Oscar3

Oscar3 is a tool for shallow, chemistry-specific parsing of chemical documents. It identifies (or attempts to identify):

• Chemical names: singular nouns, plurals, verbs etc., also formulae and acronyms, some enzymes and reaction names.
• * Ontology terms: if you can do it by string-matching, you can get OSCAR to do it.
• * Chemical data: Spectra, melting/boiling point, yield etc. in experimental sections.

In addition, where possible the chemical names that are detected are annotated with structures, either via lookup or name-to-structure parsing ("OPSIN"), and with identifiers from the chemical ontology ChEBI.

OSCAR3 also includes the Oscar Server, a Jetty-powered set of servlets. These provide the following services:

• Parsing of text/HTML by OSCAR.
• Text/InChI/SMILES/SMILES substructues/SMILES similarity search of papers, coupled with keyword and ontology-based search, using Lucene and the CDK.
• List of all names found / all names that co-occur with a search term or terms.
• Online management of a chemical/stopword lexicon.
• Manual editing of SciXML fragments containing named entities, for creating of gold standards and training data.

Oscar3 files may be downloaded from the sourceforge download page. As well as Oscar3 itself, two Oscar3 components have been separated out, and made available as separate modules: OPSIN, a chemical name-to-structure converter, and ChemTok, a tokeniser optimised for text containing chemical names.

News

07/01/08: Oscar3 alpha 4 released

This fixes a small but critical bug in alpha 3 which caused workspaces to be set up badly. A bug concerning the resources browser was also fixed.

21/12/07: Oscar3 alpha 3 released

Much like alpha2, this release adds extra documentation, algorithm improvements and some UI tweaks. In particular Oscar3 can now give confidence estimates. Another improvement is in the search UI.

22/06/07: Oscar3 alpha 2 released

This release adds extra documentation, algorithm improvements and some UI tweaks.

21/12/06: Oscar3 goes alpha

Oscar3 files may be downloaded from the sourceforge download page.

This release has been made possible by a lot of different people. The OSCAR project has been going for several years at various rates, under the supervision of Prof. Peter Murray-Rust, and has had input from a large number of different contributors (these are listed in the THANKS.txt files in the distributions). However, I'd like to single out one organisation: the Royal Society of Chemistry. The OSCAR project started out with summer students funded by the RSC, and as well as providing considerable funding and test corpora to the project, they have also been able to dedicate large amounts of staff time and expertise to it. Getting this far (and there's still a way to go before the full release) would not have been possible without them.

Oscar3 is hosted by sourceforge.net