Quick reference
List of endpoints and parameters!
4 minute read
API call format
base-URL + ‘/api/v0/’ + endpoint + ‘?’ + request-parametersTaxons endpoint example
http://opendb.inpa.gov.br/api/v0/taxons?valid=1&limit=2&offset=10GET DATA (downloads)
Shared get-parameters
When multiple parameters are specified, they are combined with an AND operator
All endpoints share these GET parameters:
id
return only the specified resource. May be number or a comma delimited list, such asapi/v0/locations?id=1,50,124
limit
: the number of items that should be returned (must be greater than 0). Example:api/v0/taxons?limit=10
offset
: the initial record to extract, to be used with limit when trying to download a large amount of data. Example:api/v0/taxons?offset=10000&limit=10000
returns 10K records starting from the 10K position of the current query.fields
: the field or fields that should be returned. Each endpoint has its own fields but there are two special words, simple (default) and all, which return different collection of fields.fields=all
may return sub-objects for each object. Example:api/v0/taxons?fields=id,scientificName,valid
wildcards
Some parameters accept an asterisk as wildcard, soapi/v0/taxons?name=Euterpe
will return taxons with name exactly as “Euterpe”, while api/v0/taxons?name=Eut*
will return names starting with “Eut”.
Endpoint parameters
Endpoint | Description | Possible parameters |
---|---|---|
/ | Tests your access | none |
bibreferences | Lists of bibliographic references | id , bibkey |
biocollections | List of Biocollections and other vouchers Repositories | id |
datasets | Lists registered datasets | id |
individuals | Lists registered individuals | id , location , location_root ,taxon , taxon_root , tag ,project , dataset |
individual-locations | Lists occurrences for individuals | individual_id , location , location_root ,taxon , taxon_root , dataset |
languages | Lists registered languages | |
measurements | Lists Measurements | id , taxon ,dataset ,trait ,individual ,voucher ,location |
locations | Lists locations | root , id , parent_id ,adm_level , name , limit , querytype , lat , long ,project ,dataset |
persons | Lists registered people | id , search , name , abbrev , email |
projects | Lists registered projects | id only |
taxons | Lists taxonomic names | root , id , name ,level , valid , external , project ,dataset |
traits | Lists variables (traits) list | id , name |
vouchers | Lists registered voucher specimens | id , number , individual , location , collector , location_root ,taxon , taxon_root , project , dataset |
userjobs | Lists user Jobs | id , status |
POST DATA (imports)
Web-interface note
- Importing data from files through the web-interface require specifying the POST verb parameters of the ODB API
- Batch imports of Bibliographic References and MediaFiles are possible only through the web interface.
Endpoint | Description | POST Fields |
---|---|---|
biocollections | Import BioCollections | name , acronym |
individuals | Import individuals | collector , tag , dataset , date , (location or latitude + longitude )**, altitude , location_notes , location_date_time , x , y , distance , angle , notes , taxon , identifier , identification_date , modifier , identification_notes , identification_based_on_biocollection , identification_based_on_biocollection_id , identification_individual |
individual-locations | Import IndividualLocations | individual , (location or latitude + longitude ), altitude , location_notes , location_date_time , x , y , distance , angle |
locations | Import locations | name , adm_level , (geom or lat +long )** , parent , altitude , datum , x , y , startx , starty , notes , ismarine |
measurements | Import Measurements to Datasets | dataset , date , object_type , object_type , person , trait_id , value **, link_id , bibreference , notes , duplicated |
persons | Imports a list of people | full_name **, abbreviation , email , institution , biocollection |
traits | Import traits | export_name , type , objects , name , description **, units , range_min , range_max , categories , wavenumber_min and wavenumber_max , value_length , link_type , bibreference |
taxons | Imports taxonomic names | name **, level , parent , bibreference , author , author_id or person , valid , mobot , ipni , mycobank , zoobank , gbif |
vouchers | Imports voucher specimens | individual , biocollection , biocollection_type , biocollection_number , number , collector , date , dataset , notes |
PUT DATA (updates)
Attention
Only the endpoints listed below can be updated using the API and only the listed PUT fields can be updated on each endpoint. Field values are as explained for the POST API endpoints, except that in all cases you must also provide theid
of the record to be updated.
Endpoint | Description | PUT Fields |
---|---|---|
individuals | Update Individuals | (id or individual_id ),collector , tag , dataset , date , notes , taxon , identifier , identification_date , modifier , identification_notes , identification_based_on_biocollection , identification_based_on_biocollection_id , identification_individual |
individual-locations | Update Individual Locations | (id or individual_location_id ), individual , (location or latitude + longitude ), altitude , location_notes , location_date_time , x , y , distance , angle |
locations | Update Locations | (id or location_id ), name , adm_level , (geom or lat +long ) , parent , altitude , datum , x , y , startx , starty , notes , ismarine |
measurements | Update Measurements | (id or measurement_id ), dataset , date , object_type , object_type , person , trait_id , value , link_id , bibreference , notes , duplicated |
persons | Update Persons | (id or person_id ),full_name , abbreviation , email , institution , biocollection |
vouchers | Update Vouchers | (id or voucher_id ),individual , biocollection , biocollection_type , biocollection_number , number , collector , date , dataset , notes |
Nomenclature types
Nomenclature types numeric codes | |
---|---|
NotType : 0 | Isosyntype : 8 |
Type : 1 | Neotype : 9 |
Holotype : 2 | Epitype : 10 |
Isotype : 3 | Isoepitype : 11 |
Paratype : 4 | Cultivartype : 12 |
Lectotype : 5 | Clonotype : 13 |
Isolectotype : 6 | Topotype : 14 |
Syntype : 7 | Phototype : 15 |
Taxon Level (Rank)
Level | Level | Level | Level |
---|---|---|---|
-100 clade |
60 cl., class |
120 fam., family |
210 section, sp., spec., species |
0 kingdom |
70 subcl., subclass |
130 subfam., subfamily |
220 subsp., subspecies |
10 subkingd. |
80 superord., superorder |
150 tr., tribe |
240 var., variety |
30 div., phyl., phylum, division |
90 ord., order |
180 gen., genus |
270 f., fo., form |
40 subdiv. |
100 subord. |
190 subg., subgenus, sect. |
Last modified
January 11, 2022
: Add PUT API info and how to customize layout (12ea724)