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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


  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 : Built around ISA, has a notion of a Protocol and Application of a protocol to a Study
  6. BASE


  2. CDISC

Ontology repositories

  1. EBI Ontology Lookup Service; publications: doi:10.1186/1471-2105-7-97, doi: 10.1093/nar/gkn252
    1. Experimental Factor Ontology EFO @ BioPortal
  1. NCBO BioPortal; publications: doi: 10.1093/nar/gkp440
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