RDF extension or transformation

Support and Helpdesk
1

Hello,

I am trying to convert a tsv file into RDF. In Linux, I downloaded OpenRefine 3.6.2, and it loads fine in the website. I can import my tsv file, etc… but the extension to convert the columns into RDF is not uploaded when I run OpenRefine. For that , what I have done is downloaded RDF extension (in a folder named extensions/rdf-extension, according to the Instructions). That folder extensions is in the same folder as the downloaded openrefine.
I have also tried with RDF transform, which is newer version of RDF extension and a new version of OpenRefine, but even when they run fine, there are not extensions running along.
I installed and reinstalled, but it is not working.

Andy suggestion? Thank you in advance,
Maria

2

Hello and welcome @Maria

Just some things to check:

  • Which version of the RDF Transform extension have you used?
  • Extensions need to be added to the ‘extensions’ directory at the path /<OpenRefine-root-dir>/webapp/extensions (where <OpenRefine-root-dir> is the directory containing the refine script etc.)
  • What browser are you using to access OpenRefine? I’ve found that the RDF Transform extension does not work with Safari, but is OK with Chrome (on macOS this is)

Best wishes

Owen

3

Hi Owen,

I finally was able to install the extension successfully. There was a problem probably in the Installation folder that I have selected.

Do you know if there are any tutorials for gene/genomics files like gff files, which use custom ontologies?

Thank you for taking your time to answer my questions.

Best regards,
Maria

4

Hi @Maria

There are several papers that reference the use of OpenRefine with genomics data (e.g. see the first four references in this funding proposal https://openrefine.org/uploads/czi-eoss-proposal.pdf) and specifically this paper QTLTableMiner++: semantic mining of QTL tables in scientific articles | BMC Bioinformatics | Full Text mentions the use of OpenRefine to produce RDF from QTL data … but seems light on the details!

I’m sorry to say I’ve not come across any specific tutorials for using OpenRefine to work with GFF. Since it’s a tab separated value format OpenRefine will read it (although since I suspect these are generally quite large files, you will probably need a generous amount of memory allocated to OpenRefine)

I’m not at all familiar with GFF or genomics data generally, but if you could share some information on exactly what you are trying to do with some example data then it maybe I can provide some pointers as to how you can use OpenRefine in this context

Best wishes

Owen