Global Biodiversity Information Facility – 1. About GBIF – 2. Definitions

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Global Biodiversity Information Facility – 1. About GBIF – 2. Definitions

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GBIFDay2014

HTML presentation for GBIF Days

On Github andrejjh / GBIFDay2014

Global Biodiversity Information Facility

Free and Open Access to Biodiversity Datadiscover, query, download and use GBIF mediated data

Seminar at Biodiversity Research Centre, UCL20th Novembre 2014

André Heughebaert Belgian Biodiversity Platform

Contents

About GBIF Definitions Services Discovering Querying Downloading Using Publishing

1. About GBIF

  • GBIF arose from a recommendation in 1999 by the Biodiversity Informatics Subgroup of the Megascience Forum, set up by the Organization for Economic Cooperation and Development (OECD).
  • GBIF vision: "A world in which biodiversity information is freely and universally available for science, society and a sustainable future."
  • By encouraging and helping institutions to publish data according to common standards, GBIF enables research not possible before, and informs better decisions to conserve and sustainably use the biological resources of the planet.

see GBIF and Open Access

1. About GBIF

Governance

  • GBIF is an international open data infrastructure, funded by governments.
  • It operates through a network of nodes, coordinating the biodiversity information facilities of Participant countries and organizations, collaborating with each other and the Secretariat to share skills, experiences and technical capacity.
  • Secretariat is located at Copenhagen, Denmark.
  • Governing board is convened once a year.

1. About GBIF

Key Documents

1. About GBIF

Participants

53 Countries Participants + 40 Associated Participants

2. Definitions

  • Open data is the idea that certain data should be freely available to everyone to use and republish as they wish, without restrictions from copyright, patents or other mechanisms of control.
  • (Species) Occurrence Data: evidence of the presence(or absence) of a species at certain time, at certain place.
  • (Species) Checklist: A list of accepted (or not) taxa assembled for a certain purpose.
  • DarwinCore Archive (DwC-A): is a Biodiversity informatics data standard that makes use of the Darwin Core terms to produce a single, self-contained dataset for species occurrence or checklist data.
  • Metadata: Data about the data such as author, geographic and time scope, methodology...

3. Services

Portal for visitors and webservices for applications.

3. Services

GBIF.org

  • Data Users
    • Discovery
    • Query
    • Download
  • Data Publishers
    • Usage statistics
    • Indexing issues

3. Services

Web services (JSON)

  • Species names (fuzzy) matching
  • Data Download
  • Registry (metadata)
{"usageKey":2440447,"scientificName":"Tursiops truncatus (Montagu, 1821)",
"canonicalName":"Tursiops truncatus","rank":"SPECIES","synonym":false,
"confidence":100,"matchType":"EXACT","kingdom":"Animalia","phylum":"Chordata",
"order":"Cetacea","family":"Delphinidae","genus":"Tursiops","species":"Tursiops truncatus",
"kingdomKey":1,"phylumKey":44,"classKey":359,"orderKey":733,"familyKey":5314,
"genusKey":2440446,"speciesKey":2440447,"class":"Mammalia"}

3. Services

Mendeley GBIF Library

Close to 2.000 peer-reviewed research publications have cited GBIF as a source of data, in studies spanning the impacts of climate change, the spread of pests and diseases, priority areas for conservation and food security. About 20 such papers are published each month.

3. Services

Other tools

Live Demo Signin to GBIF.org How to Dowload? Explore data+metadata Play with data
  • Paraguayan Types : SQLite, LibreOffice, multimedia
  • Milvus milvus : SQLite, OpenRefine, QGIS
  • ARABEL : SQLite, QGIS
Feedback to GBIF and Data Publishers

4. Discovering

Prerequisite: Signin on www.gbif.org Accept the Data Use Agreement

4. Discovering

Data distribution

Density of georeferenced species occurrence records through GBIF

500 millions occurrences records on 1.5 million species

4. Discovering

Explore occurrences

5. Querying

Adding Multimedia filter on Paraguayan Types

6. Downloading

6. Downloading

  • Citations.txt: How to cite your sources?
  • Occurrence.txt: Data indexed by GBIF
  • Rights.txt: Some possible restriction of use
  • Verbatim.txt: Original Data by data publisher
  • Multimedia.txt: related Mutlimedia URL

6. Downloading

Indexed

931143641 PRESERVED_SPECIMEN PY Tetragonoschema Thomson, 1857 National Museum of the Czech Republic Paraguay San Bernardino LECTOTYPE 167acd5c-9459-4e2d-86a1-ee9d6f5e5893 BIOCASE	2014-07-30T20:50Z 2014-11-07T14:19Z

Verbatim

931143641 PreservedSpecimen Paraguay Tetragonoschema medium Obenberger, National Museum of the Czech Republic Paraguay San Bernardino 1922 lectotype

6. Downloading

Multimedia

Tetragono schema Thomson, 1857. Lectotype from National Museum of the Czech Republic

885974538				http://collections.mnh.si.edu/media/index.php?irn=10064047										
888459823				http://collections.mnh.si.edu/media/index.php?irn=10089749										
931143641	StillImage	image/jpeg	http://pm.nm.cz/OpenUpData/Entomologie/Fotky/E143.jpg										Creative Commons (CC-by)	
888458933				http://collections.mnh.si.edu/media/index.php?irn=10050268

6. Downloading

Back to your downloads

7. Using

Data User Agreement

The quality and completeness of data cannot be guaranteed. Users employ these data at their own risk. Users shall respect restrictions of access to sensitive data. In order to make attribution of use for owners of the data possible, the identifier of ownership of data must be retained with every data record. Users must publicly acknowledge, in conjunction with the use of the data, the Data Publishers whose biodiversity data they have used. Data Publishers may require additional attribution of specific collections within their institution. Users must comply with additional terms and conditions of use set by the Data Publisher. Where these exist they will be available through the metadata associated with the data.
Will evolve towards CC0 or CC-BY

7. Using

Free to use Tools

7. Using

SQLite

7. Using

LibreOffice

7. Using

OpenRefine

7. Using

QuantumGIS

7. Using

Featured GBIF Data Use

Building national watch lists for invasive alien species Mapping the niche of Ebola host animals Using models to inform conservation policies

7. Using

Feedback

8. Publishing

Data publishing is the act of making data available on the Internet, so that they can be accessed, downloaded, analysed and reused by anyone for research or other purposes.

8. Publishing

Why publish my data?

  • You contribute to global knowledge about biodiversity
  • You receive proper credit for creating/curating data
  • You increase visibility of publishing institutions through good metadata authoring
  • You create new opportunities for collaboration

see How to publish your data through GBIF

Thank you for your attention

André Heughebaert, Belgian Biodiversity Platform

a.heughebaert@biodiversity.be

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