Lecture 24

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Interaction Databases used in Computational Biology

 

BCH441 Guest lecture:

Francis Ouellette

Associate Director, Informatics and Biocomputing and Senior Scientist, OICR

 

Links summary

• IntAct - The EBI open access, archival interaction database
  
• BioGRID
  
• DIP (archival, not open access)
  
• MINT Topical, curatedl interaction sets
  
• Mpact
  
• BIND (non-commercial component not curated since 2003)
  
• HPRD
  

• Gary Bader's pathguide database
  
• Ulysses: Projection of Protein Networks across Species
  
• Lu et al. (2005) Assessing the limits of genomic data integration for predicting protein networks.
  
• YPL240c
  

• Creative Commons License: atribution, share alike.
  
• Open Access overview
  
• Open Access Now
  
• DOAJ
  
• CIHR Open Access policy
  

 

Lecture slides

 

 

Introduction

 

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The way this works is shown in the example from the lecture notes: Boris Steipe has lifted some material from Francis Ouellettte's lecture slides. He is allowed to do so, since he has attributed the source of the material and is sharing the results under the same conditions.

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Bioinformatics and Databases

 

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Interaction Databases

 

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Gary Bader's pathguide database

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• The IntAct database
  

[The BioGrid database ]]

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Ulysses: Projection of Protein Networks across Species

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Lu et al. (2005) Assessing the limits of genomic data integration for predicting protein networks.

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Genetic Interaction Networks

 

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YPL240c

 

Open Access

 

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*DIP (archival, not open access)
*IntAct - The EBI open access, archival interaction database
*MINT Topical, curatedl interaction sets
*Mpact
*BioGRID
*BIND (non-commercial component not curated since 2003)
*HPRD
*Open Access overview
*Open Access Now
*DOAJ
*CIHR Open Access policy

 

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