BioGroovy 1.0 Classes Released

It’s been a pretty busy weekend, and the recent work on BioGroovy 1.0 is part of the reason.  One of the goals of the BioGroovy project has been to leverage the Java libraries that are currently available, and the samples shown on the BioGroovy website reflect its ties to the BioJava library.

With this latest release however, we’ve created a compiled library which can be used in Groovy scripting projects to access NCBI’s EUtils RESTful services.  This makes it possible to search and fetch data from PubMed, Entrez Gene, and other databases and return BioGroovy objects as your results.  These objects can then be embedded in web pages, or simply used to generate files.

In addition to accessing EUtil’s services, we’ve added support for NCI’s Pathway Interaction Database (PID).  You can use BioGroovy to fetch the genes associated with a particular pathway.

The library also includes a number of model objects (such as Gene’s, Transcripts and Proteins) which have been semantically tagged.  You can use these objects to fetch data from databases, and then generate RDF in the results.

You’ll can find more information about the BioGroovy project here.


About Mark Fortner

I write software for scientists doing drug discovery and cancer research. I'm interested in Design Thinking, Agile Software Development, Web Components, Java, Javascript, Groovy, Grails, MongoDB, Firebase, microservices, the Semantic Web Drug Discovery and Cancer Biology.
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