Version 43 (modified by tkappler, 14 years ago)

Perl and RDF

Open Bio* Semantic Web tools


(Please add your name!)

  • Toshiaki Katayama
  • Erick Antezana
  • Shuichi Kawashima
  • Mitsuteru Nakao
  • Brad Chapman
  • Peter Cock
  • Jan Aearts
  • Kyung-Hoon Kwon
  • Raoul Bonnal
  • Christian Zmasek
  • Keun-Joon Park
  • Thomas Kappler

RDF libraries in each language

(Please add other languages as well!)

Name of the available libraries:


  • RDF reader (in)
  • RDF generator (out)
  • SPARQL query helpers
language in out query
Ruby ? ? ?
Python o ? ?
Perl o o o

Tools to manipulate RDF data

  • RDF grep
  • RDF diff
  • RDF sort
  • RDF uniq
  • RDF wc (triple count)
  • RDF cat (combine)
    • (most of) these commands will output RDF graph :)
    • "sort" before "diff" is better.
    • it would be great if "diff" can have an option to ignore "empty node" which can shift internal IDs even if the graphs are almost same.

RDF converters

Interface for SPARQL endpoint

DBI like interface to Query and obtain Result by SPARQL.

  • automatically map to the relevant language object
  • we can use SPARQL endpoint as a data source for  Galaxy, for example.
  • sometimes, results can be huge

Language availability

language generic  4store
Ruby o o
Python o o
Perl o x
Java o o
R ? ?

Try "short read archive (metadata) SPARQL endpoint" which will be developed by the NextGenSeq? open space discussion group.

Galaxy integration

  • Plugin development
  • Documentation


RDF manipulation tools and library to produce RDF from biological objects are important for data providers, but most users are consumers of the data, so we will focus on how to access public biological SPARQL endpoint easily in each Open Bio* library.

Suggested endpoint to play with:



  • Survey existing SPARQL library in each language


  • Can we have common interface for major biological SPARQL endpoints?
  • Can we have nice SPARQL query builder? (see below for OWL notes)
  • Convert retrieved results into language's object?
  • What about getting not only a tabular result but also a result displaying a graph (nodes + edges)? (See  BioGateway browser)
  • Map directly on Bio* interal objects


  • Half of the BioRuby group will also tackle with to develop the DB (e.g. KEGG) -> RDF generator (will be used in Bio2RDF and TogoWS)

Using OWL to support dynamic queries and exploration of RDF data

This a short summary of a discussion on Friday, 2010-02-12.

The plan is to work on a nice SPARQL query builder, as a joint effort between the Bio* communities. It could make use of an OWL ontology as a description of the data: it lists what things there are, and how they are related. These relations could be offered to the user, via a simple API to the programmer or even on a web page to the biologist.

Erick pointed out the  Manchester OWL Syntax as a possibly related effort.