Open Access; Open Data I647 Fall 2006 Budapest Open Access Initiative • Based on: – Self archiving by authors – Open Access journals, e.g., BioMed Central • http://www.soros.org/openaccess/ Open Access • Institute of Physics: most papers free for 30 days after publication – http://www.iop.org/EJ/ and http://www.iop.org/EJ/journal/NJP • Public Library of Science – http://www.publiclibraryofscience.org • Highwire Press – http://www.highwire.org/ • PubMed Central – http://www.pubmedcentral.nih.gov/ Opposition to Open Access • Reacting to NIH’s proposed policy on open access, C&EN Editor Rudy Baum says: “[This] action will inflict long-term damage on the communication of scientific results and on maintenance of the archive of scientific knowledge.” -- C&EN, September 20, 2004, p. 7 Open Access + Semantic Web • "Almost all of an author's output (compounds, spectra, reactions, properties, etc.) is nowadays computerised and in principle redistributable to the community for re-use. Few journals actively validate the primary data (e.g. spectra) involved in a publication (chemical crystallography being a clear exception where data are intensively reviewed by machine). We reassert that chemists must now move towards publishing their collective knowledge in a systematic and easily accessible form for re-use and innovation.... Open Access + Semantic Web • We urge that authors, funders, editors, publishers and readers move further towards the following protocol:  All information should be ultimately machine- understandable in XML....  Machine-understandable information for a compound should include a connection table, the IUPAC unique identifier (INChI) which guarantees that the connection table can be checked and regenerated, and a name....  Rights metadata.” -- Murray-Rust, Rzepa, Tyrrella, Zhanga (2004) Google Digitization Plans • Digitize all content of: – University of Michigan • committed to complete digitization of all 7 million volumes in its collection, excluding its rare books and other fragile material – Harvard University – New York Public Library – Stanford University • Aimed at out-of-print material, whether public domain or in copyright • Opportunity for libraries to concentrate on truly unique or special holdings to digitize locally Getting at the Data • New CAS Information Use Policies – http://www.cas.org/infopolicy.html • STN’s Information Keep & Share Program – http://info.cas.org/copyright/index.html • SciFinder Scholar download restrictions: 100 items at a time Data Analysis Tools • STN’s Analyze and Tabulate feature • STN Express with Discover! (Analysis Edition) • Limited access because of A&I publishers’ reluctance to turn loose of the data InChI • IUPAC-NIST Chemical Identifier • a unique label which would be a non-proprietary identifier for chemical substances that could be used in printed and electronic data sources thus enabling easier linking of diverse data compilations • latest version handles: – organic, covalent structures – inorganic and organometallic compounds • http://chemdata.nist.gov/IChI/INChIv11b.zip Future • XML and metadata – Dymond (DYnamic Metadata ON Demand) • Virtual journals (Virtual Journal of Nanoscale Science and Technology) • Copyright question and open access resolution • Legal protection of databases • Impact of InChI and CML • Demise of Abstracting and Indexing Services? Conclusion • “The main challenge is for chemists to recognise the value of making their data machine-understandable, rather than destroying it with traditional paper or slide- focused publication and dissemination processes.” -- Murray-Rust, Rzepa, Tyrrella, Zhanga (2004) Parting words . . . If you're not part of the solution, you're part of the precipitate! Bibliography • Gasaway, Laura. “The open archives movement.” Information Outlook October 2004, 8(10), 36, 39-40. • Murray-Rust, Peter; Rzepa, Henry S.; Tyrrell, Simon M.; Zhang, Yong. “Representation and use of chemistry in the global electronic age.” Organic & Biomolecular Chemistry 2004, 2(22), 3192-3203. http://www.ch.ic.ac.uk/rzepa/obc/ (preprint) • Townsend, Joe A.; Adams, Sam E.; Waudby, Christopher A.; de Souza, Vanessa K.; Goodman, Jonathan M.; Murray-Rust, Peter. “Chemical documents: machine understanding and automated information extraction.” Organic & Biomolecular Chemistry 2004, 2(22), 3294-3300.
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