Category Archives: Semantic Web

Google IO, Schemas, and the Network of BioThings

Last week’s Google IO conference came with a slew of announcements, and videos, but perhaps the most interesting idea, wasn’t accompanied by a flashy announcement.  It did have some intriguing video’s though.  The first of which is shown below. Building a … Continue reading

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Network of BioThings: Making PDFs Useful

Recently, Andrew Su of Scripps posted a series of blog entries on the Network of Biothings (NoB) efforts, especially their efforts to uncover use cases that could aid medical research. In a nutshell,”The Network of BioThings aims to structure the … Continue reading

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Tinkering With Semantic Markup

One of the key challenges for bioinformaticians in this age is extracting meaningful findings from abstracts and full text articles. Text mining solutions can only take it so far, and previous comparative studies have shown that Amazon Mechanical Turk solutions and … 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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The Secret Names of Things

There is a belief among certain peoples in the world, that knowing the true name of a thing gives one some degree of power over it. One of the challenges for anyone writing software in a scientific setting, is figuring … 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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Adding Semantics to XML Schemas

Recently, I was working on a UniProt parser for the next BioGroovy release, and while looking through the UniProt schema I started to wonder why the elements in schemas weren’t annotated with references to ontologies?  Let’s take a look at … Continue reading

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