Implementation

Implementation details of projects using OBI

• ISA infrastructure - http://isatab.sourceforge.net

1. ISAcreator and ISAconfigurator

 - guiding users to use OBI (and other ontologies) in the annotation of multi-assays studies

2. BioInvestigation, a public ISA-based repository instance

 - using OBI in the annotation of multi-assays studies

(Contact Person: Philippe Rocca-Serra and Susanna-Assunta Sansone)

• Eagle-i - http://www.eagle-i.org/home

(Contact Person: Melissa Haendel, Carlo Torniai)

 - instruments
 - services

• Neuroscience Information Framework (NIF) - http://nif.nih.gov/

(Contact Person: Fahim Imam)

 - Developed based on OBI (old version)
 - Data transformation

• Biomedical Informatics Research Network (BIRN) - http://www.birncommunity.org/

(Contact Person: Jessica Turner)

 - data scale types
 - independent/dependent variables 
 - analyses

• The Immune Epitope Database (IEDB) - http://www.immuneepitope.org/

(Contact Person: Bjoern Peters)

 -assay

• Biomedical Resource Ontology (BRO) - http://bioportal.bioontology.org/ontologies/39002

(Contact Person: Trish Whetzel)

 - instruments

• Vaccine Investigation and OnLine Information Network (VIOLIN) - http://www.violinet.org/index.php

(Contact Person: Oliver He, Zuoshuang "Allen" Xiang)

 - independent/dependent variables, statistical analysis (ANOVA)

• ArrayExpress and other microarray experiments database - http://www.ebi.ac.uk/microarray-as/ae/

(Contact Person: Helen Parkinson, James Malone, Jie Zheng, Chris Stoekert)

 - mapping the MGED ontology to OBI
 - using OBI in the annotation of microarray experiments

Comments and responses on NBT paper
http://docs.google.com/Doc?docid=0AaEXoAK_iKrtZGhnbXQ1azZfMjE0ZnhjeDlyY2I&hl=en&pli=1