Web Crawling Chemistry

Weaving a New Web for Chemistry Antony Williams

Searching from the Structure Balloon

Imagine a time when …. ,[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]

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

Links out to KEGG Kyoto Encyclopedia of Genes and Genomes

Text- Indexing and ChemSpider? ,[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

Wikipedia – Crowdsourcing Chemistry

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

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

Differences between ChemSpider/Wikipedia No Analytical Data Active editors – about 50 (?) Active depositors/curators – 30 No Prediction of properties ???? 5000 people/day; 1100 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 Chemistry is the focus of ‘Spider Chemistry is a subset of the ‘Pedia Mixed “licensing” GFL licensing for everything Growing team of WP:Chem advocates, curators and admins 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]

Multi-level Curation and Approval

Post Comments ,[object Object]

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

But, when registered and logged in… ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Adding to the Database - Structure

Adding New Text Data Add Publication Add Identifier Add URL

Adding Supplementary Info to a Structure

Structure-Centric ,[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]

Name Recognition ,[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]

Conversion of Structure Images ,[object Object],[object Object]

Structure Conversion from Images-CLiDE ,[object Object]

Extensible Markup Process ,[object Object],[object Object],[object Object]

Tipping Point ,[object Object]

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

What’s Coming? ,[object Object],[object Object],[object Object],[object Object],[object Object]

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

Further reading ,[object Object],[object Object],[object Object]

ChemSpider Forums/Blogs ,[object Object],[object Object]

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

Web Crawling Chemistry

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Web Crawling Chemistry