Chem4Word Wade

Director, Scholarly Communications Corporate VPMicrosoft Research Connections Microsoft Research Connections

http://research.microsoft.com/connections/ 2 GEPS2011

Envisioning a New Era of Research ReportingImagine…• Live research reports that had multiple end-user ‘views’ and which could dynamically tailor their presentation to each user Reproducible• An authoring environment that absorbs Research and encapsulates research workflows and outputs from the lab experiments• A report that can be dropped into an Interactive Collaboration electronic lab workbench in order to Data reconstitute an entire experiment• A researcher working with multiple reports on a Surface and having the Dynamic ability to mash up data and workflows Documents across experiments• The ability to apply new analyses and Reputation visualizations and to perform new in & Influence silico experiments

Words & Pictures• Papers/reports today describe chemical reactions/entities in a variety of ways: – common (or brand-name) labels – identifiers and shorthand notations – chemical formulae – two- (and three-) dimensional graphical images of molecular structure.• Describing chemical data becomes an exercise in typesetting and/or graphics, and cross- and re-referencing existing chemical entities is labor intensive. – The resulting text is usually interpretable by humans but chemical data are lost in the process, making it difficult to programmatically extract meaningful information from such reports.• The goals of Chem4Word are to: – simplify the task of authoring a chemical document, – do so in a way that produces a semantically meaningful document, facilitating downstream tasks such as publishers workflows, entity extraction, and semantic applications.

Chemistry Add-in for Word aka Chem4Word• Chem4Word allows chemists to create, edit and manipulate chemistry in the Word environment, by – Providing a built in dictionary of chemical structures – Enabling online lookup of further structures via web services (e.g. Pubchem) – Facilitating linking/embedding chemical structures inside a Word document – Modification of chemical structures & representations of those structures• Authoring is backed by semantic data in Chemical Markup Language (CML), enabling: – novel functionality in data checking during the authoring process – chemistry-centric article reading support – data-mining applications.• Open source project (Outercurve Foundation); Apache 2.0 license• ~500K downloads to date

Word UI Extensibility• Ribbon• Task Pane• Gallery• Templates• Recognizers• Applications

FILE FORMATS: OFFICE OPEN XML DOCUMENTSThanks to: http://www.slideshare.net/HollowKnight/a-quick-tour-of-open-xml-format

Binary Office Open XMLformat format

Binaryformat

Office Open XML format

THEY LOOK IDENTICAL, BUT …

Binaryformat

Office Open XML format

Office Open XML is a ZIP file …

That contains XML parts

Images stored in native format(JPEG, PNG, GIF, …)

Programmer View of Open XML Files• ZIP Archive• Document Parts – XML Parts – Binary Parts – Typed (RFC 2616)• Relationships – Connections between parts• Content Type Stream – A specially-named stream – Defines mappings from part names to content types – Not itself a part, not URI addressable• Folder structure for convenience only

Multiple ‘views’ backed by a single CML data file

EXAMPLE OF GETTING CML DATABACK OUT OF A DOCUMENT

To conclude..Current publishing With Chem4Word … is broken for data-rich science … the cycle is closedData publication difficult and unsupported Data preparation integrated into user workflowInsufficient data to fully support research Open Standards promote Open Semantic Science

Important Details• Project Site – http://research.microsoft.com/chem4word• Binaries and source code – http://chem4word.codeplex.com• Facebook Page – http://www.facebook.com/groups/186300551397797/• Outercurve Foundation – http://www.outercurve.org

ContributorsUniversity of Cambridge Microsoft Research• Peter Murray-Rust • Alex D. Wade• Jim Downing • Savas Parastatidis• Joe Townsend • Oscar Naim • Pablo Fernicola • Murray Sargent • Geraldine Wade • Tola Chhoeun • Anthony Hanses • Jim McGill

Chem4Word Wade

by Alex Wade on Aug 23, 2012

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