By Kihara Absolomon
Table of Contents
Data and sample collection using the Open Data Kit with sample processing in the field
Points to be strictly followed
A smart phone or tablet running on Android will suffice. The Open Data Kit (ODK) suite of tools will be used for sample collection. ODK only runs on the Android OS.
The external Bluetooth dongle is only used when conducting a rapid collection of samples from animals, where even a 1 second delay can cumulatively cause delays in the sampling exercise. While the smart phones or tablets have inbuilt GPS which is good for general use it is not suitable for rapid data collection. The built in GPS of the smart phones and tablets takes about 2-3 minutes to capture GPS coordinates and this will cause delay in the sampling process.
The barcode scanners are necessary for scanning the barcodes on the vacutainers and on the cryo vials.
Designing the form is usually done in the traditional way where the team decides which kind of data needs to be collected from the field. In many instances, this is usually household level data and animal data. In addition to all the data that the scientists want to collect, a GPS coordinate must be captured at every point possible. Once the form has been encoded, it must be converted to an excel spreadsheet. This is a fairly technical process though very straightforward. Using the guidelines which can be found at: http://opendatakit.org/help/form-design/xlsform/ users can be able to transform the designed form into an excel spreadsheet.
On uploading the excel spreadsheet to the server, the systems will verify the correctness of the spreadsheet, convert it to an xml format if all is ok and then automatically upload it to the ODK server, ready to be used in a sampling exercise.
The mock exercise is extremely important especially for first time users. It presents an opportunity to do a mock field exercise and test the systems in a near real field situation. It also helps users know what to expect at the end of the sampling exercise.
Different sample types have different label prefixes, eg. Prefix BDT for vacutainers with EDTA, BSR for plain tube vacutainers, WBL for whole blood in cryo vials, SER for serum in cryo vials, etc. All the barcodes generated are unique and are tracked by the label generation software. All vacutainers and cryo vials will bear unique random labels.
This allows room for a random vacutainer to be associated to a randomly sampled animal during sampling and a random cryo vial to be associated to a random vacutainer during aliquoting.
For each aliquot scanned after a parent sample, ukasimu interprets that that aliquot belongs to the earlier scanned parent sample.
In addition ukasimu determines the name of the box and the position to store the aliquot in. This is based on the box label format entered in the Sort Samples Home Page. This information can be edited before scanning the next sample. The action of scanning the next aliquot/parent sample will save the previous aliquot. Confirm the determined box name before scanning the next aliquots.
While saving the aliquots ukasimu ensures that:
The parent format, is the format of the parent label. eg. Whole Blood parent samples in vacutainers will have a barcode like BDT007852 or BDT078514. The barcode is composed of a prefix of 3 letters “BDT” and a suffix of 6 digits “007852” or “078514”. All vacutainers labels will follow this form of coding a set number of letters comprising the prefix and a set number of digits comprising the suffix, in this case BDT is the prefix followed by 6 digits as the suffix. The parent format is the prefix followed by a space and then the number of suffix, ie. “BDT 6”, meaning a prefix of BDT followed by 6 digits.
The aliquot format and box label format follows the same principle as the parent sample format above.
Sample and Data Collection Protocol Page