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Manual for spreadsheet data submission

This manual provides guidance for the submission of laboratory data to iSIKHNAS using and Excel spreadsheet.

Introduction and overview

The overall process is simple:

• Open the spreadsheet template (and the linked data standards spreadsheet)
• Enter the lab submission data
• Send the spreadsheet by email to iSIKHNAS

iSIKHNAS automatically checks the data and, if it is valid, inserts it into the national database. An email is sent with confirmation that the data has been correctly submitted, as well as an automatically generated client report for printing in the lab.

To use the system, laboratory staff must:

• register with iSIKHNAS (talk to your local coordinator)
• have permissions set to be allowed to submit laboratory data (again, talk to your coordinator)
• set up their computer
  • get a copy of the submission template
  • get a copy of the lab standards spreadsheet

As the system works with Excel and email, you naturally must have

• a recent copy of Excel installed on your computer (one that can handle the newer '.xlsx' file formats), and
• an email address and internet connection to send and receive emails. To send and receive emails you can use
  • a web-mail interface (like gmail) through a web browser (like Chrome, Internet Explorer or Firefox), or
  • an email client (like Microsoft Outlook or Thunderbird)

Setting up

To be able to use the system you must have two spreadsheets:

1. the template
2. 'lab standards.xlsx' - which contains the Indonesian national laboratory data standards to ensure that all data is compatible and able to be analysed.

Both can be downloaded from the iSIKHNAS web site

Data submission template spreadsheet

This is used to enter the data, and is sent by email to iSIKHNAS. Click on the link below to download the latest version of the data submission spreadsheet:

Submission spreadsheet

The template may be updated from time to time. Your iSIKHNAS coordinator will either send you the updated spreadsheet by email, or let you know that a new version is available on this web site for download.

Laboratory standards spreadsheet

The lab standards.xlsx file is automatically linked to the template, to ensure that all data submitted conforms to the national data standards. This is automatically customised for each different lab, and is generated by iSIKHNAS. Once it is generated and downloaded, you never need to edit it. If changes are required, they can be made on-line on the iSIKHNAS web site, and a new version downloaded.

The spreadsheet can be downloaded from the iSIKHNAS secure web site. Log in and go to:

• Manage | Export Lab standards

or click on the following link to go straight to the download page (you must already be logged in for this link to work)

https://www.isikhnas.com/en/exportlabstandards

1. Select 'Custom lab references'
2. Select your lab from the drop down list
3. Either
   1. Click on 'Export'
      1. This will send a copy of the standards to your registered email address, or
   2. Click on 'Export to lab contact'
      1. This will send a copy to the lab contact person, as recorded in the iSIKHNAS list of laboratories (infrastructure table).

Important tips for spreadsheet management

Always save the template spreadsheet and the standards spreadsheet in the same directory

If they are in different directories, the automatic links will not work.

The standards spreadsheet must always have the same name: lab standards.xlsx.

If the name is changed, it will not work.

When you download the standards spreadsheet from the web, sometimes your computer will automatically change the name to something like lab standards(2).xlsx. If this happens, you need to delete the old copy, and rename the file back to lab standards.xlsx as well as placing it in the correct directory.

You can copy and rename the template file as many times as you like (but not the standards file)

You may want to keep a copy of every submission you send, so saving each file with the epi number is a good way to keep track of the files. They can all be in the same directory, as long as the lab standards.xlsx file is in the same directory.

Entering data

To enter data into the template spreadsheet:

1. Open the lab standards.xlsx spreadsheet
2. Open the template spreadsheet

Both spreadsheets must be open at the same time so that template can successfully link to the standards spreadsheet

Enter data into the required cells by clicking on the cell and typing, or clicking on the arrow to select from the drop-down list.

Controlled cells

The spreadsheet is protected to avoid entering data in the wrong places. You can only select cells intended for data entry

Drop down lists

There are many cells with drop down lists. These ensure that data follows the national laboratory data standards. You can only choose one of the values from the list

Required values

When a value is required but missing, the cell is highlighted with a red border.

Hints

Many cells contain hints to guide you. These are marked with a small triangle in the corner of the cell.

To view the hint, float your mouse over the triangle and the text will pop up.

Findings, results, diagnosis

In iSIKHNAS each of these has a special meaning.

Findings

This is what the lab test tells you. Findings can be

• qualitative (for example, Coliforms were detected in a sample ) or
• quantitative (an HI test gave a titre of 1/40)

Some tests may give both qualitative and quantitative findings (for example a faecal sample contained 300 Strongyloides eggs per gram)

Result

This is our interpretation of what the findings mean. Normally the result is either positive or negative. For example, the finding for an antibody ELISA may be an optical density of 200. If we use a cut-off of 150, this means that our interpretation of the finding is that the animal is positive - it has antibodies to the pathogen. Other possible results include protective or non-protective when doing post-vaccination surveillance; within acceptable limits or outside acceptable limits (food safety testing); light, medium or heavy load (worm eggs).

Diagnosis

This is our conclusion, based on all the available information, as to what disease is causing the problem. A diagnosis is only meaningful when disease is present and the purpose of the submission is diagnostic. Some key points:

• For surveillance, movement or other purposes, there is no diagnosis as there is no (known) disease
• AI negative is not a diagnosis. It is a result (our interpretation of the information that the test gave). It does not tell us what disease is causing the problem.

Guidelines for specific fields

Pengajuan uji laboratorium

Information about the submission.

Nomor Epi

Required. A unique submission number assigned by the laboratory.

When samples are sent from one laboratory to another, the original epi number should always be used (do not create a new one in the referral lab).

Tujuan

Required. The reason for submission of the specimen.

ID kejadian iSIKHNAS

Required for some reasons. This is the iSIKHNAS reference number, to link laboratory data to other data in iSIKHNAS.

This is should be used for:

• Diagnostic cases: The iSIKHNAS case ID
• Movement permits: The iSIKHNAS SKKH ID
• Surveillance: The iSIKHNAS surveillance program ID
• Post vaccination monitoring: The iSIKHNAS vaccination program ID

While iSIKHNAS is being rolled out, not all kabupaten will be using it, so some submissions will not have an iSIKHNAS ID even if they are meant to. In this case, leave the field empty

Pemilik dan pengirim

Information about the location, submitter and owner. The location should always be the location of the animal.

Lokasi (PKKD)

Required. Select the location from the four drop down lists.

If there location name has changed because of changes in administrative boundaries, try to find the old name and use that.

If the detailed location is not known, enter as much information as is available (at least the province and kabupaten)

Kode lokasi

This is automatically generated from the information supplied above. You cannot edit this.

Jenis Pengirim

Required. Pick from the drop down list.

Nama Pengirim

Optional. This is included on the client report

Alamat Pengirim

Optional. This is included on the client report

Nomor HP Pengirim

Optional. If available, enter the mobile phone number. This is used to identify the submitter so that it is possible to link all their submissions for consolidated reporting.

Nama Pemilik

Optional. This is included on the client report

Alamat Pemilik

Optional. This is included on the client report

Nomor HP Pemilik

Optional. If available, enter the mobile number. This allows different submissions from the same owner to be linked.

Spesimen dan uji

Information about the specimen and test. Each separate specimen and test combination should be entered in a different column.

If there are multiple qualitative findings for a particular test (see below), these should be entered in new columns with the other details blank)

Kelompok spesimen and Jenis specsimen

Required. Use these two fields to select the type of specimen (what it is or what part of the animal it came from)

Bentuk spesimen

Required. This indicates how the specimen has been handled, prepared or treated. This may be the way it is collected (swab) prepared (smear) or preserved (formalin).

Jenis Uji

Required. This specifies the lab section conducting the test. The tests listed in the next drop down depend on the custom list of tests for each laboratory and lab section (see below).

Uji

Required. The test performed.

Temuan kual.

The qualitative finding of a test. If a test produces one or more qualitative findings (e.g. bacterial or parasite species detected, or histopathological findings) each finding should be entered into a separate column on row 29. One test can therefore have multiple findings and use multiple columns.

Animal details

The bottom of the template contains information about each animal. There should be one animal per row. Each animal must have results for every test.

Jenis kelamin

Optional.Enter the sex of each animal, if known

Umur and Unit Umur

Optional. Enter the age of each animal, if known. The age is split into two columns. The first column (Umur) contains only numbers (whole numbers or decimals). The second column contains the units (days, weeks, months or years), selected from the drop down list. Only one unit can be used, so if an animal is 2 years and 3 months, enter the age as 2.25 years.

You cannot use other symbols such as > 3. Use your best estimate if the age is unknown.

Spesies

Required. Pick from the list.

Ras

Optional. Some species have a number of different breeds available. Add this if it is known. Sometimes there are different options - for exmaple, cattle (sapi) can be identified as beef (potong) or dairy (perah), or can be classified by their breed (limousin, friesian). Use the most detailed information known.

ID hewan

Required. If the animals are individually uniquely identified (for example, with ear tags) then use these identifiers. If no information is available, you can simply give each animal a serial number starting at 1.

If the animals are in a mixed group, you can add other information in this field. For example, if they come from several owners, you could identify each animal with the owner name and the animal number.

Temuan kuant.

Quantitative finding. This is required for tests that produce quantitative outputs. It must be a whole number or a decimal number.

There is a plan to allow uncertainty qualifiers, such as > (greater than), < (less than), ~ approximately, however this feature has not yet been implemented.

Hasil

Required. Pick from the drop down list.

Submitting data

Saving and sending the data

1. Once data entry is complete, save the template spreadsheet to your local hard drive. You may want to change the name using the Epi Number to make finding the data again easier.
2. Create a new e-mail
3. The address should be labdata@isikhnas.com
4. Type the Epi number in the subject line (this is optional but will help you keep track of which data has been submitted and which hasn't, when you look at your 'sent mail' folder)
5. Attach the template spreadsheet that you just saved
6. Send the e-mail

If you have a local e-mail client installed on your computer (such as Thunderbird or Outlook), sending messages can be made faster and easier:

1. In Excel go to the File menu, select Save and send, then click on the Send as attachment button. This automatically creates an email with the file attached.
2. Enter the address labdata@isikhnas.com and click send

Responses from iSIKHNAS

Whenever data is submitted to iSIKHNAS, there will be an automatic response which should arrive within a minute or two. The contents of the response depends on the data sent:

Successful submission - client report

If the data is all correct, then it will be automatically inserted into iSIKHNAS.

You will then receive an email confirming that the data has been accepted, with a summary of the data.

You will also receive a second email containing an automatically generated client report. This is in ODT format which can be opened and edited in Libre Office Writer (free) or in Microsoft Word.

Once the file has been opened, you can add any further details, save it, and print it.

Errors detected in the data

If there are any errors in the submitted data, you will receive an email listing the errors and cell references.

The email will also have an attachment which is copy of the spreadsheet submitted. In this spreadsheet, the cells with errors are highlighted in yellow, with pop-up comments to explain the error.

If there were errors, fix these in your original spreadsheet and submit again in a new email.

System errors

If there is an error in the system, you may receive an email with a system error message, instructing you to contact your coordinator.

Forward the message to your iSIKHNAS coordinator or one of the iSIKHNAS champions who will help solve the problem.

Customising test details for your lab

The list of laboratory sections, and tests performed by each of those sections, needs to be customised for each different laboratory.

To set up the list of tests, log in to the iSIKHNAS web site and go to Manage | Laboratory Tests.

1. Choose the test from the drop down list. These are national standards so if there is a test that is not present, you must contact the iSIKHNAS champions to update the standards.
2. Choose the laboratory section that does the test
3. Choose your laboratory from the list
4. If the test has a qualitative finding, check the box. For example, bacterial or parasitic identification produce qualitative findings - the names of the bacteria or parasites, while an AI ELISA doesn't - it is always just testing for AI.
5. If the test produces a quantitative finding, check the box. For example, an ELISA produces an optical density which is a number (quantitative), a faecal egg count produces a number. However a Rose Bengal Test just has either positive or negative result, so no quantitative finding.
6. If a quantitative finding is produced, select the units from the list
7. If your lab is officially accredited to perform this test, check the box
8. Enter a reference to the specific method used in the test (to be printed on the client report)

Updating data standards

The national laboratory standards are managed centrally to ensure consistency and the ability to analyse the data automatically. iSIKHNAS enforces these standards, so that it is not permissible to submit data that does not use the standards.

The standards cover all aspects of the data managed, including:

• species
• tests
• findings
• animal sex and ages
• specimens

These standards are contained in the lab standards.xlsx spreadsheet and are available in the drop down lists on the submission template.

If you ever find that there is a value missing from the standard list, it is possible to have new values added. To ensure that there is consistency, this process is managed by the iSIKHNAS champions.

Please contact the iSIKHNAS champions to request a new value to be added to the standards.