BioGRID: Biological General Repository for Interaction Datasets

Slides:



Advertisements
Similar presentations
GridWorld Case Study Part 4 Classes that Extend the Critter Interface A Summary by Jim Mims.
Advertisements

Bioinformatics growth curves Medline records Computer power DNA sequences 3-D structures.
© Wiley Publishing All Rights Reserved. Using Nucleotide Sequence Databases.
Creating NCBI The late Senator Claude Pepper recognized the importance of computerized information processing methods for the conduct of biomedical research.
Urchin & Website Usability. Usability Study Usability study is a repetitive process that involves testing a site and then using the test results to change.
Working with gene lists: Finding data using GEO & BioMart June 5, 2014.
Pathways & Networks analysis COST Functional Modeling Workshop April, Helsinki.
Basic Genomic Characteristic  AIM: to collect as much general information as possible about your gene: Nucleotide sequence Databases ○ NCBI GenBank ○
GENBANK, SWISSPROT AND OTHERS As Problem Sources for CSE 549 Andriy Tovkach Genetics.
Tutorial 7 Genome browser. Free, open source, on-line broswer for genomes Contains ~100 genomes, from nematodes to human. Many tools that can be used.
Chapter 3 Database Management
Biological Databases Notes adapted from lecture notes of Dr. Larry Hunter at the University of Colorado.
Biological networks Tutorial 12. Protein-Protein interactions –STRING Protein and genetic interactions –BioGRID Signaling pathways –SPIKE Network visualization.
Progress Report 11/1/01 Matt Bridges. Overview Data collection and analysis tool for web site traffic Lets website administrators know who is on their.
DEMO CSE fall. What is GeneMANIA GeneMANIA finds other genes that are related to a set of input genes, using a very large set of functional.
SCONUL Access Contacts’ meeting: website report Wayne Connolly 3 July 2013.
Biological Databases By : Lim Yun Ping E mail :
Use cases for Tools at the Bovine Genome Database Apollo and Bovine QTL viewer.
Creating Metabolic Network Models using Text Mining and Expert Knowledge J.A. Dickerson, D. Berleant, Z. Cox, W. Qi, and E. Wurtele Iowa State University.
ISpheresImage iSpheresImage Feature Overview and Progress Summary.
Robin Mullinix Systems Analyst GeorgiaFIRST Financials PeopleSoft Query: The Next Step.
GO-based tools for functional modeling TAMU GO Workshop 17 May 2010.
Introduction to Bioinformatics Dr. Rybarczyk, PhD University of North Carolina-Chapel Hill
Copyright OpenHelix. No use or reproduction without express written consent1.
Generic Database. What should a genome database do? Search Browse Collect Download results Multiple format Genome Browser Information Genomic Proteomic.
Lesson 2: Designing a Database and Creating Tables.
SRI International Bioinformatics 1 Editing Pathway/Genome Databases Ron Caspi.
© 2003 Prentice Hall, Inc.3-1 Chapter 3 Database Management Information Systems Today Leonard Jessup and Joseph Valacich.
Getting GO: how to get GO for functional modeling Iowa State Workshop 11 June 2009.
PubChem: An Open Repository for Chemical Structure and Biological Activity Information Steve Bryant The NIH Biowulf Cluster: 10 Years of Scientific Supercomputing.
An Introduction to NCBI & BLAST National Center for Biotechnology Information Richard Johnston Pasadena City College.
LinkOut® in STAT!Ref LinkOut Feature. LinkOut is a service of Entrez that allows you to link directly from PubMed and other Entrez databases to a wide.
After FactFinder: The future of data dissemination at Census Bureau December 17,
Amyotrophic Lateral Sclerosis Online Database (ALSOD) Presenter : Olubunmi Abel.
NCBI: something old, something new. What is NCBI? Create automated systems for knowledge about molecular biology, biochemistry, and genetics. Perform.
BUSINESS SENSITIVE 1 SAAW - Sequence Annotation and Analysis Workshop Boyu Yang and Gene Godbold Battelle Memorial Institute, Charlottesville Operations.
A New Interface to GeneKeyDB Methods for analyzing relationships among proteins based on shared motifs Chris Symons & Xinxia Peng.
GEO (Gene Expression Omnibus) Deepak Sambhara Georgia Institute of Technology 21 June, 2006.
UK CropNet Software Development. UK CropNet Software Development Goals z Improve user access to data via user- friendly graphical displays. z Development.
Entrez, dbSNP, GEO, OMIM & LinkOut JanPlan Entrez Distributed by NCBI in 1991 on CD-ROM Included linked nodes: GenBank & PDB Translated GenBank,
Views: From the Beginning John Fiala Twitter: jcfiala Vintage Digital.
MTA ETA. Product Description A real-time simulation system that estimates the expected time that it will take a certain bus to arrive at an end- user’s.
Sequence: PFAM Used example: Database of protein domain families. It is based on manually curated alignments.
BME435 BIOINFORMATICS.
Getting GO annotation for your dataset
CellExpress Tutorial A Comprehensive Microarray-Based Cancer Cell Line and Clinical Sample Gene Expression Analysis Online System :8080 NTU.
Comparative Analysis in BioCyc
Biological Databases By: Komal Arora.
Query Design View To create an Access query, you use the Query Design window. Youspecify a few data sources and fields, add a criteria expression or two,and.
Tutorial 12 Biological networks.
Pathway Visualization
Saccharomyces Genome Database (SGD)
Department of Genetics • Stanford University School of Medicine
What’s New in Colectica 5.3 Part 1
Concepts, Specifications, and Diagrams
Data Content of BioCyc Ingrid Keseler 1.
PIR: Protein Information Resource
Gene Expression Omnibus (GEO)
INFORMATION FLOW AARTHI & NEHA.
Data Content of BioCyc Ingrid Keseler 1.
Ensembl Genome Repository.
KEY CONCEPT Entire genomes are sequenced, studied, and compared.
Basic Local Alignment Search Tool
Chapter 3 Database Management
Bill to ID - Manage by Number: Delete from Cisco
Pathway Visualization
Problems from last section
Dr.s Khem Ghusinga and Alan Jones
Stephen Bridgett, James Campbell, Christopher J. Lord, Colm J. Ryan 
Partner Portal Training document
Presentation transcript:

BioGRID: Biological General Repository for Interaction Datasets Ben Bachman Georgia Institute of Technology 28 June, 2006

Overview Database of protein-protein interactions Removes redundancies Search protein of interest Retrieve primary information Physical and genetic interaction data Links to other databases http://www.thebiogrid.org

Features Overview Realtime site statistics Can search an organism by Genebank ID Entrez-Gene ID SGD ID Gene name Links to all known related enzymes Links to information in other databases

Statistics

Search Criteria

Example Search

Example Results

Osprey Visualization tool Powered by BioGRID Shows graphical relationships between proteins Links to information included in BioGRID

Features Overview Add in known enzymes Shows BioGRID data on the enzyme Visualize links to related enzymes Extended visualization View information on relationship between enzymes Links to database websites with more information

Osprey Example

Osprey Example

Osprey Example

Osprey Example

Osprey Example

Osprey Example

Summary BioGRID sometimes lacking in information, but instead displays error message Very well manicured database Osprey could use a way to find the path between two enzymes A few small UI problems Many useful features

Feedback: Privacy Policy Feedback
Do Not Sell My Personal Information
About project: SlidePlayer Terms of Service

© 2025 SlidePlayer.com. Inc. All rights reserved.