The source code for Numbat is available on Github.
Numbat is free software first developed by Benjamin Carlisle in 2014 for use by the STREAM research group1 in the Biomedical Ethics Unit at McGill University to facilitate systematic review work for the Animals, Humans and the Continuity of Evidence grant as well as the Signals, Safety and Success grant. This work was funded by the Canadian Institutes of Health Research (MOP 119574), and it is released as free and open-source under the GNU AGPL v 3.
It is named after the numbat, because numbats feed on termites by extracting them from their hiding places with very long and flexible tongues.
Numbat is a piece of software designed for managing the extraction of large volumes of data from primary sources among multiple users, and then reconciling the differences between them. It is designed for use in systematic review projects in an academic context.
The following are the intended uses of Numbat.
- Manage large databases of references ("large" here means: in the hundreds to thousands range; there's no built-in limit on Numbat, but your server may time out or something if you tell it to run a PHP script that takes too long)
- Different levels of extraction (e.g. title-and-abstract vs full extraction)
- Multiple extraction forms / codebooks
- Double, triple or n extractors, with an assignment manager
- Generate reference networks among the publications in the database
- Statistical analysis of results
- Calculating inter-rater reliability estimates (but it will export
extractions in a format that the
irrR package expects!) - Semantic analysis of papers to extract (you have to read the papers yourself)
- Magic
- No user lock-in as a philosophy for data in Numbat—data entered in Numbat should be easily imported and exported, so that users are never trapped
- Open formats
- Usability
- Expandability / modularity of software
- Ownership of one's own data
- Low barriers to entry
- Ease of back-up
- Google has a bad record for keeping private data private
- Google has an extremely bad habit of closing services regardless of whether users are still using them (remember Google Reader?)
- No good, built-in way to reconcile multiple extractions
- Built-in blinding from other extractors' work to minimise validity threats to your systematic review work
- Built-in assignment manager
- Google Forms do not accommodate certain data structures, like table data and citation networks
You may be able to install Numbat on setups different from what is described below, but the following is what it was designed for.
- Apache
- PHP
- MySQL
Copy the entire file to your web server, and navigate to the Numbat directory with your browser. You will need to know your MySQL server, username and password to complete the installation.
- Button to automate copying of all rows in table from all users to final during reconciliation
- New random references selector options for assignments
- Fix bug with table data entry
- Upload new references into an already-existing reference set
- Fixed bug where order of columns in data export sometimes doesn't match the order they appear in the extraction form
- Fixed bug where date selector would save empty fields as "0000-00-00" instead of NULL
- Removed unnecessary rows showing references without complete extractions from final table
- Implemented import/export of conditional display logic in extraction forms
- Implemented a new "tags" element for extractions and sub-extractions
- Removed Google Font, replaced with Atkinson Hyperlegible
- Fixed bug where deleting elements would fail to also delete their child conditional display triggers, resulting in unexpected behaviour
- Added IRR (inter-rater reliability, e.g. Cohen's kappa) export for
open text, single select and multi select elements to allow users to
export all extractions of a single element in a format that would be
expected by many of the functions in the
irrR package - Added drop-down selector for sorting extractions to be done on the "Do extractions" page by reference, form and assignment date (previously, extractions were sorted by assignment date only)
- Added
whenassignedandstatuscolumns to assignment export - Added new text area sub-extraction element
- Added new reference data sub-extraction element
- Added tool for uploading files, e.g. images for reference
- Fixed bug that prevents compatibility with PHP 8+
- Fixed bug where a fresh Numbat installation needs to have the
db-migrations.phprun in order to function properly - Removed default
notescolumn from extraction form (it was never used and it was causing problems) - Improved CSV import
- New screening tool
To migrate from an earlier version of Numbat, run db-migrations.php
while logged in as an administrator.
Here is a BibTeX entry for Numbat:
@Manual{numbat-carlisle,
Title = {Numbat {S}ystematic {R}eview {M}anager},
Author = {Carlisle, Benjamin Gregory},
Organization = {The Grey Literature},
Address = {Berlin, Germany},
url = {https://numbat.bgcarlisle.com},
year = 2014
}
You may also cite this resource as: (Numbat, RRID:SCR_019207).
If you use my software to complete a systematic review and you found it useful, I would take it as a kindness if you cited it.
Best,
Benjamin Gregory Carlisle PhD