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 »
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
Semantic Web Technology in Clinical Informatics Read More »
At some point in the evolution of every biopharmaceutical company, they’re faced with the problem of finding new targets to keep their pipeline fully loaded. Usually, they’ve exhausted the existing set of targets that they were working on, and are trying to decide what’s next? The answer to that question results from a lot of
Public Cloud Databases For Bioinformatics Read More »
At this week’s Bioinformatics Lunch Forum we discussed the first in the upcoming series of Hackathons designed to help bioinformatics and cheminformatics professionals learn about new technologies in an informal and hands-on environment. In general, Hackathons are intended to be free, informal gatherings, with an emphasis on practical, hands-on learning. They can also serve as
San Diego Bioinformatics Lunch Forum: Hackathons Read More »
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
BioGroovy 1.0 Classes Released Read More »
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 disciplines. The topic arose because although the Semantic Web has been talked about for nearly
The Semantic Web and Drug Discovery Read More »
The PubMed Central Open Access archive, contains the full text of a subset of the articles available through PubMed. It’s very useful for text mining. In this blog entry, I’ll show you how to search for and download the XML-encoded articles using a simple BioGroovy shell script. To perform the search, we’re going to use
Downloading PubMed Articles Read More »
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 persist Genes, Proteins, and PubMed articles into a relational database. However, I always ask myself
BioGroovy and the Semantic Web Read More »
As many Perl programmers know CPAN (the Comprehensive Perl Archive Network) is an invaluable repository for Perl modules. You can easily download and install a module and add its functionality to your script. In order for scripting languages like Groovy to gain some traction with the bioinformatics crowd there needs to be a similar repository
BioGroovy and Grapes Read More »
As part of the series of blog entries on BioGroovy, I thought I’d start with some rather simple tasks using some of the functionality found in NCBI’s eUtils API. NCBI has both RESTful and SOAP APIs that you can use. But in the interests of keeping this simple, I’m going to stick with the REST
BioGroovy: Fetching PubMed Data Read More »
