IDigBio API v1 Examples
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This document is a list of examples for using the iDigBio API but may not be comprehensive. See IDigBio API for full documentation on the API including all of the available endpoints and parameters.
Viewing JSON Output
A short JSON document is returned by the API when calling the GET method against the base URL:
$ curl -s http://api.idigbio.org/
{"v1":"http://api.idigbio.org/v1/","v0":"http://api.idigbio.org/v0/","check":"http://api.idigbio.org/check"}
For best viewing of JSON results in a browser, one may wish to use the JSONView Extension for Chrome and Firefox.
JSONView Browser Extension Example
If using a command-line tool (such as curl), you may wish to format the output of the JSON document using a "pretty printing" feature of some kind. This will make it more readable by humans and also allow it to be more easily filtered using tools such as grep. Here are some of the more commonly used curl options (from the curl man page):
$ man curl
...
-s, --silent
-i, --include
-v, --verbose
-d, --data <data>
-G, --get
...
Two common tools available on Unix/Linux are python's json.tool or the json_pp command-line Perl script (JSON::PP). These tools can receive input from a pipe in the normal Unix fashion to chain multiple commands together.
json.tool Example
$ curl -s http://api.idigbio.org/ | python -m json.tool
{
"check": "http://api.idigbio.org/check",
"v0": "http://api.idigbio.org/v0/",
"v1": "http://api.idigbio.org/v1/"
}
json_pp Example
$ curl -s http://api.idigbio.org/ | json_pp
{
"v1" : "http://api.idigbio.org/v1/",
"check" : "http://api.idigbio.org/check",
"v0" : "http://api.idigbio.org/v0/"
}
Three ways to fetch a specific record based on iDigBio GUID
- 1. Use the API
The complete record that was provided to iDigBio is stored in the API and can be retrieved by referencing the iDigBio GUID ("idigbio:uuid").
$ curl -s -XGET https://api.idigbio.org/v1/records/0cec43d8-9ad5-478a-bea1-397ab5cc4430 | json_pp
{
"idigbio:uuid" : "0cec43d8-9ad5-478a-bea1-397ab5cc4430",
"idigbio:etag" : "2682a8f2fb77d59d50442925a80fe58a2ad51e9c",
"idigbio:links" : {
"mediarecord" : [
"http://api.idigbio.org/v1/mediarecords/db38f86b-99f5-4dc4-b4a6-a045a9c35323"
],
"owner" : [
"872733a2-67a3-4c54-aa76-862735a5f334"
],
"recordset" : [
"http://api.idigbio.org/v1/recordsets/40250f4d-7aa6-4fcc-ac38-2868fa4846bd"
]
},
"idigbio:version" : 1,
"idigbio:createdBy" : "872733a2-67a3-4c54-aa76-862735a5f334",
"idigbio:recordIds" : [
"urn:uuid:5f5e476f-ee39-41c9-8b25-c929f85a773a"
],
"idigbio:dateModified" : "2014-04-20T23:11:09.437Z",
"idigbio:data" : {
"dwc:catalogNumber" : "ASU0000166",
"dwc:basisOfRecord" : "PreservedSpecimen",
"symbiotaverbatimScientificName" : "Abies",
"dwc:collectionCode" : "Plants",
"dwc:decimalLongitude" : "-105.859665870667",
"dcterms:references" : "http://swbiodiversity.org/seinet/collections/individual/index.php?occid=784316",
"dwc:scientificNameAuthorship" : "P. Mill.",
"dwc:collectionID" : "urn:uuid:a2e32c87-d320-4a01-bafd-a9182ae2e191",
"dwc:minimumElevationInMeters" : "2316",
"dwc:georeferenceSources" : "georef batch tool 2013-05-10",
"dwc:georeferenceVerificationStatus" : "reviewed - high confidence",
"dwc:occurrenceRemarks" : "Tree to 4 m; occasional in N-facing barranca",
"dwc:otherCatalogNumbers" : "153418",
"dwc:rights" : "http://creativecommons.org/licenses/by-nc-sa/3.0/",
"dwc:decimalLatitude" : "23.5821004818154",
"dwc:day" : "14",
"idigbio:recordId" : "urn:uuid:5f5e476f-ee39-41c9-8b25-c929f85a773a",
"dwc:locality" : "Ca. 1 mi N of Hwy 40 between Villa Union and Cd. Durango, and ca. 5 mi W of Durango state border.",
"dwc:occurrenceID" : "784316",
"dwc:year" : "1985",
"dwc:recordedBy" : "T. F. Daniel; ",
"dwc:family" : "Pinaceae",
"dwc:scientificName" : "Abies",
"dwc:georeferencedBy" : "cjsdavis",
"dwc:recordNumber" : "4031",
"dcterms:modified" : "2013-05-10 13:39:12",
"dwc:country" : "Mexico",
"dwc:eventDate" : "1985-03-14",
"dwc:verbatimElevation" : "7600ft",
"dwc:startDayOfYear" : "73",
"dwc:habitat" : "Pine-oak forest, in N-facing barranca.",
"dwc:dynamicProperties" : "Tree to 4 m; occasional in N-facing barranca",
"dwc:month" : "3",
"dwc:stateProvince" : "Sinaloa",
"dwc:genus" : "Abies",
"dwc:coordinateUncertaintyInMeters" : "1000",
"dwc:institutionCode" : "ASU"
}
}
- 2. Use the Elasticsearch URL interface with query parameter
The data provided by the Elasticsearch interface may differ from the raw API record, especially with regards to field names, since the Elasticsearch data has been normalized and indexed for consumption by the search portal.
$ curl -s -XGET https://search.idigbio.org/idigbio/records/_search?q=uuid:0cec43d8-9ad5-478a-bea1-397ab5cc4430 | json_pp
{
"hits" : {
"hits" : [
{
"_source" : {
"collectioncode" : "plants",
"datecollected" : "1985-03-14",
"uuid" : "0cec43d8-9ad5-478a-bea1-397ab5cc4430",
"geopoint_geohash_6" : "9shwph",
"locality" : "ca. 1 mi n of hwy 40 between villa union and cd. durango, and ca. 5 mi w of durango state border.",
"minelevation" : 231,
"collectionid" : "urn:uuid:a2e32c87-d320-4a01-bafd-a9182ae2e191",
"datecollected_rejected" : false,
"datemodified_rejected" : false,
"geopoint_geohash_5" : "9shwp",
"recordset" : "40250f4d-7aa6-4fcc-ac38-2868fa4846bd",
"geopoint_rejected" : false,
"hasImage" : true,
"data" : {
"idigbio:uuid" : "0cec43d8-9ad5-478a-bea1-397ab5cc4430",
"idigbio:etag" : "2682a8f2fb77d59d50442925a80fe58a2ad51e9c",
"idigbio:links" : {
"mediarecord" : [
"http://api.idigbio.org/v1/mediarecords/db38f86b-99f5-4dc4-b4a6-a045a9c35323"
],
"owner" : [
"872733a2-67a3-4c54-aa76-862735a5f334"
],
"recordset" : [
"http://api.idigbio.org/v1/recordsets/40250f4d-7aa6-4fcc-ac38-2868fa4846bd"
]
},
"idigbio:version" : 1,
"idigbio:createdBy" : "872733a2-67a3-4c54-aa76-862735a5f334",
"idigbio:recordIds" : [
"urn:uuid:5f5e476f-ee39-41c9-8b25-c929f85a773a"
],
"idigbio:data" : {
"dwc:catalogNumber" : "ASU0000166",
"dwc:basisOfRecord" : "PreservedSpecimen",
"symbiotaverbatimScientificName" : "Abies",
"idigbio:links" : {
"mediarecord" : [
"http://api.idigbio.org/v1/mediarecords/db38f86b-99f5-4dc4-b4a6-a045a9c35323"
],
"owner" : [
"872733a2-67a3-4c54-aa76-862735a5f334"
],
"recordset" : [
"http://api.idigbio.org/v1/recordsets/40250f4d-7aa6-4fcc-ac38-2868fa4846bd"
]
},
"dwc:collectionCode" : "Plants",
"dwc:decimalLongitude" : "-105.859665870667",
"dcterms:references" : "http://swbiodiversity.org/seinet/collections/individual/index.php?occid=784316",
"dwc:scientificNameAuthorship" : "P. Mill.",
"dwc:collectionID" : "urn:uuid:a2e32c87-d320-4a01-bafd-a9182ae2e191",
"dwc:minimumElevationInMeters" : "2316",
"dwc:georeferenceSources" : "georef batch tool 2013-05-10",
"dwc:georeferenceVerificationStatus" : "reviewed - high confidence",
"dwc:occurrenceRemarks" : "Tree to 4 m; occasional in N-facing barranca",
"dwc:otherCatalogNumbers" : "153418",
"dwc:rights" : "http://creativecommons.org/licenses/by-nc-sa/3.0/",
"idigbio:version" : 1,
"idigbio:recordIds" : [
"urn:uuid:5f5e476f-ee39-41c9-8b25-c929f85a773a"
],
"dwc:decimalLatitude" : "23.5821004818154",
"dwc:day" : "14",
"idigbio:recordId" : "urn:uuid:5f5e476f-ee39-41c9-8b25-c929f85a773a",
"dwc:locality" : "Ca. 1 mi N of Hwy 40 between Villa Union and Cd. Durango, and ca. 5 mi W of Durango state border.",
"dwc:occurrenceID" : "784316",
"idigbio:etag" : "2682a8f2fb77d59d50442925a80fe58a2ad51e9c",
"dwc:year" : "1985",
"dwc:recordedBy" : "T. F. Daniel; ",
"dwc:recordNumber" : "4031",
"dwc:georeferencedBy" : "cjsdavis",
"dwc:scientificName" : "Abies",
"dwc:family" : "Pinaceae",
"dcterms:modified" : "2013-05-10 13:39:12",
"idigbio:createdBy" : "872733a2-67a3-4c54-aa76-862735a5f334",
"dwc:country" : "Mexico",
"idigbio:dateModified" : "2014-04-20T23:11:09.437Z",
"dwc:eventDate" : "1985-03-14",
"dwc:verbatimElevation" : "7600ft",
"idigbio:uuid" : "0cec43d8-9ad5-478a-bea1-397ab5cc4430",
"dwc:startDayOfYear" : "73",
"dwc:habitat" : "Pine-oak forest, in N-facing barranca.",
"dwc:dynamicProperties" : "Tree to 4 m; occasional in N-facing barranca",
"dwc:month" : "3",
"dwc:stateProvince" : "Sinaloa",
"dwc:genus" : "Abies",
"dwc:coordinateUncertaintyInMeters" : "1000",
"dwc:institutionCode" : "ASU"
},
"idigbio:dateModified" : "2014-04-20T23:11:09.437Z"
},
"scientificname" : "abies",
"minelevation_rejected" : false,
"etag" : "2682a8f2fb77d59d50442925a80fe58a2ad51e9c",
"maxdepth_rejected" : false,
"family" : "pinaceae",
"institutioncode" : "asu",
"geopoint" : {
"lat" : 23.5821004818154,
"lon" : -105.859665870667
},
"fieldnumber" : "4031",
"geopoint_geohash_2" : "9s",
"stateprovince" : "sinaloa",
"mediarecords" : [
"db38f86b-99f5-4dc4-b4a6-a045a9c35323"
],
"country" : "mexico",
"collector" : "t. f. daniel;",
"geopoint_geohash_4" : "9shw",
"version" : 1,
"genus" : "abies",
"geopoint_geohash_3" : "9sh",
"datemodified" : "2014-04-20",
"catalognumber" : "asu0000166",
"mindepth_rejected" : false,
"maxelevation_rejected" : false
},
"_score" : 14.695786,
"_index" : "idigbio-1.0.0",
"_id" : "0cec43d8-9ad5-478a-bea1-397ab5cc4430",
"_type" : "records"
}
],
"max_score" : 14.695786,
"total" : 1
},
"timed_out" : false,
"_shards" : {
"failed" : 0,
"successful" : 10,
"total" : 10
},
"took" : 4
}
- 3. Use the Elasticsearch URL interface with json-formatted filter query in the message body
Given a json-formatted query body stored in a file named uuid.json:
$ cat uuid.json
{
"filter" : {
"term" : { "uuid" : "0cec43d8-9ad5-478a-bea1-397ab5cc4430" }
}
}
We get the same results in the data fields as the previous search:
$ curl -s -XGET https://search.idigbio.org/idigbio/records/_search -d@uuid.json | json_pp
{
"hits" : {
"hits" : [
{
"_source" : {
"collectioncode" : "plants",
"datecollected" : "1985-03-14",
"uuid" : "0cec43d8-9ad5-478a-bea1-397ab5cc4430",
"geopoint_geohash_6" : "9shwph",
"locality" : "ca. 1 mi n of hwy 40 between villa union and cd. durango, and ca. 5 mi w of durango state border.",
"minelevation" : 231,
"collectionid" : "urn:uuid:a2e32c87-d320-4a01-bafd-a9182ae2e191",
"datecollected_rejected" : false,
"datemodified_rejected" : false,
"geopoint_geohash_5" : "9shwp",
"recordset" : "40250f4d-7aa6-4fcc-ac38-2868fa4846bd",
"geopoint_rejected" : false,
"hasImage" : true,
"data" : {
"idigbio:uuid" : "0cec43d8-9ad5-478a-bea1-397ab5cc4430",
"idigbio:etag" : "2682a8f2fb77d59d50442925a80fe58a2ad51e9c",
"idigbio:links" : {
"mediarecord" : [
"http://api.idigbio.org/v1/mediarecords/db38f86b-99f5-4dc4-b4a6-a045a9c35323"
],
"owner" : [
"872733a2-67a3-4c54-aa76-862735a5f334"
],
"recordset" : [
"http://api.idigbio.org/v1/recordsets/40250f4d-7aa6-4fcc-ac38-2868fa4846bd"
]
},
"idigbio:version" : 1,
"idigbio:createdBy" : "872733a2-67a3-4c54-aa76-862735a5f334",
"idigbio:recordIds" : [
"urn:uuid:5f5e476f-ee39-41c9-8b25-c929f85a773a"
],
"idigbio:data" : {
"dwc:catalogNumber" : "ASU0000166",
"dwc:basisOfRecord" : "PreservedSpecimen",
"symbiotaverbatimScientificName" : "Abies",
"idigbio:links" : {
"mediarecord" : [
"http://api.idigbio.org/v1/mediarecords/db38f86b-99f5-4dc4-b4a6-a045a9c35323"
],
"owner" : [
"872733a2-67a3-4c54-aa76-862735a5f334"
],
"recordset" : [
"http://api.idigbio.org/v1/recordsets/40250f4d-7aa6-4fcc-ac38-2868fa4846bd"
]
},
"dwc:collectionCode" : "Plants",
"dwc:decimalLongitude" : "-105.859665870667",
"dcterms:references" : "http://swbiodiversity.org/seinet/collections/individual/index.php?occid=784316",
"dwc:scientificNameAuthorship" : "P. Mill.",
"dwc:collectionID" : "urn:uuid:a2e32c87-d320-4a01-bafd-a9182ae2e191",
"dwc:minimumElevationInMeters" : "2316",
"dwc:georeferenceSources" : "georef batch tool 2013-05-10",
"dwc:georeferenceVerificationStatus" : "reviewed - high confidence",
"dwc:occurrenceRemarks" : "Tree to 4 m; occasional in N-facing barranca",
"dwc:otherCatalogNumbers" : "153418",
"dwc:rights" : "http://creativecommons.org/licenses/by-nc-sa/3.0/",
"idigbio:version" : 1,
"idigbio:recordIds" : [
"urn:uuid:5f5e476f-ee39-41c9-8b25-c929f85a773a"
],
"dwc:decimalLatitude" : "23.5821004818154",
"dwc:day" : "14",
"idigbio:recordId" : "urn:uuid:5f5e476f-ee39-41c9-8b25-c929f85a773a",
"dwc:locality" : "Ca. 1 mi N of Hwy 40 between Villa Union and Cd. Durango, and ca. 5 mi W of Durango state border.",
"dwc:occurrenceID" : "784316",
"idigbio:etag" : "2682a8f2fb77d59d50442925a80fe58a2ad51e9c",
"dwc:year" : "1985",
"dwc:recordedBy" : "T. F. Daniel; ",
"dwc:recordNumber" : "4031",
"dwc:georeferencedBy" : "cjsdavis",
"dwc:scientificName" : "Abies",
"dwc:family" : "Pinaceae",
"dcterms:modified" : "2013-05-10 13:39:12",
"idigbio:createdBy" : "872733a2-67a3-4c54-aa76-862735a5f334",
"dwc:country" : "Mexico",
"idigbio:dateModified" : "2014-04-20T23:11:09.437Z",
"dwc:eventDate" : "1985-03-14",
"dwc:verbatimElevation" : "7600ft",
"idigbio:uuid" : "0cec43d8-9ad5-478a-bea1-397ab5cc4430",
"dwc:startDayOfYear" : "73",
"dwc:habitat" : "Pine-oak forest, in N-facing barranca.",
"dwc:dynamicProperties" : "Tree to 4 m; occasional in N-facing barranca",
"dwc:month" : "3",
"dwc:stateProvince" : "Sinaloa",
"dwc:genus" : "Abies",
"dwc:coordinateUncertaintyInMeters" : "1000",
"dwc:institutionCode" : "ASU"
},
"idigbio:dateModified" : "2014-04-20T23:11:09.437Z"
},
"scientificname" : "abies",
"minelevation_rejected" : false,
"etag" : "2682a8f2fb77d59d50442925a80fe58a2ad51e9c",
"maxdepth_rejected" : false,
"family" : "pinaceae",
"institutioncode" : "asu",
"geopoint" : {
"lat" : 23.5821004818154,
"lon" : -105.859665870667
},
"fieldnumber" : "4031",
"geopoint_geohash_2" : "9s",
"stateprovince" : "sinaloa",
"mediarecords" : [
"db38f86b-99f5-4dc4-b4a6-a045a9c35323"
],
"country" : "mexico",
"collector" : "t. f. daniel;",
"geopoint_geohash_4" : "9shw",
"version" : 1,
"genus" : "abies",
"geopoint_geohash_3" : "9sh",
"datemodified" : "2014-04-20",
"catalognumber" : "asu0000166",
"mindepth_rejected" : false,
"maxelevation_rejected" : false
},
"_score" : 1,
"_index" : "idigbio-1.0.0",
"_id" : "0cec43d8-9ad5-478a-bea1-397ab5cc4430",
"_type" : "records"
}
],
"max_score" : 1,
"total" : 1
},
"timed_out" : false,
"_shards" : {
"failed" : 0,
"successful" : 10,
"total" : 10
},
"took" : 64
}
Fetch five MediaRecord IDs (endpoints) from the API
Example URL:
http://api.idigbio.org/v1/mediarecords?limit=5
Example API Results:
curl -s http://api.idigbio.org/v1/mediarecords?limit=5 | json_pp
{
"idigbio:errors" : [],
"idigbio:links" : {
"idigbio:nextPage" : "http://api.idigbio.org/v1/mediarecords?limit=5&offset=5"
},
"idigbio:items" : [
{
"idigbio:links" : {
"mediarecord" : "http://api.idigbio.org/v1/mediarecords/000003cd-0cca-421b-8f26-f557a26b0393"
},
"idigbio:uuid" : "000003cd-0cca-421b-8f26-f557a26b0393",
"idigbio:version" : 1,
"idigbio:etag" : "ce3e2f7272ec996bb479c87549ba90c15ba96426",
"idigbio:dateModified" : "2014-04-21T22:19:27.436Z"
},
{
"idigbio:links" : {
"mediarecord" : "http://api.idigbio.org/v1/mediarecords/00000728-ffb3-4a68-9f93-137f19961121"
},
"idigbio:uuid" : "00000728-ffb3-4a68-9f93-137f19961121",
"idigbio:version" : 2,
"idigbio:etag" : "c13b10675b4a83031b1dc7a24c1f5c4e443b1939",
"idigbio:dateModified" : "2014-04-03T17:43:18.145Z"
},
{
"idigbio:links" : {
"mediarecord" : "http://api.idigbio.org/v1/mediarecords/00000b03-e208-4d22-983b-506ad2842f7c"
},
"idigbio:uuid" : "00000b03-e208-4d22-983b-506ad2842f7c",
"idigbio:version" : 2,
"idigbio:etag" : "bc118a7ea53e004c82ab9b7e813e1010ae5f8e17",
"idigbio:dateModified" : "2014-04-20T05:16:20.389Z"
},
{
"idigbio:links" : {
"mediarecord" : "http://api.idigbio.org/v1/mediarecords/000010bc-a4d4-483d-b71d-0dbdd4fd2d5a"
},
"idigbio:uuid" : "000010bc-a4d4-483d-b71d-0dbdd4fd2d5a",
"idigbio:version" : 0,
"idigbio:etag" : "68c441bd3c49507bf930f3b278f2c58f9cb792ec",
"idigbio:dateModified" : "2014-04-20T21:38:46.679Z"
},
{
"idigbio:links" : {
"mediarecord" : "http://api.idigbio.org/v1/mediarecords/000012f9-d288-4a14-b898-77430e0a137a"
},
"idigbio:uuid" : "000012f9-d288-4a14-b898-77430e0a137a",
"idigbio:version" : 0,
"idigbio:etag" : "0357f74dada8b21a69281b042a52f47a172fa33b",
"idigbio:dateModified" : "2014-01-20T20:19:29.754Z"
}
],
"idigbio:itemCount" : "2199334"
}
To Do: Provide examples of displaying multiple images accessed via the mediarecord API endpoint.
https://api.idigbio.org/v1/records/4e98d066-f35f-4cc0-ad7c-b5b5f2175521/media?quality=thumbnail
https://api.idigbio.org/v1/mediarecords/4c4c5008-5444-4348-85f5-34112b46169b/media?quality=web
Elasticsearch Examples
Find all specimen records that meet the following criteia:
- Have an image (mediarecord) associated with the specimen record
- Are from Hocking or Fairfield County, Ohio.
To resolve this criteria, we need the following (expressed in pseudocode):
- hasImage is true
- county is equal to "Hocking" or "Fairfield"
- stateprovince is equal to "Ohio" (there is a Fairfield county in multiple locations around the world)
API Performance
For large numbers of records or bulk data aquisition, please use the Download features available in the Portal. https://www.idigbio.org/portal
See also iDigBio API Performance.