chem spider introduction spring 2011

ChemSpider: A chemistry resource

Community Contribution and Innovation

ChemSpider 2010 Bio-IT World Best Practices Award for contributions to community chemistry

ChemSpider Innovation Software Award at the iExpo/KM Forum, June 2010

ChemSpider names as winner for the 2010 ALPSP Award for Publishing Innovation, September 2010

ChemSpider has won several awards for innovation since its acquisition by the RSC

ChemSpider Agenda

What is ChemSpider? How to conduct a search What do you get?

Our Agenda is to look at the content of ChemSpider and how to approach searching

What is ChemSpider?

Building a Structure Centric Community for Chemists

A deposition and curation platform A publishing platform for the community Grows daily – more depositions, more links,

more data sources ChemSpider SyntheticPages

• An online database of synthetic procedures

ChemSpider is a FREE resource which provides access to more than 25 M compounds and more than 400

data sources

What is ChemSpider? Largely small organic molecules

No support, YET, for:• Polymers• Minerals• Markush structures• Biological Macromolecules

ChemSpider relies upon InChIs• International Chemical Identifier

Std. InChIKey for the drug Fluconazole is:RFHAOTPXVQNOHP-UHFFFAOYSA-N

Can be used to search in Google

ChemSpider as Chemical Search Single search across 400 data sources Text, structure and substructure

search tools• Simple and very advanced Validated names for external

search expansion• Google Scholar• RSC publications and PubMed

Links to original sources Mobile version

• cs.m.chemspider

ChemSpider can be accessed at anytime with any Web browser, including mobile devices and tablets

ChemSpider Search

Chemical Name Tradename (Synonym) CAS Registry Number or other Identifier (SMILES, InChI)

ChemSpider Links

Data Sources

Patents

Literature Sources• Google Scholar• RSC Journals• RSC Databases• PubMed Articles

Search by Chemical Name The Record View

Expand a literature search in Google Scholar using validated names from ChemSpider

Search by Chemical Name Chemical Names, Synonyms and other Identifiers

Chemical names are listed in the Identifiers box. Those in bold are approved as validated names

Synonyms give expanded results via Google ScholarChemSpider Results

ChemSpider Results Supplier catalogs and links to other data sources

Clicking on any of the tabs will link you to other Internet resources – mostly free

ChemSpider Results Property Data from ACD/Labs and others

Options to select alternative algorithms for property prediction

ChemSpider Results Find articles on this compound from RSC Journals and Books

Titles link through to full-text articles in RSC Publishing platform

ChemSpider Results Find articles in RSC Abstract & Indexing Databases

Subject specific articles from all publishers

ChemSpider Results User or publisher recommended articles

Specific articles on this compound added by users or publishers

ChemSpider Results Expanded compound search on PubMed titles and abstracts

ChemSpider Results Patents from SureChem and Google Patents

SureChem provides access to patents from the USPTO, EPO and PCT filings, Japanese Abstracts

ChemSpider Result Links Click on a title to view the patent document

Search by Structure Auto-generate structure from chemical

name or SMILES or InChI

To search by structure: click on the search menu from the top navigation bar and select structure search from the drop down

menu. The structure drawing applet is then activated by clicking on the structure image

Search by Structure Draw a structure using Java applet

There are several structure drawing applets available. Need Java enabled

Search by Structure Load a mol file from another drawing package –

such as ChemSketch, ChemDraw or SymyxDraw

Search by Structure LOAD the molfile into the structure drawing applet

When happy with the structure, click Accept

Search by Structure Accept the loaded structure

Choose between an Exact or Substructure search

Search by Structure

Expand these links to see more properties, names, identifiers

The Record view for Codeine

ChemSpider Results Embedded spectra

Results can also include spectra. Options to download (if a registered user and logged in) and print

ChemSpider as WikiAdds quality and quantity…

Users can comment for others to action Registered users can curate names, add

links, spectra, data and multimedia resources

Depositors can load data sets which are curated on load

Curators and Master Curators approve additions and decide what is the correct structure

Anyone can comment on records, but you need to be a registered user to curate names or deposit structures and

spectra

ChemSpider as Wiki Users can contribute data and use as

a shared resource for research group

Jacqueline Bennett’s group use ChemSpider as a repository of their research to give easy access, for themselves and other ChemSpider

users

ChemSpider as a Resource

Download and reuse structures Download and reuse search

structure set 2D and 3D images Embed and link - never draw

a structure again Spectra, crystal structures ChemSpider SyntheticPages

Registered users can download the results set from a substructure search and can embed structures in a blog or wiki

ChemSpider – What we’re working on…

Working with our users to give you what you need to do your job

Adding more pharmacological data (Open PHACTS project)

Creating an eLearning resource for 16-19 yrs – to be released later in 2011

Growing the community of data depositors and curators

Putting ChemSpider at the heart of publicly accessible chemistry data

Thank you for your attentionTwitter: ChemSpiderwww.chemspider.com/blogchemspider@rsc.org