Subscribe:
RSS feed
This and That
Browsing All posts tagged under »pubmed2ensembl«
pubmed2ensembl: Query Improvements
Following my first post of the relatively new “mini” series, I have made some further improvements to the pubmed2ensembl query wrapper. Two new features are now implemented in bioknack‘s bk_pubmed2ensembl.rb script: retrieval of PubMed Central IDs besides the already retrievable PubMed IDs, and querying of Ensembl gene IDs by PubMed Central/PubMed ID Brief Recap www.pubmed2ensembl.org is a […]
pubmed2ensembl: Tweet Clarification
August 26, 2011
In my first year as postdoc I have worked on the project called pubmed2ensembl – a web resource that links publications and genes. The web-site is powered by BioMart 0.7, which we used to expose the various datasources that we provide in form of a customised Ensembl Genes mart. I have recently posted a controversial tweet about […]
opacmo: Introducing the Open Access Mortar
July 25, 2011
Today a new web-resource — www.opacmo.org — has been born that will support biologists, physicists and life sciences researchers in general to find publications linked to genes, species, diseases, cellular components, biological processes and molecular functions. This blog post gives a brief introduction to opacmo’s features, swiftly explores the background behind its development, highlights opacmo’s […]
Evaluating bioknack’s Gene Normalisation on BioCreative 3
June 29, 2011
In a previous postdoc placement I developed and set-up the customised BioMart pubmed2ensembl, which links publications to genes. Keeping pubmed2ensembl’s data sources up-to-date proved to be complicated, especially as the gene name recognition runs of the tool GNAT/LINNAEUS that we used took weeks to complete on the local computing cluster. With the recent presentation of […]
bioknack’s pubmed2ensembl Query Wrapper
June 17, 2011
This is the first post in a new “mini” series of tool features and research results. Unlike previous long winded blog posts, the mini series only features a very short description of the topic, gives an example and concludes. bioknack‘s collection of tools has been extended with a small command line tool for retrieving the […]
Portfolio
October 8, 2011
0