Navigating an Internet of Chemistry via ChemSpider

Navigating an Internet of Chemistry via ChemSpider

Antony WilliamsUniversity of Arkansas, Little Rock, October 2011

UALR Chemistry Seminar Guest Lecture

Overview

What type of chemistry is available on the internet?

Representative flavors of chemistry

How can the internet be searched by chemical?

Quality on the Internet

Contributing to the chemistry internet

Where is chemistry online? Encyclopedic articles (Wikipedia) Chemical vendor databases Metabolic pathway databases Property databases Patents with chemical structures Drug Discovery data Scientific publications Compound aggregators Blogs/Wikis and Open Notebook Science

Representative Flavors of Chemistry

Molfiles Molfiles are the primary exchange format between

structure drawing packages Can be different between different drawing packages Most commonly carry X,Y coordinates for layout Can support polymers, organometallics, etc. Can carry 3D coordinates

Molfiles 10 9 0 0 1 0 0 0 0 0 1 V2000 31.2937 -9.0366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 26.6526 -9.0366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 31.2937 -7.7066 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 30.1161 -9.6877 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 25.5096 -9.6877 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 28.9731 -9.0366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 27.8163 -9.7016 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 26.6664 -7.7066 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 32.4367 -9.6877 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 30.1161 -11.0177 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 3 1 2 0 0 0 0 4 1 1 0 0 0 0 9 1 1 0 0 0 0 7 2 1 0 0 0 0 5 2 2 0 0 0 0 8 2 1 0 0 0 0 6 4 1 0 0 0 0 4 10 1 6 0 0 0 7 6 1 0 0 0 0 M END

SMILES (http://en.wikipedia.org/wiki/SMILES)

SMILES is a common format Can support polymers,

organometallics, etc. Does NOT carry X,Y or Z

coordinates for layout so requires layout algorithms – can be problematic!

Generally different between drawing packages

Stereo

Tautomeric forms

Vendor-dependent SMILES ACD/LabsCC(C)CCC[C@@H](C)CCC[C@@H](C)CCCC(\

C)=C\CC2=C(C)C(=O)c1ccccc1C2=O

OpenEyeCC1=C(C(=O)c2ccccc2C1=O)C/C=C(\C)/

CCC[C@H](C)CCC[C@H](C)CCCC(C)C

ChEMBLCC(C)CCC[C@@H](C)CCC[C@@H](C)CCC\C(=C\

CC1=C(C)C(=O)c2ccccc2C1=O)\C

The InChI Identifier

InChI

SINGLE code base managed by IUPAC – integrated into drawing packages. No variability as with SMILES

InChI Strings can be reversed to structures – same problem as with SMILES – no layout

Adopted by the community (databases, blogs, Wikipedia) – good for searching the internet

Multiple Layers

Tautomers – “Mobile H Perception”

Stereo

Checking for Stereochemistry

Checking for StereochemistryUse your drawing package!

Checking for Stereochemistry

Checking for Stereochemistry

Checking for Stereochemistry

Databases and Standardization

Databases and Standardization

InChIStrings Hash to InChIKeys

Vancomycin

Vancomycin

Search Molecular SKELETON

Search Full Molecule

Searching Chemistry on the Internet

Searching Vincristine Name searching Google Name searching Wikipedia Name searching Wolfram Alpha Name, name, name, name…searching Structure searching DOZENS of websites,

each with different information or…

Searching Chemistry on the Internet

Searching Vincristine Name searching Google Name searching Wikipedia Name searching Wolfram Alpha Name, name, name, name…searching Structure searching DOZENS of websites,

each with different information or…

Search ONE website integrating the others!

www.chemspider.com

I want to know about “Vincristine”

Vincristine: Identifiers and Properties

Vincristine: Identifiers and Properties

Vincristine: Vendors and Sources

Vincristine: Patents

Vincristine: Articles

Vancomycin

Search Molecular SKELETON

Search Full Molecule

Full Skeleton Search: 104 Hits

Full Molecule Search: 4 Hits

Quality on the Internet

Trust everything on the web???

What’s said on the web is true…

What’s said on the web is true…

What’s said on the web is true…

“We then established a collaboration with professor Sum Ting Wong, a fugitive from the North Korean University Hu Yu Hai Ding, currently in Rome (Italy).”

“This was identified as the new protein Wai So Dim (WSD).”

Contributing Chemistry to the Web If it was not just about me

Contributing Chemistry to the Web 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

Contributing Chemistry to the Web 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

Contributing Chemistry to the Web

ChemSpider as a host for community contributions Curation and validation input Structures Movies Images Analytical data – especially spectra

Contributing Chemistry to the Web

Sites allow direct feedback – leave it!

Sites allow deposition of data Text – chemical names, properties Structures Spectra

Curation of existing data

Spectra

ChemSpider SyntheticPages

Submission Process Simple template-based submission process

Submissions reviewed by editorial board. Published as is or comments sent to author

Online Peer Review process

Data supported include web movies, images, live spectra etc.

DOI issued to author

Conclusion

Diverse types of chemistry are available on the web Searching of the internet is possible based on

Text Structure searching Substructure searching

The InChI has enabled linking on the internet Quality on the Internet is diverse – separating the

wheat from the chaff is not always easy! It is possible to contribute to the chemistry internet!

Thank you

Email: [email protected] Twitter: ChemConnectorBlog: www.chemspider.com/blogPersonal Blog: www.chemconnector.comSLIDES: www.slideshare.net/AntonyWilliams