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Ontologies in Physical Science Onto Workshop, ed.ac.uk 2013-04-11 An #animalgarden production Peter Murray-Rust, University of Cambridge & Open Knowledge Foundation

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PMR and friends want us to help build a computational chemistry ontology Is it an important problem? $1,000,000,000/yr for compchem They need OWL Problem: How to build ontologies when people are uninterested or antagonistic even though we have the technology

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Chemists dont use ontologies Perhaps the chemists could use OWL-DL Top-down schemas like AniML havent (yet) taken off

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Are there any ontologies in physical science that work? Crystallo- graphers build CIF dictionaries The IUCr, right? Tell us about CIF IUCr: International Union of Crystallography

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CIF Core defines 500 common concepts CIF: http://www.iucr.org/cif Or the volume of the crystal cell Like the wavelength of the radiation used

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Core dictionary (coreCIF) version 2.4.3 _diffrn_ambient_temperature Definition: The mean temperature in kelvins at which the intensities were measured. Range: 0.0 -> infinity Type: numb An example ? ID For humans For machines: Constraint + type http://www.iucr.org/__data/iucr/cifdic_html/1/ cif_core.dic/Idiffrn_ambient_temperature.html

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Definition: The mean temperature in kelvins at which the intensities were measured. So everyone converts temperatures to use K? Yes! today I swam at 273K But chemists want to use all sorts of different units We MUST have a units ontology

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OWL? Is CIF a proper ontology? Its not RDF but weve global URIs, like cif:_diffrn_ambient_temperature Because IUCr controls the namespace prefix: cif= http://www.iucr.org/cif

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CIF had 20 years of community involvement through IUCr But most top- down chemistry projects dont work So well do this bottom-up.

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Every compchem program uses basically the same scientific concepts We think each should build its own dictionary so we understand the output Wont that just be a mess? No. Its the first step to interoperability.

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Chemical Markup Language PMR/Rzepa http://www.xml-cml.org Hyperchem builds ITS dictionary Each annotates their own program output NWChem builds ITS dictionary The programs will use CML* for chemical output

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in a communal cml:compchem dictionary that everyone uses We agree they are the same so create compchem:alphae Alpha-electrons: Hyperchem uses hchem:e_alpha NWChem has nwchem:_alpha_elec

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What if the data structure or concepts dont map CML provides conventions so each group can define their data structure Data can then be machine validated against each convention!

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But there are over 20 program codes. Weve prototyped with many before. Theyll be encouraged I think its going to work. BUT TTT* GULP, DPOLY, CASTEP, SIESTA, MOPAC TTT: Things Take Time (Piet Hein)

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Will it work? It depends on people National labs CSIRO/AU and PNNL/US are committed And we have companies like Hyperchem and Kitware I wish we had some publishers

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Well need tools Weve got FoX* for FORTRAN output JUMBOTemplates to parse logfiles RDF for navigating dictionaries FoX*: XML/FORTRAN Toby White, Andrew Walker

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Benefits of semantic dictionaries: FORTRAN logfile can be made semantic High degree of interoperability in chemistry Semantic publication (HTML5, CML, MathML) Interoperates with mainstream Web Easily scalable to other phys sci. Problems: Closed code/minds is short-term market advantage Non-trivial commitment (updates, code revision) Getting top-down approval (e.g. IUPAC)

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Benefits of semantic dictionaries: FORTRAN logfile can be made semantic High degree of interoperability in chemistry Semantic publication (HTML5, CML, MathML) Interoperates with mainstream Web Easily scalable to other phys sci. Problems: Closed code/minds is short-term market advantage Non-trivial commitment (updates, code revision) Getting top-down approval (e.g. IUPAC)

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Benefits of semantic dictionaries: FORTRAN logfile can be made semantic High degree of interoperability in chemistry Semantic publication (HTML5, CML, MathML) Interoperates with mainstream Web Easily scalable to other phys sci. Problems: Closed code/minds is short-term market advantage Non-trivial commitment (updates, code revision) Getting top-down approval (e.g. IUPAC)

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Benefits of semantic dictionaries: FORTRAN logfile can be made semantic High degree of interoperability in chemistry Semantic publication (HTML5, CML, MathML) Interoperates with mainstream Web Easily scalable to other phys sci. Problems: Closed code/minds is short-term market advantage Non-trivial commitment (updates, code revision) Getting top-down approval (e.g. IUPAC)

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Benefits of semantic dictionaries: FORTRAN logfile can be made semantic High degree of interoperability in chemistry Semantic publication (HTML5, CML, MathML) Interoperates with mainstream Web Easily scalable to other phys sci. Problems: Closed code/minds is short-term market advantage Non-trivial commitment (updates, code revision) Getting top-down approval (e.g. IUPAC)

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Top-down schemas like AniML havent (yet) taken off Chemists dont use ANY ontologies Perhaps the chemists could use OWL-DL