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I am not a PDBid I am a Biological Macromolecule
Philip E. Bourne
University of California San Diego
Striving to be Recognized
• The “identity” of a macromolecular structure – functional and structural features and its broad role in a living system – is not established very easily by the majority of biologists. Given the technology available to us today surely it is time that this situation changed?
This is Not to Say that the Identity has not Improved
• Improved chemical description of polymers and monomers
• Remove sequence and taxonomic inconsistencies
• Improved representation of viruses
• Primary citation assignments
• REMARKS, SF files, NMR restraints….
Henrick et al. NAR 2008 36: D426-D433
For Example…• Chemical Components Dictionary:
– Model and idealized coordinates
– Chemical descriptors (e.g. SMILES) and systematic names
– Stereochemical assignments and aromatic bond assignments
– IUPAC nomenclature for standard amino acids and nucleotides with the exception of the well-established convention for C-terminal atoms OXT and HXT
– More conventional atom labeling
– Removal of redundant ligands
– Additional description of protonation states
This now sets the stage for the next stage of identity
development
The Problem Can be Defined as A Need to Change the Workflow
Workflow
Entry Point
Sequence
Literature
Structure
Function
Pathway…
The best way to change the workflow is to remove the barrier
between the literature (knowledge) and the PDB (data)
How Can This Happen?
Possibility 1 – ProteopediaA Completely New Beginning
• Advantages– Anyone can contribute simply – Community consensus seems to support
quality (e.g. Wikipedia)
• Disadvantages– Where is the reward?– Wiki format limited for providing a structural
identity
http://www.proteopedia.orgEran Hodis, Eric Martz, Jaime Prilusky, Joel L. Sussman
Possibility 2 - iSee
• Advantages– High quality annotation
• Disadvantages– Time consuming– Does not scale
http://www.sgc.ox.ac.uk/iSee
Possibility 3 – Database and Literature Integration
• Advantages– Reward through publication– Potentially comprehensive– Retains full power of the database and
literature
• Disadvantages– Literature accessibility– Harder to do
The Disadvantage of Literature Accessibility is Disappearing
Slowly
• The NIH Public Access Policy is a Term and Condition of Award for all grants and cooperative agreements active in Fiscal Year 2008 (October 1, 2007- September 30, 2008) or beyond, and for all contracts awarded after April 7, 2008.
So What is the Policy for NIH Sponsored Research?
• You can only agree to a journal copyright policy if that policy allows you to deposit the paper in PubMed Central (PMC)
• The paper must be deposited in PMC
• How this happens depends on the journal
BioLit http://biolit.ucsd.eduOur Effort at Database-Literature Integration
• J.L.Fink, S. Kushch, P. Williams & P.E.Bourne 2008 BioLit: Integrating Biological Literature with Databases NAR 36(S2) W385-389
• P.E.Bourne, J.L.Fink, M.Gerstein 2008 Open Access: Taking Full Advantage of the Content PLoS Comp. Biol. (Editorial) 4(3) e1000037
1. A link brings up figures from the paper
0. Full text of PLoS papers stored in a database
2. Clicking the paper figure retrievesdata from the PDB which is
analyzed
3. A composite view ofjournal and database
content results
BioLit: Tools for New Modes of Scientific Dissemination
• Biolit integrates biological literature and biological databases and includes:– A database of journal
text– Authoring tools to
facilitate database storage of journal text
– Tools to make static tables and figures interactive
4. The composite view haslinks to pertinent blocks
of literature text and back to the PDB
1.
2.
3.
4.
The Knowledge and Data Cycle
http://biolit.ucsd.edu
How Much of the Structure Literature is Currently Found in the Accessible PMC?
PMC Growth
0
2000
4000
6000
8000
10000
12000
14000
16000
1974
1976
1978
1980
1982
1984
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1988
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1992
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2000
2002
2004
2006
2008
Year
Art
icle
s D
epo
site
d
• 74127 articles• 17161 were not
parasable• 7% - 3814 PDBids out
of 51633 referenced in ?? PMC articles
• 338 Figures have legends that include PDBids
ICTP Trieste, December 10, 2007
Where Can we Go From Here with BioLit?
The Ideal Situation is to Capture Relationships as the Paper is
Written
BioLit Plugin ProjectRather than Post-processing the Document the
Author Controls the Semantic Tagging
Author Paper
Word File in Docx formatPublisher
BioLit Plugin Project
Plugin Architecture
Context-Sensitive Data Access
• Display of information of database entries when the user clicks on the ID in the document
• Display of ontology terms related to terms in the document text, using local database search
Ontologies are Stored in a Local Database
User Configurable Selection
• Fully user configuration ontology and database identifier selection
• All searches occur within the user’s desktop computer
• Desired ontologies are downloaded and installed automatically, and update periodically
• BioLit installer XML file provides the application with the information needed to download and install ontologies.
Possibility 4. SciVee - A Different Kind of Learning Experience
Why not listen to the enthusiastic author talk about the structure
while you see the structure respond to their dialog?
YouTube for Scientists www.scivee.tv
Motivation
Pubcast – Video Integrated with the Full Text of the Paper
Pubcast - Making
PSP Washington DC Feb. 2008
Professional Profile
ICTP Trieste, December 2007
Create & Join Communities and Discussion Groups
ICTP Trieste, December 2007
Finding What you Want
• Tag clouds generated automatically from MESH headings
• Full text of the papers indexed
• Browsing by audience type, subject, language etc.
SciVee – Viral Projects
• Sweetwater School District
• “Postercasts”
• Science video competitions
• “Pubumentaries”
Summary
• New modes of learning about structure are possible
• Number 6 never did get identified
• Time will tell whether a PDBid will become more than a number
Acknowledgements
• SciVee Team– Apryl Bailey– Tim Beck
– Leo Chalupa
– Marc Friedman– Alex Ramos– Willy Suwanto
• BioLit Team• J. Lynn Fink• Sergey Kushch• Parker Williams• Greg Quinn
CT Watch 2007, 3(3) 26-31
