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. | ||
− | + | == 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://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] | ||
+ | ##[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 == | ||
+ | # [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] | ||
+ | #[http://symba.sourceforge.net/ SyMBA] | ||
+ | #[http://www.sysmo-db.org/ SysMO-DB] | ||
+ | #[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 | ||
+ | #[http://base.thep.lu.se/ BASE] | ||
+ | |||
+ | == Standards == | ||
+ | |||
+ | #[http://biosharing.org/standards Biosharing.org] | ||
+ | #[http://www.cdisc.org/ CDISC] | ||
+ | |||
+ | == Ontology repositories == | ||
+ | |||
+ | #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] | ||
+ | ## [http://www.ebi.ac.uk/efo/ Experimental Factor Ontology] [http://bioportal.bioontology.org/ontologies/39885 EFO @ BioPortal] | ||
+ | |||
+ | #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 |
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Contents |
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
All identified by URIs
Software
- BioInvestigationIndex web application
- SIMBioMS
- SyMBA
- SysMO-DB
- XperimentR : Built around ISA, has a notion of a Protocol and Application of a protocol to a Study
- BASE
Standards
Ontology repositories
- EBI Ontology Lookup Service http://www.ebi.ac.uk/ontology-lookup; publications: doi:10.1186/1471-2105-7-97, doi: 10.1093/nar/gkn252
- NCBO BioPortal http://bioportal.bioontology.org/; publications: doi: 10.1093/nar/gkp440