ChemSpider SyntheticPages and the benefits of publishing chemical syntheses online

ChemSpider SyntheticPages – the Benefits of Publishing Chemical Syntheses Online

If it was not just about me…

If it was not just about me… We might have a community built encyclopedia I might know where the best restaurants are I might get good advice on books to read I might know which movies to watch I might know which plumber to call Data might just be Open

ChemSpider SyntheticPages Many syntheses are not published but are of value A database of synthesis procedures built for the community, by the community. Peer-reviewed by the community Each contribution DOI’ed. Develop online scientific reputation at a time of “micro-publications” Integrates semantic mark-up and visualization tools

ChemSpider SyntheticPageshttp://cssp.chemspider.com

ChemSpider SyntheticPages

Submission process Register as a user Use the Submit button and fill in the fields…

Submission Process Submissions reviewed by editorial board Published as is or comments sent to author Online Peer Review process – engage chemists in ongoing discussions and feedback loop Data supported include web movies, images, live spectra etc.

Recent Submissions

Semantic Markup: Project Prospect

Entity-Extraction, Mark-up, Annotate

Success Depends on Dictionaries Link to a Structure or the Right Structure?

Name-Structure Pairs

Semantic Linking of Structures What would you want to link off a structure?  Chemical suppliers  Other publications  Analytical Data  Related Reactions  Wikipedia  Patents  “Everything”

ChemSpider The Free Chemical Database A central hub for chemists to source information  >28 million unique chemical records  Aggregated from >400 data sources  Chemicals, spectra, CIF files, movies, images, podcasts, links to patents, publications, predictions A central hub for chemists to deposit & curate data

Answer Questions with ChemSpider Questions a chemist might ask…  What is the melting point of n-heptanol?  What is the chemical structure of Xanax?  Chemically, what is phenolphthalein?  What are the stereocenters of cholesterol?  Where can I find publications about xylene?  What are the different trade names for Ketoconazole?  What is the NMR spectrum of Aspirin?  What are the safety handling issues for Thymol Blue?

I want to know about “Vincristine”

I want to know about “Vincristine” If all algorithms work then everything on the page is correct by default except the name!

Vincristine: Identifiers and Properties

Vincristine: Vendors and Sources

Vincristine: Patents

Vincristine: Articles

Searches: The INTERNETAll ChemSpider and Internet searches are “simply algorithms”but synonym searching is based on an assertion

InChIs

Validated Names for Searching…

Interactive Data

Most Accessed

Is it working? Show of hands…  How many of you know CSSP?  Have any of you submitted to CSSP? Low submissions but some dedicated authors

Popular Authors

Is it working? Show of hands…  How many of you know CSSP?  Have any of you submitted to CSSP? Low submissions but some dedicated authors What reasons are there you would not publish?  Time  Approval from supervisor  Need to keep the science quiet  Publishing on CSSP prevents future publishing?

How will it improve? Participation and contribution

The Social Network Career-wise NOT having a personal presence online will be a detriment  Self-marketing  Establishing a profile  Getting on the record  Collaborative Science  Demonstrating a skill set  Measured using alternative metrics  Contributing to the public peer review process

Social Networking Tools A growing number of social networking tools:  Facebook  Twitter  Linked-In  Flickr  YouTube  Blogs  Communities  Collaborative environments

Chemistry Social Networking Methods of sharing MY chemistry online include:  Wikis or blogs  Slideshare for presentations  YouTube for videos  Flickr, Wikimedia etc. for images  PubChem for assay data  NMRShiftDB for NMR assignments  GoogleDocs for data

Drivers in the Social Network Anonymity is a choice in the social networks Anonymity in peer-review will likely become less important and may be generational I may want acknowledgment if…  I share my data  I review a paper  I share my expertise

The Alt-Metrics Manifesto http://altmetrics.org/manifesto/

Enabled by ORCID…

The Joint Responsibility of Authors

What is my ImpactStory?

ImpactStory

The Linked Network

Imperial College Data repository activities initiated with Imperial  Storage of research data from electronic lab notebook  Chemicals  Reactions  Analytical data – spectra  Experimental data points  Open Data with CC licenses of NC-SA

Feeding ELN Data into ChemSpider Integrate e-Notebooks into ChemSpider  IDBS e-Workbook plug-in allows direct deposition of chemical structures  Can be extended to more ELN content  Spectra  Reactions  Properties etc.  Integration Video http://tinyurl.com/9xnprqr

Feeding ELN Data into ChemSpider

What is already in testing… ChemSpider Google  Searching Google Scholar, Google Books and Google Patents by chemical structure ChemSpider reactions – alpha version  300,000 reactions extracted from US patents  ChemSpider SyntheticPages container  Container for future RSC Archive reactions  Accepting Electronic Lab Notebook depositions  Successful AND Failed Reactions

Work in Progress – 300k Reactions

Data Enabling the RSC Archive An archive going back to 1841. Project underway to “data enable” the archive:  Extract chemistry – chemicals, reactions, experimental data points, complex data  Semantic enriching of the articles for interactive viewing and crowdsourced annotation/curation  Dramatically enables the type of queries possible across the archive

EPSRC National Chemical Database RSC is preferred bidder for the EPSRC national chemical database tender – presently completing legal documentation etc. Will deliver federated access to a series of commercial databases plus data repository – personal, group and institutional Citable data objects for papers, supplementary info, non-published work

A model for data segregation Integrate to Institutional repositories Access to Theses and Dissertations

Model Building with Community Data Community data can be the basis of model building  Consume data from available databases, RSC archive, new publications and build predictive algorithms for the community  Accept research data from the community and include into predictions

An Open Data-Centric Chemistry Hub Internet Data Small organic molecules Commercial Software Undefined materials Pre-competitive Data Organometallics Open Science Nanomaterials Open Data Polymers Publishers Minerals Educators Particle bound Open Databases Links to Biologicals Chemical Vendors

Benefits of PublishingChemical Syntheses Online Not all syntheses will be “published” Publishing is changing and has many forms Online exposure develops reputation, benefits the community, engages discussion and collaboration. Peer review in the open. CSSP offers a platform for exposure, linking to ChemSpider, interactive visualization and is a feed to ChemSpider reactions ELNs are a natural feed to the CSSP micro- publishing platform

Acknowledgments RSC|ChemSpider team CSSP Editorial Team All data source providers Curators and annotators Service providers:  ACD/Labs  OpenEye  GGA Software Services  Many others….

Thank youEmail: williamsa@rsc.orgTwitter: ChemConnectorPersonal Blog: www.chemconnector.comSLIDES: www.slideshare.net/AntonyWilliams

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ChemSpider SyntheticPages and the benefits of publishing chemical syntheses online

by Antony Williams, ChemConnector on Oct 01, 2012

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