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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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 Bioseminar on Tuesdays at 3pm in room 10 of Forskningsparken at. Gaustadalléen 21 (see map here).

The Bioinformatics Seminars are held every Wednesday at 12:15 by the Joint Centre for Bioinformatics in Oslo, located at Gaustadalléen 25 (see map here).

Courses

A new, two-week, intensive bioinformatics course is being prepared for September of 2009. You can view a preliminary schedule here http://bioinformatics.uio.no/wiki/Bioinformatics_course. This will replace MBV-INF4410 taught in previous years.

Introductory Perl is taught by Antonio Mora and Ian Donaldson as part of the MBV3070 course.


Contact

ian.donaldson at biotek.uio.no