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Cocoa Compact cover annotator for biological noun phrases

Using Cocoa with Brat

Brat is an online annotation tool that has excellent editing and viewing capabilities. Many corpora are available in a Brat-compatible ann/A1 standoff format. Brat allows integration of automatic annotation tools to pre-annotate the current document (see the section "Integration with automatic annotation tools" in Brat's features page)

Cocoa can return its output in a format that is compatible with Brat. To access Cocoa from Brat, we only need to add Cocoa to the list of annotators that Brat knows about. This is done in the tools configuration file of Brat, namely tools.conf (see the tool configuration page of Brat) This file is present in the Brat installation directory. Add the following line in this tools.conf file, just below the [annotators] section (similar to the Examples already there):

Cocoa_NER      tool:Cocoa, model:NER, <URL>:http://npjoint.com/Cocoa/bratapi/
That should be all. Cocoa will now be displayed in the list of available tools shown upon pressing the "Data" button in the Brat menu. Press the "NER" button next to "Cocoa" to get Brat to retrieve and display Cocoa annotations for the current document.

Note

Brat fills the data portion of the POST request with the input document. and does not push any parameters. Otherwise, the access mode for Brat is a specialization of the general Cocoa WebAPI call with the following defaults: the 'outputFormat' parameter is set to the value 'a1j', the formula mode is set to 'noform' and acronyms are set to null.

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