We have developed a novel, comprehensive technology to automatically extract structure-activity relationships from chemistry patents.  First, named entities are annotated: using large dictionaries and name-to-structure tools, chemical entities and compound classes from our chemical ontology are annotated.  Similarly, diseases, biological, pharmaceutical and physiological effects are annotated.  In a second step, potential anaphora are resolved, e.g. numbers or underdetermined entities are replaced by their more precise meaning.  In a third step, sentences that contain relationships about chemical compounds and effects are analyzed for their syntax using automated tools that determine potential relationship types using a fine grained relation specific relationship ontology.  As a last step, the output of normalized relationship triples or n-tuples is generated. These results are than analyzed for their quality using statistical and other criteria to derive a validated SAR that could be used as input for databases or search engines.

Automated extraction of structure-activity relationships from chemistry patents

244th National Meeting (2012)

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