Crawling Across the Web of Chemistry Using ChemSpider
Crawling Across the Web of Chemistry Using ChemSpider
May 10, 2015
ChemSpider is a free access website for chemists built with the intention of providing a structure centric community for chemists. It was developed to index available sources of chemical structures and their associated data into a single searchable repository and making it available to everybody, at no charge. While there are a large number of databases containing chemical compounds and data available online their inherent quality, accuracy and completeness is severely lacking. ChemSpider has provided a platform so that the chemistry community could contribute to improving the quality of data online and expanding the information to include data such as reaction syntheses, analytical data, experimental properties and linkages to other valuable resources. It has grown into a resource containing over 21 million unique chemical structures from over 200 data sources.
This presentation will provide an overview of ChemSpider and its value to chemists as a search tool, as a public repository of information and how it can become one of the primary foundations of internet-based chemistry. I will also discuss the vision for ChemSpider and some of the lofty goals we are setting for the system moving forward.
This presentation will provide an overview of ChemSpider and its value to chemists as a search tool, as a public repository of information and how it can become one of the primary foundations of internet-based chemistry. I will also discuss the vision for ChemSpider and some of the lofty goals we are setting for the system moving forward.
Welcome message from author
This document is posted to help you gain knowledge. Please leave a comment to let me know what you think about it! Share it to your friends and learn new things together.
Transcript
Crawling Across the Web of Chemistry Using ChemSpider
Citizen Scientists Enable the Web
Who is writing about chemical compounds on Wikipedia?
Who is writing critical reviews of Chemistry online?
Who is blogging about chemistry on the web?
For Synthesis…TotallySynthetic.com
Org Prep Daily (Blog)
Molbank (Open Access Journal)
Synthetic Pages (Website)
Encyclopedic Articles (Wikipedia)
Chemistry online – An Overview Encyclopedic articles (Wikipedia) Chemical vendor databases Metabolic pathway databases Property databases Chemical Synthesis procedures Scientific publications Chemical vendors Blogs Wikis Open Notebook Science
What and who do you trust?
Compounds and Identifiers
What is ChemSpider? ChemSpider is:
Building a Structure Centric Community for Chemists >23 million compounds, ca. 250 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
Linked across the internet
Link off a structure in ChemSpider
Chemical suppliers Other publications Analytical Data Related Reactions Wikipedia Patents “Everything”
Linked to Millions of Articles
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?
What is the structure of Flibanserin?
What is the structure of Flibanserin?
Complex Data and Information
Various Searches
Structure searching
Substructure searching
Subset searching – choose from 200 data sources
Property searching
Searches are used in various ways by different types of chemists…
ChemSpider Searches
ChemSpider Searches
Caution! Question Everything!
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)
“Lathosterol”
“Lathosterol”
“Lathosterol”
“Lathosterol” Removed
“Lathosterol” on PubChem
Crowd-sourcing Chemistry Curation
Crowd-sourced curation: identify/tag errors, edit names, synonyms, identify records to deprecate
Citizen Scientists
Become a Data Source
Synthesis Procedures
Links to Data or Deposit Data
Your Blog Posted Online?
Upload Spectral Data, OPEN Data?
Data as DOIs
Primary Data for Chemistry Available for the First Time
…Thieme is the first publisher to make primary chemistry data accessible worldwide
Analytical data, from various experiments, is the foundation of research work and scientific papers
From now on, primary data will be registered and made available online using digital object recognition in the form of Digital Object Identifiers (DOI)
Linking Data By DOI
Semantic Mark-up for Chemistry
Semantic mark-up for chemistry is here
RSC project prospect (structure linking, IUPAC Gold Book ontology and other ontologies). Based on the OSCAR system
ChemSpider Journal of Chemistry
Nature publishing group compound linking
ChemSpider and Publishing
Curation led to a set of validated dictionaries
Integrated entity extraction with validated name dictionaries
Additional dictionaries gave reactions, groups, families, hardware and software vendors etc
ChemMantis and CJOC
Name-Structure Pairs
Deposit Structures
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
Online Journals and Live Data
ChemSpider Everywhere : Embed
ChemSpider Everywhere: Spectral Game
ChemSpider EverywhereCrowdsourced Curation of Spectra
Building a Structure Centric Community for Chemists
ChemSpider EverywhereChemMobi
ChemSpider Web Services
ChemSpider Everywhere Linked from Wikipedia
Linked from Open Notebook Science sites
Linked from Blogs using Structure/Spectra
Integrated into structure drawing packages such as ACD/ChemSketch, Symyx Draw, Open Source applets
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
Enable discovery via the semantic web (RDF)
Integrate software: Symyx Jdraw, NMRShiftDB
Integrate RSC content – a massive archive!
Integrate RSC publishing workflows and databases
Continue Building Community for Chemistry
Building a Public ADME/Tox database
Delivering ChemSpider Synthetic Pages
Delivering ChemSpider Analytical Data
Delivering ChemSpider Education
Project Focus
People Make Change HappenYou are invited.. Curate ChemSpider data and link to us
Deposit your data with us Structures Spectra Synthesis procedures
ChemSpider Synthesis is under development
People Make Change Happen 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
ca. 6000 visitors a day, >50,000 transactions daily
Organizations Scale Innovation
There is a Downside…
There is a Downside…
Thank you
[email protected]: ChemSpidermanwww.chemspider.com/blogSLIDES: www.slideshare.net/AntonyWilliams
Related Documents
