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Ontologies, RDF-generators, and a web interface for querying it all.
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README.md

SPARQLing genomics

This project provides programs to extract RDF triplets from commonly used file formats in genomics. It also provides a web-based environment to explore the RDF triplets once inserted in a triple store. The complete documentation is available in the doc/ directory.

Dependencies

To build the programs in this repository, the following tools are required:

  • GNU Autoconf, GNU Automake, pkg-config and GNU Make
  • HTSlib
  • Libgcrypt
  • Raptor2
  • GNU Guile

Installation and development environment with GNU Guix

The following command creates an environment wherein all required tools to construct the project's programs are available:

$ guix environment -l environment.scm

Do the usual autotools dance to build everything:

[env]$ autoreconf -vfi
[env]$ ./configure
[env]$ make

Or change the last step to build individual components, like vcf2rdf:

[env]$ make -C tools/vcf2rdf

Starting the web interface

To start the web interface, run:

[env]$ web/sg-web

Web interface screenshot

Further reading

Please read the manual in the doc/ directory. A PDF can be built using:

$ guix environment -l environment.scm --ad-hoc texlive
[env]$ make doc

Alternatively, a pre-built PDF is also available.

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