chemspider – a platform to gather, host and integrate structure based data across the web
DESCRIPTION
ChemSpider was developed with the intention of aggregating and indexing available sources of chemical structures and their associated information into a single searchable repository and making it available to everybody, at no charge. There are many tens of chemical structure databases such as literature data, chemical vendor catalogs, molecular properties, environmental data, toxicity data, analytical data etc. and no single way to search across them. Despite the diversity of databases available online their inherent quality, accuracy and completeness is lacking in many regards. ChemSpider was established to provide a platform whereby the chemistry community could contribute to cleaning up the data, improving the quality of data online and expanding the information available to include data such as reaction syntheses, analytical data and experimental properties. ChemSpider has now grown into a database of well over 20 million chemical substances integrated with over 300 disparate data sources, many of these directly supporting the Life Sciences. This presentation will provide an overview of our efforts to improve the quality of data online, to provide a foundation for the semantic web for chemistry and to provide access to a set online tools and services to support access to these data. I will also discuss how ChemSpider is being used to enhance Semantic Publishing in Chemistry at RSC.TRANSCRIPT
ChemSpider – A Platform to Gather, Host and Integrate Structure Based Data Across the Web
Declaration
ChemSpider does NOT do toxicity prediction, yet We are building a content database for you to use
What ChemSpider does can be invaluable to those who do toxicity prediction Find “correct” chemical structures Find associated data (experimental/predicted) Link out to rich sources of information online Engage the community in sharing data
A Pragmatic Vision in 2006
“Build a Structure Centric Community”
December 2006 – A project initiated to connect chemistry on the web
Integrate chemical structure data on the web Create a “structure-based hub” to information and
data Provide access to structure-based “algorithms” Let chemists contribute their own data Allow the community to curate/correct data
Three Years of Experience Internet-based chemistry is a mess!
Most public compound databases on the web are contaminated. Including ours!
The annotation/curation of data online is difficult
Most database hosts are non-responsive to feedback – “We are a host/repository of data”
Who cares?
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
What is the Structure of Vitamin K?
MeSH – Medical Subject Headings
A lipid cofactor that is required for normal blood clotting. Several forms of vitamin K have been identified: VITAMIN K 1 (phytomenadione) derived from plants, VITAMIN K 2 (menaquinone) from bacteria, and synthetic naphthoquinone provitamins, VITAMIN K 3 (menadione). Vitamin K 3 provitamins, after being alkylated in vivo, exhibit the antifibrinolytic activity of vitamin K. Green leafy vegetables, liver, cheese, butter, and egg yolk are good sources of vitamin K
What is the Structure of Vitamin K1?
What is the Structure of Vitamin K1?
Chemical Abstracts“Common Chemistry” Database
Wikipedia
Incorrect Structures
Wow!
Lack of Stereochemistry
Does stereochemistry matter?
Distaval, Talimol, Nibrol, Sedimide, Quietoplex, Contergan, Neurosedyn, Softenon, Thalidomide
Comparative Toxigenomics Database
PubChem
“2-methyl-3-(3,7,11,15-tetramethylhexadec-2-enyl)naphthalene-1,4-dione”
Variants of systematic names on PubChem
2-methyl-3-[(E,7R,11R)-3,7,11,15-tetramethyl 2-methyl-3-[(E,7S,11R)-3,7,11,15-tetramethyl 2-methyl-3-[(E,7R,11S)-3,7,11,15-tetramethyl 2-methyl-3-[(E,7S,11S)-3,7,11,15-tetramethyl 2-methyl-3-[(E,11S)-3,7,11,15-tetramethyl 2-methyl-3-[(E)-3,7,11,15-tetramethyl 2-methyl-3-(3,7,11,15-tetramethyl 2-methyl-3-[(E)-3,7,11,15-tetramethyl
ChEBI – Manual Curation
What’s Methane?
What’s Methane?
What ELSE is Methane???
The EXPERTS must get it right?!
Wikipedia, C&E News, PubChem C&E News (from ACS)
Online Datasets
Online Datasets
Online Datasets
O
O
H
H H
HH
H
H
HH
HH
H HH H
H
HH HH H
H
H
H
H
H
H
H
Online Datasets
O
O
H
H H
HH
H
H
HH
HH
H HH H
H
HH HH H
H
H
H
H
H
H
H
H
H
H
O
OH
Online Datasets
O
OH
O
O
OH
O
O
O
N
O
O
OH
OH
OH
Online Datasets
O
OH
O
O
OH
O
O
O
N
O
O
OH
OH
OH
O O
OO
O
OH OH
OH
O
O
OH
O
OH N
What Sources Do You Trust?
QSAR World
Online Datasets
The dataset for QSAR appears to have been generated with Name-to-Structure algorithms
Many systematic errors in the data – non-curated? Using such data for modeling is risky
Online Datasets
Internet-Based Chemistry is a Mess
Algorithms can get you so far in data cleaning
Human curation is necessary
Only the crowds can help with big data…
But, if we DID have a highly curated dataset… Reference database/dictionary of chemicals High quality data for modeling Centralized repository for models/data?
www.chemspider.com
We Answer Questions for Chemists 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 Aspirin? What is the NMR spectrum of Benzoic Acid? What are the safety handling issues for toluene?
Search for a Chemical…by name
Available Information…
Linked to vendors, safety data, toxicity, metabolism
Available Information….
Search for chemicals
ChemSpider Today
24.8 million structures 400 data sources Grows daily Community annotation and curation
We curate, edit, change, enhance data daily
Search “Vitamin H”
Search “Vitamin H”
“Curate” Identifiers
“Curate” Identifiers
“Curate” Identifiers
“Curate” Identifiers
General curation activities Remove incorrect names Correct spellings Add multilingual names Add alternative names
In 3 years over 1 million structure-identifier relationships have been validated – robotically and manually
130 people have participated in validation or annotation. “Crowds” can be quite small!
Crowdsourced “Annotations”
Registered Users can add Descriptions/Syntheses/Commentaries Links to articles, blogs, wikis etc Add spectral data Add photos Add MP3 files Add Videos
Data Validation – ONE CymarinQuestion Quality in Big Databases
Data Validation – Cortisol
Data Validation in Databases
ADNPLDHMAVUMIW 509 WQZGKKKJIJFFOK 119 RUDATBOHQWOJDD 118 Ursodeoxycholic
acid GUBGYTABKSRVRQ 89 Lactose BHQCQFFYRZLCQQ 80 Cholic acid RCINICONZNJXQF 76 Taxol KXGVEGMKQFWNSR 73 Deoxycholic acid PXGPLTODNUVGFL 71 HVYWMOMLDIMFJA 69 QGXBDMJGAMFCBF 63
First request to Database Hosts!
Every public compound database host should add ONE feature – “Leave Comments”
Second request to Database Hosts! Show Comments
Linked Data on the Web
Taken from: Rafael Sidis’ Blog
What is a compound?
The InChI Identifier
Linking and Modeling Bad Data
What is the value of linking bad data?
How can we model suspect data efficiently?
Commonly data are incorrect Measured data are suspect Structures associated with data are not correct Identifiers are incorrectly associated
Properties on the Database
Properties on the Database
Properties on the Database
Linked Out to Resources
Properties Linked Off the Database
LASSO uses 23 kinds of Interactive Surface Point Descriptors and is conformation independent screens at 1 million structures/min is proven to enrich screened
databases provides scaffold hopping
Hbond Donors (5 kinds) Acceptors (5 kinds) Ambivalent H donor/acceptor Aromatic Pi-stacking (5 kinds) Hydrophobic (3 kinds) Metal ions Misc (Sulfur, Halogens)
http://dx.doi.org/10.1007/s10822-007-9164-5
SimBioSys LASSO
SimBioSys LASSO
LASSO Linked Out
Present Activities
Enhancing data model to manage more experimental properties – data available for download and modeling
Developing relationships with other software vendors and model developers for integration
Curating QSARWorld datasets for deposition
ChemSpider Tomorrow
6 months: >1.2M compounds/month 6 months: >800,000 new uniques 6 months: >60 new data sources added
Continue the curation effort and keep cleaning Finish depositions – millions left to deposit Integrate RSC content – a massive archive! Integrate RSC publishing workflows and databases Enable the semantic web for chemistry – RDF
Future Activities – Data Management
Future Activities – Data Management
Aggregating and managing data from publications
Specifically aggregating: Data from MedChemComm Reaction Data (SyntheticPages) Spectral Data
Access Data Through Web Services
Mobile Data Access
The Future of Linked Chemistry on the Internet? Public compound databases federate to build a
truly linked environment of validated data! Data validation needs are not ignored Publishers layer on information to make
publications discoverable Public-Private databases can be linked Open Data proliferate RDF is everywhere
ChemSpider & Toxicity Prediction
Continue the curation effort and keep cleaning Web services allow integration and data download Presently collaborating with groups to provide
access to data for modeling Intention is to provide the highest quality online
database with associated data
Community Contribution and Innovation “Community contribution”
best practice award”
i-Expo Innovation Award:June 2010 ALPSP Innovation Award: September 2010
Thank you
Email: [email protected] Twitter: ChemConnectorBlog: www.chemspider.com/blogPersonal Blog: www.chemconnector.comSLIDES: www.slideshare.net/AntonyWilliams