Enabling Academic Research: Office Add-ins Alex Wade Director – Scholarly Communication Microsoft External Research

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

Add-inBinarySourceOS License Article AuthoringY Creative CommonsYYMs-PL Chem4WordYYApache 2.0 GenePattern Reproducible ResearchYYMs-PL NodeXLYYMs-PL Ontology Add-inYYMs-PL Project Trident Add-inYYApache 2.0

Office Open XML (OOXML) –.docx,.xlsx,.pptx – ZIP compatible Open Packaging Convention (OPC) container – XML content, as well as other file formats

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

Remove confidential information, tracked changes or metadata from outbound documents: Remove macros, inappropriate language, or other content from inbound documents: Open XML Processing Open XML Processing

Back-end system (LOB/CRM/etc.) Create expense reports as spreadsheet documents, which are loaded into a back-end system on the server: Open XML Processing Authoring environment (Microsoft Office, etc.)

Create sales reports from financial and forecast data stored in a CRM system: Calculated data Manual entries Existing content Web client or rich client allows user to select or enter content criteria

Tagging document content with custom semantics for processing by a back-end system. Authoring environment Open XML Processing

Custom-defined XML part Stored separately from document body Any XML can be stored – Document properties – WSS meta-data – Custom XML (with or without XML schema) External applications can easily read or write the custom XML part True separation of data and presentation Doc/Template Doc Parts XML External App

Formed by 40 companies to share developer information about the Office Open XML file formats Articles with full source code for C#, VB, Java, XSLT Forums for posting technical questions

Intent: Insert Creative Commons licenses from within Office 2007 Relationships: license information stored as RDF XML within the document OOXML Source code and binary: Services: Integrates with Creative Commons Web API to create new licenses

Binary (v.2 beta 3): Relationships: ORE Resource Map creation Structure: Read, convert, and author NLM XML documents Structure: Client-side XML validation Services: repository deposit via SWORD This work is licensed under a Creative Commons Attribution 3.0 United States License.Creative Commons Attribution 3.0 United States License Relationships: Citation lookup and reference management

Scientific, Technical, and Medical publishing (STM) Accelerating move to electronic publishing and consumption of journals – Semantics over presentation at authoring Open Access publishing and repositories – High Energy Physics – arXiv.org – Biomedical – PubMed Central

National Institute of Health’s National Library of Medicine – PubMed Central repository – Archiving mandated by law as part of funding – Conversion usually done by publisher NLM XML formats – Light on presentation, extensive metadata – Used in the publishing and archiving process, even outside of biomed – Article publishing and book formats

Opening and saving of NLM XML files – Preserving metadata and semantics Article templates – Simplify authoring experience – Package and convey requirements to authors Metadata access and editing – Author view - simple – Editor view - extensive

For Authors - rely on native Word functionality/concepts as much as possible – Add-in and file formats should be invisible – Try to gather metadata from authors Reduce data entry errors Provide Editors and staff with full access to metadata, format concepts, and validation – Likely to know at least parts of the format or metadata in depth – Need full extent of the format presented in the UI

Custom ribbon Side Panel InfoPath integration Content control and custom elements Format SDK and packaging functionality MathML XSLT (two way)

This work is licensed under a Creative Commons Attribution 3.0 United States License.Creative Commons Attribution 3.0 United States License

Direct upload/submission from Word using the Authoring Add-in through SWORD – Simplified experience for authors – Some data validation before submission – Data ready for use by intake infrastructure Embedding data within articles and referencing data stored online based on ORE – Enable an additional dimension to the content

Version 2 Beta 3 available for free download – Great community participation and engagement – Valuable feedback from the National Library of Medicine, Hindawi Publishing, and other Beta participants

Relationships: Navigate and link referenced chemistry Peter Murray-Rust Joe Townsend Jim Downing Available soon: Data: Semantics stored in Chemistry Markup Language Intent: Recognizes chemical dictionary and ontology terms Author/edit 1D and 2D chemistry. Change chemical layout styles. Intelligence: Verifies validity of authored chemistry