Introduction to Using the VecTraits Database

VectorByte Methods Training

The VectorByte Team (Cat Lippi, PhD, Virginia Tech)

Overview of VectorByte

VectorBiTE RCN
VectorByte \(\Rightarrow\) two databases
VecDyn and VecTraits

VecDyn

Vector abundance
Typically field-collected surveillance data

VecTraits

Biological trait data
Typically results from controlled laboratory experiments

Vector Trait Data

Vector trait: measurable biological aspects of life-history, behavior, or vector competence

Because we are dealing with ectothermic vectors, these are often measured against temperature in controlled laboratory environments

Examples of Studies

Flexible Framework

VecTraits template provides a starting point
Required fields
Commonly used fields
Each column has data format requirements (e.g., text, numeric, etc)
NO strict format for most study aspects (e.g., units used in study, taxonomy)
Can be expanded as needed to accommodate study designs with more interactors

VecTraits Column Definitions

VecTraits Required Columns

A minimum set of columns required in the dataset for successful upload

These cannot be missing

They should include all available data

If a required column is missing, file may fail to upload without any error

VecTraits Required Columns

Original Trait Value
Original Trait Unit
Original ID
Location
Location Date Precision

Submitted By
Contributor Email
Citation
Embargo Release

More Column Definitions

Original Trait Name: trait as named in source
Original Trait Def: definition of trait as named in source
Original Error: error recorded in study (additional column for units)
Interactor1: lowest taxonomic identity of main study organism
Interactor1 Number: if grouped, number of individuals (i.e., experiment sample size)
Interactor1 Temp: experimental temperature (additional column for units)

More Column Definitions

Interactor2: lowest taxonomic identity of additional organisms in experiment Note: can be expanded to accomodate experimental design
Second Stressor: additional experimental factors (e.g., CO2)
Notes: any additional information not captured with existing fields

Where to Find Template and Instructions

Note: Must be logged into VectorByte account

VecTraits Template

EXERCISE: Take a moment to download the VecTraits template

Formatting Your Data

Do not need to natively format experimental data for VecTraits
Should still adhere to minimum information standard (MIReVTD)

Study Traits

What is the main trait or outcome being measured in your study?
Sometimes multiple traits measured at once
May require formatting into separate datasets

Individual Observations vs Grouped Data

How were data recorded in the study?
Individual measurements
Group averages (include sample sizes!)
Repeated measurements

Formatting Dates

Most fields do not have strict formatting guidelines to ensure flexibility
Dates are an exception
There could be errors due to ambiguity based on localization
For example, 5/2/2021 could refer to the 5th of February or the 2nd of May
The desired date format is YYYY-MM-DD
This is the only way to minimize errors and guarantee that dates are recorded as expected

Study Parameters

Record all controlled aspects of experiment
Anything that was manipulated in the study (e.g., temperature, humidity, food concentration)
Ideally enough information to replicate experiment

Other Experimental Stressors

Some studies may include other factors in addition to trait and main experimental parameters (e.g., temperature)
Some common examples are CO2 concentrations or pesticide exposure

Vector Taxonomy

Full taxonomic grouping in study/paper \(\rightarrow\) ‘interactorx’ column
Can include information on subspecies, species complex, biotype, etc
Dedicated columns for taxonomic groupings (Kingdom, Phylum, etc.)

‘interactorxspecies’ column should only contain specific epithet
Add additional interactors (e.g., interactor2…) with associated taxonomy for other organisms in study
Interactors may include pathogens, hosts, and plants

Laboratory Conditions

What factors were controlled in the laboratory?
These need to be recorded!
Ambient holding temperature, relative humidity, photoperiod, rearing temperature, feeding concentrations, etc.
Anything that was not an experimental parameter, but still controlled or recorded as part of the experiment

Geographic Information

GPS coordinates or location description of where field-collected specimens orginate
DO NOT put location of laboratory or facility where experiment was conducted
DO NOT put coordinates for established lab colonies
These details can be recorded in other fields

Additional Interactors

Interactor1 is typically the vector being studied
Additional interactors can be recorded for other named organisms in study
The VecTraits template can be expanded to accommodate additional species
These may include parasites, hosts, viruses, plant substrate, etc

Digitizing Trait Data

Full data not always available
Try to contact study authors
Some data and results are only provided in tables and figures

Digitizing Published Studies

Check supplemental materials first
Consider reaching out to CA
Identify where requisite data are in paper
Tables are typically easier
Make sure to check text!
Make sure figures are displaying unique data
Check for data that will ensure usability (e.g., sample sizes, error, etc)

Manual Digitization

Time consuming
May not be practical for large groups
Great deal of control
Issues with agreement between digitizers
More of an issue when digitizing figures

Figure Digitization Tools

PlotDigitizer (plotdigitizer.com)
GraphReader (www.graphreader.com)
WebPlotDigitizer (automeris.io)

Finding Data in VecTraits

Downloading Data from VecTraits

Exercise: search the database and download a dataset

Choose a vector (or trait) and search the database
Review search results
Find a dataset and view details
Download and view dataset on your computer

Contributing Data to VecTraits

Common Sources of Upload Errors

Missing required columns
Special characters and accents (e.g., check citations, units, and names)
Incorrect character type for column (e.g., characters in numeric)
Autofill for unique ID or citation columns (e.g., spreadsheet autofill options will increase numbers incrementally)
If there are multiple errors, may not get a specific warning

Citing VecTraits/Data Ecosystem

LR Johnson, L Cator, SSC Rund, SJ Ryan, PJ Huxley, and S Pawar. 2023. “VecTraits Explorer”. University of Notre Dame. DOI: 10.7274/28020782
SJ Ryan, LR. Johnson, CA Lippi, L Cator, S Pawar, and SSC Rund. 2023. “The Vector Data Ecosystem.” University of Notre Dame. DOI: 10.7274/27854508 or
CA Lippi, SSC Rund, SJ Ryan, Characterizing the Vector Data Ecosystem, Journal of Medical Entomology, Volume 60, Issue 2, March 2023, Pages 247–254

For more info: www.vectorbyte.org/blog/how-to-cite-us