UI Description ============== Main Screen ----------- .. image:: images/mainscreen.png :width: 600 Permanently available components, all specific to the main screen: - Rail on the left side, containing: - Info button - Settings button, see below - Exit button - New Query button, see below - Top bar, with Sorting controls - List space (empty after install) containing Query cards, see below Settings ^^^^^^^^ The Settings button opens the General Settings dialog. Settings consist of ``String``: ``String`` pairs that are saved in the installation directory as JSON file. - ``path-to-queries``: absolute path of the directory where your queries will be saved and, on start up, read from. Use this to organise if you have a lot of queries, e.g. create a new directory and change this setting to it, so you can archive the old one. Or switch back and forth. - ``directory-prefix``: regarding the single query directories below the above mentioned directory, they get a name consisting of prefix and query name. Install default is ``Query-``. - ``path-to-YDF``: on Linux, if you want to use a ML classifier, set this to the path of your YDF installation - ``path-to-classifiers``: as per above, the path under which there are ready trained ML classifiers; LitBall ships the ``virus-EXP`` model - ``query-sort-type``: permanent sort setting that is changed by clicking on the sorting controls on the main screen - ``paper-sort-type``: permanent sort setting that is changed by clicking on the sorting controls on the two paper list screens New Query ^^^^^^^^^ This button asks you for - the name of the to-be-created query. This should be short, optimally an abbreviation - one or more DOIs of the core papers, with which the first expansion is performed. Please input the part starting with ``10.`` which all DOIs start with Query cards ^^^^^^^^^^^ .. image:: images/card.png :width: 800 Once you complete the set up of a query (see :doc:`quick`), query cards are visible in the List space of the main screen. They contain (from left): - a Settings button for specific query settings, see below - the query name, framed and emphasized - the string :literal:`Accepted:\ `, indicating the number of papers you chose as core articles, plus all others you accepted later in the Supervised filtering steps. Set in bold if the last round of expansion/filtering didn't get any new papers that you accepted - the string :literal:`Rejected:\ `, indicating the number of papers that were rejected during both filtering steps, i.e. those rejected because their title/abstract/TLDR didn't contain one of the mandatory keywords; their title contained one of the forbidden keywords; or they were manually rejected by you - the string :literal:`Status:\ `, indicating one of three states the query can be in: ``EXPANDED``, ``FILTERED1``, and ``FILTERED2`` - the string :literal:`Last expansion:\ `, indicating the last time an expansion was performed - the Action button, showing one of three actions: ``Start expansion``, ``Automatic filtering``, or ``Supervised filtering`` - the Annotate button, which leads you to a paper list screen, showing details of all accepted papers, and where you can put these articles into further categories, and export them Query Settings ^^^^^^^^^^^^^^ .. image:: images/qsettings.png :width: 600 In the query-specific settings dialog, the following can be set: - Mandatory keywords. In the automatic filtering step, words from title/abstract/TLDR of articles are matched against these keywords. You must set at least one keyword before expansion - (optional) Forbidden keywords. If the article title contains one of these, the paper gets rejected during automatic filtering - (optional) Classifier model name. If set, the Apply Classifier button becomes available during Supervised filtering - (optional) Annotation classes. Comma-separated names of classes that can be set for each paper in the annotation screen, affecting the export of data Supervised Filtering Screen --------------------------- .. image:: images/filtering2.png :width: 600 This screen shows - a Rail containing - Save Button. Saves current list with Rejected/Accepted settings in query directory - Finish Button. Finalizes the supervised filtering step. Rejected papers will no longer be considered - Main Button. Saves and returns to main screen. You come back by clicking ``Supervised filtering`` again - Exit button - Top bar, with Sorting controls - List space showing titles of all papers that need decision whether to accept them; use the radio buttons to the right. Clicking on the title opens a dialog showing details. On the left of the title, the web page symbol opens in your browser the PubMed or Google Scholar search results for this title. Annotating Screen ----------------- .. image:: images/annotating.png :width: 600 This screen shows - a Rail containing - Save Button. Saves current list with Annotated settings in query directory - Export Button. Writes CSV into query directory - Main Button. Saves and returns to main screen. You come back by clicking ``Annotate accepted`` again - Exit button - Top bar, with Sorting controls - List space showing titles of all papers that optionally need association with categories; after setting annotation classes in query settings, use the flag boxes to the right. Clicking on the title opens a dialog showing details. On the left of the title, the web page symbol opens in your browser the Google Scholar search results for this title.