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Chem spider introduction spring 2011
 

Chem spider introduction spring 2011

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An introduction to Chemspider

An introduction to Chemspider

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  • ChemSpider: An introduction to conducting a chemical name or structure search
  • ChemSpider has won several awards for innovation since its acquisition by the RSC just over a year ago.
  • Our Agenda is to look at the content of ChemSpider and how to approach searching.
  • ChemSpider is a FREE resource which provides access to more than 25 M compounds and more than 400 data sources.
  • ChemSpider can be accessed at anytime using a PC with any Web browser, mobile devices and tablets.
  • Search with a chemical name, common name, tradename or other identifier.
  • The results page has links to data sources, patent information and literature sources such as RSC Journals, Google Scholar and PubMed.
  • The top of the record view will give structure, common name and other identifiers for a compound. There is also a link to Google Scholar for an extended search based on validated names.
  • Chemical names are listed in the Identifiers box. Those in bold are known as validated names.
  • Validated names are used to extend the search to literature references from all publishers via Google Scholar. Answers are displayed in best match order, but can be changed to most recent first.
  • Scroll down to find Associated Data Sources & Commercial Suppliers. Clicking on any of the hyperlinks will take you out to the supplier websites. ChemSpider is not a chemical supplier. You need to contact the vendors for prices and ordering. Other tabs will take you to other Internet resources – mostly free.
  • Scroll down the results page to find predicted properties for a substance Options to select alternative algorithms for property prediction.
  • Links to RSC Publishing platform for full-text.
  • Results may include links to article from other publishers as well as RSC
  • Can contain links to other publishers or other articles that may not be published elsewhere
  • Similarly links to PubMed.
  • SureChem provides access to patents from the USPTO, EPO and PCT filings, Japanese Abstracts.
  • Click on the title to view the record (full-text available)
  • 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. The structure drawing applet can auto-generate a structure based on a chemical name, SMILES, InChIKey, JPEG or TIFF image. The structure skeleton can be edited if required. You can also draw a structure in another drawing package and save as a molfile, then load into the applet.
  • There are several structure drawing applets available. Need Java enabled.
  • Alternatively, use your favourite drawing package – ChemSketch or ChemDraw.
  • When happy with the structure, click Accept.
  • Choose between an Exact or Substructure search
  • By clicking on a particular structure more details can be viewed, For example the InChI Key for the compound. The first part of the INCHI Key is indicative of the structure skeleton, the second part confirms the bond arrangement and stereo indicators.
  • Results can also include Spectra. Options to download (if a registered user and logged in) and print.
  • Registered users can comment on records, curate names or deposit structures and spectra.
  • The SUNY group is an example of a research group using ChemSpider as a repository of their research enabling sharing of information with others as well as round the clock access.
  • Registered users can download the results set from a substructure search and can embed structures in a blog or wiki.

Chem spider introduction spring 2011 Chem spider introduction spring 2011 Presentation Transcript

  • 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 Scholar
    ChemSpider 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
    • The Record view for Codeine
    Expand these links to see more properties, names, identifiers
  • ChemSpider Results
    • Embedded spectra
    Results can also include spectra. Options to download (if a registered user and logged in) and print
  • ChemSpider as Wiki
    • Adds 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 attention Twitter: ChemSpider www.chemspider.com/blog [email_address]