Protocols vs. methods

Understanding differences to better collect data

November 2026

Sophie Pamerlon

Yvan Le Bras

Olivier Norvez

Data engineer
@GBIF-France  

Scientific and technical coordinator
@PNDB  
@DataTerra  

Animation coordinator
@PNDB  
@DataTerra  
@Theia  

Data lifecycle

Data lifecycle

Context and issues

Context and issues :

  • Heterogeneity (data types, origin, standards) & diversity of “objects” to be linked together1
  • Loss of information over time2
  • Toward a better open science and reproducibility 3, 4

Context and issues : biodiversity monitoring

A monitoring scheme is the result of a compromise between three parameters: the size of the area surveyed, the density of sites sampled within this area and the observation effort per site1.

In the realm of biodiversity conservation, the imperative to harmonise monitoring protocols is paramount, driven by the need to enhance the comparability of data and thereby facilitate more effective conservation measures2.


Contrasted options for monitoring biodiversity, depending on the size of the area monitored, the density of sites and the observation effort per site, with different consequences on the grain of resolution and spatial variation and, therefore, on precision and generality of the observed ecological patterns3.

Couvet et al. (2011)

Definitions

A protocol is a detailed study plan explaining how data should be collected to answer a scientific question. It comprises: - a sampling plan that defines the rules for selecting the units; - one or more techniques and/or methods to be applied; - additional application rules (e.g. frequency, weather conditions, etc.). A protocol is standardised when it is precisely defined in a reference document and applicable by different operators in various territories1.

A method is a reproducible process with the aim of achieving an objective (e.g. estimation of a population size) by data collection. A method mobilises one or more techniques for the acquisition of data in the field, and can be part of a standardised protocol23.

A technique refers to the set of specific skills, processes, and/or tools employed to collect data associated with a parameter under observation. This concept is concrete in nature; a technique is implemented with the aim of achieving a precise result (Le Robert, 2022)4.

Definitions

Source : CAMPanule, 2022

Definitions




Table 1: Conditions proposed for extensive monitoring protocols over a large territory to maximise scientific output1
Characteristics of the protocol Scientific advantages
Density of sites sampled Assessment of fine-grained spatial variation, of diffuse cumulative interactions and of remote environmental effects
Monitoring of each species within a community Assessment of the state of the community Distinction of specific versus general impacts, comparing species responses based on their ecological traits
Standardised methods of observation Biodiversity measures can be compared in space and time (phenology, abundance, etc.)
Regular sampling (depends on generation times: annual for long-lived species like birds, but might be shorter for other species, and different in non-seasonal environments) Assessment of fine-grained temporal variation, which can be related to environmental factors of comparable variability such as climate and land-use factors

Good Level of FAIRness during data acquisition

  • Open data (CC-BY 4.0 compatible with Etalab)
  • Mandatory license
  • Direct link to download raw datasets
  • Thematic scope (All biodiversity including paleo- and archaeo-biodiversity)
  • Geographic scope (Data produced by France)
  • Temporal coverage (at least one data acquisition date)
  • Abstract
  • Title, authors and contacts
  • Acquisition framework (at least via a text field)
  • DOI / Unique identifiers
  • Taxonomic coverage (if taxa are present)
  • Keywords related to the Thesaurus
  • Data attributes (Dictionary of data attributes with units and descriptions)
  • Semantic annotation (Keywords and attribute names, unlimited usable resources)

Protocols.io

By sharing methods on protocols.io in your company or lab, you make sure that knowledge stays with the team, even if the scientist leaves. It also helps to keep the protocols up-to-date and make sure everyone is using the most recent version.

To discover Protocols.io Link

Protocols.io1

Protocols.io1

Protocols.io1

CAMPanule project

The CAMPanule project (CAtalogue of Methods and Protocols) aims to identify and characterize the techniques, methods and protocols for acquiring naturalist data in France.


Example of collection technique: Installation of a “Malaise” type entomological trap.
© Laura Savio

Example of protocol: Setting up an ultrasound recording device for a study on bats.
© Camille Gazay

CAMPanule project

The PROTOCOL spreadsheet


 For more information: CAMPanule => temporary link

CAMPanule project

The METHOD spreadsheet


 For more information: CAMPanule => temporary link

 Resources

Resources

  • Guide technique de la base de données CAMPanule - version 1 Gazay C., 2022. PatriNat. 25 p. Link

  • CAMPanule : partager les protocoles, méthodes et techniques de collecte de données naturalistes. Rapport d’accompagnement de la version 1. Gazay C., de Lacoste N., King-Gillies N., 2022. PatriNat. 43 p. Link

  • CAMPanule Link => temporary link

  • Protocols.io Link

  • PNDB resources on data collecting link

  • GBIF resources on biodiversity data mobilization link

  • Guide on harmonising biodiversity monitoring protocols across scales. Biodiversa + link