Comparative Genomics of Non-Model Invertebrates

ESR Project 15: Semantic publication, dissemination, visualization and re-use of biodiversity-related genomic and metagenomic data

Supervisor: Lyubomir Penev (Pensoft Publishers, Sofia), Co-supervisor Michael Schrödl (Zoological State Collection Munich)

Student: Mariya Dimitrova 

Objectives: One of the increasingly worrying impediments in biodiversity sciences and genomics is the continuing use of non-machine-readable formats, for example PDF, HTML or even paper. To extract and reuse data from these formats a significant post-publication effort is needed.

O1: Integrate academic peer-review and publishing practices with the research process, so that to increase machine-readability, interoperability and reuse of the published content to the maximum extent possible.

O2: Deliver machine-readable content through XML and Application Programming Interface (API) to data aggregators and end users.

O3: Survey, develop and implement novel methods and workflows, including nano- and micro-publications, for genomic and metagenomic data publishing, visualisation, dissemination and reuse. A core part of the work for all three objectives will be the integration between leading genomic data management platforms (INSDC, BOLD, PlutoF, Galaxy, and others) with the ARPHA XML-based publishing platform for online collaborative peer review and publication, through implementation of community-accepted standards for genomic / metagenomic data and metadata.

The applicants must have a basic knowledge and experience in informatics and software development and programming. Educational degrees in the above fields and especially in Linked Open Data, RDF and OWL will be considered as a major advantage.
Agostinho Antunes (Porto), Michael Schrödl (Munich), Yu Wang (Leibniz-Supercomputing Centre of the Bavarian Academy of Science and Humanities, Munich).

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