NOTES

Please notice that OntoGene/ODIN is currently being revised for the BioCreative 2015 IAT task. Therefore you might experience occasional problems or malfunctions. Please bear with us.

Update June 2015: We have added a set of short screencast videos which describe how to use ODIN.

Comments and suggestions

Reports of problems and suggestions for improvements are extremely welcome! Please contact us at odin@ontogene.org.

Documentation

Please also notice that documentation within the help menus might not be totally accurate or up-to-date. The most up-to-date documentation can be found by following the link on the bottom left corner of the ODIN interface ("Documentation as PDF").

Supported browsers

ODIN has been optimized for firefox, however it should work also on other browsers. We recommend the following browsers (in order of preference):

• 1. Firefox
• 2. Safari
• 3. Chrome (some bugs still unresolved)

Known bugs

Occasionally when the user asks ODIN to process a novel pubmed id (i.e. not already previously processed), the interface will hang up without delivering any result. In this case, simply try to process AGAIN the same pubmed id, and you should get the expected results

In chrome the color-coded underlying of terms (which should depend on the term type), does not seem to work correctly

Usage

This interface allows the reviewing and curation of term-annotated XML documents.

File Menu

• Reload: reloads the current document.
• Open Pubmed Abstract: prompts the user to select a Pubmedcentral abstract number.
• Save: stores back in the server the current document as modified by the curator.
• Show XML: opens the formular containing the raw XML of the current document for copy and paste.
• Select Sample File: offers the user a pop-up menu of a selection of Pubmedcentral file numbers
• Set Curator Identifier: allows to modify the current email address (which is used as an identifier for the curator)
• Show Logged Actions: displays a log of the user interactions for the current session

View Menu

Once a document is loaded, the corresponding annotations can be inspected in the Annotation panel on the right side of ODIN. There are several types of annotations which can be inspected within this panel: the options in the 'View' menu allow the user to toggle which information should be visualized (concepts, interactions, terms, and others depending on the specific application).

• Show Term Table: Shows the individual occurrences of each term as they appear in the document and the concept(s) to which they link. Click a table row to show the document occurrence.
• Show Concept Table: Show the entities detected in the document, i.e. if several term occurrences correspond to the same entity, they will be shown only once in this table. Concepts are linked to their occurrences in the document: selecting a concept results in highlighting all the occurrences of associated terms in the document.
• Show Interaction Table: Shows the interactions in the text, with confidence score, and the types of concepts of the two participating entitities.
• Show Organisms Table: Organisms and their probability in the current document are shown. The annotator can e.g. delete all false positives that arise from a wrong organism. (Not available in all versions of ODIN)

Mode Menu

Currently two options are available: single term mode and repeated term mode.

• In single term mode, single terms are displayed and curated in the term inspector panel on mouse click. New terms are created by mouse clicks on adjacent words.
• In repeated term mode, every term of the term can be mass edited.