gem install publisci
Most of the gem's functions can be accessed through its DSL
require 'publisci'
include PubliSci::DSL
# Specify input data
data do
# use local or remote paths
source 'https://github.com/wstrinz/publisci/raw/master/spec/csv/bacon.csv'
# specify datacube properties
dimension 'producer', 'pricerange'
measure 'chunkiness'
# set parser specific options
option 'label_column', 'producer'
end
# Describe dataset
metadata do
dataset 'bacon'
title 'Bacon dataset'
creator 'Will Strinz'
description 'some data about bacon'
date '1-10-2010'
end
# Send output to an RDF::Repository
# can also use 'generate_n3' to output a turtle string
repo = to_repository
# run SPARQL queries on the dataset
PubliSci::QueryHelper.execute('select * where {?s ?p ?o} limit 5', repo)
# export in other formats
PubliSci::Writers::ARFF.new.from_store(repo)
Running the gem using the publisci
executable will attempt to find and run
an triplifier for your input.
For example, the following
publisci https://github.com/wstrinz/publisci/raw/master/spec/csv/bacon.csv
Is equivalent to the DSL code
require 'publisci'
include PubliSci::DSL
data do
source 'https://github.com/wstrinz/publisci/raw/master/spec/csv/bacon.csv'
end
generate_n3
The API doc is online. For more code examples see the test files in the source tree.
Building a parser simply requires you to implement a generate_n3
method, either at the class or instance level. Then register it using Publisci::Dataset.register_reader(extension, class)
using your reader's preferred file extension and its class. This way, if you call the Dataset.for
method on a file with the given extension it will use your reader class.
Including or extending the Publisci::Readers::Base
will give you access to many helpful methods for creating a triplifying your data. There is a post on the project blog with further details about how to design and implement a parser.
The interface is in the process of being more rigdly defined to separate parsing, generation, and output, and it is advisable to you make your parsing code as stateless as possible for better handling of large inputs. Pull requests with parsers for new formats are greatly appreciated however!
Information on the source tree, documentation, examples, issues and how to contribute, see
http://github.com/wstrinz/publisci
The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
If you use this software, please cite
and one of
- BioRuby: bioinformatics software for the Ruby programming language
- Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics
This Biogem is published at (http://biogems.info/index.html#publisci)
Copyright (c) 2013 wstrinz. See LICENSE.txt for further details.