Table 1.
A sampling of (some of the) standards related to microarray-based transcriptomics, generated by non-experts for evaluation of relevance to a project involving microarray-based transcriptomics data
| Standard | Type | Description |
|---|---|---|
| MIAME | Reporting guideline | Minimum Information About a Microarray Experiment Specifies six components that must be included to describe a microarray experiment, for example, raw and processed data, experimental design, sample annotation, protocols. MIAME does not specify how these components must be represented, for example, in any given format, or using any given terminology |
| ISA-TAB | Exchange format | Generic format for experimental representations; conversion tools to MAGE-Tab, MIMiML and other formats exist |
| MAGE-TAB | Exchange format | MicroArray and Gene Expression-Tabular Simple tab-delimited, spreadsheet-based format. Used by ArrayExpress |
| MAGE-ML | Exchange format | MicroArray and Gene Expression-Markup Language. No longer supported |
| SOFT | Exchange format | Simple Omnibus Format in Text. Line-based, plain text format designed for rapid batch submission of data. Used by GEO |
| MIMiML | Exchange format | MIAME Notation in Markup Language. Optimized for microarray and other high-throughput molecular abundance data Used by GEO |
| GO | Terminology artifact | Gene Ontology. Controlled vocabulary for annotation of gene function and cellular location. Part of the OBO Foundry |
| EFO | Terminology artifact | Experimental Factor Ontology. Provides a systematic description of many experimental variables. Used by ArrayExpress |
| OBI | Terminology artifact | Broader scope for experimental representations. Part of the OBO Foundry |
| MGED Ontology | Terminology artifact | Integrated in OBI |
| MAGE-OM | Object model | MicroArray and Gene Expression—Object Model. The object model from which MAGE-ML was derived |
| FuGE | Object model | Generic object model for functional genomics |
| SEND | Exchange format | Standard for Exchange of Nonclinical Data—an implementation of the CDISC (Clinical Data Interchange Standards Consortium) SDTM (Standard Data Tabulation Model) |
| GEML | Exchange format | These three standards have since been deprecated and/or replaced by other standards, but that progression may not always be clear to novice users |
| FUGO | Terminology artifact | |
| MAML | Exchange format | |