MIAREMIBBI Portal Project Update

2nd MIBBI Workshop

Nigel Binns

1-2 December 2010

MIARE : Biology and Scope

MIARE (www.miare.org) Minimum Information About an RNAi Experiment

RNA interference (RNAi) natural post-transcriptional gene-silencing

High-throughput genome-wide gene knockdown screens small interfering RNA (siRNA) or expressed small hairpin RNA

(shRNA)

High content phenotypic screens (phenome)

MIARE : Implementation

Status of specification: transitioning from draft to mature guidelines

Tools: MIARE-Tab: simple Microsoft Excel-based data exchange format PubChem Deposition Template and guidance notes: deposit MIARE-compliant

RNAi screening data into PubChem (http://pubchem.ncbi.nlm.nih.gov)

Database support: NCBI/PubChem RNAi Deposition Gateway implements MIARE-compliance via a

flexible tag/value pair container

Controlled Vocabulary: Defines a number of reporting requirements contained in the MIARE reporting

guidelines

MIARE : Status and Support Project status:

PubChem RNAi deposition gateway is actively being developed

Contributors: Division of Pathway Medicine (www.ed.ac.uk/pathway-medicine)

Peter Ghazal, Graeme Grimes, Javier Santoyo-Lopez, Nigel Binns RNAi Global Initiative (www.rnaiglobal.org)

Amanda Birmingham, Queta Smith PubChem developers (http://pubchem.ncbi.nlm.nih.gov)

Yanli Wang, Steve Bryant

This work is/was supported by: INFOBIOMED (www.infobiomed.org) - EC-IST 2001-35024 eScience Data Information & Knowledge Transformation (www.edikt.org.uk) - SFC HR04019

Publications: Statistical methods for analysis of high-throughput RNA interference screens

Birmingham, A. et al Nat Methods 6 (2009) p569-75