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README.md Update outliers taxon docs Mar 5, 2018

README.md

api-docs

This is the documentation for the OBIS API. Paged responses include the fields count, offset, limit, lastpage, and results. Some arguments accept multiple, comma-separated, values.

Occurrence

URL Description Parameters Example
/occurrence/{id} Get single occurrence
/occurrence Find occurrences scientificname,
obisid,
aphiaid,
resourceid,
nodeid,
year,
startdate,
enddate,
groupid,
areaid,
startdepth,
enddepth,
geometry,
qc,
fields,
offset,
limit
http://api.iobis.org/occurrence?year=2005&scientificname=Cetacea&limit=100

http://api.iobis.org/occurrence?&scientificname=Abra,Lanice,Pectinaria&year=2005,2006

Occurrence download

Large result sets can be downloaded as a single CSV file using the download API. The initial search request will return a UUID, which can be used to retrieve the file when it is ready. Files will be removed after a few days.

URL Description Parameters Example
/occurrence/download Find occurrences See /occurrence for parameters. offset and limit do not apply. http://api.iobis.org/occurrence/download?year=2005&scientificname=Cetacea
/download/{uuid}/status Get download status http://api.iobis.org/download/d5d40adb-5920-3659-956e-94bbaf352b73/status
/download/{uuid} Download file http://api.iobis.org/download/d5d40adb-5920-3659-956e-94bbaf352b73

Checklist

URL Description Parameters Example
/checklist Generate checklist scientificname,
obisid,
aphiaid,
resourceid,
groupid,
areaid,
year,
startdate,
enddate,
startdepth,
enddepth,
geometry,
offset,
limit
http://api.iobis.org/checklist?resourceid=3013

http://api.iobis.org/checklist?year=2005&scientificname=Cetacea

http://api.iobis.org/checklist?eezid=59&scientificname=Mollusca&limit=100

Resource

URL Description Parameters Example
/resource/{id} Get single resource /resource/3013
/resource Find resources scientificname,
q,
obisid,
aphiaid,
groupid,
areaid,
nodeid,
year,
startdate,
enddate,
startdepth,
enddepth,
geometry,
offset,
limit
http://api.iobis.org/resource?startdate=2010-01-01&scientificname=Cetacea

http://api.iobis.org/resource?q=sediment

Groups

URL Description Parameters Example
/group Find groups offset,
limit
http://api.iobis.org/group

Areas

URL Description Parameters Example
/area Find areas offset,
limit
http://api.iobis.org/area

Nodes

URL Description Parameters Example
/node Find nodes offset,
limit
http://api.iobis.org/node

Taxon

URL Description Parameters Example
/taxon/{id} Get single taxon
/taxon/{id}/common Get common names
/taxon Find taxon scientificname,
obisid,
aphiaid

Lookup XY

URLDescriptionParametersExample
/xylookup Endpoint for looking up environmental and societal spatial information based on coordinates.

For more info see https://iobis.github.io/xylookup/.
POST bodies may also be msgpack encoded.
x: array of x-coordinate(s) (longitude). Required for GET requests.
y: array of y-coordinate(s) (latitude). Required for GET requests.
points: nested array of x, y pairs (longitude, latitude). Required for POST requests.
areas: Should areas be returned (default: true).
grids: Should grid values be returned (bathymetry, ...) (default: true).
shoredistance: Should the distance the coastline be returned (default: true).
http://api.iobis.org/xylookup?x=2.90,2.1&y=51.2,51.1

Outliers taxon

URLDescriptionParametersExample
/outlierstaxon Endpoint for identifying spatial and environmental outlier records for points of a taxon.

For more info see https://iobis.github.io/qc-service/.
POST bodies may also be msgpack encoded.
x: array of x-coordinate(s) (longitude). Required for GET requests.
y: array of y-coordinate(s) (latitude). Required for GET requests.
points: nested array of x, y pairs (longitude, latitude). Required for POST requests.
mad_coef: Coefficient to multiply the median absolute deviation (MAD) by in order to determine the range of valid values (default: 6).
iqr_coef (optional): Coefficient to multiply the interquartile range (IQR) by in order to determine the range of valid values (default: 3).
aphiaid (optional): taxonomic identifier as provided by the world register of marine species (WoRMS). Can be used for checking new records of a known taxon.
http://api.iobis.org/outliersspecies?x=50.1936,...,-177.6604&y=55.0475,...,13.9234

Outliers dataset

URLDescriptionParametersExample
/outliersdataset Endpoint for identifying spatial outliers for points of a dataset.

For more info see https://iobis.github.io/qc-service/.
POST bodies may also be msgpack encoded.
x: array of x-coordinate(s) (longitude). Required for GET requests.
y: array of y-coordinate(s) (latitude). Required for GET requests.
points: nested array of x, y pairs (longitude, latitude). Required for POST requests.
mad_coef: Coefficient to multiply the median absolute deviation (MAD) by in order to determine the range of valid values (default: 6).
iqr_coef (optional): Coefficient to multiply the interquartile range (IQR) by in order to determine the range of valid values (default: 3).
http://api.iobis.org/outliersdataset?x=50.1936,...,-177.6604&y=55.0475,...,13.9234