Database manager (DBM) in the Integrative Biomedical Informatics (IBI) group of GRIB (IMIM-UPF)

Deadline:
30/04/2017
Centre / Institution:
Pompeu Fabra University
Bioinformatics expertise:
Bioinformatics of Disease and Treatment, Biomedical Informatics, Integrative Bioinformatics
Keywords:
Medical informatics; Database; Data Management; semantic web

Job description

A position for a database manager (DBM) is available in the Integrative Biomedical Informatics (IBI) group led by Ferran Sanz and Laura I. Furlong at GRIB (IMIM-UPF) in Barcelona.

General description

The successful candidate will work in the development and management of several biomedical databases in the group. These databases include clinical data from electronic health records, and also different types of biomedical data from public repositories. Examples of the latter are the DisGeNET (http://www.disgenet.org) and PsyGeNET (http://www.psygenet.org) resources developed in our group. The tasks of the Database manager include the design, development, administration, and maintainance of the integrity, security, and availability of the different relational databases in our group. These tasks include data transformation, database analysis,  tuning, backup and migration between different RDBMS. In addition, the candidate will work in close collaboration with other members of the group in a variety of interdisciplinary projects in the area of translational bioinformatics in which these databases are used.

Desired skills and expertise

Required

  • University degree in informatics, medical informatics, bioinformatics or related area
  • Proficiency with SQL
  • Knowledge of relational database analysis and design using MySQL/MariaDB, Postgres, Oracle and SQLite
  • Must be able to create and modify database queries, views, and related objects.
  • Familiarity with scripting languages (Python, Perl, R, Shell Scripting, etc.)
  • Demonstrated strong verbal and written communication skills
  • Good English communication skills
  • Excellent attention to detail and organization skills
  • Must be able to multi-task, meet deadlines, and work within a team

Desirable

  • Knowledge/expertise on Semantic Web technologies: RDF, OWL, SPARQL and semantic Web services
  • Expertise in RDF/graph databases (Virtuoso, neo4j)
  • Knowledge/experience in working with biomedical ontologies and controlled vocabularies
  • Expertise on Data Management using no relational databases (e.g. MongoDB)

 

The IBI group is an international research group with interdisciplinary expertise in biology, medicine, pharmacology, chemistry, psychology and informatics. It has a unique experience in the fields of network medicine, systems toxicology and biomedical text mining. Recent achievements include: 

  1. development of the DisGeNET and PsyGeNET knowledge platforms
  2. development and application of biocuration approaches
  3. development of network biology approaches to study the mechanisms leading to adverse drug reactions and disease comorbidities
  4. semantic web approaches for life sciences
  5. strategies for the reuse of clinical data in biomedical research
  6. participation in international projects in the aforementioned fields (EMIF, eTOX, Open PHACTS, MedBioinformatics, iPiE, TransQST)

Contract duration and other benefits

Until December, 31st 2017 with possibility of extension one or more years.

Required information and contact

Please send a CV, letter of interest and the contact information for 2-3 referees by email to chus.donlo(ELIMINAR)@upf.edu with reference to IBI-DBM.