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Ana Carolina Peralta

Marine Biologist - USF

Caribbean OBIS Node Manager

Tylar Murray

MBON

Data Management - USF

Nuno Álvaro

Marine Ecologist

University of the Azores

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Meet the instructors!

Gonzalo Bravo CENPAT - MBON Pole to Pole data manager

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Adriano Lima �AIR Centre

Researcher �MBON Scientific Programmer

Joana Soares AIR Centre Researcher MBON Ex. Secretary

Meet the Expert Advisors!

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Participants introduction:

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Name, affiliation/country and research area.

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AIR Centre’s Mission & Strategy

An organisation based on science

PEOPLE

PLANET

PARTNERSHIPS

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BRAZIL

PORTUGAL

CABO

VERDE

SPAIN

Headquarters

Terceira Island, Azores

Secretariat

Lisbon Office

ANGOLA

SOUTH

AFRICA

NAMIBIA

Headquarters: TERINOV, Science and Technology Park

Terceira Island, Azores

FRANCE

COLOMBIA

GUATEMALA

MOROCCO

NIGERIA

PERU

UK

SÃO TOMÉ AND PRÍNCIPE

AIR Centre’s Network

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Space Systems & Applications

Data Science, Cloud Infrastructure, & Development

Biodiversity &

Blue Economy

Ocean Policy

& Stakeholder Engagement

  • Marine Biodiversity
  • Blue Economy
  • Sustainable Fisheries & Aquaculture

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  • Stakeholders' engagement
  • Ocean Literacy
  • Awareness & Advocacy

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Earth Observation Lab, ESA LAB@Azores

Secretariat

AIR Datacentre

Data centre +

Direct Receiving Station

AIR Centre’s Thematic Programmes

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Co-Chairs & Executive Secretariat

Joana Soares

Adriano Lima

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MBON (Marine Biodiversity Observation Network)

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Stay connected

Mailing list

To join the MBON, go to the GEO BON website and select MBON as one of the interests in your profile. You will join the MBON List server and receive our news.

LinkedIn

linkedin.com/in/marine-biodiversity-observation-network-mbon-8a0905397

X

x.com/MarineBON1

WhatsApp community

chat.whatsapp.com/IqqB2mRuNfIIEaCkdd1H7B

Website

marinebon.org

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Watch the recordings: youtube.com/playlist?list=PL-3G0PUXakeY0GBp-VI6yRSfUb-GRiOCx

Contact: joana.soares@aircentre.org

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Enhancing Marine Biodiversity Data Collection and Publication: 2025

Data standards

Following good practices for standardising biological data, using widely accepted biodiversity standards like Darwin Core.

Field workday

Collection and processing of benthic photo-quadrat imagery and their analysis following MBON Pole to Pole monitoring protocols, aiming to enhance capacity for long-term monitoring of rocky intertidal communities.

Dataset published in OBIS: ipt.iobis.org/caribbeanobis/resource?r=rockyshore_mbon_azores&v=1.8

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Open Network With Regional & Thematic Working Groups

https://marinebon.org/

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Marine Biodiversity Observation Network - MBON

  • Not a formal institution but a networking mechanism
  • Community of practice focused on operational monitoring of biodiversity

Anyone interested in marine life and biodiversity research can participate and help accomplish this goal.

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Biodiversity data available in open, standardized formats is a foundation of global biodiversity assessment.

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https://marinebon.org/about-us/

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MBON dataset highlight

  • Zooplankton net tows
  • Taxa imaged using
    • Microscopy
    • PlanktoScope
    • OceanSpace Aquatic Imager
  • Taxa identified with
    • Taxonomist expertise
    • EcoTaxa for machine classifications

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  • Taxonomic Occurrence Data -

When, where, & what Taxa?

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https://marinebon.github.io/p2p/about.html

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Workshop Schedule & Software Setup

marinebon.org/mbon-air-workshop-2026

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Module 1: Planning for your data collection

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Research Data Life Cycle

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Azores Intertidal:

  • Mostly rocky coast with boulders and cobbles
  • Dominated by macroalgae
  • Poor in animal diversity

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- Three levels:

  • High shore
  • Middle shore
  • Low shore

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Azores Subtidal:

  • Rocky substrates,
  • Sand
  • Mixed (sand with ricky reefs or boulders

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  • Dominated by macroalgae
  • Invertebrates:
    • Macro
    • Micro
  • fish

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Sampling Site: Porto e Piscina Natural de São Fernando

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https://www.exploreterceiraisland.com/mapa-interativo/local/63343/

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Collecting data: sampling collection (methods), materials, instruments, equipments etc.

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Sampling collection method

Find tides suitable for sampling

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Selection of sampling site

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Sampling collection method

Identification of intertidal levels (e.g. presence of Macroalgae, Barnacles, Mussels, bare substrate)

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Photographic record

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Workshop Fieldwork 2025

Based on MBON Pole-2-Pole Protocol : https://marinebon.org/p2p/methods_field_protocols.html

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Processing the photos and data generation

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MBON Pole to Pole Protocol 2019

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Processing and analysis:

-Rocky Shore Image collection

- CoralNet Image processing web service

https://coralnet.ucsd.edu/

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Research Data Life Cycle

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Sharing Data: OBIS data structure

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Example of an Occurrence Table

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Experiential learning section

Planning for your data collection

Exercise 1

  • Take a moment to explore this section of the OBIS manual before starting with your data collection templates: https://manual.obis.org/formatting.html (10 minutes)
  • Create your own data template (spreadsheet) for the samples you will be collecting tomorrow. You can use any of the data formatting tools suggested by OBIS:https://gbif-norway.github.io/dwc-excel-template-generator-js/ .

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BioData Mobilization Workshop - Azores, November 2025

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Module 2: Data Access from OBIS

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What is OBIS?

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www.obis.org

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28 Regional Nodes

7 Thematic Nodes

What are OBIS Nodes?

  • The main entry point to the OBIS Community.
  • They support data holders in integrating their data into OBIS.

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What does OBIS Nodes do?

  • Data Stewards
  • Data management
  • Community engagement
  • Capacity Building
  • Product development (stakeholder support)

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obis.org

An open database for Taxonomic Occurrence Data

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Uses Darwin Core (DwC) Framework

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https://obis.org/

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Experiential learning section

Data Access from OBIS

Exercise 2

  • Go to the OBIS website (www.obis.org) and click on the SEARCH button. Search for any options you have in the drop down menu and explore what you find.
  • Repeat the search by Area and type Azores. Select the option Portugal: Azores. You will get a general overview of the biodiversity recorded for the selected area: all datasets shared in OBIS for that area, the list of taxa registered. Click “Open in Mapper” and “Explore Occurrences” to explore further.
  • Repeat the search by Area and type your Area of Interest (your home country, continent or research area). Play around and explore the data.
  • For a more comprehensive explanation visit the OBIS manual: https://manual.obis.org/access.html

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Data Access from OBIS

OBIS YouTube channel - How-To videos - Accessing OBIS data from the Mapper and Portal

https://www.youtube.com/watch?v=9PSPEtqgjUI&t=225s

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Experiential learning section

Data Access from OBIS - part II

Exercise 2

  • Go to the OBIS website, click on Data menu>Mapper and create filters/layers of your interest. Try downloading the dataset; keep in mind that the download time could depend on your internet capacity and the amount of records. (15 min)
  • Click on Data>Mapper and create a polygon on your Area Of Interest (AOI). Apply all filters you want and play around with the tool. Try downloading the datasets. (15 min)

Note: We will go through the data content and formats in another section of the training.

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Data access

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Why Use DwC?

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  • Increased Reproducibility
  • Use shared analyses
    • Species Distribution Modeling
    • Change over time
    • Data visualizations
  • Contribute to global assessments

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  • Richness Estimate : ES50 (Hurlbert Index)
  • Estimated Species; 50 samples

https://app.marinesensitivity.org/h3-db/

cumulative sample count

number unique species

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  • The API is *the* way to access a database directly
    • Access all data in OBIS
    • Select and download a subset of data

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How to use and access the OBIS API Video

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Application Programming Interface (API)

https://blog.postman.com/api-diagram-guide/

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  • URL parameters : request data encoded in the URL. ? initiates, & separates, special characters are "url-encoded"
    • https://api.obis.org/v3/occurrence?scientificname=Larus%20fuscus&extensions=MeasurementOrFact
      • scientificname is first parameter
        • argument to the parameter is Larus%20fuscus
          • %20 is a "url-encoded" space (" ")
      • extensions is second parameter with argument MeasurmentOrFact
  • curl : a bash program for performing http requests
  • JSON : JavaScript Serial Object Notation : a generic data structure
  • pagination : API will show subset of data, you need to iterate through the "pages"

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Activity: Test out the API with the swagger interface:

https://api.obis.org/

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Application Programming Interface (API)

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  • Libraries exist to make using the API easier in a programming language.
    • builds the URLs for the API
    • does requests
    • handles pagination
    • more features - e.g. DataType conversion (JSON-to-DataFrame)

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OBIS API "Driver" Libraries

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  • R : robis

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  • https://posit.cloud/

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OBIS API "Driver" Libraries

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  • python : pyOBIS

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OBIS API "Driver" Libraries

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  • OBIS harvests from a Federated Network of IPT Servers
    • Anyone can create an IPT and request OBIS harvest from it
    • Regional OBIS Nodes manage IPTs & help researchers publish

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  • OBIS Manual on downloading & uploading with an IPT

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https://lifebit.ai/blog/federated-data-governance/

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IPT : Integrated Publishing Toolkit

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  • For global-scale analyses, download all OBIS records

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Full OBIS Exports

columnar format on-disk:

tabular abstraction:

[1] https://en.wikipedia.org/wiki/Data_orientation#Column-oriented

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"User Story"

  • Specific stories about what a specific user wants to do.
  • Often hypothetical.
  • "As ______ I want _______ so that _________."

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  • "As a researcher I want to seasonally-decompose my time-series data so that I can see anomalies in the residuals."
  • "As a researcher I want a function to calculate R^2 so that I can assess statistical significance."

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END of DAY 1

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