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Question: Should I use the Annotations tab or MAGE-TAB annotation Files to annotate my experiment?
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Topic: caArray Usage
Release: Up to caArray 2.2
Date entered: 02/12/2009
Question
Annotation Tab vs. MAGE-TAB Annotation Files in caArray
Answer
caArray offers two options to annotate the experiment.
- You can annotate the experiment
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- automatically (recommended) by uploading/Importing MAGE-TAB formatted annotation files (caArray 007 - MAGE-TAB Files).
- You can annotate the experiment manually by entering data using the Annotations tab, as described in the caArray User's Guide.
caArray007) or manually entering data via the annotation user interface (Annotation Tab). Refer to the caArray User Guide (page 34). This knowledge base entry aims to clarify the difference and helps help you to find an efficient way to annotate your experiment.
Differences between
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Annotations Tab and MAGE-TAB annotation files
The Annotation Annotations tab opens with seven subtabs for entering annotation data for the experiment you are creating: Experimental Design, Experiment Factors, Source, Extracts, Labeled Extract and Hybridizations, as shown in the illustration. Detailed definitions and explanations for each subtab can be found in the Annotations tabs section, of the caArray User Guide(page 34)'s Guide..
Subtabs of the Annotation Tab
A MAGE-TAB file (caArray007) is a simple tab-delimited, spreadsheet-based file. IDF and SDRF are the related MAGE-TAB annotation files.
The table below compares using Annotation Tab and MAGE-TAB annotation files.
Features Task | Annotation Annotations Tab | MAGE-TAB File |
|---|---|---|
Entering Annotation Annotations Data | Click on "Annotation Tab" to annotation user interfacethe Annotations Tab in caArray. Enter annotation annotations field by field. | Upload pre-created Tabtab-delimited Data MAGE-TAB files (IDF and SDRF filesformat). Annotation data need needs to be validated and imported together with the array data files referred referenced in SDRF filesfile(s). |
Modifying Annotation Data | Flexible. Your unpublished annotation data can be modified on the annotation user interface in caArray | Flexible with some limitations. Biomaterial related characteristics/attributes can be modified or added via annotation user interface. |
Auto Generated Annotation | During data import, caArray offers options of associating array data with the existing annotations or auto-creating new annotations for a Source - Sample - Extract - Labeled Extract - Hybridization chain based on the data imported. You may can enter the rest of the annotations on the annotation interface after the auto reactionchain has been created. | The Annotation information in IDF & and SDRF files will be is automatically assigned to each annotation field during the data import. If a biomaterial node is missing in the Source - Sample - Extract - Labeled Extract - Hybridization chain, appropriate intermediate nodes are automatically generated to complete the chain. |
Portability | Annotation can not Annotations cannot be downloaded. Only the data file associated with annotation annotations can be downloaded. | Annotation files can be downloaded. However, the annotation annotations added or modified via the Annotation interface will not be downloaded. |
Re-usability | Vocabulary entered can be reused by the other experiments. But annotations need to , but the annotations must be selected or entered in each new experiment. | Annotation files can be downloaded and reused for different experiments with the necessary modifications, such as the name of the data files. |
Best Usage | Experiments with few sources or samples. Useful for the experiments which can be described with the generic annotation data in caArray. | Complex experiments with large set of data, or experiments with many specific characteristics. |
Summary
In summary, the annotation user interface (annotation Annotation tab) offers a straight forward and quick way to enter annotation data. MAGE-TAB annotation files allow the user to create complex annotations and keep annotation editing and maintenance manageable at the same time. MAGE-TAB files allow users to enter the annotations that are not displayed as generically available and editable fields in the annotation user interface. These customized annotation data entered via MAGE-TAB files will be are visible but un-editable on caArray. Furthermore, MAGE-TAB files are portable and reusable, which can save a lot of time or thus saving time and effort, especially when a large set of samples are collected from the same source.
For more information about about MAGE-TAB related files, refer to caArray007 caArray 007 - MAGE-TAB Files.
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