Getting Started with Bio2RDF

[Christian Stackhouse]

I am attempting to convert my normalized/annotated affymetrix array data to RDF format. I found the bio2rdf affymetrix php script for this, but I am unsure how to run it. I am also going to be converting fasta/fastq files, VCF (variant call format), and other data types. I think the bio2rdf project could be helpful in this, but I do not have any experience with php and little experience programming outside of R. Any help or advice would be greatly appreciated

I'm running windows 10 pro 64bit

[Michel Dumontier]

Hi Christian,
The Bio2RDF script converts the array metadata that Affymetrix
provides. here's an example entry:

http://bio2rdf.org/affymetrix:246305_at

here's a list of the arrays

http://bio2rdf.org/affymetrix_vocabulary:Genechip-Array

we don't currently have the actual array results such as what you find
in GEO or Array Express, in RDF - although we are working on GEO at
the moment.

m.
Michel Dumontier
Associate Professor of Medicine (Biomedical Informatics), Stanford University
Chair, W3C Semantic Web for Health Care and the Life Sciences Interest Group
http://dumontierlab.com

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[Michel Dumontier]

Christian,
You're in luck! We're just working on a docker deployment for
Bio2RDF. I'll let Maxime talk more about it

m.
Michel Dumontier
Associate Professor of Medicine (Biomedical Informatics), Stanford University
Chair, W3C Semantic Web for Health Care and the Life Sciences Interest Group
http://dumontierlab.com

On Fri, Feb 19, 2016 at 8:06 AM, Christian T Stackhouse (Campus)
<ctst...@uab.edu> wrote:
> Dr. Dumontier,
>
> Thank you very much for your follow up. Do you have installation instructions and/or a vignette for bio2rdf? I'd like to try and install the api and run scripts on a VM. Do you have recommendations for OS and configuration? I would like to help contribute to this project, though right now I'm not able to offer much. Again, thank you for your assistance and I hope you have a pleasant day!
>
> Best,
>
> Christian T. Stackhouse | Graduate Student
> GBS Neuroscience Theme
> Department of Neurosurgery
> Department of Radiation Oncology
> UAB | The University of Alabama at Birmingham
> Hazelrig-Salter Radiation Oncology Center | 1700 6th Ave S | Birmingham, AL 35233
> M: 919.724.6890 | ctst...@uab.edu | cstac...@uabmc.edu | ctst...@gmail.com
>
> uab.edu
> Knowledge that will change your world
>
>
> ________________________________________
> From: Michel Dumontier <michel.d...@gmail.com>
> Sent: Thursday, February 18, 2016 11:40 AM
> To: bio2rdf
> Cc: Christian T Stackhouse (Campus)
> Subject: Re: Getting Started with Bio2RDF

[Maxime Déraspe]

Hi Christian,

it is in our agenda to package the bio2rdf scripts with docker which will enable us to make the conversion in containers.

Docker is a container engine which offers several advantages over VM.

But right now if you want to launch a instance of a database locally  I would suggest to download the virtuoso db from download.bio2rdf.org and launch it in a virtuoso container - the triple store engine.

You will need to install docker first.

docker pull zorino/docker-virtuoso
mkdir data; cd data;
wget https://raw.githubusercontent.com/zorino/docker-virtuoso/master/virtuoso.ini .

wget http://download.openbiocloud.org/current/affymetrix/affymetrix.virtuoso.gz
gunzip -c affymetrix.virtuoso.gz > virtuoso.db
cd ../
docker run --name affymetrix -v `pwd`/data:/mnt/graphs/ -p 9000:9000 zorino/docker-virtuoso

You now have a working instance of the latest bio2rdf release for affymetrix.

http://localhost:9000/fct 

http://localhost:9000/sparql

Maxime

[mahmut...@gmail.com]

While I was trying to use the given container for bio2rdf drugbank virtuoso db I had the following error on my SELinux enabled box.

    "Unable to create file /mnt/graphs/virtuoso.lck (Permission denied)"

Adding "--privileged=true" option to the docker run command line has solved the above error.

Mahmut