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GBIF Governing Board 20
Module 6B: New GBIF Tools II
2013 Portal and NPT Startup
Daniel Amariles
IT Leader, National Biodi...
SUMMARY
The development of the new GBIF portal offers
in a complete API to query data published in
the network.
This is an...
INDEX
1. Introduction to NPT Startup
2. Introduction to the 2013 Data Portal
3. The Data Portal API
4. From the Portal to ...
INTRODUCTION TO
NPT STARTUP
“NPT Startup is a
Drupal site that sets
up a web presence
for GBIF Participant
Nodes.”
INTRODUCTION TO
NPT STARTUP
Demo site
http://nptstartup.gbif.org/
https://github.com/gbif/gbif-npt-startup/releases
GitHub...
NPT STARTUP FEATURES
• Biodiversity information coming from the GBIF Data
Portal and from the Encyclopedia of Life.
NPT STARTUP FEATURES
• Common website features like news, forums and blogs
so the website can be used by a GBIF Participan...
NPT STARTUP FEATURES
• Includes an initial country checklist, generated by assembling
scientific names that are extracted ...
NPT STARTUP FEATURES
• Further information available about a species includes
a species description and media from the Enc...
NPT STARTUP FEATURES
• At the country level, NPT Startup provides some basic
facts on data publishing activities.
NPT STARTUP FEATURES
• Shows scientific articles and reports using GBIF-
mediated data, published by authors from the coun...
INDEX
1. Introduction to NPT Startup
2. Introduction to the 2013 Data Portal
3. The Data Portal API
4. From the Portal to ...
INTRODUCTION TO
THE 2013 DATA PORTAL
MAIN SECTIONS
SPECIES SEARCH
Search
results
Filters
- Base taxonomy
- Higher taxon
- Rank
- Status
- Habitat
- Name Type
SPECIE OVERVIEW
General
information
External
Content
Basic stats
Taxonomic
information
Occurrences distribution
INDEX
1. Introduction to NPT Startup
2. Introduction to the 2013 Data Portal
3. The Data Portal API
4. From the Portal to ...
DATA PORTAL API
An interface to
access the data
published through the
GBIF network using
Web Services.
DATA PORTAL API
GBIF Portal Registry API:
http://portaldev.gbif.org/developer/registry
GBIF All Webservices API:
http://de...
AVAILABLE API
• Checklist Bank Services: Name usage
• Checklist Bank Services: GBIF Backbone Taxon Lookup
• Checklist Bank...
Names API
http://api.gbif.org/lookup/name_usage/?name=oenanthe&kingdom=plants
Dataset API
http://api.gbif.org/dataset/52a4...
INDEX
1. Introduction to NPT Startup
2. Introduction to the 2013 Data Portal
3. The Data Portal API
4. From the Portal to ...
QUERYING
ORGANIZATION Get organization UUID
10980920-6dad-11da-ad13-b8a03c50a86210980920-6dad-11da-ad13-b8a03c50a862
API Base URL + Endpoint URL + Organization UUID
QUERYING AN
ORGANIZATION
http://api.gbif.org/organization/10980920-6dad-11...
USE THE API DATA
Example: http://data.sibcolombia.net/publicadores/provider/3
INDEX
1. Introduction to NPT Startup
2. Introduction to the 2013 Data Portal
3. The Data Portal API
4. From the Portal to ...
MAPPING API v1.0
“Looking to overlay GBIF content on
your maps? Try this simple to use and
flexible tile rendering service...
This service is intended for use with commonly used map clients
such as the Google Maps API or Leaflet JS library.
These l...
CUSTOMIZING LAYER CONTENT
El formato de la URL es el siguiente:
With the following required parameters:
type: TAXON, DATAS...
CUSTOMIZING LAYER CONTENT
• Basis of record
– Fossil
– Living specimen
• Year Range
– Observations year range
– Specimens’...
STYLING A LAYER
“Styling the configured layer is controlled through either the
colors parameter or the palette parameter.”...
INDEX
1. Introduction to NPT Startup
2. Introduction to the 2013 Data Portal
3. The Data Portal API
4. From the Portal to ...
USE THE API DATA
Build query to the GBIF MAPS API
Set the layer on your map browser
USE THE API DATA
Example: http://maps.sibcolombia.net/
INDEX
1. Introduction to NPT Startup
2. Introduction to the 2013 Data Portal
3. The Data Portal API
4. From the Portal to ...
PRACTICAL EXERCISE:
PLAYING WITH PORTAL API
1. Explore data with a REST Client
2. Try to imagine how would you like to use...
WEB SERVICES TOOLS
Some recommended REST clients
Advanced REST client
Google Chrome extensions
http://code.google.com/p/re...
WIREFRAMING
Recommended wireframing tool
https://cacoo.com/
GBIF Governing Board 20
Module 6B: New GBIF Tools II
2013 Portal and NPT Startup
Daniel Amariles
IT Leader, National Biodi...
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Module 6B - New GBIF Tools II 2013: Portal and NPT Startup

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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.

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  • NPT Startup
  • NPT Startup
  • NPT Features
  • NPT Features
  • NPT Features
  • NPT Features
  • NPT Features
  • NPT Features
  • This is the GBIF 2013 Data Portal
  • These are the main sections of the Data Portal, exploring by occurrences, datasets, species and countries
  • Navigating though an specie search, show the results related with the search and also there is the capability to filter the results.
  • The specie overview show some helpful sections, besides the data access.
  • What ’ s the Data Portal API? An interface to access the data published through the GBIF network using Web Services.
  • These are the current available services
  • API Examples
  • Get the organization UUID
  • Getting information for an organization
  • The API may be used to show information in your website/portal
  • This is the GBIF 2013 Data Portal
  • The mapping API
  • Tha mapping API is designed to used over map clients
  • The layer may be customized by using the following filters
  • The layer may be customized by using the following filters
  • The layer may be styled by using a default color palette or defining exactly what colors to use
  • Integrate the layers from GBIF Maps Service into your map browser development
  • Integrated density layer from GBIF Maps Service into SiB Colombia Map platform
  • This is a practical excercise
  • Recomended rest clients
  • Recomended for wireframing
  • Transcript of "Module 6B - New GBIF Tools II 2013: Portal and NPT Startup"

    1. 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. 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. 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. 4. INTRODUCTION TO NPT STARTUP “NPT Startup is a Drupal site that sets up a web presence for GBIF Participant Nodes.”
    5. 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. 6. NPT STARTUP FEATURES • Biodiversity information coming from the GBIF Data Portal and from the Encyclopedia of Life.
    7. 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. 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. 9. NPT STARTUP FEATURES • Further information available about a species includes a species description and media from the Encyclopedia of Life (EOL).
    10. 10. NPT STARTUP FEATURES • At the country level, NPT Startup provides some basic facts on data publishing activities.
    11. 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. 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. 13. INTRODUCTION TO THE 2013 DATA PORTAL
    14. 14. MAIN SECTIONS
    15. 15. SPECIES SEARCH Search results Filters - Base taxonomy - Higher taxon - Rank - Status - Habitat - Name Type
    16. 16. SPECIE OVERVIEW General information External Content Basic stats Taxonomic information Occurrences distribution
    17. 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. 18. DATA PORTAL API An interface to access the data published through the GBIF network using Web Services.
    19. 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. 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. 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. 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. 23. QUERYING ORGANIZATION Get organization UUID 10980920-6dad-11da-ad13-b8a03c50a86210980920-6dad-11da-ad13-b8a03c50a862
    24. 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. 25. USE THE API DATA Example: http://data.sibcolombia.net/publicadores/provider/3
    26. 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. 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. 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. 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. 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. 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. 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. 33. USE THE API DATA Build query to the GBIF MAPS API Set the layer on your map browser
    34. 34. USE THE API DATA Example: http://maps.sibcolombia.net/
    35. 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. 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. 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. 38. WIREFRAMING Recommended wireframing tool https://cacoo.com/
    39. 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
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