Web Links

AGRON-OMICS

AGRON-OMICS Wiki: Discussion pages for AGRON-OMICS topics (requires registration)

AGRON-OMICS Molecular Scaffold: Database for gene-centered queries (AGRON-OMICS members only)

BIO-ONTOLOGIES

IFOMIS: Institute for Formal Ontology and Medical Information Science

OBO: Open Biomedical Ontology project

OLS: Ontology Look-up Service at EBI

Web-ontology  explorer: BRENDA website

GO: Gene Ontology

PO: Plant Ontology consortium (NEW release available Sept 2007)

CCO: Cell Cycle Ontology

SO: Sequence Ontology

MeSH: Medical Subjects Headings

BIOLOGICAL PATHWAYS

Reactome: curated database of biological processes

Arabidopsis Reactome: curated database of Arabidopsis biological processes

KEGG: Kyoto Encyclopedia of Genes and Genomes – pathway database

AraCyc: Arabidopsis pathways and metabolic maps database at TAIR

Wiki Pathways: Open platform dedicated to the curation of biological pathways

SOFTWARE AND DATABASES

Data analysis

Arabidopsis eFP browser: visualization tool for gene expression and other data types

BioModels: data resource at EBI that allows biologists to store, search and retrieve published mathematical models of biological interests

Genevestigator: software for microarray experiments mining: requires subscription

MapMan: software for the mapping of plant gene expression onto biological pathways

PageMan: software for quick overview of multi-parallel experiments

At TAX: expression data for Arabidopsis TILING arrays data

Bio-ontologies

OBO-Edit: software for viewing and editing bio-ontologies

Protégé: ontology editor

COBrA: an ontology browser and editor for anatomy allowing mapping between ontologies

Phenote: software toolkit for the annotation of phenotypes

Data Integration and Systems Biology

AtPID: Arabidopsis thaliana protein interaction database

Biomart:  a query-oriented data management system developed jointly by the EBI and Cold Spring Harbor Laboratory

CellDesigner: a modeling tool of biochemical networks with graphical user interface

Cytoscape: an open source bioinformatics software platform for visualizing molecular interaction

networks and integrating these interactions with gene expression profiles and other state data

BioGRID: General Repository for Interaction Datasets

BioMoby: system for inter-operability between biological data hosts and analytical services

Taverna: software to create workflows and facilitate data integration in biological sciences

VirtualPlant: integration of genomic data and provides visualization and analysis tools for rapid and efficient exploration of genomic data.

Image Analysis

Image J: image processing analysis toolbox software in Java

STANDARDS

MIAME: Minimum Information About a Microarray Experiment

MIAPE: Minimum Information About a Proteomics Experiment

MIBBI: Minimum Information for Biological and Biomedical Investigations

MGED: Microarray Gene Expression Data Society

EMERALD: EU project on Standards and Standardization of Microarray Technology and Data Analysis

SBML: Systems Biology Markup Language, computer-readable format for representing models of biochemical reaction networks


TEXT MINING

Textpresso for Arabidopsis: Online text mining tool based on a literature corpus of over 15000 full text papers

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