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h1. 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

h2. Answer

caArray offers two options to annotate the experiment. 
* You can annotate the experiment 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|https://wiki.nci.nih.gov/x/Nho9Ag#5-CreatingandManagingExperiments-AnnotationsTab], as described in the [caArray User's Guide|https://wiki.nci.nih.gov/x/LBo9Ag]. 

This knowledge base entry aims to clarify the difference and help you find an efficient way to annotate your experiment. 

h3. Differences between Annotations Tab and MAGE-TAB annotation files

The 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|https://wiki.nci.nih.gov/x/Nho9Ag#5-CreatingandManagingExperiments-AnnotationsTab], of the caArray User's Guide.. 

*Subtabs of the Annotation Tab*
!annotation-tab.JPG|vspace=4, align=center,alt="Screenshot showing Subtabs of the Annotations Tab"!

A [MAGE-TAB file|https://wiki.nci.nih.gov/x/zZCNAg] 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. 


|| Task || Annotations Tab || MAGE-TAB File ||
| Entering Annotations Data | Click on the *Annotations Tab* in caArray. Enter annotations field by field. | Upload pre-created tab-delimited MAGE-TAB files (IDF and SDRF format). Annotation data needs to be validated and imported together with the array data files referenced in SDRF file(s). |
| Modifying Annotation Data | Flexible. Your unpublished annotation data can be modified the annotation user interface in caArray | Flexible with some limitations. Biomaterial related characteristics/attributes can be modified or added via annotation user interface.
Experimental factor, protocol, design, or publication related attributes cannot be changed. They become read-only after files are imported. 
Additional annotation data added through annotation interface cannot be downloaded (see below). |
| 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 can enter the rest of the annotations on the annotation interface after the chain has been created. | The Annotation information in IDF and SDRF files is automatically assigned to each annotation field during 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 | Annotations cannot be downloaded. Only the data file associated with annotations can be downloaded. | Annotation files can be downloaded. However, annotations added or modified via the Annotation interface will not be downloaded. |
| Re-usability | Vocabulary entered can be reused other experiments, but the annotations must be selected or entered in each new experiment. | Annotation files can be downloaded and reused for different experiments with 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. |

h3. Summary

In summary, the annotation user interface (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 are visible but un-editable on caArray. Furthermore, MAGE-TAB files are portable and reusable, 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 [caArray 007 - MAGE-TAB Files].

h2. Have a comment?

Please leave your comment in the [caArray End User Forum|https://cabig-kc.nci.nih.gov/Molecular/forums/viewtopic.php?f=6&t=577].

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