Data
From ToxBank API Wiki
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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. | ||
− | + | == Dataset format / examples == | |
− | # [[OpenTox_API_1.2_Dataset]] + | + | # [[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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## 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 == | ||
+ | # [https://github.com/ISA-tools/BioInvIndex BioInvestigationIndex web application] | ||
+ | ## [http://bii.nwl.ac.uk/bioinvindex NERC Environmental Bioinformatics data center] | ||
+ | ## [http://discovery.hsci.harvard.edu/bioinvindex/ Harvard Stem cell discovery engine] | ||
+ | ## [http://www.ebi.ac.uk/bioinvindex/ EBI BioInvestigation Index] | ||
+ | #[http://simbioms.org SIMBioMS] |
Revision as of 08:09, 20 October 2011
Data |
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Datasets
Datasets are considered to be generated by experiments (described by Study) and associated with Protocols via Assays container.
Dataset format / examples
- OpenTox_API_1.2_Dataset +
- modified OT datasets to include BioEntities
- other types of datasets
- [ISA-TAB]
- TG-GATES .cel files
- BioAssay ontology
All identified by URIs