IDigBio API: Difference between revisions

Latest revision as of 07:05, 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.

@@ Line 9: / Line 9: @@
 [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]. Although our portal has many features, 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.
+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 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.
-== iDigBio API Mailing List ==
+All iDigBio APIs are publicly available with no user authentication required or rate limits applied.
-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.
+== Quick Start Example ==
-You can join via the web at: http://lists.ufl.edu/cgi-bin/wa?A0=IDIGBIO-API-USERS-L
+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:
-== Specification ==
+[https://search.idigbio.org/v2/search/records?rq={%22genus%22:%22acer%22} https://search.idigbio.org/v2/search/records?rq={"genus":"acer"}]
-The [https://github.com/idigbio/idigbio-search-api/wiki iDigBio API v2 / iDigBio Search API specification] includes detailed information about the Search API endpoints, parameters, query format, values, and returns. It is available in the github wiki associated with the [https://github.com/iDigBio/idigbio-search-api code repository]. The iDigBio Search API was released to production in June 2015.
+(You might want to install a JSON viewing plugin in your browser such as JSONView for Chrome.)
-iDigBio transitioned from version 1 to version 2 (v1 to v2) of the API. All v1 endpoints and documentation should be considered deprecated, even if they continue to function. Programmers who are interested in accessing data directly in iDigBio via an API should consult the v2 API documentation. '''The v2 API is also known as the iDigBio Search API.'''
+== iDigBio API Mailing List ==
-The now-deprecated [[iDigBio API v1 Specification]] includes detailed information about the old v1 API endpoints, parameters, values, and returns. In most cases, the only reason to use the v1 API was to retrieve raw, unprocessed versions of a record (e.g. no iDigBio data quality enhancements) or to access previous versions of a particular record.
+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.
-== Examples ==
+You can join via the web at: http://lists.ufl.edu/cgi-bin/wa?A0=IDIGBIO-API-USERS-L
-See [https://github.com/iDigBio/idigbio-search-api/wiki/Examples iDigBio API v2 / iDigBio Search API Examples] in the [https://github.com/iDigBio/idigbio-search-api/wiki idigbio-search-api github wiki].
+== iDigBio APIs ==
-== Quick Start ==
+There are several APIs you can use to retrieve data from iDigBio: Search, Download, Record, and Media.
-iDigBio API endpoints follow the general form:
+=== Search API ===
-;<pre>https://search.idigbio.org/{api_version}/{endpoint}{optional_parameters}</pre>
-In nearly all cases, a successful API request returns data as a JSON-formatted document.
+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.
-Many error cases will also return a JSON-formatted document rather than a bare HTTP status failure.
+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].
-== Searching iDigBio ==
+=== Download API ===
-=== Search Portal and Bulk Record Downloads ===
+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.
-The easiest method for searching iDigBio is to use the Portal website search features, not the API. The portal also provides bulk download capabilities for acquiring larger sets of data.  See: https://www.idigbio.org/portal
+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.
-=== Search API ===
+=== Record & Media APIs ===
-The [https://github.com/idigbio/idigbio-search-api/wiki iDigBio Search API] has be released and the June 2015 version of the portal is based on this API.
+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 APIs ===
+'''ToDo:''' Make documentation for v2 of this API publicly accessible.
-[[iDigBio Download API]]
-[https://docs.google.com/document/d/1C75oUWk7Wbbo81-ldh-ogOurNjbIQ-ZLPqSQVR-hc5A/edit?usp=sharing Media API Working Docs]
+== 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. Go to the [[Specimen Map]] page for details on using the map.
+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.
-== Full Recordset Downloads ==
-Instead of generating large queries in the portal or with the API, it may be easier to download iDigBio data from regular dumps of all data in iDigBio. These dumps are available from [http://s.idigbio.org/idigbio-static-downloads?max-keys=10000 s.idigbio.org]. This is an S3-compatible object store (although it can be treated as a web server if that is easier) that contains .zip files of each record set in iDigBio named by recordset uuid as well as files containing all data across all records sets.
+=== Client Libraries ===
-== 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:
-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.
+==== ridigbio R Package for the Search API ====
-=== ridigbio R Package for 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.
@@ Line 76: / Line 69: @@
 The ridigbio R package is an "official" client library in the iDigBio code repository.
-=== iDigBio Python Library for Search API ===
+==== iDigBio Python Library for Search API ====
 The Python client library is available via PyPI:
@@ Line 92: / Line 85: @@
 The iDigBio Python library is an "official" client library in the iDigBio code repository.
-=== idigbio_client Ruby Gem ===
+==== idigbio_client Ruby Gem for the Search API ====
 The idigbio_client ruby gem is available:
@@ Line 109: / Line 102: @@
 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.