CVBDataGuide Page 1 of 38 20 May 2019

CVB DATA GUIDE 

HOW TO SUBMIT DATA

This document describes how to submit data for studies reported to CVB. 

1 Overview – How to submit data

• Organize the data set according to a data format.

• Save the data set in Comma Separated Value (CSV) files.

• Use this data set in your own data analysis.

• Submit the CSV files to CVB.

2 Data Formats

2.1 What is a data format?

A data format is a defined way of arraying data. A data format definition specifies one or more related 

tables that have a particular structure.

2.2 What does a data format do? 

Data formats provide a common “language” for sharing data sets. The CVB data formats are designed for 

several characteristics. One of the most important is to facilitate machine reading and processing.

2.3 Data Format definitions are found in the Appendix

3 CSV Files

A CSV file is a type of text file. 

• Use CSV files, not another electronic file type. (If you think an exception is warranted, please check first.)

• Each table in a data format should be in a separate CSV file.

• Files should be named according the naming convention of its data format.

• See Appendix Section 3.2: Creating CSV Files for CVB Statistics for more information.

4 Before submission

4.1 Prepare the data set

• Select the appropriate Data Format

• Take into account Data Principles

• Perform quality checks for internal consistency

4.2 Use the data set 

• First prepare the data set, then use the data set in your analysis (if you choose to do a statistical analysis). 

• By working with the data set before submitting it to CVB, your analysis serves as a final check of the 

validity and quality of the data set before submission. Don’t leave the preparation of the data set for 

submission to the end.

• Your programming code should usually show how you read in the data from the CSV files.
CVBDataGuide Page 2 of 38 20 May 2019

• See the NCAH Portal Guidance web page for instructions on submitting the data files.

5 Help

• See the Appendix for a number of helpful documents and tools. 

• If you need technical support from a person, contact: CVB.Data.Help@aphis.usda.gov 
CVBDataGuide – Appendix Page 3 of 38 20 May 2019

APPENDIX

1 Data Formats................................................................................................................................................................... 4

1.1 Introduction............................................................................................................................................................. 4

1.2 ELISA Format......................................................................................................................................................... 5

1.3 Clinical Format ....................................................................................................................................................... 8

1.4 Multi-well Assay Format ...................................................................................................................................... 10

1.5 Dichotomous Format............................................................................................................................................. 14

1.6 General Field Safety Format................................................................................................................................. 17

1.7 Poultry/Fish Field Safety Format.......................................................................................................................... 19

1.8 Diagnostic Kit Format - Dichotomous.................................................................................................................. 21

1.9 Diagnostic Kit Format - Quantitative.................................................................................................................... 23

1.10 Checkerboard Format............................................................................................................................................ 25

1.11 Build Your Own Format ....................................................................................................................................... 27

1.12 Glossary of Mandatory Columns.......................................................................................................................... 29

2 Expectations for all data submissions........................................................................................................................... 31

2.1 Use CSV Files....................................................................................................................................................... 31

2.2 Data Principles...................................................................................................................................................... 31

2.3 Data Types and Variable Roles............................................................................................................................. 32

3 Tools, troubleshooting and help.................................................................................................................................... 34

3.1 Common Data Formatting Issues.......................................................................................................................... 34

3.2 Creating CSV files for CVB Statistics.................................................................................................................. 36

3.3 Optional data entry tools....................................................................................................................................... 37

3.4 Contact CVB Statistics.......................................................................................................................................... 37

4 Revision History ........................................................................................................................................................... 38
CVBDataGuide – Appendix Page 4 of 38 20 May 2019

1 Data Formats

1.1 Introduction

A data format is a defined way of arraying data. A data format definition specifies one or more related tables that 

have a particular structure. The table specifications include “mandatory columns” – those that are always 

necessary, and “other columns” – those that may be necessary for specific studies. Both have required naming 

conventions.

The data formats are designed for the types of studies commonly submitted to CVB. To help choose a suitable 

data format, below is a list of study types with a suggested data format that often works. However if you think 

that your data doesn’t quite fit, feel free to Build Your Own Format or contact CVB statistics for advice.

POSSIBLE DATA FORMATS FOR SOME COMMON STUDY TYPES

Category Study Type Data Format

Efficacy Vaccination/Challenge Clinical

Serology or other efficacy surrogate Clinical

Natural exposure field efficacy Clinical

Field Safety

FST by VSM 800.204

FST in target species General Field Safety

FST in target species – poultry or fish Poultry/Fish Field Safety

Clinical Safety Designed safety study Clinical

Assay

e.g. Assay validation

Reagent change

Manufacturing process

Inactivation kinetics

Stability

Relative potency ELISA ELISA

Checkerboard ELISA optimization Checkerboard

Titration Multi-well Assay

Count Multi-well Assay

Conventional PCR Multi-well Assay

Other dilution assays (e.g. RID, dot blot, etc.) Multi-well Assay

Dichotomous response (pos/neg) Dichotomous

Diagnostic Test Kit Dichotomous response (e.g. single use device) Diagnostic Kit-Dichotomous

Quantitative response (e.g. OD, Ct) Diagnostic Kit-Quantitative

Other Serological equivalence Clinical
CVBDataGuide – ELISA Page 5 of 38 20 May 2019

1.2 ELISA Format

1.2.1 Introduction

This format is for enzyme-linked immunosorbent assays (ELISA) used to estimate relative potency or 

analyte concentration. This assay is performed in a 96-well microtiter plate. For assays that are performed 

on a 96-well microtiter plate, but is not an RP ELISA, please see the Multi-well Assay Format.

1.2.2 What to Submit

When submitting electronic data that correspond to relative potency ELISA data format, include a total of 

four (4) CSV files, one corresponding to each of the 4 tables labeled below.

1.2.3 Tables

This format includes four tables, named plateinfo, od, layout, and dilution. Except for plateinfo, the 

tables are laid out as stacked 8×12 arrays of plate information, with one additional column. The data 

should be presented exactly as arrayed on the plate. In other words, the rows are A-H and the columns are 

1-12.

1.2.4 Submission subtypes with additional required information

Assay validation: Please provide the Relative Potency (RP), product code (prod_code), and plate role 

(plate_role). The RP and product codes can be added as columns to the serialtesting table. The plate role, 

which would identify the aspect of the assay validation the plate was used in, should be added as a 

column to the plateinfo table (add multiple columns if a plate has more than one role). 

Table Description Mandatory 

Columns

Other Columns

plateinfo Information about each individual plate. plateID

date

technician

capture antibody

antigen

role

etc.

od The optical density readings of the wells. Every well should 

have a numeric result.

1-12

plateID

none

layout The contents of each well, usually the preparation identifier.

Include information on every well. 

For columns 1-12, if no material was added to the well, use 

“NA”. Note that the word “blank” should not be used for an 

empty well, since it usually refers to the preparation known as 

the reagent blank. For wells that are not part of the study, please 

use “NPS”.

1-12

plateID

none

dilution The dilution of the material in each well.

For columns 1-12, specify “undiluted” wells as 1. Use number 

(8, 0.125, NA) not text (1:8, 1/8, NPS). Do not use commas 

(1,024) that might cause a number to be interpreted as text. For 

ten-fold dilutions, scientific notation (1e9) may be used to avoid 

data entry errors of large dilutions (1000000000).

1-12

plateID

none

serialtesting (optional) Relationships between serial number, product code 

number and test data results.

plateID serial ID

product code

test outcome

relative potency

etc.
CVBDataGuide – ELISA Page 6 of 38 20 May 2019

Stability – product: Please add a column for the Relative Potency (RP) results, serial fill date (fill_date), 

and bulk date (bulk_date) for each serial to the serialtesting table. If testing is conducted on bulk and final 

container, please add the column MaterialTested.

Stability - reference: Please provide the product code (prod_code) for each serial by adding a column to 

the serialtesting table.

Note: When submitting the Relative Potency (RP) results which rely on a linear model fit, please also 

provide the start and end dilutions1 used for each serial and reference that the linear model was fit to. 

Please see the serialtesting table example below for prefered column names.

1.2.5 Example

Below are examples of the 4 tables in the format that should be included when submitting a study to the 

CVB. The fifth table, serialtesting, is used when specific serial information needs to be included.

 

1 Integer where 1 is the first dilution in the series, 2 is the second, etc. Not the same as dil, and not the column number. In example 

1.2.5, the linear model is fit to the 1st – 4th dilutions for the reference (dil 1:1 – 1:8) and the linear model is fit to the 2nd to 5th dilutions 

for the serial (dil 1:2 – 1:16). 
CVBDataGuide – ELISA Page 7 of 38 20 May 2019
CVBDataGuide – Clinical Format 8 of 38 20 May 2019

1.3 Clinical Format

1.3.1 Introduction

This format is intended for designed experiments with live animals. This includes vaccination-challenge 

efficacy studies, natural exposure or field efficacy studies, other experimental efficacy studies without a 

challenge, feasibility studies involving target species or laboratory surrogates, and serological studies. It is 

not intended for simple in vivo titrations involving lab animals, for those studies see Dichotomous 

Format.

1.3.2 What to Submit

When submitting electronic data in the Clinical Format, include a total of three (3) CSV files, one 

corresponding to each of the 3 tables listed below. If no daily observations are taken, a repeated table may 

not be necessary.

1.3.3 Tables

Table Description Mandatory 

Columns

Other Columns

individual This table will contain all the information for the individual 

animal. Include any information that pertains to housing or 

litter (if applicable). It may also include any observations that 

are made once, usually at necropsy.

animalID

group

sex

date of birth

litter

pen

lung lesions

lymphoid depletion

etc.

repeated This table will contain information on outcomes that were 

observed more than once. In most cases this means the daily 

observations. It should have an animal ID (identical to the 

one used in the individual table), a day column, and other 

observation columns.

animalID

day

temperature

coughing

diarrhea

etc.

variables This table is for the explanation of all the columns names in 

the previous two tables. You will provide the column name 

exactly as it appears in the previous two tables, a brief 

description of the column, and what table the column belongs 

to.

variable

table

description

comments
CVBDataGuide – Clinical Format 9 of 38 20 May 2019

1.3.4 Example

Below are examples of the three tables in the format that should be included when submitting a 

study to the CVB with the Clinical format.
CVBDataGuide – Multi-well Assay Format 10 of 38 20 May 2019

1.4 Multi-well Assay Format

1.4.1 Introduction

This format is designed for any assay that uses multiple wells or vessels for a single test. It is particularly 

suited for microtiter (multi-well) plates that can be of any shape or size.

1.4.2 What to Submit

When submitting electronic data that corresponds to the Multi-well Assay Format, include a total of three

(3) CSV files, one corresponding to each of the 3 tables listed below.

1.4.3 Tables

1.4.4 Submission subtypes with additional required information

Stability – product: Please provide the results of the test as a column on the plateinfo table. If you have 

more than one serial/test per plate, please provide a testinfo table. The testinfo table would include 

columns for testID, plateID, date, serialID, fill_date, bulk_date and results. If testing is conducted on 

bulk and final container, please add the column MaterialTested.

Assay validation: Please provide the potency, product code, and plate role. These can be added to the 

plateinfo table using column names: potency, prod_code, plate_role. If you have more than one serial/test 

per plate, please provide a testinfo table for the results instead of reporting on the plateinfo table.

1.4.5 Example 1

Example of the three tables in the Multi-well Assay Format that should be included when submitting a 

study like a count assay to the CVB.

Table Description Mandatory 

Columns

Other Columns

plateinfo This table is designed to give us all the information that is 

specific to the plate or test.

plateID

date

technician

role

etc.

wellinfo This table is designed to give us all the information on the 

individual wells. This file will include the plate ID (this needs 

to match exactly with the plateinfo table), the reading, the well 

position, the layout (content of well), and any other information

plateID od

count

area

layout

position

dilution

etc.

variables This table is for the explanation of all the columns names in the 

previous two tables. You will provide the column name 

exactly as it appears in the previous two tables, a brief 

description of the column, and what table the column belongs 

to.

variable

table

description

comments
CVBDataGuide – Multi-well Assay Format 11 of 38 20 May 2019

1.4.6 Example 2

Example of the three tables in the Multi-well Assay Format that should be included when submitting a 

study like a Western Blot to the CVB.
CVBDataGuide – Multi-well Assay Format 12 of 38 20 May 2019

1.4.7 Example 3

Example of the three tables in the Multi-well Assay Format that should be included when submitting a 

study like a PCR to the CVB.
CVBDataGuide – Multi-well Assay Format 13 of 38 20 May 2019
CVBDataGuide – Dichotomous Format 14 of 38 20 May 2019

1.5 Dichotomous Format

1.5.1 Introduction

The Dichotomous Format is for studies where results are reported as positive (or negative) out of a total. 

For submissions where results are not dichotomous (such as continuous or integer readings like counts, 

etc.), please review the Multi-Well Assay Format. The Dichotomous Format can also be used for live lab 

animal vaccination/challenge with challenge back-titration studies.2

1.5.2 What to Submit

When submitting electronic data that corresponds to the Dichotomous Format, include at least three (3) 

CSV files, one corresponding to each of the three tables listed below. If the study also has a challenge 

with a back-titration, also include a fourth challenge table.

1.5.3 Tables

1.5.4 Submission subtypes with additional required information

Stability –product: Please make sure to add the titer results, fill date (fill_date), and bulk date (bulk_date)

for each test to the testinfo table. If testing is conducted on bulk and final container, please add the 

column MaterialTested.

 

2 This was formerly known as the Bioassay Format

Table Description Mandatory 

Columns

Other Columns

testinfo This table contains information about each individual test. testID

date

challenge date

vaccination date

back-titer date

technician

results

vial

comments 

product code

etc.

titration This table contains information about each titration within a 

test.

testID

prepID

prepRole

dil

positive

total

comments

etc.

variables This table is for the explanation of all the columns names in the 

previous two tables. You will provide the column name 

exactly as it appears in the previous two tables, a brief 

description of the column, and what table the column belongs 

to.

variable

table

description

comments

challenge (optional) This table contains information on the animals that 

were used in the back-titration of the challenge material.

prepID

dil

positive

total

testID
CVBDataGuide – Dichotomous Format 15 of 38 20 May 2019

1.5.5 Example 1

Below are examples of the three tables in the format that should be included when submitting a study to 

the CVB when performing assays with dichotomous results.

1.5.6 Example 2

Below are examples of the four tables in the format that should be included when submitting a study to 

the CVB that has a live lab animal component where animals were vaccinated, challenged, and 

monitored. A third table has the challenge back-titration information.
CVBDataGuide – Dichotomous Format 16 of 38 20 May 2019
CVBDataGuide – General Field Safety Format 17 of 38 20 May 2019

1.6 General Field Safety Format

1.6.1 Introduction

This format is designed mainly for Field Safety Trials (FST) done in accordance with VSM 800.204. 

FSTs are observational studies done at several sites without much in the way of experimental design other 

than observing what happens after the product is administered under everyday conditions. This format is 

intended for use with all animals, except poultry and fish (see Poultry/Fish Field Safety Format).

1.6.2 What to Submit

When submitting electronic data that corresponds to the General Field Safety Format, include a total of 

three (3) CSV files, one corresponding to each of the 3 tables listed below.

1.6.3 Tables

1.6.4 Example

Below are examples of the three tables in the format that should be included when submitting a study to 

the CVB with the General Field Safety Format. Please note this is a very brief example. It is understood

that each site can have 100 or more animals and may go on for many days. These files can be very large.

Table Description Mandatory 

Columns

Other Columns

individual This table will provide us with the information on the 

individual animal.

animalID

siteID

group

sex

age

repeated This table will provide us with the observations on each 

animal. It will have a unique animal ID (exactly the same that 

was provided in the individual table). Then we need a date

column, a column that states whether an adverse event was 

observed, and the VEDDRA term if an AE was observed (If 

there is more than one AE for an animal on the same day, 

please add an additional row with that animal and that 

day). Please click here for further information about the 

formatting for the VEDDRA term. You may also add a nonVEDDRA term and any other pertinent information about the 

animal on that date.

animalID

date

ae

veddra

altetiology

nonveddra

localsite

localsize

comments

etc.

variables This table is for the explanation of all the column names in the 

previous two tables. You will provide the column name 

exactly as it appears in the previous two tables, a brief 

description of the column, and what table the column belongs 

to.

variable

table

description

comments
CVBDataGuide – General Field Safety Format 18 of 38 20 May 2019
CVBDataGuide – Poultry/Fish Field Safety Format 19 of 38 20 May 2019

1.7 Poultry/Fish Field Safety Format

1.7.1 Introduction

This format is designed mainly for Field Safety Trials (FST) done in accordance with VSM 800.204. 

FSTs are observational studies done at several sites without much in the way of experimental design other 

than observing what happens after the product is administered under everyday conditions. This FST 

Format is intended for use with poultry and fish.

1.7.2 What to Submit

When submitting electronic data that corresponds to Poultry/Fish Field Safety Format, include a total of 

four (4) CSV files, one corresponding to each of the 4 tables listed below.

1.7.3 Tables

1.7.4 Example

Below are examples of the four tables in the format that should be included when submitting a study to 

the CVB with the Poultry/Fish Field Safety Format.

Table Description Mandatory 

Columns

Other Columns

siteinfo This table will provide us with the information on the treatment 

groups for each site.

siteID

group

total

dead

tanks

isolators

etc.

repeated This table will provide us with the mortality for each group at 

each site. It will have the site ID and the group (exactly the 

same that was provided in the individual table). Then we need 

a date column and a column for mortality for that date.

siteID

group

date

dead

comments

etc.

hatchability This table will provide us with the number of eggs that hatched 

per group.

siteID

group

total

hatched

variables This table is for the explanation of all the columns in the 

previous two tables. You will provide the column name 

exactly as it appears in the previous two tables, a brief 

description of the column, and what table the column belongs 

to. 

variable

table

description

comments
CVBDataGuide – Poultry/Fish Field Safety Format 20 of 38 20 May 2019
CVBDataGuide – Diagnostic Kit Dichotomous 21 of 38 20 May 2019

1.8 Diagnostic Kit Format - Dichotomous

1.8.1 Introduction

This format is designed for diagnostic test kits with a dichotomous response such as lateral flow 

devices, or similar single use devices where a positive/negative determination is made by the 

presence or absence of a visible dot or line. 

1.8.2 What to Submit

When submitting electronic data that corresponds to Diagnostic Kit - Dichotomous data format 

the number of tables submitted is dependent on the study type. Not all study types for diagnostic 

testing are listed below, such as confirmation of dating. However, formatting of those data may 

be similar to one of the study types described. 

1.8.3 Tables

Table Description Mandatory 

Columns

Other Columns

deviceinfo This table is designed to give us the results from each 

device and information about that device. Each device ID 

should only appear once. If the device has more than one 

spot or line that is read, like a control line, then add 

columns for additional readings. 

deviceID

serialID

visual_read

date

sample ID

specimen

species

manufacture date

test session

panel member

instrument reading

reference result

population

product code

etc.

labinfo This table contains information for each lab for 

interlaboratory testing. Information about the lab will 

include the lab name, technician, and other columns may 

be appropriate also.

testsession

labID

date

technician

etc.

panelinfo This table is designed to give us the information on the 

panel members. Information will include the panel 

member description, specimen type and species. 

panelmember

memberdesc

blind ID code

species

specimen

etc.

testinfo If multiple devices are used to report one derived value, 

such as a mean instrument result, then report the derived 

information on this table.

sampleID

variables This table is for the explanation of all the column names 

in the previous tables. You will provide the column name 

exactly as it appears in the previous tables, a brief 

description of the column, and what table the column 

belongs to.

variable

table

description

comments

1.8.4 Tables to submit for submission subtypes

Assay Validation – Sensitivity and Specificity: Please submit a deviceinfo and variables table. 

Additional mandatory columns to those listed above for this study type on the deviceinfo table 

include: sampleID, date, and ref_result. If the reference test was not conducted concurrently, 

then please provide a reference date column indicating what date the reference test was initiated.

If more than one reference test is conducted, columns can be numbered (ref1_result, ref2_result).
CVBDataGuide – Diagnostic Kit Dichotomous 22 of 38 20 May 2019

Assay Validation – Interlaboratory Comparison (Diagnostic Field Study): Please submit a 

deviceinfo, labinfo, panelinfo, and variables table. An additional mandatory column to those 

listed above for this study type on the deviceinfo table include: panelmember and testsession. For 

the panelinfo table, information such as blinding code, the description of the panel member 

(negative, weak positive, strong positive), species, and specimen should be included.

Serial Release Panel Validation (Diagnostic Panel Validation): Please submit a deviceinfo, 

panelinfo and variables table. Additional mandatory columns to those listed above for this study 

type on the deviceinfo table include: panelmember, and date. If multiple devices are used to 

report one derived value, such as a mean instrument result, then report the derived information 

on the testinfo table.

1.8.5 Example

An example of tables to submit for each of the three types of studies (1.8.4) is included in the 

following zip file.

https://www.aphis.usda.gov/animal_health/vet_biologics/publications/DiagnosticKitDichotomous.zip
CVBDataGuide – Diagnostic Kit Quantitative 23 of 38 20 May 2019

1.9 Diagnostic Kit Format - Quantitative

1.9.1 Introduction

This format is designed for diagnostic test kits with a quantitative response such as OD or Ct, 

which are usually conducted on multi-well plates and read by a machine. 

1.9.2 What to Submit

When submitting electronic data that corresponds to Diagnostic Kit - Quantitative data format 

the number of tables submitted is dependent on the study type. Not all study types for diagnostic 

testing are listed below, such as confirmation of dating. However, formatting for those data may 

be similar to one of the study types described. 

1.9.3 Tables

Table Description Mandatory Columns Other Columns

plateinfo This table is designed to give us the information about 

the plate. Each plateID should only appear once on the 

plateinfo table. 

plateID

date

serialID

lab ID

technician

manufacture date

product code

etc.

wellinfo This table is designed to give us all the information on 

the well readings (such as od). If the results are

calculated for an individual well, then also include 

derived result, interpretation (pos/neg) and any other 

information necessary.

plateID

row

col

sample ID

sample specimen

sample species

panel member

raw well reading

derived result

population

etc.

panelinfo This table is designed to give us the information about 

the panel member. Include information such as the 

description of the panel member, species, and specimen. 

Other columns may be appropriate also.

panelmember

memberdesc

blind code

member species

member specimen

etc.

testinfo This table is for derived information on a plate that is 

across multiple wells (similar to serialtesting table in

the ELISA Format). Example, the SP Ratio is calculated 

using average of three wells on the plate.

plateID derived result 

panel member

etc.

variables This table is for the explanation of all the column names 

in the previous tables. You will provide the column 

name exactly as it appears in the previous tables, a brief 

description of the column, and what table the column 

belongs to.

variable

table

description

comments

1.9.4 Table to submit for submission subtypes

Assay Validation – Sensitivity and Specificity: Please submit a plateinfo, wellinfo, and variables

table. Additional mandatory columns to those listed in the Tables above for this study type on the 

wellinfo table include: sampleID, and raw well reading (od, etc.). Information about the 

reference result (ref_result), and reference date (if the test was not conducted concurrently) may 

be appropriate on any of the tables listed, and are mandatory columns. If more than one reference 

test is conducted, columns can be numbered (ref1_result, ref2_result). If information is derived 

from multiple wells, please include this on the testinfo table.

Assay Validation – Interlaboratory Comparison (Diagnostic Field Study): Please submit a 

plateinfo, wellinfo, panelinfo and variables table. Additional mandatory columns to those listed 
CVBDataGuide – Diagnostic Kit Quantitative 24 of 38 20 May 2019

above for this study type on the wellinfo table include: panelmember, and well reading (od, etc.). 

Information about each lab that performed testing should be included on the plateinfo table. If 

information is derived from multiple wells, please include this on the testinfo table.

Serial Release Panel Validation (Diagnostic Panel Validation): Please submit a plateinfo, 

wellinfo, panelinfo and variables table. Additional mandatory columns to those listed above for 

this study type on the wellinfo table include: panelmember, and well reading (od, etc.). If 

information is derived from multiple wells, please include this on the testinfo table.

1.9.5 Example

An example of tables to submit for each of the three types of studies (1.9.4) is included in the 

following zip file.

https://www.aphis.usda.gov/animal_health/vet_biologics/publications/DiagnosticKitQuantitative.zip
CVBDataGuide – Checkerboard 25 of 38 20 May 2019

1.10 Checkerboard Format

1.10.1 Introduction

The checkerboard format is usually used when optimizing an assay for an assay validation submission 

subtype. 

1.10.2 What to Submit

When submitting electronic data that corresponds to checkerboard data format, include a total of two CSV 

files, one corresponding to each of the 2 tables labeled below.

1.10.3 Tables

1.10.4 Example

Below are examples of the 2 tables in the format that should be included when submitting a study to the 

CVB.

Table Description Mandatory Columns Other Columns

plateinfo Information about each individual plate. Each unique 

dilution series on a plate is designated “A”, “B”, etc.

plateID

date

series name

series 

pre-dilution

technician

role

etc.

stacked This table contains information about the well including the 

plate ID, the location of the well (row and column), the 

optical density reading, and the dilution. There will be a 

row of data for each well on the plate.

plateID

row

col

od

dil_A (and other 

dilution series, dil_B, 

etc.)
CVBDataGuide – Checkerboard 26 of 38 20 May 2019
CVBDataGuide – BYO Format 27 of 38 20 May 2019

1.11 Build Your Own Format

1.11.1 Introduction

The Build Your Own Format goes over the basic formatting ideas that you need in order to submit 

electronic data if none of the prior formats fit your study design. If you like you may email STAT the 

format you determined was appropriate, and we can provide feedback.

1.11.2 What to Submit

When submitting electronic data, there will probably be 2-3 tables that are saved as CSV files. Depending 

on your data, there may be different combinations of the three tables that follow. However, the variables

table should always be one of them.

1.11.3 Tables

Table Description Mandatory 

Columns

Other Columns

individual A table that has unique information in each row. You will 

have one column that links this file to your repeated table; like 

ID. Other columns in this table describe that key identifier 

column.

ID conjugate

plate role

date of birth

group

tech

etc.

repeated A table that has one column that has a repeated entry in 

several rows of the table but is the key identifier that ties it to 

the individual table, and all other columns have unique entries 

to their row in the table.

ID day of study

daily observations

well position

well readings

counts

etc.

variables A table that describes the columns in the other two tables. The 

column (variable) names that you choose for the individual

and repeated tables, might be obvious, or they might not be. In 

order to make the submission as clear as possible, the 

variables table should describe the column names that are 

used.

variable

description

table

comments
CVBDataGuide – BYO Format 28 of 38 20 May 2019

1.11.4 Example

Below are examples of 3 tables in the format could be included when submitting a study to the CVB.
CVBDataGuide – Glossary 29 of 38 20 May 2019

1.12 Glossary

This glossary includes the names of Columns (Variables) that are mandatory, and some non-mandatory, with a 

description of the column. It also includes some non-mandatory columns if their names are fixed and should not 

be altered. Not all column names will apply to every submission. Please review specific formats to determine 

which column names your table will need.

1-12 The twelve columns that relate to the 96-well plate used in relative potency ELISA

ae Whether an Adverse Event is observed (Yes, No).

age Age of the animal when vaccination is administered

alive The number of animals that did not die or were not affected by the challenge

altetiology Use “affirm” or NA. The licensee affirms that there is diagnostic or clinical support for a 

possible cause of this AE other than vaccination (alternative etiology).

animalID Unique identifier for an animal

bulk_date The date (preferably formatted “YYYY-MM-DD”) in which the serial in bulk was produced to final 

form and composition.

col Most commonly a number (1-12) that corresponds to the numbered row on a 96-well microtiter plate

date Start date of the test, assay, or observation, including month, day and year. Preferably in the format 

“YYYY-MM-DD”. The start date is considered to be the date the product is introduced into the test 

system (the first day the product is injected into the animal or the first day the product is added to an in 

vitro test plate).”

day A number to either indicate the day of the study, or day post challenge. It is not a date, but a count of 

the days since time point 0 (vaccination, challenge, etc.)

dead The number of animals in the group that died

description Description of the column

deviceID A single use device identifier that is unique to the table. The use of special characters such as periods, 

hyphens, spaces, arithmetic operators, etc. is discouraged. Limiting the length of the string to fewer 

than 16 alphanumeric characters is encouraged.

dil The dilution administered to the animal or used in a well. Specify “undiluted” wells as 1. Use number 

(8, 0.125) not text (1:8, 1/8). Do not use commas (1,024) that might cause a number to be interpreted 

as text. For ten-fold dilutions, scientific notation (1e9) may be used to avoid data entry errors of large 

dilutions (1000000000).

fill_date The date (preferably formatted “YYYY-MM-DD”) in which the serial was filled into final containers.

group Treatment group assigned to an animal

hatched Number of birds hatched

ID Generic Identifier for a plate, gel, animal, test, etc.

labID Unique identifier for the laboratory that is performing testing. The use of special characters such as 

periods, hyphens, spaces, arithmetic operators, etc. is discouraged.

localsite For injection site reactions only, identify the injection site if there is more than one vaccination: e.g. 1 

for 1st vaccination and 2 for 2nd vaccination.

localsize For injection site reactions only, provide the size.

memberdesc Description of the panel member. Usually described as “negative”, “weak positive”, or “strong 

positive”.

MaterialTested Use ‘bulk’ or ‘final container’. The completed product material that was used in testing. If the testing 

was conducted on a serial that was filled into final container, use ‘final container’. If the testing was 

conducted on a serial in final formulation bulk form, use ‘bulk’.

nonveddra Can be used to apply a non-VEDDRA category term to the event.

od Optical density reading.

panelmember Unique identifier for the panel member being tested. The use of special characters such as 

periods, hyphens, spaces, arithmetic operators, etc. is discouraged.

plateID A plate identifier that is unique to the table. The use of special characters such as periods, 

hyphens, spaces, arithmetic operators, etc. is discouraged. Limiting the length of the string to 

fewer than 16 alphanumeric characters is encouraged.

plate_role Role of the plate in an assay validation (i.e. precision, ruggedness, specificity)
CVBDataGuide – Glossary 30 of 38 20 May 2019

positive Total number of positive readings (tubes or wells) or animals affected by challenge.

potency potency of a product

prepID The identifier of the preparation used. This will usually be a lot or serial number of a vaccine

prepRole The role of the preparation. This must be reference, test, or other

prod_code Veterinary Services Product Code

ref_result Reference test result which is usually a dichotomous result, “positive” or “negative”. In some 

cases, a result of “suspect” may be appropriate. If multiple reference tests are performed, 

please report results in multiple columns with the reference tests numbered, refX_result. i.e. 

ref1_result, ref2_result, etc. Information about each of the tests can be included in the 

variables table.

results The outcome of a test

row Most commonly a letter (A-H) that corresponds to the lettered row on a 96-well microtiter 

plate.

RP Relative potency calculated

sampleID Unique identifier for the sample being tested. The use of special characters such as periods, 

hyphens, spaces, arithmetic operators, etc. is discouraged.

serialID The identifier of the preparation used. This will usually be a lot or serial number of a vaccine

sex sex of animal; Male (M) or Female (F)

siteID Site location that animals were held at for observation

table Name of the table that the column is found on

testID A test identifier that is unique in the table. Every test must have a test identifier

testsession An identifier that can be used to group individual identifiers together.

total The total number of animals/tubes/wells in a group (treatment group or at a specified dilution)

variable Names of the columns that are used in the corresponding data files

veddra From the VEDDRA List of Clinical Terms select the appropriate Low Level Term (LLT) or Preferred 

Term (PT). 

visual_read For tests that require a visual read per the SO or OP, include the visual read result.
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2 Expectations for all data submissions

2.1 Use CSV Files

Comma Separated Value (CSV) files are a portable standard that allows for quick importation into statistics 

analytical programs. Occasionally there may be a reason to submit some other file type to CVB Statistics. In such 

cases, please email STAT. Note that the CVB Portal for electronic submission does not accept all file types.

When preparing your CSV files:

• Include only one table per file.

• If you use spreadsheet software to prepare the CSV file:

o Do not encode information via text formatting (e.g. italics, bold, color). This information is ignored 

when converting to CSV.

o Do not encode information by formatting the table (e.g. background color). This information is 

ignored when converting to CSV.

o Values in merged cells will be arbitrarily assigned to a single cell (merging lost) when converting to 

CSV. This will result in empty cells on the table which may extend analysis time.

• Name individual CSV files using the structure SUBMISSIONFILENAME_tablename.csv, where 

SUBMISSIONFILENAME prefix is common to all tables of a single data set, and tablename matches the table 

names specified for the particular data format exactly (case-sensitive).

See Appendix Section 3 for troubleshooting technical help.

2.2 Data Principles 

Basic principles for data sets that should be followed for all submissions. Consideration of competing goals prior 

to analysis can help identify the best data structure for a particular submission.

2.2.1 Principles

• Each variable is in a column, each observation is in a row. 

o Some data formats may have an exception to this rule. That occurs when certain types of 

multivariate data are handled as a chunk, such as when 96-well plate data are included as they 

are captured by a plate reader.

• Each column contains one data type. 

o For example, do not include the text “undiluted” in a column of numeric dilutions.

o See list of data types (Section 2.3.1)

• Derived information.

o Do not include derived information, such as averages, in the same column as the raw data. 

o If it is needed for submission, derived information should be included in a separate column or 

table. 

Example: the relative potency of two preparations on a plate. 

Example: lung lesion score calculated as the weighted sum of individual lobes.

• Include an entry in every cell of a table.

o Indicate missing data with NA (not N/A, na, or other code).

o If using spreadsheet software, such as Excel, to create a CSV file, be sure to start the table in 

the first row and column of the spreadsheet (cell A1). Otherwise, there will be empty cells.
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• Avoid redundant data.

o If the same data are used to support different aspects of the same study (e.g. accuracy and 

parallelism in an assay validation study) do not submit those data twice. Submit them in one 

data set. An additional variable can be used to indicate the roles of various subsets of the data.

2.2.2 Points to consider

• The number of data sets for a single study is sometimes a judgment call, and must balance design 

needs for data entry with demands for efficient analysis workflows.

o Sometimes it’s better to use multiple data sets

Example: An efficacy study has daily clinical signs, nasal swabs every other day, and blood 

work weekly. It is convenient to use a separate repeated table for each observation sequence.

o Sometimes it’s better to use a single data set.

Example: An assay validation study includes experiments for accuracy, parallelism, and 

freeze/thaw effects. Their data may be included in a single set, with a variable indicating 

which experiment they are from. The reason for using a single data set for similar data of this 

type is that statistical modeling may need to include all of them to estimate certain 

parameters.

2.3 Data Types and Variable Roles

2.3.1 Data Types

Data Type Description

Continuous A measurement on a continuous scale, such as body temperature. Large imprecise integer counts, 

such as blood cell counts, are often considered continuous. Interval censored continuous data, 

such as duration in days, may at times be treated as either continuous or integer.

Count Integer counts, such as frequencies.

Ranked A numerical value that reflects a valid ordering but a unit spacing that is not calibrated. For 

example, a valid clinical scoring scheme may produce integers from 0 to 16, where a higher 

number always indicates more severe disease than a lower number but the severity difference 

between any two adjacent scores is not necessarily the same.

Dichotomous A binary response that can only take two values, such as dead or alive

Ordinal Categories that are ordered, such as those applied to disease severity. The number of categories 

should be as few as possible and ideally would reflect distinct states, such as dead, sick, normal. 

(Excessive categories lead to issues of discreteness and sparseness.) Simple grading scales may 

generate ordinal categories.

Nominal Categories without any natural ordering, such as breed of cattle.

Date Date

Censored Measurements that have an upper or lower observational limit imposed by the instrument. 

(example: colony counts greater than 300 may be reported as “TNTC” [too numerous to count])
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2.3.2 Variable Roles

Variable Type Role

Identifier Unique identification given to each unit (or possibly subunit). The identifier also serves as the 

grouping factor for repeated observations made on the individual. (Data type: nominal)

Grouping Grouping factors are nominal categories important in study design, such as treatments or 

clusters. All efficacy studies have treatment groups, such as vaccine or placebo. Many have 

clusters, such as litter or pen. (Data type: nominal.)

Observation Direct observations or measurements. (Data types: continuous, count, ranked, dichotomous, 

ordinal, nominal.)

Derived Value calculated or derived from other variables. (Data types: continuous, count, ranked, 

dichotomous, ordinal, nominal.)

Timing Date or time. May be an actual date or time (Data type: date), or may be a count, such as the 

number of days in relation to an event such as challenge, or continuous, such as the number of 

minutes from inactivation. (Data type: count or continuous.)

Units The units of measurement. Units must be indicated for continuous and count data types. Leave 

blank otherwise.
CVBDataGuide – Troubleshooting 34 of 38 20 May 2019

3 Tools, troubleshooting and help

3.1 Common Data Formatting Issues

3.1.1 Proper Formatting

Properly formatted data is suitable for immediate use in other software without need for additional 

manipulation that may delay analysis or introduce errors. Tables and screenshots in this document 

addresses common issues that occur when formatting data tables for submission as one of the CVB data 

formats.

DO DON’T

Start data entry in first row, first column of 

table (position ‘A1’ in Excel, OpenOffice)

DON’T Include empty rows and/or columns

Indicate missing data by NA DON’T Indicate missing data by ‘NA’, na, 

n/a or N/A

Report dilution units (1,2,4,8,etc.) DON’T Report log dilution values

DON’T Report dilution values as ratios 

‘1:10’, ‘1/10’

Include an entry (data or NA) for every cell in 

each row and column of the table

DON’T Leave cells empty 

DON’T Merge cells

Follow nomenclature outlined in Appendix

Section 1: Data Formats

DON’T Include multiple tables in a single 

file

Report raw data once per observation DON’T include raw data multiple times if 

different analysis is performed

Decimal separators should be the decimal 

point. (Standard in the US)

DON’T use decimal commas.

Use commas to separate text fields, since it is 

a comma separated value file.

DON’T use commas in numbers or commas 

in text in cells.

Use alpha-numeric characters or 

underscore in column names

DON’T use special characters such as %, 

#, space, period, etc. in column names
CVBDataGuide – Troubleshooting 35 of 38 20 May 2019

3.1.2 Example

Figure 1: Common formatting errors that delay analysis (lower) and correct formatting for the same data (upper).
CVBDataGuide – Troubleshooting 36 of 38 20 May 2019

3.2 Creating CSV files for CVB Statistics

CSV tables created from user-specified files must follow a specific nomenclature to facilitate automated 

data management tools. Follow the nomenclature and conventions described in Appendix Section 1: Data 

Formats.

3.2.1 Starting from statistical software

• In R, use: write.csv(...)

• In SAS, use: proc export

3.2.2 Starting from Excel

• Use the “Save As” option to designate “CSV” as the file type.

o Merged cells will be ignored.

o Text and border formatting (font, color, background) will be lost.

o Only one worksheet will be saved per destination file.

In Office 2013, the “Save As” option 

is on the “File” page. Pick “CSV” as 

the file type from the drop down.
CVBDataGuide – Troubleshooting 37 of 38 20 May 2019

3.3 Optional data entry tools

CVB Statistics is in the process of creating tools to support creating CSV files that conform to the data formats 

described above. These tools are completely optional to use. Please check back later for details.

These tools can be found at:

https://www.aphis.usda.gov/animal_health/vet_biologics/publications/OptionalDataEntryTools.zip

3.4 Contact CVB Statistics

If your question is in regards to one of the following areas, ask to speak to a Statistician:

• Identifying the best Data Format for a specific submission

• Troubleshooting creating Data Format tables for submission

• Bug fixes/upgrades to optional data entry tools.

• Informal feedback regarding experimental design prior to submission

Email: CVB.Data.Help@aphis.usda.gov
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4 Revision History

Date Affected Sections

2017-02-07 Appendix Sections 1.2.4, 1.2.5, 1.4.3, 1.4.4, 1.4.5, 1.4.6, 1.4.7, 1.5.2, 1.5.3, 1.5.4, 1.5.5, 1.5.6, 1.6.3, 

1.6.4, 1.9.4, 1.10, 3.3

2017-09-26 Overview 1; Appendix Sections 1.1, 1.2.3, 1.2.4, 1.2.5, 1.4.4, 1.4.5, 1.4.6, 1.5.6, 1.6, 1.8, 1.9, 1.12, 

3.1.1

2017-11-20 Appendix Sections 1.6.3, 1.6.4, 1.10.2, 1.10.3, 1.10.4, 1.12, 2.2.2

2019-05-20 Overview 2.2, 3, 5; Appendix Sections 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 1.10.2, 1.11,

1.12, 2.1, 3.1, 3.2, 3.4