Biomedical Engineering Reference
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different color codes, each denoting a different category. The extracted data can be
useful, among other applications, to create and automatically populate a database
of toxic effects of nanoparticles, or to semantically annotate and search the manu-
scripts based on the different entities that appear in them.
We have recently also developed an automated text indexing and retrieval engine
that links scientific articles to mention of concepts from the Nanoparticle Ontology
(Thomas et al. 2010) and the Foundational Model of Anatomy (Rosse and Mejino
2003 ). The indexing engine was built following a dictionary-based approach, similar
to that adopted in (Garten and Altman 2009 ). Using the search engine, users can
search for papers reporting which nanoparticles are more suitable for delivering a
certain drug to a given anatomical location, or on the other hand, identifying which
nanoparticles are toxic to a specific anatomical part. Figure 2 shows the interface
of the search engine after executing a query for retrieving all documents in the
database that were semantically annotated with the nanoparticle “Paclitaxel” (concept
Fig. 2 Screenshot of the search engine linking manuscripts to mentions of nanoparticles and
anatomical targets belonging to the Nanoparticle Ontology and to the Foundational Model of
Anatomy, respectively
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