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RSC Project Prospect
RSC Project Prospect Introducing semantics into chemical science publishing RSC Publishing a la Web 2.0 User Generated Content 1841 Discussion Forums 1947 …and flame wars Social Networking Interactivity Aims of Project Prospect Preserve authors’ science Capture the science as XML Apply ontologies to find meaning Make it part of the publishing process Provide new views to readers Computer-readable chemistry Meaningful searches Why is it hard for chemistry? Searching Free text or proprietary Related articles No standards Animal ontology those that belong to the Emperor, embalmed ones, those that are trained, suckling pigs, mermaids, fabulous ones, stray dogs, those included in the present classification, those that tremble as if they were mad, innumerable ones, those drawn with a very fine camelhair brush, others, those that have just broken a flower vase, those that from a long way off look like flies. Allegedly from “Celestial Emporium of Benevolent Knowledge” The Analytical Language of John Wilkins, Jorge Luis Borges Classification problems 2,4,6-trinitrotoluene biosynthesis “This term is obsolete as 2,4,6-trinitrotoluene is not synthesized by living organisms“ From the Gene Ontology The RSC Prospect model Enhance existing publications Attract authors Add value for subscribers Promote dissemination of chemical science Build straight into existing workflow Marked small molecule libraries… …lysyl oxidase in zebrafish notochord morphogenesis How? Collaborations Unilever Centre/Computer Lab Others Technology OSCAR text mining Standards Workflow RSS feeds OSCAR text mining Open Source Chemical Analysis Routines University of Cambridge: Chemistry (Unilever Centre) –Computer Lab collaboration SciBorg Analyses single words and short chemical-looking phrases to determine structure Attaches structures to text Extended to subjects InChI IUPAC International Chemical Identifier InChI=1/C8H10N4O2/c110-4-9-6-5(10)7(13)12 (3)8(14)11(6)2/h4H,13H3 Machine readable InChIkey RYYVLZVUVIJVGHUHFFFAOYAW Subject terms Open Biomedical Ontologies Gene Ontology (GO) Sequence Ontology (SO) Cell Ontology (CL) IUPAC Gold Book Dictionary of chemical terminology RSC Publishing process XML up front Technical editors edit and correct the XML, then publish throughout the day Understanding of XML and context, and the subject areas RSC Publishing process Editing Mining Add & Tidy Enhanced RSS feeds Make available chemical structures and subject terms Subject terms and structures in plain text Subject term IDs and InChI in RDF metadata OWL for the subject terms InChI for compounds Enhanced RSS feeds New data standards Experimental data checker Validation Visualisation Role for publishers Feeding back into Open projects Improving chemistry recognition within Project SciBorg Improving Gene Ontology (10,000 enzyme terms added) Tidying the Sequence Ontology It was like a researchers Aladdin's cave… …it was fantastic to dig around the subject area and discover things I never knew existed. My only criticism would be the need for a time warning! I spent 4 hours digging about which generated at least six new research ideas, printed half a ream of paper and I missed my bus home... …At least it was a new excuse my wife had not heard, so another first. Well done to you all but I don't think my wife is that keen on it. Steve Haswell, Hull What’s unique? Technology Semantic enrichment Compounds Ontology terms Enhanced RSS feeds Implementation across existing portfolio Incorporation into workflow Shows the possibilities for structured science For other publishers? Building up new open ontologies Publishers will compete on display and application, but can still share links …via CrossRef? Future for RSC Project Prospect Experimental data Linguistics Extensive linking Other subject areas E-books, databases and backfile Peer review Prospect services RSC Project Prospect Richard Kidd Manager, Informatics [email protected] "My first forays show [Project Prospect is] brilliant. [It's] great to see the compounds and have machine readable SMILES and InChIs" "Your new system is very impressive, I am sure it will become very useful to a large community” •It is great and exciting!! Just from the very few minutes I looked into it I realized its great potential and immediately ran to show it to my students!" “This is a fantastic resource for the community, and a great use of the GO and SO. Nice work" ”I have … found it very intuitive/ straightforward to use.[I] believe that it will make the manuscript even more appealing to readers."
