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ODIN-pharmgkb: basic instructions

1)  Initial access

When a user first access the ODIN-pharmgkb, he/she will be asked to enter an email address, which is then used as an identifier of the user. All the actions performed by the user (e.g. editing a term) will be logged and associated with his/her identifier (this could allow for example undoing of selected actions). In the current version it is not strictly necessary to enter an email address: any string will be accepted. Notice also that in this demo version the actions of the curator have no permanent effect.

2) How to load an abstract

The next step is to load an abstract. This can be done
either by using "Select Sample File" in the "File" menu, or by entering a PubMed ID (using "Open PubMed abstract" in the "File" menu).  If the abstract has already been processed by ODIN, it will be loaded immediately. A previously unseen abstract will be processed "on the fly" and then presented to the user (this process can take a few seconds - please be patient).

3) The three panels

The left-hand-side panel ("Term Inspector") is used for inspection and modification of a single annotation by a curator. The central panel shows the annotated document. The right-hand-side panel ("Annotation") contains a number of tabs which can be used to inspect the entities and interactions detected in the document. Notice that entities are always referred to by their PharmGKB identifier.

4) Inspecting Entities

The right-hand-side panel contains two tabs: "concepts" and "interactions". The former is used to inspect the annotated entities. The latter shows the candidate interactions that the system has detected in the abstract. Select the "Concepts" tab in the right-hand-side panel. Each entity that the system has detected in the abstract is listed using its PharmGKB identifier. If the corresponding tickbox is selected, the entity is highlighted in the abstract.

5) Inspecting Candidate Interactions

Select the "Interactions" tab in the right-hand-side panel. Candidate Interactions are listed in the order of probability (most likely first). Checking the tickbox will result in a red frame being added to the two entities which participate in the interaction. Notice that for this demo we have used a rather crude method of computing candidate interactions, which however has the advantage of achieving the maximum possible recall using abstracts only (60%). We have done experiments with more precise approaches, which we will integrate into the demo at a later stage.

6) Modifying a term

Select (with a mouse click) a term in the central panel: the term will be highlighted in red and all the related information will be displayed in the term inspector (right panel), where it can be modified by the curator. When the "save" button on top of the panel is pressed, this information is stored within the document. When the document is saved (by selecting File->Save) the modified document is sent back to the server and can be accessed again for later inspection. This could be used to pause a curation session and resume it later. Notice that in the demo version the "Save" menu option is disabled.

Important notice: ODIN should work on any recent browser,
however we recommend using Firefox.

Temporary notice: the help menus, as well as the pdf documentation accessible from the demonstrator, are currently out of date (they refer to the version of ODIN which was used for the BioCreative III interactive curation task).