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 Knowledge Graph (Part 2)</> Building a Knowledge Graph (Part 3)</> Getting Your Events Into The […]
Google IO, Schemas, and the Network of BioThings Read More »
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 biological knowledge found in biomedical research articles by comprehensively annotating BioThings (genes, proteins, mutations, diseases,
Network of BioThings: Making PDFs Useful Read More »
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 automated text mining solutions have similar levels of success when it comes to identifying terms
Tinkering With Semantic Markup Read More »
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 out the true (and sometimes unintentionally hidden) names of things. Imagine for a moment that
The Secret Names of Things Read More »
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 an example. A typical UniProt record contains many “reference” elements like this: <reference key=”2″> <citation
Adding Semantics to XML Schemas Read More »
Every weekend my PubMed search agent sends me a slew of papers to review. The interesting ones I add to the Pancreatic Cancer Genomics group in Mendeley — and at last count there are over 500 papers that have found their way into the collection. The hard part of this process is simply reviewing the
Utopia Docs: Making Scientific Literature More Useful Read More »
PubMed is an indispensible resource for scientists engaged in drug discovery and medical research. However, getting useful results from it can be a hit-or-miss proposition some times when your query returns thousands of results. For the work that I do curating the Pancreatic Cancer Genomics collection in Mendeley, I use a number of tools and
Getting the Most From PubMed Read More »
