Data

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Datasets are considered to be generated by experiments (described by [[Study]]) and associated with [[Protocol|Protocols]] via [[Study#Assays|Assays]] container.
 
Datasets are considered to be generated by experiments (described by [[Study]]) and associated with [[Protocol|Protocols]] via [[Study#Assays|Assays]] container.
  
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TBD
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== Dataset format / examples ==
  
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# [[OpenTox_API_1.2_Dataset]] +  
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# [[OpenTox_API_1.2_Dataset]] +
 
# modified OT datasets to include BioEntities
 
# modified OT datasets to include BioEntities
 
# other types of datasets
 
# other types of datasets
 
## [[http://isatab.sourceforge.net/docs/ISA-TAB_release-candidate-1_v1.0_24nov08.pdf ISA-TAB]]
 
## [[http://isatab.sourceforge.net/docs/ISA-TAB_release-candidate-1_v1.0_24nov08.pdf ISA-TAB]]
 
### [http://isatab.sourceforge.net/isaconfig.html ISA Configurator]
 
### [http://isatab.sourceforge.net/isaconfig.html ISA Configurator]
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### [[https://github.com/ISA-tools/BioInvIndex BioInvestigationIndex web application]
 
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#### [http://bii.nwl.ac.uk/bioinvindex NERC Environmental Bioinformatics data center]
 
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#### [http://discovery.hsci.harvard.edu/bioinvindex/ Harvard Stem cell discovery engine]
 
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#### [http://www.ebi.ac.uk/bioinvindex/ EBI BioInvestigation Index]
 
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#### []
 
 
## TG-GATES .cel files
 
## TG-GATES .cel files
 
### [http://toxico.nibio.go.jp/open-tggates/compound_search/screen3/compound?compound_id=00001&design_name=HG-U133_Plus_2&organ_id=ORGA0010&test_type=in+vitro Acetaminophen]
 
### [http://toxico.nibio.go.jp/open-tggates/compound_search/screen3/compound?compound_id=00001&design_name=HG-U133_Plus_2&organ_id=ORGA0010&test_type=in+vitro Acetaminophen]
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### [http://www.bioassayontology.org/index.php?option=com_content&view=article&id=97&Itemid=140 Assay Annotation Template]
 
### [http://www.bioassayontology.org/index.php?option=com_content&view=article&id=97&Itemid=140 Assay Annotation Template]
 
All identified by URIs
 
All identified by URIs
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== Open source software ==
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# [https://github.com/ISA-tools/BioInvIndex BioInvestigationIndex web application]
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## [http://bii.nwl.ac.uk/bioinvindex NERC Environmental Bioinformatics data center]
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## [http://discovery.hsci.harvard.edu/bioinvindex/ Harvard Stem cell discovery engine]
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## [http://www.ebi.ac.uk/bioinvindex/ EBI BioInvestigation Index]
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#[http://simbioms.org SIMBioMS]

Revision as of 08:09, 20 October 2011

Data


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

All identified by URIs


Open source software

  1. BioInvestigationIndex web application
    1. NERC Environmental Bioinformatics data center
    2. Harvard Stem cell discovery engine
    3. EBI BioInvestigation Index
  2. SIMBioMS
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