This presentation is an introduction to the new GBIF Portal API. It explores the possibilities of using it to connect GBIF mediated data to existing systems.

1. GBIF Governing Board 20
Module 6B: New GBIF Tools II
2013 Portal and NPT Startup
Daniel Amariles
IT Leader, National Biodiversity Information System of Colombia
Global Biodiversity Information Facility (GBIF)
Saturday, October 5th
, 2013

2. SUMMARY
The development of the new GBIF portal offers
in a complete API to query data published in
the network.
This is an introduction to the new system, for
those who are considering building (web)
applications using the API.
This presentation corresponds
to module 6B of the GB20
training course for Nodes
held in October 2013 in
Berlin, Germany.
Also, Here it will presented an introduction of
the NPT Startup and its main features.

3. INDEX
1. Introduction to NPT Startup
2. Introduction to the 2013 Data Portal
3. The Data Portal API
4. From the Portal to the API
5. The mapping API
6. Use the API data
7. Practical exercise

4. INTRODUCTION TO
NPT STARTUP
“NPT Startup is a
Drupal site that sets
up a web presence
for GBIF Participant
Nodes.”

5. INTRODUCTION TO
NPT STARTUP
Demo site
http://nptstartup.gbif.org/
https://github.com/gbif/gbif-npt-startup/releases
GitHub Repository
http://vimeo.com/63640790
Presentation video

6. NPT STARTUP FEATURES
• Biodiversity information coming from the GBIF Data
Portal and from the Encyclopedia of Life.

7. NPT STARTUP FEATURES
• Common website features like news, forums and blogs
so the website can be used by a GBIF Participant Node
as a communication website.

8. NPT STARTUP FEATURES
• Includes an initial country checklist, generated by assembling
scientific names that are extracted from species occurrence
data within a country available in the GBIF network.
• Biodiversity data of a species are shown as static species
distribution maps.

9. NPT STARTUP FEATURES
• Further information available about a species includes
a species description and media from the Encyclopedia
of Life (EOL).

10. NPT STARTUP FEATURES
• At the country level, NPT Startup provides some basic
facts on data publishing activities.

11. NPT STARTUP FEATURES
• Shows scientific articles and reports using GBIF-
mediated data, published by authors from the country
and/or about the biodiversity of the country.

12. INDEX
1. Introduction to NPT Startup
2. Introduction to the 2013 Data Portal
3. The Data Portal API
4. From the Portal to the API
5. The mapping API
6. Use the API data
7. Practical exercise

13. INTRODUCTION TO
THE 2013 DATA PORTAL

14. MAIN SECTIONS

15. SPECIES SEARCH
Search
results
Filters
- Base taxonomy
- Higher taxon
- Rank
- Status
- Habitat
- Name Type

16. SPECIE OVERVIEW
General
information
External
Content
Basic stats
Taxonomic
information
Occurrences distribution

17. INDEX
1. Introduction to NPT Startup
2. Introduction to the 2013 Data Portal
3. The Data Portal API
4. From the Portal to the API
5. The mapping API
6. Use the API data
7. Practical exercise

18. DATA PORTAL API
An interface to
access the data
published through the
GBIF network using
Web Services.

19. DATA PORTAL API
GBIF Portal Registry API:
http://portaldev.gbif.org/developer/registry
GBIF All Webservices API:
http://dev.gbif.org/wiki/display/POR/Webservice+API
“All services take parameters as query string
encoded GET key=value parameters and
respond with an json content type”

20. AVAILABLE API
• Checklist Bank Services: Name usage
• Checklist Bank Services: GBIF Backbone Taxon Lookup
• Checklist Bank Services: Search Service
• Checklist Bank Services: Metrics
• Registry Services: Node
• Registry Services: Organization
• Registry Services: Network
• Registry Services: Technical Installation
• Registry Services: Dataset
• Registry Services: Dataset Search Service
• Occurrence Services: Occurrence Record
• Occurrence Services: Search Service
• Occurrence Services: Download Service
• Cube Metrics Services: Occurrence Service
• Crawler Services: Dataset Crawl Service

21. Names API
http://api.gbif.org/lookup/name_usage/?name=oenanthe&kingdom=plants
Dataset API
http://api.gbif.org/dataset/52a423d2-0486-4e77-bcee-6350d708d6ff
Organization API
http://api.gbif.org/organization/10980920-6dad-11da-ad13-b8a03c50a862
Names Usage API
http://api.gbif.org/name_usage/1
Occurrence search API
http://api.gbif.org/occurrence/search?TAXON_KEY=6746
API CALL EXAMPLES

22. INDEX
1. Introduction to NPT Startup
2. Introduction to the 2013 Data Portal
3. The Data Portal API
4. From the Portal to the API
5. The mapping API
6. Use the API data
7. Practical exercise

23. QUERYING
ORGANIZATION Get organization UUID
10980920-6dad-11da-ad13-b8a03c50a86210980920-6dad-11da-ad13-b8a03c50a862

24. API Base URL + Endpoint URL + Organization UUID
QUERYING AN
ORGANIZATION
http://api.gbif.org/organization/10980920-6dad-11da-ad13-b8a03c50a86210980920-6dad-11da-ad13-b8a03c50a86210980920-6dad-11da-ad13-b8a03c50a862
To build the API call URL:
Use REST client to
EXPLORE THE CODE

25. USE THE API DATA
Example: http://data.sibcolombia.net/publicadores/provider/3

26. INDEX
1. Introduction to NPT Startup
2. Introduction to the 2013 Data Portal
3. The Data Portal API
4. From the Portal to the API
5. The mapping API
6. Use the API data
7. Practical exercise

27. MAPPING API v1.0
“Looking to overlay GBIF content on
your maps? Try this simple to use and
flexible tile rendering service”
http://uat.gbif.org/developer/maps

28. This service is intended for use with commonly used map clients
such as the Google Maps API or Leaflet JS library.
These libraries allow the GBIF layers to be visualized with other
content, such as those coming from Web Map Service (WMS)
providers. It should be noted that the mapping API is not a WMS
service, nor does it support WFS capabilities.
http://leafletjs.com/
MAPPING API v1.0

29. CUSTOMIZING LAYER CONTENT
El formato de la URL es el siguiente:
With the following required parameters:
type: TAXON, DATASET, COUNTRY or PUBLISHER
key : The appropriate key for the chosen type (a taxon key,
dataset/publisher UUID or 2 letter ISO country code)
http://api.gbif.org/map/density/tile?x={x}&y={y}&z={z}

30. CUSTOMIZING LAYER CONTENT
• Basis of record
– Fossil
– Living specimen
• Year Range
– Observations year range
– Specimens’ year range
– Other year ranges
The layer parameter is an optional multi-evaluated field in which
it is declared the layers to be combined by the server for this tile.
&layer=OBS_2010_2020&layer=SP_2010_2020&layer=OTH
_2010_2020&layer=LIVING&layer=FOSSIL
Example:

31. STYLING A LAYER
“Styling the configured layer is controlled through either the
colors parameter or the palette parameter.”
&colors=%2C100%2C%23FF000033%7C100%2C10000%2C
%2300FF0033%7C10000%2C%2C%230000FF33
Using colors parameter:
&palette=greens
Using palette parameter:

32. INDEX
1. Introduction to NPT Startup
2. Introduction to the 2013 Data Portal
3. The Data Portal API
4. From the Portal to the API
5. The mapping API
6. Use the mapping API layers
7. Practical exercise

33. USE THE API DATA
Build query to the GBIF MAPS API
Set the layer on your map browser

34. USE THE API DATA
Example: http://maps.sibcolombia.net/

35. INDEX
1. Introduction to NPT Startup
2. Introduction to the 2013 Data Portal
3. The Data Portal API
4. From the Portal to the API
5. The mapping API
6. Use the API data
7. Practical exercise

36. PRACTICAL EXERCISE:
PLAYING WITH PORTAL API
1. Explore data with a REST Client
2. Try to imagine how would you like to use those
data in your portal or application
3. Make one or more wireframes about how to
integrate the data
4. Homework: Implement a JSON client to get the
data

37. WEB SERVICES TOOLS
Some recommended REST clients
Advanced REST client
Google Chrome extensions
http://code.google.com/p/rest-client/
https://chrome.google.com/webstore/detail/advanced-rest-client/hgmloofddffdnphfgcellkdfbfbjeloo

38. WIREFRAMING
Recommended wireframing tool
https://cacoo.com/

39. GBIF Governing Board 20
Module 6B: New GBIF Tools II
2013 Portal and NPT Startup
Daniel Amariles
IT Leader, National Biodiversity Information System of Colombia
Global Biodiversity Information Facility (GBIF)
Saturday, October 5th
, 2013