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    The annotator is where you will view and edit annotations. All phenotypes are categorized by systems, such as “abnormality of the nervous system” and “abnormality of the cardiovascular system”. Importantly, each exercise may have multiple diseases to annotate. Use the dropdown menu to select the disease that you would like to annotate.

    Editing annotations

    To add a phenotype, begin typing the phenotype name in the Add a phenotype input box on the bottom bar. Phenotate will attempt to autocomplete the phenotype when you stop typing. You can view the definition of the phenotype (if available) by hovering over a phenotype name. Click on the phenotype you would like to add. Proceed to set attributes as needed.

    The attributes you can change are:

    Observed: Select Y if the phenotype is observed in certain or all patients with this disease. Otherwise, click N if none of the patients with this disease present this phenotype. Note that phenotypes irrelevant for the disease should not be listed.
    Frequency: Select the most accurate percentage of patients with this disease who will present this phenotype.
    Onset: Select the most accurate age at which patients with this disease will present this phenotype.
    Details: Here, you can specify additional details, i.e. pace of progression, severity, temporal pattern, spatial pattern, and laterality. If you have selected antenatal or adult onset, you can also select a more specific age of onset, such as fetal, middle age, etc.

    Note: It is up to the professor whether or not he/she will grade the details. In any case, if you are sure of the details, it is better to provide them.

    You can also remove irrelevant phenotypes.

    On the right-hand pane, you can view the list of references. You can add references using the Add a reference input box on the bottom bar. As with phenotypes, Phenotate will attempt to autocomplete the title of the article you are adding. You can also enter the authors’ names or PubMed ID. Hover over an article’s title in the autocomplete list to view its lead author and year published. Once added, hover over the article’s lead author and year published in the references list to view its title and PubMed ID. Clicking on the title will let you view the article in PubMed.

    To cite a phenotype, drag and drop the relavant reference onto the phenotype (works in Internet Explorer, Chrome, and Firefox; does not work in Safari). You can also add a citation by hovering over the phenotype and clicking on the plus sign on a paper icon, then entering the reference number. Clicking on a reference number on a paper icon will remove the citation.

    Finally, click Submit to submit the exercise. Submitted annotations cannot be modified later. To successfully submit an exercise, all references must be used. Furthermore, you must cite all phenotypes and annotate every disease in the exercise.

    Note: You must submit completed exercises for them to be graded. If you do not submit your responses, your professor will not be able to view them.

    Note: There is no save button. Your annotation is saved automatically every time you edit it. So, do not feel pressured to complete your annotation in one sitting.

    Viewing annotations

    Each phenotype is preceded with a widget indicating, from left to right, the stated frequency and age of onset. The frequency is illustrated with a pie graph indicating the percentage. A line indicates that the author is unsure of the frequency. The age of onset is indicated using a three-letter abbreviation (e.g. JUV for juvenile onset). A line indicates that the author is unsure of the age of onset. The frequency and age of onset can be clarified by hovering over the widget.

    Next, the phenotype name is written in full. If available, a definition of the phenotype can be viewed by hovering over the phenotype name. If the phenotype name is blue, you can click on it for further details, such as spatial pattern and severity.

    References are listed on the right-hand pane. Hovering over a reference will reveal the title of the article. Clicking on the title will allow you to view the article in PubMed. The number in superscript next to phenotype name indicates the cited article, as numbered on the paper icon.

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