CHIC – Converting Hamburgers Into Cows

Joseph Townsendjat45@cam.ac.uk

The Scholarly Publication Cycle

Generate

Publish

Capture

Use

What is a Cow?

• the character encoding is clearly stated• the document uses a mark-up technology to

identify components • the components have meaning and possibly

behaviour associated with them• unreduced data available

What we thought the workflow should look like

Standoff Annotation File

OSCAR

http://sourceforge.net/projects/oscar3-chem/http://www.omii.ac.uk/wiki/Nwsltr1209OSCAR

http://tinyurl.com/yakzgkd

Front Matter

Abstract

Introduction

Discussion

Experimental

References

Results

Article

Front Matter

Abstract

Introduction

Discussion

Experimental

References

Results

Synthesis

Set up

Analysis

Compound Name

Experimental

DOCX Workflow (part 1)

DOCX Workflow (part 2)

OREChemPSU Soton

IU

Atom

Atom

Cam

Atom

Molecules

SVG

PDF

Text

CrystalEye PubChem

Gaussian workflow ORE Triplestore

http://research.microsoft.com/en-us/projects/orechem/

What can we do with a Cow?

5-Cyclobutyl-2,3-dihydro-[1H]-2-benzazepine 82:

Potassium carbonate (0.63 g, 4.56 mmol) and thiophenol (0.19 g, 1.69 mmol) were added to the 2- nitrobenzene sulfonamide 50 (0.50 g, 1.302 mmol) in N,N-dimethylformamide (33 cm3) at room temperature and the mixture was stirred for 16 h. Deionised water (50 cm3) was added and the aqueous phase was extracted with ethyl acetate (5 x 50 cm3). The organic extracts were dried (MgSO4) and concentrated under reduced pressure to give the title compound 82 (0.259 g, 1.302 mmol, ca. 100%) as an oil used without further purification.

Parsing and Semantics

Tokenization and Chunking

Phrase identification

RDF of reaction components

• 3D Boxes: Solid• Double Circles: Oil• Octagon: Gum• Triple Octagon: Foam• Diamond: Crystals or

Needles• Ellipses: Unknown or

Unspecified

Semantic Authoring

• ICE-TheOREM– http://tinyurl.com/y85vh22

• Chem4Word– http://research.microsoft.com/en-us/projects/ch

em4word/– http://bit.ly/c4w