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Donaldson Group

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The Donaldson Group at the Biotechnology Centre of Oslo

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Research Interests

Our primary interests include protein interaction data consolidation, text mining and data mining especially with respect to diseases.

Our recent work on a consolidated protein interaction database can be found at http://irefindex.uio.no/ .

Projects

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iRefIndex http://irefindex.uio.no/
iRefIndex (interaction Reference Index) provides an index of protein interactions available in a number of primary interaction databases including BIND, BioGRID, CORUM, DIP, HPRD, IntAct, MINT, MPact, MPPI and OPHID. This index allows the user to search for a protein and retrieve a non-redundant list of interactors for that protein.

iRefIndex uses the Sequence Global Unique Identifier (SEGUID) to group proteins and interactions into redundant groups. This method allows users to integrate their own data with the iRefIndex in a way that ensures proteins with the exact same sequence will be represented only once.

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iRefWeb http://wodaklab.org/iRefWeb/
iRefWeb provides a searchable web interface to the iRefIndex. iRefWeb also provides visualization of statistics related to iRefIndex and allows users to compare annotation of the same publication by multiple interaction databases.

iRefWeb is a collaborative project with the Wodak group at the Hospital for Sick Children in Toronto.

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Magrathea http://magrathea.uio.no/
Magrathea is prototype software demostrating the principals of coordinated agent modeling.
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The Biolibrarian Proposal

The Biolibrarian proposal proposes the creation of new positions at university libraries around the world. These people would act as local biocurators that help local university researchers submit data to relevant biological databases.

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DiG: Disease Groups http://donaldson.uio.no/wiki/DiG:_Disease_groups
The Disease Groups project groups together phenotypically related disease-gene associations found in OMIM's Morbid Map. The resulting map of disease genes may be used to explore relationships between disease genes in the human protein-interactome.
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Bioscape http://bioscape.uio.no/
Bioscape is our in-house text-mining system used to locate gene and protein mentions in PubMed abstracts.

Group Members

Past Group Members

  • Katerina Michalickova
  • Hanna Nemchenko

Local Seminar Series

The Biotechnology Centre of Oslo holds a weekly Tuesday seminar at Forskningsparken, Gaustadalléen 21, Oslo.

The Computational Life Science seminars are held every Wednesday at Ole-Johan Dahls hus, located at Gaustadalléen 23D, Oslo (opposite the Forskningsparken main entrance).

Courses

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Bioinformatics for molecular biology

A new, two-week, intensive bioinformatics course that covers various aspects of bioinformatics analyses for molecular biology. Statistics, multiple hypothesis testing, microarray analysis, sequence alignments, working with protein structures, protein interaction networks and more. The schedule can be viewed here http://bioinformatics.uio.no/wiki/Bioinformatics_course along with all material used in the course. The course is composed of lectures and practical tutorials.

Introductory Perl is taught by Antonio Mora and Ian Donaldson as part of the MBV3070 course. The slides for these lectures are available here at Perl lectures for MBV3070

Contact

ian.donaldson at biotek.uio.no