Alan Tonge Semantic Web Data Repositories from Chemistry e-Thesis Data Mining Open Repositories 2008 Southampton University 2 April 2008 SPECTRa-T Project

12-month project between University of Cambridge and Imperial College London to develop text- and data-mining tools to extract chemical data from e-theses Part of the JISC Digital Repositories programme Project Overview Submission, Preservation and Exposure of Chemistry Teaching and Research Data – in Theses

Background Chemistry is an experimental science Synthetic Organic Chemistry is the basis of Pharmaceutical and Agrochemical industries Where does the information to make this molecule come from? Ethyl 4,5-epoxy-hex-2-enolate C8H12O3 Systematic Name : Molecular Formula :

Chemical Abstracts (9000+ journals - 12,000 structures/day) Beilstein (180 core journals) Patents (CAS, Derwent, MDL) (400,000 /annum) Academic chemistry publications largely derived from PhD Theses Perhaps ~10K published per year worldwide Synthetic : contains preparations – only 20% published in detail Search Chemical patent & journal abstracting services – e.g.

List of Starting Materials & Reagents Recipe: Reactions Conditions & Work-up Product Characterization – spectroscopic & physical properties

Sample preparation from synthetic chemistry thesis

~80% of (academic) synthetic preparations remain locked in theses Manual abstraction (cf journals/patents) not an option The Problem The Solution OSCAR3 : Automatic high-throughput chemical name and chemical term recognition Open Source Chemistry Analysis Routines is an extensible Open Source framework which can identify much of the chemical terminology in electronic articles Semantic Web : Deposit extracted terms in searchable RDF triplestore

OSCAR Name recognition: 1. Dictionary of chemical names/terms (ChEBI Ontology) 2. Rules; chemical suffix filters 3. Regular expressions to recognise: data, formulae

Input: PDF Legacy Format PDF is the de facto format for electronic document deposition in digital repositories Problem: irregular word order line-breaks: loss of continuous text; paragraphs difficult to identify loss of subscripts and superscripts non-printing characters erroneous character assignment with OCR. PDF text is a Page Description Format – optimized for human, not machine, readability

Remove linebreaks from extended chemical names Remove text fragments derived from Figures and Tables Correct whitespace in chemical names PDF UTF-8 text OSCAR3 SAF XMLRDF statements XSLT Used ‘as is’ OSCAR used ‘as is’ on PDF e-theses : Gives 5000 terms / thess Gives 5000 terms / thesis (80% duplicates) Cannot identify chemical objects (spectra assignments; properties) Programmatic modifications to:

Input: MS Office Open XML – ‘docx’ No information loss from student’s deposited thesis (written with MS software ) Identification of experimental sections no longer a problem - > Chemical Objects Conversion of CO’s into Chemical Markup Language DocX Extract chemical terms OSCAR3 Link together RDF statements Extract chemical objects CML data files Data Repository URI

Sample preparation from synthetic chemistry thesis Sample preparation from chemistry thesis

CML Infra-Red ASSIGNMENTS - film - CML C-13 NMR ASSIGNMENTS

RDF - Resource Description Framework. A component of the Semantic Web, it is based upon the idea of making statements about resources/data in the form of a subject-predicate-object ( or resource-property-value) expression (called a triple) e.g. : My_thesis has_chemical_entity 2,4-dinitrobenzene The value of one property can in turn be used as the resource for another.

RDF TRIPLESTORE ENTRY <rdf:RDF xmlns:dc=" xmlns:dcrdf=" xmlns:rdf=" xmlns:spectra-t=" - CDCl3 ClC([2H])(Cl)Cl InChI=1/CHCl3/c2-1(3)4/h1H/i1D - 1-Benzyloxy-but-3-yne C#CCCOCC1=CC=CC=C1 InChI=1/C11H12O/c /h1,4-8H,3,9-10H (3E,5S,6S)-8-(p-Methoxy-benzyloxy)-5,6-epoxy-6-methyl-oct-3-en-2-one SPARQL QUERY PREFIX st: PREFIX dcrdf: CONSTRUCT { ?thesis st:hasBicycloMoleculeAndHNMR ?chemical. ?thesis dcrdf:author ?author } WHERE { ?thesis dcrdf:creator ?author. ?thesis st:hasChemicalName ?annot. ?annot st:chemicalName ?chemical. ?annot st:hasHNMRSpectrum ?hnmr. FILTER regex(?chemical, ".*bicyclo.*"). } RESULT 5-Acetyl-7,8-bis(trimethylsilyl)bicyclo[4.2.1]nona-4,7-diene N.R.Champness 5-Acetyl-bicyclo[4.2.1]nona-4,7-diene N.R.Champness 5-Phenyl-bicyclo[4.2.1]nona-3,7-diene N.R.Champness 5-Acetyl-7,8-bis(trimethylsilyl)bicyclo[4.2.1]nona-4,7-diene N.R.Champness 5-Acetyl-bicyclo[4.2.1]nona-4,7-diene N.R.Champness 5-Phenyl-bicyclo[4.2.1]nona-3,7-diene N.R.Champness

Caveats (Proof-of-concept): Single subject area (synthetic organic chemistry) Single institution docx (limited variation in document structure) Limited thesis availability Solutions : Domain ontology development Make your e-theses public! Message to repository managers: PDF is a limited format for data extraction from e-theses Docx allows chemical data object extraction (~80% precision / recall)

Acknowledgements Project Director:Peter Morgan UL Cambridge Chemistry leads:Henry Rzepa, Peter Murray-Rust Developers:Jim Downing, Diana Stewart, Joe Townsend, Matt Harvey Project Manager:Alan Tonge /

SPECTRa Tools Workshop Autumn 2008 Unilever Centre, Cambridge, UK Contact: Peter Murray-Rust Peter Morgan