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Chem spider introduction spring 2011
ChemSpider is a free online database of over 25 million chemical structures and properties from 400 data sources. It allows users to search by chemical name, structure, or other identifiers. Search results provide links to related literature, patents, and other data sources. ChemSpider has won several awards for its contributions to open chemistry data sharing and innovations in online chemical information. The database continues to grow through community contributions of additional data and curation of existing records.
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Chem spider introduction spring 2011
- 1. ChemSpider: Achemistry resource
- 2. Community Contribution andInnovation 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
- 3. ChemSpider AgendaWhat 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
- 4. 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
- 5. 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
- 6. ChemSpider asChemical 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
- 7. ChemSpider SearchChemical Name Tradename (Synonym) CAS Registry Number or other Identifier (SMILES, InChI)
- 8. ChemSpider LinksData Sources Patents Literature Sources Google Scholar RSC Journals RSC Databases PubMed Articles
- 9. Search by ChemicalName The Record View Expand a literature search in Google Scholar using validated names from ChemSpider
- 10. Search by ChemicalName Chemical Names, Synonyms and other Identifiers Chemical names are listed in the Identifiers box. Those in bold are approved as validated names
- 11. Synonyms give expandedresults via Google Scholar ChemSpider Results
- 12. ChemSpider ResultsSupplier catalogs and links to other data sources Clicking on any of the tabs will link you to other Internet resources – mostly free
- 13. ChemSpider ResultsProperty Data from ACD/Labs and others Options to select alternative algorithms for property prediction
- 14. ChemSpider ResultsFind articles on this compound from RSC Journals and Books Titles link through to full-text articles in RSC Publishing platform
- 15. ChemSpider ResultsFind articles in RSC Abstract & Indexing Databases Subject specific articles from all publishers
- 16. ChemSpider ResultsUser or publisher recommended articles Specific articles on this compound added by users or publishers
- 17. ChemSpider ResultsExpanded compound search on PubMed titles and abstracts
- 18. ChemSpider ResultsPatents from SureChem and Google Patents SureChem provides access to patents from the USPTO, EPO and PCT filings, Japanese Abstracts
- 19. ChemSpider ResultLinks Click on a title to view the patent document
- 20. Search by StructureAuto-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
- 21. Search by StructureDraw a structure using Java applet There are several structure drawing applets available. Need Java enabled
- 22. Search by StructureLoad a mol file from another drawing package – such as ChemSketch, ChemDraw or SymyxDraw
- 23. Search by StructureLOAD the molfile into the structure drawing applet When happy with the structure, click Accept
- 24. Search by StructureAccept the loaded structure Choose between an Exact or Substructure search
- 25. Search by StructureThe Record view for Codeine Expand these links to see more properties, names, identifiers
- 26. ChemSpider ResultsEmbedded spectra Results can also include spectra. Options to download (if a registered user and logged in) and print
- 27. ChemSpider asWiki 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
- 28. ChemSpider asWiki 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
- 29. ChemSpider asa 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
- 30. 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
- 31. Thank you foryour attention Twitter: ChemSpider www.chemspider.com/blog [email_address]
Editor's Notes
- #2Â ChemSpider: An introduction to conducting a chemical name or structure search
- #3Â ChemSpider has won several awards for innovation since its acquisition by the RSC just over a year ago.
- #4Â Our Agenda is to look at the content of ChemSpider and how to approach searching.
- #5Â ChemSpider is a FREE resource which provides access to more than 25 M compounds and more than 400 data sources.
- #7Â ChemSpider can be accessed at anytime using a PC with any Web browser, mobile devices and tablets.
- #8Â Search with a chemical name, common name, tradename or other identifier.
- #9Â The results page has links to data sources, patent information and literature sources such as RSC Journals, Google Scholar and PubMed.
- #10Â 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.
- #11Â Chemical names are listed in the Identifiers box. Those in bold are known as validated names.
- #12Â 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.
- #13 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.
- #14Â Scroll down the results page to find predicted properties for a substance Options to select alternative algorithms for property prediction.
- #15Â Links to RSC Publishing platform for full-text.
- #16Â Results may include links to article from other publishers as well as RSC
- #17Â Can contain links to other publishers or other articles that may not be published elsewhere
- #18Â Similarly links to PubMed.
- #19Â SureChem provides access to patents from the USPTO, EPO and PCT filings, Japanese Abstracts.
- #20Â Click on the title to view the record (full-text available)
- #21Â 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.
- #22Â There are several structure drawing applets available. Need Java enabled.
- #23 Alternatively, use your favourite drawing package – ChemSketch or ChemDraw.
- #24Â When happy with the structure, click Accept.
- #25Â Choose between an Exact or Substructure search
- #26Â 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.
- #27Â Results can also include Spectra. Options to download (if a registered user and logged in) and print.
- #28Â Registered users can comment on records, curate names or deposit structures and spectra.
- #29Â 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.
- #30Â Registered users can download the results set from a substructure search and can embed structures in a blog or wiki.