Data

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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 ==
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== Ontology repositories ==
 
== Ontology repositories ==
  
#EBI Ontology Lookup Service [http://www.ebi.ac.uk/ontology-lookup http://www.ebi.ac.uk/ontology-lookup]
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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]
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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#NCBO BioPortal [http://bioportal.bioontology.org/ http://bioportal.bioontology.org/]
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Publications: [http://dx.crossref.org/10.1093/nar/gkp440 doi: 10.1093/nar/gkp440]
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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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