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Biological Storytelling A Software Tool for Biological Information Organization Based upon Narrative Structure Presented by Anjani K Dhrangadhariya Junior Student, M.S. Life Science Informatics Bonn-Aachen International Center for Information Technology B-IT Allan Kuchinsky, Kathy Graham, David Moh, Annette Adler, Ketan Babaria, Michael L. Creech; Biological storytelling: a software tool for biological information organization based upon narrative structure; ACM Siggroup Bulletin 01/2002; DOI:10.1145/1556262.1556315 ISBN: 1-58113-537-8
Biological storytelling: A Software Tool for Biological Information Organization Based upon Narrative Structure
Allan Kuchinsky, Kathy Graham, David Moh, Annette Adler, Ketan Babaria, Michael L. Creech; Biological storytelling: a software tool for biological information organization based upon narrative structure; ACM Siggroup Bulletin 01/2002; DOI:10.1145/1556262.1556315 ISBN: 1-58113-537-8 Presented by Anjani K Dhrangadhariya Junior Student, M.S. Life Science Informatics Bonn-Aachen International Center for Information Technology B-IT
Text of Biological storytelling: A Software Tool for Biological Information Organization Based upon...
Biological Storytelling A Software Tool for Biological
Information Organization Based upon Narrative Structure Presented
by Anjani K Dhrangadhariya Junior Student, M.S. Life Science
Informatics Bonn-Aachen International Center for Information
Technology B-IT Allan Kuchinsky, Kathy Graham, David Moh, Annette
Adler, Ketan Babaria, Michael L. Creech; Biological storytelling: a
software tool for biological information organization based upon
narrative structure; ACM Siggroup Bulletin 01/2002;
DOI:10.1145/1556262.1556315 ISBN: 1-58113-537-8
Way research really is
Your preference ?
or...This Protein A with 2 active sites interacts with Protein
B having 1 active site and 1 allosteric site, in presence of
co-enzyme X under high concentration of XYZ in ABC pathway and BBC
temperature in XOX fish found in XXX ocean.
INTRODUCTION Drug designing/discovery and treatment for life
threatening diseases is a mind mapping process which takes into
account piecing together the story of how genes and proteins behave
in pathway (in disease pathogenesis). Paradigm is Personalized
medicine which involves taking into account peculiar genomic
information and tailoring drugs for individuals according to their
genetic makeup. Microarray: Made it possible for researchers to
correlate gene expression with disease progression, screen for
mutations, and treat patients according to their genetic profiles.
Yu X, Schneiderhan-Marra N, Joos TO.;Protein microarrays
forpersonalized medicine.; Clin Chem. 2010 Mar;56(3):376-87. doi:
10.1373/clinchem.2009.137158. Epub 2010 Jan 14.
DNA Microarray DNA microarray made Paradigm shift in Medicine
possible and GAVE HUGE AMOUNT OF RAW DATA which remains to be sense
of....by researchers
Analysis and Synthesis
http://en.wikipedia.org/wiki/List_of_open-source_bioinformatics_software
Synthesis Task Synthesis is a Greek word meaning "to put
together" Procedure to combine separate elements or components in
order to form a coherent whole Synthesis and Analysis task go hand
in hand and complement each other. Every synthesis is built upon
the results of a preceding analysis, and every analysis requires a
subsequent synthesis in order to verify and correct its results.
But this simply does not seem the case in Bioinformatics whereby
huge number of Analysis softwares are available but synthesis
softwares lack. Tom Ritchey.; Analysis and synthesis: On scientific
method based on a study by bernhard riemann.; Systems Research
Volume 8, Issue 4, pages 2141, December 1991; DOI:
10.1002/sres.3850080402
Synthesis task (1) Keeping track of the diverse pieces of
information, (2) Organizing and using the diverse information, (3)
Formulating hypotheses and higher-level explanations, (4) Sharing
the information
Findings from User Research The facts gathered and hypothesis
formed during the synthesis task were usually stored in form of
printed web pages and were kept in binders but it did not serve at
later date when information was required. (Finding a needle from
haystack!!!!!!!!!!!) User research results came up that researchers
particularly have difficulty in keeping the track of diverse pieces
of information. (Hence the problem in synthesis task was
identified) From user studies and other collaborative design
sessions with researchers at Cancer Genetics lab, a number of
themes for navigating and interacting with this huge amount of data
was identified AND... Vicki ODay, Annette Adler, Allan Kuchinsky,
Anna Bouch.; When Worlds Collide: Molecular Biology as
Interdisciplinary Collaboration; Proceedings of European Conference
on Computer Supported Collaborative Work (ECSCW2001), Bonn,
Germany, 2001.
A Picture emerged which explained the Synthesis tasks involved
in Biological Researches NARRATIVE STRUCTURE Piecing together the
story MADE SENSE
Aspects of User Research Connecting the dots mind mapping
Information is in free form (Structure-less) Many researchers, many
fields and many hypothesis Group work, multiple perspectives
Solving the puzzle together Reasoning over data Sharing of
data
The Role of Narrative Structure Thorndyke: Comprehensibility
and recall are were a function of amount of inherent plot structure
of the story, independent of the actual content. Schank: When prior
experience is indexed cleverly, we can call it to mind to
understand current situation. This process can lead to brand new
insights. Thorndyke,P.W.; CognitiveStructures in Comprehension and
Memory of Narrative Discourses; Cognitive Psychology, 9, 1977,
pp.77-110 Schank, R, Tell Me a Story: Narrative and Intelligence,
North western University Press, 1990.
Middleton and Edwards: Telling stories preserves potentially
arcane and idiosyncratic pieces of information ... Erickson:
Depicts storytelling as an integral part of design. Stories have
informalities that are well suited to lack of certainity that
characterises much design related knowledge. Stories also provide
concrete examples that people from vastly different backgrounds can
relate to Middleton, D., and Edwards, E, Collective Remembering;
SAGE Publications;1990. Erickson, T.; Notes on Design Practice.
Stories and Prototypes as Catalysts for Communication, in Scenario
Based Design: Envisioning Work and Technology in Systems
Development (ed .J .Carroll), Wiley, 1995, pp.37-58
Birth of the Tool Thus after applying above perspectives to
user findings and drawing analogies, a prototype software tool was
developed on the concept of STORY TELLING which utilizes Narrative
Structure as framework and allows Biologists in their Synthesis
tasks- Organize and use information Build hypothesis from data
Construct alternative explantions from Biological Process share
diverse information (Labs are generally interdisciplinary with each
researcher having varied field related terms e.g. KB = KiloByte for
Computer Scientist and KB = KiloBase for a Biologist)
OVERVIEW OF THE SOFTWARE Features provided by BIOLOGICAL
STORYTELLING Free form database model Narrative framework Concrete
social aspect of information sharing Creating alternative
hypothesis with reasoning Semi-automatic clustering of biological
entities Extensive cross references to public and proprietary data
and literature
Elements There are three connecting entitites in the free form
data model of Biological Storytelling. Items Biological Stories
Collections
Items Basic unit of information Represent biological entities
like gene, proteins or other gene product like a trascript Items
contain detailed information about biological entity in form of
links to different public and proprietary databases and literature
information Data can be automatically loaded into Items (Tabular
gene expression data) Researcher can also manually add information
Viewer for dataset of Items loads from microarray experiment raw
data
Items
Collections User created and free form set of items. Analogous
to clustering Collections manager component provides tree view of
collections (Analogous to tree view panel in Windows Explorer) Data
can be manually or semi-automatically loaded into Collections.
Collections are malleable. (one can split, merge, add to
collections and/or move Items from one collection to another.
Collections can have other Collections as well as other Items
(Nested) Repositories for links to experimental data and
literature
Collections
Biological Stories Narrative structure to represent state of
Biological hypothesis Textually and graphically building up
Biological stories (Story editor) Allows to represent story in form
of themes, players and explanations Represent paths explored and
alternative hypothesis formulated Repositories for links to
experimental data and literature
Example... PAX3-FHKR oncogene activates Myogenin and MyoD
Action of myogenin and MyoD induces My14 Failure of muscle cells to
differentiate and end cycle = uncontrolled proliferation =
Cancer
Biological Stories
Grammar Top level element in story editor is a STORY.. Optimal
Themes A set of Players A set of Explanations STORY
Theme Works as an abstract ( as in a publication Entered in
free form text in Story Editor PAX3 oncogene activates a myogenic
transcription program, causing alveolar rhabdomyosarcoma
Player Items and Collections which play a role in Biological
Stories e.g. Genes and Proteins that interact in pathways or can
say kind of characters playing role in a story Myogenin and
MyoD
Explanation This forms the main plot of the Story Contains
descriptive elements about a Biological Story Explanation contains
An optimal theme A set of players A set of interactions Annotations
which support or oppose the claims made in explanation
[Theme}+Players+Explanations+[Comment] Description+[Comment]
[Player]*+[Comment] item|collection|[Player]* Description//could be
a URL for acitation
Putting the story together graphically People think Graphically
rather than Textually Diagram Editor tool Nodes = Players (Nouns)
Edges = Interactions (Verbs) Diagram Editor Tool More general
Prefeined Verbs for relationships between genes. Inhibits Binds
Promotes
Semantic Overlays A way of juxtaposing Biological Stories with
detailed experimental data Validate higher level hypothesis
Annotation and Citations Textual notes Arbitrary list of
citations (URL) Each citation can again have an arbitrary textual
note attached to it For annotating biological elements an Object
Editor is provided
Support for Group Work Annotation is tagged with user name and
timestamp Provides Support and Oppose elements in Story Editors
which can accomodate alternative hypothesis
Web repository
User Feedback Conflict about use of terms in Story Editor. Some
researchers liked literary terms while others liked scientific
terms Discussions on importance of free form data model. (which is
rather malleable) User suggestion: Able to group experiments intos
into Collections, not just Items Using Players globally v/s tagging
them with alternatives
Storyspace (EastGate Systems) Lotus Agenda STKE, BIND, KEGG,
EcoCyc, TransPath, SPAD The eLab Book Cell Space software Related
Work
Better for microarray experiments and not the generalized
research Data format for loading (Tabular data for automatic
loading into software) Cons !!
Provision for multiple data types Evolution to support Systems
approach Support Scientific publications Converting diagramatic
representation into textual stories via use of parsers Utilization
of data mining methods. (Semi-automatic in populating collections)
Future Work
Image sources
http://www.clipartheaven.com/clipart/kids_stuff/images_%28a_-_f%29/boy_-_happy_3.gif
http://www.picgifs.com/clip-art/activities/sweating/clip-art-sweating-328953.jpg
Snap shot of papers http://www.ncbi.nlm.nih.gov/pubmed/19937809
http://www.sciencedirect.com/science/article/pii/S0197458011001783
Snap shot of public databases: PubMed
http://www.ncbi.nlm.nih.gov/pubmed Pubchem:
https://pubchem.ncbi.nlm.nih.gov/ Protein DataBank:
http://www.rcsb.org/pdb/home/home.do
https://genome.unc.edu/images/microarray.jpg
http://www.bio.davidson.edu/people/macampbell/acs_magic/excel_sheet.jpg
http://www.ub.edu/stat/docencia/bioinformatica/microarrays/ADM/imatges/SingleArray1.jpg
http://upload.wikimedia.org/wikipedia/commons/thumb/a/a0/Caesar-dot-to-dot.svg/350px-Cae
sar-dot-to-dot.svg.png
