Cross Projects
Project Ideas
Cross BioInterchance
Rationale
BioInterchange Interchange
data using the Resource Description Framework (RDF) and let
BioInterchange automagically create RDF triples from your TSV, XML,
GFF3, GVF, Newick and other files common in Bioinformatics.
BioInterchange helps you transform your data sets into linked data for
sharing and data integration via command line, web-service, or API.
BioInterchange was conceived and designed during NBDC/DBCLS’s
BioHackathon 2012. Architecture and RDF
serialization implementations were provided by Joachim Baran, Geraint
Duck provided JSON and XML deserialization implementations and
contributed to architecture decisions, guidance on ontology use and
applications were given by Kevin B. Cohen and Michel Dumontier, where
Michel brought forward and extended the Semanticscience Integrated
Ontology (SIO). Jin-Dong Kim helped to define ontology relationships for
RDFizing DBCLS’ PubAnnotation category annotations. The main idea is to
have a central service with can be used as a validator and as
interchange service for different languages.
Approach
The project will identify the most common and used file formants for all
the currently used language under OBF and will design a RESTful API and
will project an implementation for all the supported languages.
BioInterchange was developed with Ruby but the scope of the project is
to have an agnostic system which let use implement a converter using the
best language for that functionality. It expected to have a high traffic
for the service so an appropriate refactoring or reimplementation using
parallel techniques or languages devoted to parallel programming would
be possible.
Difficulty and needed skills
The project is mid / high difficulty, aimed at talented students.
Previous knowledge of Ruby or other scripting language is preferred and
flexibility in learning other languages is requireed.
The project requires
Knowledge of advanced programming languages and meta-programming and
some concept in parallelizing and web services design.
Mentors
Raoul J.P. Bonnal, Francesco Strozzi, Toshiaki Katayama, Joachim Baran