Blog Archives

rrdf 2.0: Updates, some fixes, and a preprint

January 3, 2014
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rrdf 2.0: Updates, some fixes, and a preprint

It all started 3.5 years ago with a question on BioStar: how can one import RDF into R and because lack of an answer, I hacked up rrdf. Previously, I showed two examples and a vignette. Apparently, it was a niche, and I received good feedback. And...

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Pharmacology data from Open PHACTS in R

December 22, 2013
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Where I reported yesterday the initial steps of an client R package for Open PHACTS, I can now report the first pharmacology data import:

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Open PHACTS from R

December 21, 2013
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Nothing much going to say about it, and just to report some progress:

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The Dutch Dataverse Network: a host for the ChEMBL-RDF v13.5 data, and some thoughts in workflow integration

August 31, 2013
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The Dutch Dataverse Network: a host for the ChEMBL-RDF v13.5 data, and some thoughts in workflow integration

Last Thursday, there was a UM library network drink. And as I see a library where knowledge is found, and libraries still rarely think of knowledge as ever being able to be stored outside books and papers, I was happy to see the library promoting the D...

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Triples, stores, and SPARQL in R

November 27, 2012
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For some time I have been stealing an hour here and there for the rrdf package for R. This package is based on Apache Jena and allows reading and writing of RDF triples, as well as doing local and remote SPARQL querying. BTW, rrdf is not only R pa...

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My #ACSPhilly #skolnik2012 slides for “Semantic pipelines to molecular properties”

August 21, 2012
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(This article was first published on chem-bla-ics, and kindly contributed to R-bloggers) To leave a comment for the author, please follow the link and comment on his blog: chem-bla-ics. R-bloggers.com offers daily e-mail updates about R news and tutorials on topics such as: visualization (ggplot2, Boxplots, maps, animation), programming (RStudio, Sweave, LaTeX, SQL, Eclipse, git, hadoop, Web Scraping) statistics...

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Compiling R code, and speed up your computation

May 5, 2012
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I just ran into this interesting post on the R-bloggers Planet. The described R functionality allows you to compile R code (to byte code) so that it will no longer be interpreted but actually run. That is a performance boost. I guess in due time we will see R use JIT technologies, so that the difference will...

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Tricks I learned today #1: as.integer() on factor levels

October 12, 2011
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I normally work with full numerical data, not categorical data. R, when using read.csv() seems to recognize such categories and marks the column as to have factor levels. This is useful indeed. However, I wanted to make a PCA biplot on this data, so wa...

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rrdf 1.5: Accessing SMW SPARQL end points behind LDAP authentication

September 25, 2011
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rrdf 1.5: Accessing SMW SPARQL end points behind LDAP authentication

We are using a Semantic MediaWiki (SMW) for the Gold Compound selection task by the ToxBank in the SEURAT-1 cluster, funded by Colipa and the EC. I do stress that despite being funded by Colipa, they have no control over my research; they just co-...

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Plotting molecular properties for (sub)sets

August 10, 2011
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Plotting molecular properties for (sub)sets

For a toxicology paper we are writing up, I need to create a few plots showing how the toxic and non-toxic molecules differ (or not) with respect to a few molecular properties, such as logP or the molecular weight. The rcdk package provides all, of cou...

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