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 : 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 – Proteopedia A 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 Eran Hodis, Eric Martz, Jaime Prilusky, Joel L. Sussman

Possibility 2 - iSee Advantages –High quality annotation Disadvantages –Time consuming –Does not scale

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, 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 Our 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) W P.E.Bourne, J.L.Fink, M.Gerstein 2008 Open Access: Taking Full Advantage of the Content PLoS Comp. Biol. (Editorial) 4(3) e

1. A link brings up figures from the paper 0. Full text of PLoS papers stored in a database 2. Clicking the paper figure retrieves data from the PDB which is analyzed 3. A composite view of journal 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 has links to pertinent blocks of literature text and back to the PDB The Knowledge and Data Cycle

How Much of the Structure Literature is Currently Found in the Accessible PMC? articles were not parasable 7% PDBids out of 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 Project Rather than Post-processing the Document the Author Controls the Semantic Tagging

Author Paper Word File in Docx format Publisher 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

Motivation

Pubcast – Video Integrated with the Full Text of the Paper

Pubcast - Making PSP Washington DC Feb. 2008

Channels – Just Like TV ICTP Trieste, December 2007

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

Questions?

Questions?