Unlike the Agatha Christie mystery referred to in the title of this piece, there are some mysteries that seem to defy a single answer. One of those mysteries is how most scientists manage to keep up-to-date given the growing avalanche of developments in their fields. The answers I get are wide and varied, but I thought I would share a […]
A Pocketful of Rye 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 »
In my previous post on Assessing Credibility in Scientific Research, I described several ways that credibility might be tracked with respect to a paper and the methods and materials used. William Gunn at Mendeley, recently pointed me to a project that he’s become involved in, called the Reproducibility Initiative.
Assessing Credibility Via Reproducibility Read More »
Part of what makes user group meetings so interesting is getting the opportunity to peek behind the curtains and see someone else’s operation. In last night’s, KNIME user group meeting, Brock Luty of Dart NeuroScience gave an interesting perspective on Dart’s cheminformatics computing stack used to support parallel synthesis (chemical library design): OpenEye for predictive
KNIME and Cheminformatics: A Peek Behind The Curtain Read More »
One of the things that I’m always curious about, is the effect of a sequence variation on the conformation of a target. Recently I wrote about ClinVar and SwissVar, two tools for examining variants and their associations with disease. Since the PDB tends to have either wild type versions of a protein, or versions of
SwissModel: It’s not what you think Read More »
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 [Ten Simple Rules for the Care and Feeding of Scientific Data] along with some new
Reproducibility and Provenance Read More »
In a previous post, I described ClinVar, the NCBI’s database of clinically relevant protein variations. Recently, I came across SwissProt’s version of this database called SwissVar. SwissVar is designed to help you answer two questions: What diseases is this protein involved in? What proteins have been found to be mutated in a particular disease?
SwissVar: Clinically Relevant Protein Variations Read More »
Over the past few years, pharmaceutical companies have come to increasingly rely external research to help fill their pipelines. This greater reliance on academic research is not without it’s risks — chief amongst these is the lack of reproducibility. Amgen discovered that 47/53 landmark oncology papers had results that could not be reproduced, and Bayer
Assessing Credibility in Scientific Research Read More »
PubMed is one of those tools that everyone uses but not everyone uses it well. Usually your enthusiasm for investigating the search results will wane after the third or fourth page of results. Here are a few tips for making your searches more targeted and successful. Use MeSH Terms PubMed uses Medical Search Heading (MeSH)
Tips for Better PubMed Searches Read More »
