ChemSpider - Building a Foundation for the Semantic Web by Hosting a Crowd Sourced Databasing Platform for Chemistry - Presentation Transcript
Building a Foundation for the Semantic Web by Hosting a Crowdsourced Databasing Platform for Chemistry
What’s the Status of Chemistry online?
Encyclopedic articles (Wikipedia)
Chemical vendor databases
Metabolic pathway databases
Virtual Screening databases
Property databases
Screening assay results
Patents with chemical structures (IBM & SureChem)
ADME/Tox data
Scientific publications
Compound aggregators
Blogs/Wikis and Open Notebook Science
For Synthesis…TotallySynthetic.com
Org Prep Daily (Blog)
Molbank (Open Access Journal)
Synthetic Pages (Website)
Encyclopedic Articles (Wikipedia)
Lots of “Public Compound” Databases
PubChem
Drugbank
ChEBI/ChEMBL
KEGG
LipidMAPs
ChemIDPlus
eMolecules
ZINC
Lots of chemical vendors
ChemSpider
Where Would You look? What Do You Trust?
Linked Data on the Web Taken from: Rafael Sidis’ Blog
Compounds and Identifiers
Connecting Chemistry on the Web
Connections are made
actively by purposeful linking
via semantic web links (i.e. RDF and triple stores)
by integrating via identifiers (InChI, CAS #, names and web service look ups)
Connections Can Lead Anywhere
The FUTURE of Chemistry on the Web
The internet is searchable by chemical structure and substructure (e.g.Wikipedia, Google Scholar)
Chemistry articles are indexed and searchable by a free online service
Publicly funded research data can be shared and discussed in the Open, maybe as ONS?
There is structure based access to property data (ADME/Tox), spectra, clean name-structure dictionaries
What is ChemSpider?
ChemSpider is:
Building a Structure Centric Community for Chemists
>20 million compounds, >200 data sources
A deposition and curation platform
A publishing platform for the community
Grows daily – more depositions, more links, more data sources
Search Cholesterol
Search Cholesterol
Search Cholesterol
Search Cholesterol
Search Cholesterol
Search Cholesterol
Linked across the internet
Kyoto Encyclopedia of Genes and Genomes
Link off a structure in ChemSpider
Chemical suppliers
Other publications
Analytical Data
Related Reactions
Wikipedia
Patents
“ Everything”
Links to Patents based on structure
Clickthrough to Patent (SureChem)
Pubmed Articles Linked
Answering Questions for Chemists
Questions a chemist might ask…
What is the melting point of n-butanol?
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?
Complex Data and Information
ChemSpider Searches
ChemSpider Searches
ChemSpider Complex Searches
Question Everything online: www.dhmo.org
Searching Dihydrogen Monoxide…
Politicians, Chemistry and DHMO
March 2004 , Aliso Viejo, California considered banning foam containers at city-sponsored events because dihydrogen monoxide is part of their production.
2007 Jacqui Dean , New Zealand National Party MP write a letter to Associate Minister of Health Jim Anderton asking "Does the Expert Advisory Committee on Drugs have a view on the banning of this drug?"
Caution! Question Everything!
PubChem
Vancomycin
Who will curate?
PubChem is not resourced to clean these errors
How would you clean such a large dataset?
Vancomycin on ChemSpider 1 compound – discussions over 3 days
The EXPERTS must get it right?!
Wikipedia, C&E News, PubChem
C&E News (from ACS)
Feedback from Steve Ritter
“ As for where we source our structures, our primary source is the researcher and peer-reviewed papers , because many compounds are novel.
..we always double check them against one or more primary sources, typically Merck Index and SciFinder.
Although CAS and C&EN are both part of the ACS Publications Division, we at C&EN still have to pay for our SciFinder access, strangely enough.”
Feedback from Steve Ritter
“ As a rule, we at C&EN don’t use Wikipedia as a primary source for structures or chemical information, and I recommend that policy to anyone .”
“ It would be nice to have an authoritative web-based source of standard, well-drawn structures for chemists to go to so they can freely cut and paste structures into their papers, PowerPoint presentations, and anything else they might need. Maybe Wikipedia will be that source one day .”
What About Digitonin?
Comments on the Blog
Kirill Degtyarenko says:
September 15th, 2009 at 1:57 pm It looks like both ChEBI and Wikipedia structures are wrong as far as aglycon is concerned. According to http://www3.interscience.wiley.com/journal/20330/abstract
“… for the first time to confirm beyond all doubt the structure suggested by Tschesche and Wulff for digitonin by means of modern NMR techniques, and to assign all proton and carbon resonances.” Structure 1 shows methyl group at C-20 going UP, i.e. 20β (while by default spirostan is 20α).
CAS as an authority
The Blogging Community Participate
Will it ever end?
The community says the structure of digitonin has “up” 20-Methyl.
If so, then multiple substances related to digitonin have OPPOSITE stereo at 20-Methyl
The spirostane skeleton has a “ down ” Methyl group so all spirostane-related structures would be wrong
The FDA’s DailyMed
Structures on DailyMed
Lack of Stereochemisty
Incorrect Structures
Wow!
Collaborative Knowledge Management
Drugbank
Taxol on PubChem
The InChI Identifier
Multiple Layers
InChIStrings Hash to InChIKeys
InChIs for Taxol
Back to Taxol
DrugBank: RCINICONZNJXQF-CLDWUXIMDD
ChEBI: RCINICONZNJXQF-GXKQXQCDDN
Wikipedia: RCINICONZNJXQF-MZXODVADBJ
Which one is correct???
InChIKeys for Taxol
DrugBank: RCINICONZNJXQF-CLDWUXIMDD
ChEBI: RCINICONZNJXQF-GXKQXQCDDN
Wikipedia: RCINICONZNJXQF-MZXODVADBJ
ChEBI and Wikipedia are the SAME structure
Drugbank is a DIFFERENT structure – ONE stereocenter
Does one stereocenter matter?
Does one stereocenter matter?
Distaval, Talimol, Nibrol, Sedimide, Quietoplex, Contergan, Neurosedyn, and Softenon
Does one stereocenter matter?
Distaval, Talimol, Nibrol, Sedimide, Quietoplex, Contergan, Neurosedyn, and Softenon
Building a Structure Centric Community for Chemists
Content is King and Quality Costs
Chemistry “content” is big money
Patent searching
Structures and properties
Drug databases
Literature databases
Chemical Abstracts Service (CAS), the “Gold Standard” in Chemistry related information
101 years of content
$260 million revenue (2006)
>50 million substances
>60 million sequences
ChemSpider Searches
ChemSpider Searches
InChIKey Searches Work
The InChI “Resolver”
Assertion and Chemical Entities
Who says what Taxol is?
What is the “timeline” for a molecule?
How do we clean up the Public data?
Crowdsourcing
Depositions From Crowds
CAS indexes published literature, patents and chemical vendors ( indexes ChemSpider too )
“ Lost Chemistry”
syntheses in theses
lab notebooks
compounds in private collections
ChemSpider accepts public depositions: structures, text, spectra, images.
Crowd-sourcing Chemistry Curation
Crowd-sourced curation: identify/tag errors, edit names, synonyms, identify records to deprecate
“ Lathosterol”
“ Lathosterol”
“ Lathosterol”
“ Lathosterol” Removed
“ Lathosterol” on PubChem
“ Lathosterol” on PubChem
“ Lathosterol” on PubChem
Validate Names for PubMed “Caldarchaeol”
Publishers are experimenting
… invited researchers to prototype tools dealing with the ever-increasing amount of online life sciences information
The winners built:
Reflect: Automated Annotation of Scientific Terms : http://reflect.ws
Reflect
Entity-Extraction, Mark-up, Annotate
Success Depends on Dictionaries
Structure Searching Articles…
Searching articles based on chemical structure and substructure is very expensive.. but is changing
The web IS ready - when will publishers deliver?
Structures can be shown
Spectra can be interactive
Graphics don’t need to be static
Publishers can enhance their articles
Semantic Mark-up for Chemistry
Semantic mark-up for chemistry is here
RSC project prospect (structure linking, IUPAC Gold Book ontology and other ontologies
Nature publishing group compound linking
ChemSpider Journal of Chemistry
Nature Chemistry Compound Pages
ChemSpider and Publishing
Curation led to a set of validated dictionaries
Integrated best-in-class entity extraction with validated name dictionaries
Additional dictionaries gave reactions, groups, families, hardware and software vendors etc
ChemMantis and CJOC
Name-Structure Pairs
Converting Detected Names…
Names are searched against a validated dictionary (this expands as ChemSpider is curated)
If not found then they are passed through a Name to Structure algorithm
If they cannot convert then ChemSpider is searched for non-validated names
Deposit Structures
Custom Dictionaries
Entity Extraction built around modified algorithms from SureChem
Optimized for “publications”
Dictionaries for chemical entities, groups, reactions, elements, families, species…
Dictionaries can be expanded
Species – linked to Wikipedia
Semantic Linking of Structures
What would you want to link off a structure?
Chemical suppliers
Other publications
Analytical Data
Related Reactions
Wikipedia
Patents
“ Everything”
RSC’s Project Prospect
In Development ChemSpider Synthesis
ChemSpider Synthesis will be a home for all things “synthetic”
An online resource for synthetic procedures from blogs, other online resources, RSC supplementary info, other publishers etc.
Public peer-review and feedback for synthetic procedures
RSC Supplementary Info
RSC Supplementary Info
Online Journals and Live Data
ChemSpider Everywhere : Embed
ChemSpider Everywhere: Spectral Game
ChemSpider Everywhere Crowdsourced Curation of Spectra Building a Structure Centric Community for Chemists
ChemSpider Everywhere ChemMobi Building a Structure Centric Community for Chemists
ChemSpider Everywhere
Linked from Wikipedia
Linked from Open Notebook Science sites
Linked from Blogs using Structure/Spectra EMBED
Integrated into structure drawing packages such as ACD/ChemSketch, Symyx Draw, Open Source applets
Integrated to software offerings from Thermo, Waters, Agilent, Bruker
It’s a long road ahead…
More representative…
Where is ChemSpider Lacking?
ChemSpider is limited to “defined chemicals”. No support for:
Polymers
Minerals
Markush structures
ChemSpider is very dependent on InChIs
Stereochemistry around non-carbon centers
Organometallics are not correctly represented
There are millions of errors on ChemSpider
What’s next?
Keep cleaning and depositing data
Deprecate/redeposit at PubChem
Layer on RDF for the semantic web
Integrate software: Symyx Jdraw, NMRShiftDB
Integrate RSC content – a massive archive!
Integrate RSC publishing workflows and databases
You are invited..
Curate ChemSpider data and link to us
Deposit your data with us
Structures
Spectra
Synthesis procedures
ChemSpider Synthesis is under development
Help assert what is Digitonin?
How Was ChemSpider Built?
ChemSpider was a “hobby project”
Housed in a basement and running off three servers – one bought, two built
Sensitive to weather and power stability
Went live at ACS Spring 2007 in Chicago
Not in a basement now...
And the Downside
Thank you [email_address] Twitter: ChemSpiderman www.chemspider.com/blog SLIDES: www.slideshare.net/AntonyWilliams
There is an increasing availability of free and ope more
There is an increasing availability of free and open access resources for chemists to use on the internet. Coupled with the increasing availability of Open Source software tools we are in the middle of a revolution in data availability and tools to manipulate these data. ChemSpider is a free access website for chemists built with the intention of providing a structure centric community for chemists. It 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 tens if not hundreds 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 fact that there were a large number of databases containing chemical compounds and data available online their inherent quality, accuracy and completeness was lacking in many regards. The intention with ChemSpider was 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, experimental properties and linking to other valuable resources. It has grown into a resource containing over 21 million unique chemical structures from over 200 data sources.
ChemSpider has enabled real time curation of the data, association of analytical data with chemical structures, real-time deposition of single or batch chemical structures (including with activity data) and transaction-based predictions of physicochemical data. The social community aspects of the system demonstrate the potential of this approach. Curation of the data continues daily and thousands of edits and depositions by members of the community have dramatically improved the quality of the data relative to other public resources for chemistry.
This presentation will provide an overview of the history of ChemSpider, the present capabilities of the platform and how it can become one of the primary foundations of the semantic web for chemistry. It will also discuss some of the present projects underway since the acquisition of ChemSpider by the Royal Society of Chemistry.
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