folder and double click the BCDE Application icon to start BCDE.
BCDE may take up to 1 minute to open on some computers depends on the speed of the computer,
internal memory, and/or virus scanner.
To use the export function (to Visio or to PowerPoint), you must install the Microsoft Office Primary
InterOp Assembly. Also, the export functions might not support any Microsoft Office older than the
2003 edition.
We included a BioPax sample file with our release, it can be located at "<BCDE
Directory>\biopax_sample1.owl".
Linux Users:
If run-UNIX.sh file does not run, use "chmod" command to change the permission of the file to allow
execution.
If Java is not found by the run-UNIX.sh, please modify the file by changing the line
'jdkhome="/opt/jdk1.6.0/"' to the appropriate Java directory
Here is an example of how to install Java in Fedora Core 6