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'''API Basics'''
[[Category:CYWG]]
[[Category:API]]
[[Category:Documentation]]


== iDigBio API Overview ==


The iDigBio API is a RESTful pattern HTTP API that primarily delivers data in JSON format. Currently the API supports GET requests or data read operations only.  
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]).


API URLs have several parameters in them, and typically follow the form of
[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.
<pre style="color:red">
<base url>/<version>/<type>/<id>
</pre>


For example:
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.
<pre>
Using the following parameters for an API request


base url = http://api.idigbio.org
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.
version = v1
type = records
id = 00000230-01bc-4a4f-8389-204f39da9530


would produce a URL of the following form
All iDigBio APIs are publicly available with no user authentication required or rate limits applied.


"http://api.idigbio.org/v1/records/00000230-01bc-4a4f-8389-204f39da9530"
== Quick Start Example ==
</pre>


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:


There are two major types of API enpoints:  
[https://search.idigbio.org/v2/search/records?rq={%22genus%22:%22acer%22} https://search.idigbio.org/v2/search/records?rq={"genus":"acer"}]


*Collection - which is a group endpoint that returns lists of multiple records. These urls are of the form <base url>/<version>/<type>, such as http://api.idigbio.org/v1/mediarecords/ . Additionally, a collection endpoint can contain optional query parameters, [[?limit]] indicates the number of records returned in the collection and defaults to 1000 and the [[?offset]] parameter which indicates the number of records to skip before returning a set of records and defaults to 0. If a collection endpoint request finds more then the set limit of records it will include a "next page" link to retrieve the next set of records in the collection. See the [[#endpointprops|endpoint properties]] section for more information on properties returned.
(You might want to install a JSON viewing plugin in your browser such as JSONView for Chrome.)
*Entity - A single item endpoint which returns all of the data available about an object. These urls are of the form  <base url>/<version>/<type>/<id> like the example used above.


Examples:
== iDigBio API Mailing List ==


collection:
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.
"http://api.idigbio.org/v1/mediarecords"
collection w/ optional query parameters:
"http://api.idigbio.org/v1/mediarecords?limit=100&offset=100"
entity:
"http://api.idigbio.org/v1/mediarecords/00000230-01bc-4a4f-8389-204f39da9530"


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


'''Endpoint Basics'''
== iDigBio APIs ==


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


Calling just the base URL will return a list of API version endpoints. For example a GET request to "http://api.idigbio.org" will return JSON data like the example below. 
=== Search API ===


<pre>
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.
{
v1: "http://api.idigbio.org/v1/",
v0: "http://api.idigbio.org/v0/"
}
</pre>


and calling a version URL endpoint will return a list of major data types available for that version, such as:
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].


<pre>
=== Download API ===
{
recordsets: "http://api.idigbio.org/v1/recordsets",
records: "http://api.idigbio.org/v1/records",
mediarecords: "http://api.idigbio.org/v1/mediarecords",
mediaaps: "http://api.idigbio.org/v1/mediaaps",
people: "http://api.idigbio.org/v1/people",
organizations: "http://api.idigbio.org/v1/organizations",
taxa: "http://api.idigbio.org/v1/taxa",
aggregates: "http://api.idigbio.org/v1/aggregates"
}
</pre>


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.


<div id="endpointprops">
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.
'''Endpoint Properties'''
</div>


=== Record & Media APIs ===


The iDigBio API tries to follow the REST paradigm's HATEOAS (Hypermedia as the Engine of Application State) model, which basically means that within each API endpoint we provide a list of relevant links to further API actions. This list typically is stored in either the "idigbio:links" in v1 or below or the "links" property in v3. In general, the largest difference between v1 and v3 responses is that the "idigbio:" namespace has been dropped from all system-level property names.
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.


Other system level property names include
'''ToDo:''' Make documentation for v2 of this API publicly accessible.


For Entity Endpoints:
== Other Ways of Accessing Data ==
*[[wikipedia:HTTP_ETag|etag]] - the opaque identifier assigned to a specific version of a resource found at a URL
*dateModified - The date the entity was modified
*version - The entity's version number
*type - The entity's type
*uuid - The entity's uuid
*siblings - Any siblings the entity may have as a dictionary of uuids
*recordIds - A list of lookup keys for the entity
*data - The entity's encapsulated data element


For Collection Endpoints:
=== Specimen Web Map Module ===
*items - the list of items in the collection
*itemCount - the number of total items in the collection


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.


'''Entity Data'''
=== 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:


The data element for each entity can include any number of key-value pairs containing properties of the entity, including potentially values that are themselves lists or dictionaries. Typical key namespaces that might appear in each type are (in order of decreasing usefulness):
==== ridigbio R Package for the Search API ====


*Records: typically contains darwin core elements ( http://rs.tdwg.org/dwc/terms/index.htm ) describing a physical specimen, may also contain custom elements or elements defined by other standards.
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.
*MediaRecords: typically contains audubon core elements ( http://terms.gbif.org/wiki/Audubon_Core_Term_List_(1.0_normative) ) describing a media capture event, may also contain custom elements or elements defined by other standards.
*MediaAPs: defined internally, contains references to the location of binary media objects within our object stores.
*RecordSets: currently undefined, in v3 will have a fixed format derived from our collection registration parameters.
*DataFiles: defined internally, contains references to the location of binary data file objects within our object stores.
*People: defined internally, contains records of people who have interacted with the iDigBio system, such as data provider contacts, users of the system, or other related people.
*Organizations: defined internally, contains records of organizations who interact with iDigBio. Right now this primarily contains the data from our collection registrations.
*Taxa: currently undefined and unused. May eventually hold taxonomic records, most likely following the darwin core standard.
*Aggregates: currently undefined and unused. May eventual hold incrementally built lists of records, such as the cached results of search queries or manually curated record groups.


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


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


==== iDigBio Python Library for Search API ====


All endpoints follow the form of
The Python client library is available via PyPI:
"http://api.idigbio.org/{api_version}{endpoint}"


{|
https://pypi.python.org/pypi/idigbio
! align="left"| Endpoint
 
! Method
or just use pip:
! API Versions Available
 
! Description
'''pip install idigbio'''
|-
 
| '/mediarecords'
The client code can also be found at github if you wish to help develop the library:
| GET
 
| v0, v1
https://github.com/idigbio/idigbio-python-client/
| returns a collection of media record IDs
 
|-
The iDigBio Python library is an "official" client library in the iDigBio code repository.
| '/mediarecords/{ID}'
 
| GET
==== idigbio_client Ruby Gem for the Search API ====
| v0, v1
 
| returns a media record with the specific entity ID
The idigbio_client ruby gem is available:
|-
 
| '/mediaaps'
https://rubygems.org/gems/idigbio_client
| GET
 
| v0, v1
which can be installed via:
| returns a collection of media access point IDs
 
|-
'''gem install idigbio_client'''
| '/mediaaps/{ID}'
 
| GET
The idigbio_client ruby gem is a "community-supported" client library with software repository currently at:
| v0, v1
 
| returns the media with the specific entity ID
https://github.com/GlobalNamesArchitecture/idigbio_client
|-
 
| '/organizations'
== Suggestions? ==
| GET
 
| v1
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.
| returns a collection of organizations IDs
 
|-
 
| '/organizations/{ID}'
== Technical Details ==
| GET
 
| v1
We describe the [[iDigBio API Software]] used to provide these APIs in a separate document.
| returns a organization record with the specific entity ID
|-
| '/people'
| GET
| v1
| returns a collection of people IDs
|-
| '/people/{ID}'
| GET
| v1
| returns a person record with the specific entity ID
|-
| '/records'
| GET
| v0, v1
| returns a collection of record IDs
|-
| '/records/{ID}'
| GET
| v0, v1
| returns a record with the specific entity ID
|-
| '/recordsets'
| GET
| v0, v1
| returns a collection of record set IDs
|-
| '/recordsets/{ID}'
| GET
| v0, v1
| returns a record set with specific entity ID
|}

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"