fishDelish final product post

By Mark van Harmelen | Published: July 10, 2011

Here we discuss the one of the two most reusable outputs from the fishDelish Project; namely our SPARQL Explorer. This is a tool to, inter alia, help people learn to use SPARQL. Over time we expect to build content (instructional materials) to populate the tool.

The other ‘most reusable’ product is FishOMatic, which allows users to easily utilise FishBase data on their own pages to eg produce an observation log. FishOMatic can also be used to harvest observational data. As such we think the technology is helpful in educational ventures such as the BBC’s Springwatch and Autumnwatch.

Te remainder of this post focusses on the SPARQL Explorer.

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Installation overview

By David Workman | Published: May 13, 2011

Installation guides

  1. Infrastructure setup preconditions
  2. Setting up RVM, Apache, Passenger, Ruby and Rails
  3. Installing iDoc
  4. Installing 4Store
  5. Creating your Triplestore
  6. Installing MySparql
  7. Installing the Species Browser
  8. Installing Fishomatic
  9. Installing rdf_generator

All guides and software are provided as-is

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Install iDoc

By David Workman | Published: May 13, 2011

iDoc is a rails application for producing community documentation. For the Fishdelish project, it was extended to allow direct embedding of MySparql queries that would be run when a page is loaded. Read More »

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Installing rdf_generator

By David Workman | Published: May 13, 2011

The rdf_generator is a very simple rails application that bootstraps the process of providing dereferencable URIs when you only have a SPARQL endpoint. It does this by taking the URL you visit and running a CONSTRUCT SPARQL query to obtain RDF, which is then returned in RDF-XML format. Obviously, this should be running at the ‘root’ of the URL-space for your RDF URIs as otherwise the RDF URIs wouldn’t be dereferencable. In practice, this means installing it on the server that serves the root URL of your RDF uri’s, or at least proxying request’s from the main server to the application where the rdf_generator app is installed. Read More »

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Install fishomatic

By David Workman | Published: May 13, 2011

Fishomatic is a mechanism for displaying and self-publication of observations of Fish species, such as those from diving expeditions or at an aquarium. Read More »

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Installing the species browser

By David Workman | Published: May 13, 2011

This setup requires a base ubuntu install, and doesn’t need RVM or rails. Read More »

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Install MySparql

By David Workman | Published: May 13, 2011

Having set up your machine for rails (see previous post) you’re now ready to install applications. The first is MySparql. Read More »

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Creating your triplestore

By David Workman | Published: May 13, 2011

Obviously, for this you will need the Fishbase database, or access to some copy of it. You should contact FIN or fishbase.org for this.

You’ll also need the fishbase D2RQ mapping file, available here.

This also assumes that you have installed 4store (see …) and that you’re on the same machine as the 4store installation. If you are not, then you will need to transfer the file generated in step 3 to the 4store machine. Read More »

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Installing 4store

By David Workman | Published: May 13, 2011

4store is the triplestore of choice for the fishDelish project. While there is documentation on how to install it on the 4store site, the process for doing so on ubuntu does deviate slightly, so I’ll list the steps I used to install it from source. Be warned, this doesn’t include any diagnostics for if something goes wrong and if something does, your best place to resolve issues is to get in touch with knowledgable individuals on either the 4store mailing list or on their #4store IRC channel on freenode. Once again, this is being done on a fresh installation of Ubuntu 10.04 (Server). Read More »

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Setting up rvm, apache, passenger, ruby and rails

By David Workman | Published: May 13, 2011

For most of the tools built on the SPARQL endpoint you will need a machine capable of running a rails application. This guide is a quick intro to my preferred way of setting up the rails infrastructure on a server. Read More »

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