Columbia ONS Archiving May09

Libraries and digital scholarship, documenting Open Notebook Science Jean-Claude Bradley May 20, 2009 Columbia University Associate Professor of Chemistry Drexel University Andrew Lang Professor of Mathematics Oral Roberts University

Outline

ONS and Digital Scholarship

Roles and opportunities for Libraries

Open and Closed Science Traditional Lab Notebook (unpublished) Traditional Journal Article Open Access Journal Article Open Notebook Science (full transparency) CLOSED OPEN Traditional Paper Textbook F2F lectures Lectures Notes public Assigned problems public Archived Lectures Public and free online textbooks RESEARCH TEACHING

Motivation: Faster Science, Better Science

Open Notebook Science Logos (Andy Lang, Shirley Wu) Sharing: how much and when

There are NO FACTS, only measurements embedded within assumptions Open Notebook Science maintains the integrity of data provenance by making assumptions explicit

TRUST PROOF

The solubility of 4-chlorobenzaldehyde

The Log makes Assumptions Explicit

The Rationale of Findings Explicit

Raw Data Made Public Splatter? Some liquid

YouTube for demonstrating experimental set-up

Calculations Made Public on Google Spreadsheets

Revision History on Google Spreadsheets

Wiki Page History

Comparing Wiki Page Versions

Proof of Purity with interactive NMR spectrum using JSpecView and JCAMP-DX

Semi-Automated Measurement of solubility via web service analysis of JCAMP-DX files (Andy Lang)

Indexing Molecules on Google

Linking to Molecules in Chemistry Databases

Experimental Spectra and User-Deposited Data on ChemSpider

Crowdsourcing Solubility Data

ONS Challenge Students

ONS Challenge Judges

Teaching Lab: Brent Friesen (Dominican University)

Solubility Experiment List

Summary of Solubility Experiments

Solubilities collected in a Google Spreadsheet

Rajarshi Guha’s Live Web Query using Google Viz API

From Wikipedia to…

… the lab notebook and raw data

Including links to the literature

Concentration (0.4, 0.2, 0.07 M)

Solvent (methanol, ethanol, acetonitrile, THF)

Excess of some reagents (1.2 eq.)

Reaction to Optimize

Mettler-Toledo MiniMapper

Mettler-Toledo MiniBlock System

XML reports from MiniMapper robot

GoogleDoc to program and report

Paper written on Wiki

Paper on Journal of Visualized Experiments (JoVE)

References to papers, blog posts, lab notebook pages, raw data

Where’s the Beef?

Pre-print on Nature Precedings

ChemSpider Journal: Automated Mark-up of Chemical Names

Cameron Neylon’s Notebook Other Open Notebooks

Anthony Salvagno’s Notebook (Steve Koch group)

The Missing Pieces of the Puzzle

Automatic Backup of Science 2.0 Data

Archiving of Open Notebooks

Science 2.0 Community Needed Resources - Preservation, Cataloging, Archiving, Cite-ability

The ONS backup spreadsheet and ONSPreserver

Publishing Google Spreadsheets as XLS

Automatic Backup of Data

Archiving Open Notebooks

Librarians and Science 2.0 "The Internet Archive is a 501(c)(3) non-profit that was founded to build an Internet library, with the purpose of offering permanent access for researchers, historians, and scholars to historical collections that exist in digital format." The internet Archive is not practical for practitioners of Open Notebook Science or Science 2.0

Good concept but.....

Most pages look like this....

Possible role for libraries: citation to objective third party archives of digital scholarship

Acknowledgments