Software and demos for Cheminformatics Open Source meeting at EBI

#wwmm #quixotechem #blueobelisk

I do not present software through Powerpoint but through living links and demos. These all worked when they were entered here. All demos decay…

We (http://wwmm.ch.cam.ac.uk) have built a wide-ranging series of components to support Open chemistry. They are mainly based on Chemical Markup Language (CML)

• Recent presentation from Sam Adams at ACS covers much of the ground (especially Chempound)
  

http://www-pmr.ch.cam.ac.uk/mediawiki/images/9/94/Sam-Adams-CLARION-ACS-April2011.pdf

• Recent OSCAR4 symposium http://www-pmr.ch.cam.ac.uk/wiki/Presentations
  

Multicomponent demos include:

• Searching Chempound repository for a Chem4Word document and using OPSIN to translate name2structure
  
• Running Lensfield on commandline to parse directory of compchem output into CML
  

All demos and software ore Open (Artistic, GPL , CC-BY, PDDL, CC0)

(CML) infrastructure and include:

• Schemas: Version 3: http://xml-cml.org/schema/schema3/index.php
  
• Dictionaries: example (compchem): https://bitbucket.org/petermr/dictionary/raw/729a6140e282/dict/cmlcompAbstractPropertiesDict.xml
  
• Conventions: example (dictionary convention) http://xml-cml.org/convention/dictionary (includes example)
  
• Units: convention: http://xml-cml.org/convention/unit-dictionary (includes example)
  
• UnitType: convention: http://xml-cml.org/convention/unitType-dictionary (includes example)
  
• Validator: http://validator.xml-cml.org/ (example: https://bitbucket.org/petermr/jumbo-converters/raw/f7f967f569ce/jumbo-converters-compchem/jumbo-converters-compchem-gaussian/src/main/resources/org/xmlcml/cml/converters/compchem/gaussian/log/templates/testoutput.xml )
  

OSCAR4, a modular system for textmining;

• Sam Adams on Architecture of OSCAR4: http://www-pmr.ch.cam.ac.uk/mediawiki/images/b/ba/OSCAR4-architecture.pdf
  
• Bitbucket: http://bitbucket.org/wwmm/oscar4 (includes Wiki with downloads, support, tracker, mailing list…)
  
• Commandline interface for OSCAR4: http://dl.dropbox.com/u/6280676/oscar4-cli.jar (java –jar oscar4-cli.jar “this is benzene”)
  

Chem4Word

• http://research.microsoft.com/en-us/projects/chem4word/
  
• OuterCurve/codeplex: http://chem4word.codeplex.com/releases/view/63786 (11K downloads in last month)
  

OPSIN, a name2structure converter (Daniel Lowe et al.);

• OPSIN website: http://opsin.ch.cam.ac.uk/
  

ChemicalTagger, a natural language system for chemistry;

• Demo: http://chemicaltagger.ch.cam.ac.uk/
  
• Lezan Hawizy: textmining with OSCAR4: http://www-pmr.ch.cam.ac.uk/mediawiki/images/d/df/ChemicalTagger.pdf
  
• Hannah Barjat: textmining atmospheric chemistry: http://www-pmr.ch.cam.ac.uk/mediawiki/images/0/02/OSCAR4-ACP.pdf
  
• Bitbucket: https://bitbucket.org/lh359/chemicaltagger
  
• Textmining of patents: blogpost: /pmr/2011/03/29/green-chain-results-summarized-for-talk-at-acs/ commonest solvents (1 month) http://greenchain.ch.cam.ac.uk/patents/results/2008/solventFrequency.htm :
  

   

JUMBOConverters which process collections of legacy material (including computational logfiles) into semantic form;

• CMLXOM: Reference implementation of CML https://bitbucket.org/wwmm/cmlxom/overview
  
• JUMBO6. Tools for CML: https://bitbucket.org/wwmm/jumbo6/overview
  
• Bitbucket: https://bitbucket.org/petermr/jumbo-converters/src (toplevel dir for all converters (8 compchem types, Chemdraw, SDF, CIF, JCAMP, reactions, spectra, etc.)
  

Chempound, a semantic RDF repository for any chemistry;

• Bitbucket: http://bitbucket.org/chempound
  
• Demonstration Quixote repository (crystal structures are present) : http://quixote.ch.cam.ac.uk (includes *.docx, viewable in Chem4Word, includes search on structure and physical properties).
  

Crystaleye, an automatic aggregator of crystal structures and publications;

• http://wwmm.ch.cam.ac.uk/crystaleye
  

Lensfield, a make facility for data.

• Download zipfile: http://maven.ch.cam.ac.uk/m2repo/org/lensfield/lensfield2-launcher/0.2/lensfield2-launcher-0.2.zip
  
• Bitbucket: http://bitbucket.org/sea36/lensfield2
  
• Readme: https://bitbucket.org/sea36/lensfield2/src/b0268c8b398d/lensfield2-launcher/README.txt
  

Metaprint, an Open source tool for predicting sites of metabolism

• URL for source: http://www.sourceforge.net/projects/metaprint2d
  
• Freely accessible web site: http://www-metaprint2d.ch.cam.ac.uk/
  
• Bioclipse plugin (with Ola Spjuth)
  

JNI-InChI (Sam Adams)

• Sourceforge: http://jni-inchi.sourceforge.net/
  

   

See also:

• http://www.blueobelisk.org/
• http://quixote.wikispot.org/Front_Page
• http://wwmm.ch.cam.ac.uk/blogs/murrayrust
• http://wwmm.ch.cam.ac.uk/
• http://okfn.org

Much of this is being formally written up for a special issue of J. Cheminformatics (BMC).