Tag Archives: Semantic Web

Reproducibility and Provenance

One of the key problems with reproducibility in scientific research is understanding and preserving the provenance of the data, and any digital methods used to turn raw data into actionable information. The following paper recently appeared in PLoS Computational Biology … Continue reading

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The Secret Names of Things: Naming The Database

In my previous post I described how an ontology like EDAM could be used to provide applications with consistent names for objects and their attributes.  Let’s take a look at how we can add and retrieve ontology information to/from a … Continue reading

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Tinkering with OntoMaton

One of the primary challenges in open science is making the experiment data behind a paper easily accessible in a universally acceptable format.  A number of solutions have sprung up over the years to address parts of this problem; however, … Continue reading

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Semantic Web Technology in Clinical Informatics

During the recent Future of Genomics Medicine conference hosted by Scripps in La Jolla, Isaac Kohane of the Boston Children’s Hospital talked about how semantic web technologies can make a difference in federating disparate sources of data together. t

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The Semantic Web and Drug Discovery

The Semantic Web and Drug Discovery was a recent topic at the San Diego Informatics Lunch forum.  This is an informal get-together of bioinformatics and cheminformatics practitioners to share ideas and discuss how different technologies can be applied in our … Continue reading

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BioGroovy and the Semantic Web

Recently, I found myself putting together a presentation on BioGroovy.  One of the key features that I’ve been taking advantage of is the ability to use BioGroovy models as Grails domain objects.  This makes it possible to easily download and … Continue reading

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