Revision as of 14:32, 20 October 2011

Datasets

Datasets are considered to be generated by experiments (described by Study) and associated with Protocols via Assays container.

Dataset format / examples

1. OpenTox_API_1.2_Dataset +
2. modified OT datasets to include BioEntities
3. other types of datasets
   1. [ISA-TAB]
      1. ISA Configurator
   2. TG-GATES .cel files
      1. Acetaminophen
      2. Amiodarone
      3. Chlorpromazine
   3. BioAssay ontology
      1. Assay Annotation Template
   4. Study Data Tabulation model

All identified by URIs

Software

1. BioInvestigationIndex web application
   1. NERC Environmental Bioinformatics data center
   2. Harvard Stem cell discovery engine
   3. EBI BioInvestigation Index
2. SIMBioMS
3. SyMBA
4. SysMO-DB
5. XperimentR
   1. Built around ISA, has a notion of a Protocol and Application of a protocol to a Study

Standards

1. Biosharing.org
2. CDISC

Ontology repositories

1. EBI Ontology Lookup Service http://www.ebi.ac.uk/ontology-lookup; publications: doi:10.1186/1471-2105-7-97, doi: 10.1093/nar/gkn252

1. NCBO BioPortal http://bioportal.bioontology.org/; publications: doi: 10.1093/nar/gkp440