Introduction

This interface allows the reviewing and curation of term-annotated XML documents. Terms may be highlighted through the View Menu.

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 Email Address" 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

The annotation tables (which appear in the right-hand side panel) can be toggled. Tick a term or all terms to highlight them. Underlining of recognized terms is always enabled. If a table a$ Supported term types are currently:

• 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.
• 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: Gene/Protein Identifiers ('concepts'), their organism, and their frequency and salience score (if available) are displayed. It also shows the mapping of a concept to the term in the text and the term type (gene [blue], protein [green], disease [yellow]).
• Show Interaction Table: Shows the interactions in the text, with confidence score, and the types of concepts of the two participating entitities.

Each annotation table has its own help button.

Mode Menu

• In 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 same ontological class can be mass edited.

Further items on the Help Menu explain how to browse and how to annotate documents.