<img src=“https://secure.travis-ci.org/wstrinz/publisci.png” />
Note: this software is under active development!
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)
To use the library
require 'publisci'
The API doc is online. For more code examples see also the test files in the source tree.
Information on the source tree, documentation, 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 one of
-
[BioRuby: bioinformatics software for the Ruby programming language](dx.doi.org/10.1093/bioinformatics/btq475)
-
[Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](dx.doi.org/10.1093/bioinformatics/bts080)
This Biogem is published at biogems.info/index.html#publisci
Copyright © 2013 wstrinz. See LICENSE.txt for further details.