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== iDigBio API Overview ==
== iDigBio API Overview ==


This document serves as the starting page of official documentation for the iDigBio Application Programming Interface (API).
This document serves as the starting page of official documentation for the iDigBio Application Programming Interfaces ([https://en.wikipedia.org/wiki/Application_programming_interface APIs]).


[https://www.idigbio.org/ Integrated Digitized Biocollections (iDigBio)] is the National Resource for Advancing Digitization of Biodiversity Collections (ADBC) funded by the National Science Foundation. Through ADBC, data and images for millions of biological specimens are being made available in electronic format for the research community, government agencies, students, educators, and the general public. iDigBio is a data aggregator. This means that data is provided to iDigBio through various publishing mechanisms.
[https://www.idigbio.org/ Integrated Digitized Biocollections (iDigBio)] is the National Resource for Advancing Digitization of Biodiversity Collections (ADBC) funded by the National Science Foundation. Through ADBC, data and images for millions of biological specimens are being made available in electronic format for the research community, government agencies, students, educators, and the general public. iDigBio is a data aggregator. This means that data is provided to iDigBio through various publishing mechanisms.


Many consumers of the iDigBio aggregated data will choose to use the [https://www.idigbio.org/portal iDigBio Portal web site]. Additionally, to facilitate integration of iDigBio data with other web sites or services, iDigBio provides an API.
Many consumers of the iDigBio aggregated data will choose to use the [https://www.idigbio.org/portal iDigBio Portal web site]. Although our portal has many features and is the easiest interface to use, to facilitate integration of iDigBio data with other web sites, services, or research uses, iDigBio provides APIs in order to provide direct access to our data. We ourselves make use of these APIs in our portal and other data services so any functionality you see there, as well as functions not available through the portal, can be done through APIs yourself.


The iDigBio API is an abstraction layer for retrieving data from the iDigBio back-end data systems. This abstraction allows reuse and mashup of aggregated data without needing to understand the complex underlying details of the back-end data storage. Currently, the public API supports GET requests for data read operations only. The iDigBio API is a RESTful web service that delivers data primarily as JSON documents.
The iDigBio APIs are an abstraction layer for retrieving data from the iDigBio back-end data systems. This abstraction allows reuse and mashup of aggregated data without needing to understand the complex underlying details of the back-end data storage. Currently, the public APIs support HTTP GET and POST requests for data read operations only. The iDigBio APIs are RESTful web services that delivers data primarily as [https://www.json.org/ JSON] documents.


Programmatic Search is a special case. See the section [[#Searching iDigBio]] below for more information.
All iDigBio APIs are publicly available with no user authentication required or rate limits applied.


== Specification ==
== Quick Start Example ==


The current [[iDigBio API v1 Specification]] includes detailed information about the API endpoints, parameters, and values.
The search API is our most useful for most people. Below is a simple example of searching for all records in a given genus to provide you with an example of how this API looks. You can simply click the link in your browser to make the API call and get results:


The upcoming iDigBio API v2 specification is available in the [https://github.com/idigbio/idigbio-search-api/wiki iDigBio Search API github wiki].
[https://search.idigbio.org/v2/search/records?rq={%22genus%22:%22acer%22} https://search.idigbio.org/v2/search/records?rq={"genus":"acer"}]


== Examples ==
(You might want to install a JSON viewing plugin in your browser such as JSONView for Chrome.)


The [[iDigBio API Examples]] page contains many more examples of the iDigBio API in action.
== iDigBio API Mailing List ==


== Quick Start ==
Please join our list at '''idigbio-api-users-l@lists.ufl.edu''' if you are using our APIs. Besides providing notification of API changes, the mailing list gives direct access to the iDigBio API developers and is a good place to ask questions or give and receive feedback.


iDigBio API endpoints follow the general form:
You can join via the web at: http://lists.ufl.edu/cgi-bin/wa?A0=IDIGBIO-API-USERS-L


;<pre>http://api.idigbio.org/{api_version}{endpoint}{optional_parameters}</pre>
== iDigBio APIs ==


In nearly all cases, a successful API request returns data as a JSON-formatted document.
There are several APIs you can use to retrieve data from iDigBio: Search, Download, Record, and Media.


=== Quick Start Example - Family Curculionidae ===
=== Search API ===


Let us say that we have already located the specimen record for a particular Curculionidae specimen (a family of weevils). The specimen record for our particular example is identified by the following iDigBio GUID:
The version 2 Search API was released in June 2015 and is the current API that the portal and other iDigBio services are based on. Full documentation for this API is available in the [https://github.com/idigbio/idigbio-search-api/wiki idigbio-search-api Github wiki] with the source code. The search API allows you to retrieve limited sets of data in response to custom queries and is typically the one people use.


<code>
You can see more [https://github.com/iDigBio/idigbio-search-api/wiki/Examples iDigBio Search API examples] in the [https://github.com/iDigBio/idigbio-search-api/wiki/Examples github wiki].
"idigbio:uuid" : "354210ae-4aa3-49d2-8a66-78a86b019c7b"
</code>


To retrieve a specimen record from v1 of the API with the above iDigBio UUID, we issue an HTTP "GET" request to the following endpoint:
=== Download API ===


<code>
The Download API can be used to generated [https://en.wikipedia.org/wiki/Darwin_Core_Archive Darwin Core archives] containing any amount of data up to everything that is in iDigBio. This API is documented on the [[iDigBio Download API]] wiki page. This API is useful when the size of the data you want exceeds what you can get through the search API. Be aware that this is not an interactive API; requests will result in a queued job being started to make the Darwin Core archive and you will be informed when it is ready to download later.
http://api.idigbio.org/v1/records/354210ae-4aa3-49d2-8a66-78a86b019c7b
</code>


and receive the following JSON document from the API (in this case, formatted for readability):
For a detailed discussion of the data included in one of our downloads, you can read our [https://www.idigbio.org/content/understanding-idigbios-data-downloads Understanding iDigBio's Data Downloads] blog post.


<pre>
=== Record & Media APIs ===
{
  "idigbio:uuid" : "354210ae-4aa3-49d2-8a66-78a86b019c7b",
  "idigbio:etag" : "02736fd7318eafed62a4a5ff35175a27fa63983e",
  "idigbio:links" : {
      "mediarecord" : [
        "http://api.idigbio.org/v1/mediarecords/59141135-813a-4db1-a527-009ae6d17101"
      ],
      "owner" : [
        "872733a2-67a3-4c54-aa76-862735a5f334"
      ],
      "recordset" : [
        "http://api.idigbio.org/v1/recordsets/69037495-438d-4dba-bf0f-4878073766f1"
      ]
  },
  "idigbio:version" : 2,
  "idigbio:createdBy" : "872733a2-67a3-4c54-aa76-862735a5f334",
  "idigbio:recordIds" : [
      "urn:uuid:b036a012-ba1e-41e0-a39a-76fc253640cf"
  ],
  "idigbio:dateModified" : "2014-04-22T07:33:16.129Z",
  "idigbio:data" : {
      "dwc:day" : "16",
      "dwc:identifiedBy" : "CPMAB",
      "idigbio:recordId" : "urn:uuid:b036a012-ba1e-41e0-a39a-76fc253640cf",
      "dwc:catalogNumber" : "NAUF4A0013309",
      "dwc:locality" : "Box Cyn. Santa Rita Mts.",
      "dwc:occurrenceID" : "1063507",
      "dwc:year" : "1967",
      "dwc:recordedBy" : "C.D. Johnson",
      "dwc:scientificName" : "Curculionidae",
      "dwc:basisOfRecord" : "PreservedSpecimen",
      "dwc:family" : "Curculionidae",
      "symbiotaverbatimScientificName" : "Curculionidae",
      "dwc:collectionCode" : "NAUF",
      "dcterms:modified" : "2013-12-20 13:00:36",
      "dwc:country" : "USA",
      "dcterms:references" : "http://symbiota4.acis.ufl.edu/scan/portal/collections/individual/index.php?occid=1063507",
      "dwc:eventDate" : "1967-08-16",
      "dwc:scientificNameAuthorship" : "Latreille, 1802",
      "dwc:collectionID" : "urn:uuid:c87a0756-fdd7-4cb6-9921-ca5774f8330e",
      "dwc:minimumElevationInMeters" : "1524",
      "dwc:verbatimElevation" : "5000'",
      "dwc:startDayOfYear" : "228",
      "dwc:month" : "8",
      "dwc:rights" : "http://creativecommons.org/licenses/by-nc-sa/3.0/",
      "dwc:stateProvince" : "Arizona",
      "dwc:genus" : "Curculionidae",
      "dwc:institutionCode" : "NAU",
      "dwc:county" : "Pima"
  }
}
</pre>


The [[iDigBio API Examples]] page shows how we might use Search features to find specimen records that match specific criteria such as Family, Genus, or Scientific Name.
The record and media APIs are of limited use for most people outside iDigBio. They are intended to return a single specimen or media's unprocessed information. You must know the iDigBio record or media identifier to be able to request data from this API. The most common use of the media API is to retrieve a link to an image as stored at iDigBio from a media record identifier. The significant additional functionality the record API provides is access to prior versions of records stored in iDigBio. Other APIs only interact with the most recent record version.


== Searching iDigBio ==
'''ToDo:''' Make documentation for v2 of this API publicly accessible.


=== Search Portal and Bulk Record Downloads ===
== Other Ways of Accessing Data ==


The recommended method for searching iDigBio is to use the Portal search, not the API. The portal also provides bulk download capabilities for aquiring larger sets of data.  See: https://www.idigbio.org/portal
=== Specimen Web Map Module ===


=== Elasticsearch Overview ===
The iDigBio [https://www.idigbio.org/portal/search Portal Search page] map is also provided as a stand-alone module for use in any third-party web site. If you are a software developer interested in integrating this map, please see the [https://github.com/iDigBio/idb-portal/blob/master/README.md#stand-alone-map-module-use documentation on Github] provided as part of the portal source code.


The iDigBio API query/search capabilities are currently in beta testing [https://github.com/idigbio/idigbio-search-api/wiki]. At present we also provide a public-facing interface to the back-end Elasticsearch system. This is the same interface that is used by the iDigBio Portal search but allows experienced programmers to search for data in ways beyond what is provided by the Portal.
=== Client Libraries ===


'''Note: Direct queries to the iDigBio Elasticsearch service should be considered an Advanced operation.'''
Client libraries, packages, and modules are pieces of software that make it easier to interface with the iDigBio API from a specific programming language. We have developed and maintain libraries for the following languages:


According to the [http://www.elasticsearch.org/overview/elasticsearch/ Elasticsearch project site], Elasticsearch is a "flexible and powerful open source, distributed, real-time search and analytics engine."  Elasticsearch provides a RESTful web services interfaces and returns data in JSON format.
==== ridigbio R Package for the Search API ====


More detailed information on iDigBio Elasticsearch capabilities is available in [[iDigBio API v1 Specification#Search]].
R is a free software environment for statistical computing and graphics. It compiles and runs on a wide variety of UNIX platforms, Windows and MacOS.


See [[iDigBio API Examples]] for Elasticsearch query examples that are specific to iDigBio.
The production version of this package is in [http://cran.r-project.org/web/packages/ridigbio/index.html CRAN]. The latest development version is available at https://github.com/idigbio/ridigbio


== Client Libraries ==
The ridigbio R package is an "official" client library in the iDigBio code repository.


Client libraries, packages, and modules are pieces of software that make it easier to interface with the iDigBio API. The following list includes the known iDigBio libraries that are currently available.
==== iDigBio Python Library for Search API ====


=== ridigbio R Package for Search API ===
The Python client library is available via PyPI:


Coming soon!
https://pypi.python.org/pypi/idigbio
 
or just use pip:
 
'''pip install idigbio'''
 
The client code can also be found at github if you wish to help develop the library:
 
https://github.com/idigbio/idigbio-python-client/
 
The iDigBio Python library is an "official" client library in the iDigBio code repository.
 
==== idigbio_client Ruby Gem for the Search API ====
 
The idigbio_client ruby gem is available:
 
https://rubygems.org/gems/idigbio_client
 
which can be installed via:
 
'''gem install idigbio_client'''
 
The idigbio_client ruby gem is a "community-supported" client library with software repository currently at:
 
https://github.com/GlobalNamesArchitecture/idigbio_client
 
== Suggestions? ==
 
If you are in need of other client libraries or iDigBio API features, please use the [https://www.idigbio.org/modal_forms/nojs/contact feedback button] to submit your request.
 
 
== Technical Details ==
 
We describe the [[iDigBio API Software]] used to provide these APIs in a separate document.

Latest revision as of 08:05, 10 July 2018


iDigBio API Overview

This document serves as the starting page of official documentation for the iDigBio Application Programming Interfaces (APIs).

Integrated Digitized Biocollections (iDigBio) is the National Resource for Advancing Digitization of Biodiversity Collections (ADBC) funded by the National Science Foundation. Through ADBC, data and images for millions of biological specimens are being made available in electronic format for the research community, government agencies, students, educators, and the general public. iDigBio is a data aggregator. This means that data is provided to iDigBio through various publishing mechanisms.

Many consumers of the iDigBio aggregated data will choose to use the iDigBio Portal web site. Although our portal has many features and is the easiest interface to use, to facilitate integration of iDigBio data with other web sites, services, or research uses, iDigBio provides APIs in order to provide direct access to our data. We ourselves make use of these APIs in our portal and other data services so any functionality you see there, as well as functions not available through the portal, can be done through APIs yourself.

The iDigBio APIs are an abstraction layer for retrieving data from the iDigBio back-end data systems. This abstraction allows reuse and mashup of aggregated data without needing to understand the complex underlying details of the back-end data storage. Currently, the public APIs support HTTP GET and POST requests for data read operations only. The iDigBio APIs are RESTful web services that delivers data primarily as JSON documents.

All iDigBio APIs are publicly available with no user authentication required or rate limits applied.

Quick Start Example

The search API is our most useful for most people. Below is a simple example of searching for all records in a given genus to provide you with an example of how this API looks. You can simply click the link in your browser to make the API call and get results:

https://search.idigbio.org/v2/search/records?rq={"genus":"acer"}

(You might want to install a JSON viewing plugin in your browser such as JSONView for Chrome.)

iDigBio API Mailing List

Please join our list at idigbio-api-users-l@lists.ufl.edu if you are using our APIs. Besides providing notification of API changes, the mailing list gives direct access to the iDigBio API developers and is a good place to ask questions or give and receive feedback.

You can join via the web at: http://lists.ufl.edu/cgi-bin/wa?A0=IDIGBIO-API-USERS-L

iDigBio APIs

There are several APIs you can use to retrieve data from iDigBio: Search, Download, Record, and Media.

Search API

The version 2 Search API was released in June 2015 and is the current API that the portal and other iDigBio services are based on. Full documentation for this API is available in the idigbio-search-api Github wiki with the source code. The search API allows you to retrieve limited sets of data in response to custom queries and is typically the one people use.

You can see more iDigBio Search API examples in the github wiki.

Download API

The Download API can be used to generated Darwin Core archives containing any amount of data up to everything that is in iDigBio. This API is documented on the iDigBio Download API wiki page. This API is useful when the size of the data you want exceeds what you can get through the search API. Be aware that this is not an interactive API; requests will result in a queued job being started to make the Darwin Core archive and you will be informed when it is ready to download later.

For a detailed discussion of the data included in one of our downloads, you can read our Understanding iDigBio's Data Downloads blog post.

Record & Media APIs

The record and media APIs are of limited use for most people outside iDigBio. They are intended to return a single specimen or media's unprocessed information. You must know the iDigBio record or media identifier to be able to request data from this API. The most common use of the media API is to retrieve a link to an image as stored at iDigBio from a media record identifier. The significant additional functionality the record API provides is access to prior versions of records stored in iDigBio. Other APIs only interact with the most recent record version.

ToDo: Make documentation for v2 of this API publicly accessible.

Other Ways of Accessing Data

Specimen Web Map Module

The iDigBio Portal Search page map is also provided as a stand-alone module for use in any third-party web site. If you are a software developer interested in integrating this map, please see the documentation on Github provided as part of the portal source code.

Client Libraries

Client libraries, packages, and modules are pieces of software that make it easier to interface with the iDigBio API from a specific programming language. We have developed and maintain libraries for the following languages:

ridigbio R Package for the Search API

R is a free software environment for statistical computing and graphics. It compiles and runs on a wide variety of UNIX platforms, Windows and MacOS.

The production version of this package is in CRAN. The latest development version is available at https://github.com/idigbio/ridigbio

The ridigbio R package is an "official" client library in the iDigBio code repository.

iDigBio Python Library for Search API

The Python client library is available via PyPI:

https://pypi.python.org/pypi/idigbio

or just use pip:

pip install idigbio

The client code can also be found at github if you wish to help develop the library:

https://github.com/idigbio/idigbio-python-client/

The iDigBio Python library is an "official" client library in the iDigBio code repository.

idigbio_client Ruby Gem for the Search API

The idigbio_client ruby gem is available:

https://rubygems.org/gems/idigbio_client

which can be installed via:

gem install idigbio_client

The idigbio_client ruby gem is a "community-supported" client library with software repository currently at:

https://github.com/GlobalNamesArchitecture/idigbio_client

Suggestions?

If you are in need of other client libraries or iDigBio API features, please use the feedback button to submit your request.


Technical Details

We describe the iDigBio API Software used to provide these APIs in a separate document.

Retrieved from "http://www.idigbio.org/wiki/index.php?title=IDigBio_API&oldid=27663"