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.
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 5 th , 2013
Transcript
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
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