Data

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## [http://bioassayontology.org/index.php?option=com_content&view=article&id=96&Itemid=137 BioAssay ontology]
 
## [http://bioassayontology.org/index.php?option=com_content&view=article&id=96&Itemid=137 BioAssay ontology]
 
### [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]
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##[http://www.nthanalytics.com/doc/Study%20Data%20Tabulation%20Model%20v1%202%20Draft%2020070710.pdf Study Data Tabulation model]
 
All identified by URIs
 
All identified by URIs
 
  
 
== Software ==
 
== Software ==
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#[http://symba.sourceforge.net/ SyMBA]
 
#[http://symba.sourceforge.net/ SyMBA]
 
#[http://www.sysmo-db.org/ SysMO-DB]  
 
#[http://www.sysmo-db.org/ SysMO-DB]  
#[http://www3.imperial.ac.uk/bioinfsupport/resources/data_management/xperimentr XperimentR]
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#[http://www3.imperial.ac.uk/bioinfsupport/resources/data_management/xperimentr XperimentR] : Built around ISA, has a notion of a Protocol and Application of a protocol to a Study
## Built around ISA, has a notion of a Protocol and Application of a protocol to a Study
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#[http://base.thep.lu.se/ BASE]
 
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== Standards ==
 
== Standards ==
  
 
#[http://biosharing.org/standards Biosharing.org]
 
#[http://biosharing.org/standards Biosharing.org]
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#[http://www.cdisc.org/ CDISC]
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 +
== Ontology repositories ==
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#EBI Ontology Lookup Service [http://www.ebi.ac.uk/ontology-lookup http://www.ebi.ac.uk/ontology-lookup]; publications: [http://dx.crossref.org/10.1186%2F1471-2105-7-97  doi:10.1186/1471-2105-7-97], [http://dx.crossref.org/10.1093/nar/gkn252 doi: 10.1093/nar/gkn252]
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## [http://www.ebi.ac.uk/efo/ Experimental Factor Ontology]  [http://bioportal.bioontology.org/ontologies/39885 EFO @ BioPortal]
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#NCBO BioPortal [http://bioportal.bioontology.org/ http://bioportal.bioontology.org/]; publications: [http://dx.crossref.org/10.1093/nar/gkp440 doi: 10.1093/nar/gkp440]

Latest revision as of 09:21, 21 October 2011

Data


Contents

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

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. Experimental Factor Ontology EFO @ BioPortal
  1. NCBO BioPortal http://bioportal.bioontology.org/; publications: doi: 10.1093/nar/gkp440
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