What does it do?

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.