UI Description

Main Screen

_images/mainscreen.png

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

_images/card.png

Once you complete the set up of a query (see Quick start), 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 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 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 Status:, indicating one of three states the query can be in: EXPANDED, FILTERED1, and FILTERED2

  • the string 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

_images/qsettings.png
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

_images/filtering2.png
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

_images/annotating.png
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.