A Presentation At Nature Publishing Group Crowdsourcing, Collaborations And Text Mining In A World Of Open Chemistry

Crowdsourcing, Collaborations and Text-Mining in a World of Open Chemistry Nature Publishing Group 11/2008 Antony Williams

Imagine a time when …. ,[object Object],[object Object],[object Object],[object Object],[object Object]

ChemSpider - A Search Engine for Chemists ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

What is a Structure? Ask a computer…ask a chemist

Links out to KEGG Kyoto Encyclopedia of Genes and Genomes

How many names does a compound have?

ChemSpider Data Content ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Other Searches ,[object Object],[object Object]

The Quality of Data Online… ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Who holds THE Quality Authority? ,[object Object],[object Object],[object Object]

Quality is a Major Issue- Search Butanol OLD EXAMPLE..now fixed

Wikipedia Chemistry Curation project ,[object Object],[object Object],[object Object],[object Object],[object Object]

Wikipedia Curation ,[object Object],[object Object],[object Object],[object Object]

Sugars – Machine Readable vs Aesthetics Haworth Stereo Fischer

Wikipedia – Crowdsourcing Chemistry

Thymol Blue on ChemSpider ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Differences between ChemSpider/Wikipedia No, but links. Analytical Data Active editors > 50 (?) Active depositors/curators – 30 No Prediction of properties ???? 6000 people/day; 1900 registered Detailed compound monographs Compound monographs linked Text Complex queries – Properties, Text, structure/substructure, OA publishers, Data Sources, … ~5000 organics, 2000 others >21 million unique structures Wikipedia ChemSpider

Differences between Wikipedia/ChemSpider Growing reputation as focused on quality Worldwide reputation as quality source – good and bad Chemistry is the focus of ‘Spider Chemistry is a subset of the ‘Pedia Mixed “licensing” GFL licensing for everything Growing team of advocates, curators and users Strong team of WP:Chem advocates, curators and admins “ Out of a basement” on three servers and 5 volunteers Established infrastructure and Wikipedia Foundation Team Primarily Microsoft .NET technologies with OS components Supported by tried and tested Media-Wiki platform. ChemSpider Wikipedia

Crowd-sourcing Curation ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Post Comments ,[object Object]

Multi-level Curation and Approval

Crowd-sourcing Chemistry ,[object Object],[object Object],[object Object]

Structure-Centric ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

“Entity Extraction” ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Name Recognition ,[object Object],[object Object]

How Many Chemical Names? ,[object Object]

Making Open Access Articles Searchable Proof of Concept ,[object Object],[object Object],[object Object],[object Object]

Document markup ,[object Object],[object Object]

A Standard for Document Markup? ,[object Object],[object Object]

Chemistry and Biology ,[object Object]

A Platform for Markup ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Challenges ,[object Object],[object Object],[object Object]

Names and Structures ,[object Object],[object Object]

Ambiguity in Abbreviations - DPA

Ambiguity in Abbreviations - THF

Import is Easy ,[object Object],[object Object]

[object Object],[object Object],[object Object]

Entity Balloons ,[object Object],[object Object]

Other Dictionaries - Species ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Integrations Out to Other Sources

Manual Curation is Always Necessary

Text- Indexing and ChemSpider? ,[object Object],[object Object]

Conclusions ,[object Object],[object Object],[object Object],[object Object]

A Presentation At Nature Publishing Group Crowdsourcing, Collaborations And Text Mining In A World Of Open Chemistry

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A Presentation At Nature Publishing Group Crowdsourcing, Collaborations And Text Mining In A World Of Open Chemistry