SPARQL

Introduction As researchers, we give presentations. Over the last years, I gave somewhere between 2 and 10 presentations a year. What I need is a html document that lists all my presentations, their title, date of presentation and a link to the pdf document in a table. This table can then be included on my institutional home page. As a plus, I want the table to be searchable and each column to be sortable. [Read More]

Experimenting with the tripalv3 JSON+LD API Introduction In this post I'm experimenting with querying the JSON-LD (LD stands for Linked Data) API of my Tripal3 genome database for Pseudomonas fluorescens SBW25. A little bit of background: Tripal is a content management system (CMS) for genomic data, based on the Drupal CMS framework. It facilitates setting up customized genomic database webservers to publish genome assemblies, annotation tracks, experimental and modeling data for one or several organisms. [Read More]

Introduction In this post I will present example SPARQL queries against the Pseudomonas fluorescens SBW25 knowledge graph (SBW25KG). The knowlegde graph was derived from the manually created annotation in gff3 format, as explained in a previous post. The queries are run against a local instance of the apache-jena-fuseki triplestore. First, I set the endpoint URL and the maximum number of returned records: %endpoint http://micropop046:3030/plu/ %show 50 Endpoint set to: http://micropop046:3030/plu/Result maximum size: 50 Retrieve 10 CDS’s from the SBW25KG. [Read More]