Difference between revisions of "OJ Break v2 Occurrence Reference"

From xBio:D Wiki
Jump to navigation Jump to search
(→‎See also)
(→‎API Information and Access)
 
(12 intermediate revisions by one other user not shown)
Line 1: Line 1:
 
'''Introduction'''
 
'''Introduction'''
  
−
OJ_Break is the name of the xBio:D RESTful API service to facilitate discovery of data within the xBio:D database. The API can respond with JavaScript Object Notation (JSON), XML, or JSON with padding (JSONP) and accepts HTTP GET and POST requests indiscriminately. The backend of the API is written in Oracle's PL/SQL database language, which is fast but often inflexible, while a Python presentation layer mitigates request handling and authentication.
+
OJ_Break is the name of the xBio:D RESTful API service to facilitate discovery of data within the xBio:D database. The API can respond with HTML, JSON, XML, or JSON with padding (JSONP) and accepts HTTP GET and POST requests indiscriminately. The backend of the API is written in Oracle's PL/SQL database language, which is fast but often inflexible, while a Python presentation layer mitigates request handling and authentication.
  
 
OJ_Break Version 2 is a new and improved edition of the work started in Version 1. Version 2 introduces a completely restructured and standardized data model to further enhance the functionality of the xBio:D database.
 
OJ_Break Version 2 is a new and improved edition of the work started in Version 1. Version 2 introduces a completely restructured and standardized data model to further enhance the functionality of the xBio:D database.
Line 10: Line 10:
 
Using the OJ_Break Version 2 API requires calling methods with corresponding, method specific parameters (found on this page) and a few other required parameters. These required parameters include specifying a return ''format'', an API access ''key'', and a ''version'' number.  
 
Using the OJ_Break Version 2 API requires calling methods with corresponding, method specific parameters (found on this page) and a few other required parameters. These required parameters include specifying a return ''format'', an API access ''key'', and a ''version'' number.  
  
−
     Example: http://osuc.biosci.ohio-state.edu/OJ_Break/getOccurrenceInfo?occurrence_id=1&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2
+
     Example: http://osuc.biosci.ohio-state.edu/OJ_Break/getOccurrenceInfo?occurrence_id=1&format=html&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2
  
 
Notice the specification of the ''version'' parameter at the end of the example method call. With the introduction of OJ_Break Version 2, the ''version'' parameter has a default value of ''2'' making the specification in the example unnecessary. To read more about using the OJ_Break Version 2 API, go to [[OJ_Break API Access]].
 
Notice the specification of the ''version'' parameter at the end of the example method call. With the introduction of OJ_Break Version 2, the ''version'' parameter has a default value of ''2'' making the specification in the example unnecessary. To read more about using the OJ_Break Version 2 API, go to [[OJ_Break API Access]].
 +
 +
 +
[[File:OJ_Break Data Model - Occurrence.png|none|frame|Occurrence Data Model]]
  
 
== Procedural Reference ==
 
== Procedural Reference ==
Line 24: Line 27:
 
* ''version'': number
 
* ''version'': number
 
===== Return =====
 
===== Return =====
−
* [[OccurrenceExtended_.28(extends_OccurrenceBasic.29|OccurrenceExtended]]
+
* [[#OccurrenceExtended (extends OccurrenceBasic)|OccurrenceExtended]]
  
 
===== Example =====
 
===== Example =====
−
http://osuc.biosci.ohio-state.edu/OJ_Break/getOccurrenceInfo?occurrence_id=1&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2
+
http://osuc.biosci.ohio-state.edu/OJ_Break/getOccurrenceInfo?occurrence_id=1&format=html&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2
  
 
==== getOccurrencesInfo ====
 
==== getOccurrencesInfo ====
Line 37: Line 40:
 
* ''version'': number
 
* ''version'': number
 
===== Return =====
 
===== Return =====
−
* array of [[OccurrenceExtended_.28(extends_OccurrenceBasic.29|OccurrenceExtended]]
+
* array of [[#OccurrenceExtended (extends OccurrenceBasic)|OccurrenceExtended]]
  
 
===== Example =====
 
===== Example =====
−
http://osuc.biosci.ohio-state.edu/OJ_Break/getOccurrencesInfo?occurrence_ids=1,2&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2
+
http://osuc.biosci.ohio-state.edu/OJ_Break/getOccurrencesInfo?occurrence_ids=1,2&format=html&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2
  
 
== Occurrence Data Type Glossary ==
 
== Occurrence Data Type Glossary ==
Line 57: Line 60:
 
* ''start_time'': ''[[#start_time|start_time]]''
 
* ''start_time'': ''[[#start_time|start_time]]''
 
* ''end_time'': ''[[#end_time|end_time]]''
 
* ''end_time'': ''[[#end_time|end_time]]''
−
==== CollectionOccurrence (realizes [[OccurrenceExtended_.28extends_OccurrenceBasic.29|OccurrenceExtended]]) ====
+
==== CollectionOccurrence (realizes [[#OccurrenceExtended (extends OccurrenceBasic)|OccurrenceExtended]]) ====
 
* ''occurrence_type'': ''[[#occurrence_type|occurrence_type]]''
 
* ''occurrence_type'': ''[[#occurrence_type|occurrence_type]]''
 
* ''alt_ids'': array of ''[[#alt_id|alt_id]]''
 
* ''alt_ids'': array of ''[[#alt_id|alt_id]]''
Line 65: Line 68:
 
* ''coll_time'': ''[[#CollectingTime|CollectingTime]]
 
* ''coll_time'': ''[[#CollectingTime|CollectingTime]]
 
* ''field_code'': ''[[#field_code|field_code]]''
 
* ''field_code'': ''[[#field_code|field_code]]''
−
* ''determinations'': array of [[#DeterminationExtended_.28extends_DeterminationBasic.29|DeterminationExtended]]
+
* ''determinations'': array of [[#DeterminationExtended (extends DeterminationBasic)|DeterminationExtended]]
 
* ''media'': array of [[#MediaExtended|MediaExtended]]
 
* ''media'': array of [[#MediaExtended|MediaExtended]]
 
* ''sequences'': array of [[#Sequence|Sequence]]
 
* ''sequences'': array of [[#Sequence|Sequence]]
Line 72: Line 75:
  
 
==== DeterminationBasic ====
 
==== DeterminationBasic ====
−
* ''taxon'': [[OJ_Break v2 Taxon Reference#TaxonRelationship|TaxonRelationship]]
+
* ''taxon'': [[OJ_Break v2 Taxon Reference#TaxonRelationship (extends TaxonExtended)|TaxonRelationship]]
−
* ''determiner'': [[#OJ_Break v2 Agent Reference#AgentExtended_.28extends_AgentBasic.29|AgentExtended]]
+
* ''determiner'': [[#OJ_Break v2 Agent Reference#AgentExtended (extends_AgentBasic)|AgentExtended]]
−
==== DeterminationExtended ====
+
 
 +
==== DeterminationExtended (extends [[#DeterminationBasic|DeterminationBasic]]) ====
 
* ''det_id'': ''[[#det_id|det_id]]''
 
* ''det_id'': ''[[#det_id|det_id]]''
 
* ''det_date'': ''[[#det_date|det_date]]''
 
* ''det_date'': ''[[#det_date|det_date]]''
Line 81: Line 85:
 
* ''occurrence_coll_id'': ''[[#occurrence_coll_id|occurrence_coll_id]]''
 
* ''occurrence_coll_id'': ''[[#occurrence_coll_id|occurrence_coll_id]]''
 
* ''coll_id'': ''[[#coll_id|coll_id]]''
 
* ''coll_id'': ''[[#coll_id|coll_id]]''
−
==== NoncollectionOccurrence ====
+
==== NoncollectionOccurrence (realizes [[#OccurrenceExtended (extends OccurrenceBasic)|OccurrenceExtended]]) ====
 
* ''num_spms'': Number
 
* ''num_spms'': Number
 
* ''determination'': [[#DeterminationBasic|DeterminationBasic]]
 
* ''determination'': [[#DeterminationBasic|DeterminationBasic]]
−
==== OccurrenceAssociation ====
+
==== OccurrenceAssociation (extends [[#OccurrenceTrimmed (extends OccurrenceBasic)|OccurrenceTrimmed]]) ====
 
* ''assoc_type'': ''[[#assoc_type|assoc_type]]''
 
* ''assoc_type'': ''[[#assoc_type|assoc_type]]''
 
* ''assoc_type_full'': ''[[#assoc_type_full|assoc_type_full]]''
 
* ''assoc_type_full'': ''[[#assoc_type_full|assoc_type_full]]''
Line 93: Line 97:
 
* ''vouchered'': ''[[#vouchered|vouchered]]''
 
* ''vouchered'': ''[[#vouchered|vouchered]]''
 
* ''unvouchered'': ''[[#unvouchered|unvouchered]]''
 
* ''unvouchered'': ''[[#unvouchered|unvouchered]]''
−
==== OccurrenceExtended ====
+
==== OccurrenceExtended (extends [[#OccurrenceBasic|OccurrenceBasic]]) ====
−
* ''locality'': [[OJ_Break v2 Locality Reference#LocalityExtended_.28extends_LocalityBasic.29|LocalityExtended]]
+
* ''locality'': [[OJ_Break v2 Locality Reference#LocalityExtended (extends LocalityBasic)|LocalityExtended]]
 
* ''coll_date'': [[#CollectingDate|CollectingDate]]
 
* ''coll_date'': [[#CollectingDate|CollectingDate]]
 
* ''coll_method'': [[#coll_method|coll_method]]
 
* ''coll_method'': [[#coll_method|coll_method]]
−
* ''collector'': [[OJ_Break v2 Agent Reference#AgentExtended_.28extends_AgentBasic.29|AgentExtended]]
+
* ''collector'': [[OJ_Break v2 Agent Reference#AgentExtended (extends AgentBasic)|AgentExtended]]
 
* ''habitat'': ''[[#habitat|habitat]]''
 
* ''habitat'': ''[[#habitat|habitat]]''
 
* ''associations'': array of [[#OccurrenceAssociation|OccurrenceAssociation]]
 
* ''associations'': array of [[#OccurrenceAssociation|OccurrenceAssociation]]
 
* ''comments'': ''[[#comments|comments]]''
 
* ''comments'': ''[[#comments|comments]]''
−
* ''orig_citation'': [[OJ_Break v2 LiteratureCitationExtended_.28extends_LiteratureCitationBasic.29#LiteratureCitationExtended|LiteratureCitationExtended]]
+
* ''orig_citation'': [[OJ_Break v2 Literature Reference#LiteratureCitationExtended (extends LiteratureCitationBasic)|LiteratureCitationExtended]]
 
* ''enterer'': ''[[#enterer|enterer]]''
 
* ''enterer'': ''[[#enterer|enterer]]''
 
* ''last_update'': ''[[#last_update|last_update]]''
 
* ''last_update'': ''[[#last_update|last_update]]''
−
==== OccurrenceTrimmed ====
+
==== OccurrenceTrimmed (extends [[#OccurrenceBasic|OccurrenceBasic]]) ====
 
* ''alt_ids'': array of ''alt_id''
 
* ''alt_ids'': array of ''alt_id''
−
* ''institution'': [[InstitutionBasic]]
+
* ''institution'': [[OJ_Break v2 Institution Reference#InstitutionBasic|InstitutionBasic]]
 
* ''determination'': [[#DeterminationBasic|DeterminationBasic]]
 
* ''determination'': [[#DeterminationBasic|DeterminationBasic]]
 +
 
==== Preparation ====
 
==== Preparation ====
 
* ''prep_type'': ''[[#prep_type|prep_type]]''
 
* ''prep_type'': ''[[#prep_type|prep_type]]''
Line 132: Line 137:
  
 
=== Elements ===
 
=== Elements ===
 +
==== alt_id ====
 +
String - An alternate identifier for the specimen.
 +
==== assoc_type ====
 +
String - A description of the biological relationship between a specified taxon and another organism.
 +
==== assoc_type_full ====
 +
String - A complete description of the biological relationship between a specified taxon and another organism.
 +
==== ceid ====
 +
Number -
 +
==== coll_date ====
 +
String -
 +
==== coll_date_sortable ====
 +
String -
 +
==== coll_id ====
 +
Number -
 +
==== coll_method ====
 +
String
 +
==== comments ====
 +
String -
 +
==== date_recorded ====
 +
String
 +
==== det_date ====
 +
String
 +
==== det_id ====
 +
Number
 +
==== det_status ====
 +
String
 +
==== end_date ====
 +
String
 +
==== end_date_sortable ====
 +
String
 +
==== end_time ====
 +
String
 +
==== enterer ====
 +
String
 +
==== extract_quality ====
 +
String
 +
==== field_code ====
 +
String
 +
==== guid ====
 +
GUID - Globally Unique Identifier that uniquely identifies a resource.
 +
==== habitat ====
 +
String
 +
==== lab_code ====
 +
String
 +
==== last_update ====
 +
String
 +
==== life_status ====
 +
String
 +
==== num_preps ====
 +
Number - Number of preparations.
 +
==== occurrence_coll_id ====
 +
Number
 +
==== occurrence_id ====
 +
Number
 +
==== occurrence_type ====
 +
String
 +
==== seq_result ====
 +
String
 +
==== spm_sex ====
 +
String
 +
==== start_time ====
 +
String
 +
==== pcr_result ====
 +
String
 +
==== prep_contents ====
 +
String
 +
==== prep_type ====
 +
String
 +
==== type_status ====
 +
String
 +
==== unvouchered_coll ====
 +
?
 +
==== updater ====
 +
String
 +
==== vouchered ====
 +
Boolean_flag
 +
 
== See also ==
 
== See also ==
 
Visit any of the below links to find information about the other data domains defined by OJ_Break Version 2.
 
Visit any of the below links to find information about the other data domains defined by OJ_Break Version 2.

Latest revision as of 16:39, 9 June 2015

Introduction

OJ_Break is the name of the xBio:D RESTful API service to facilitate discovery of data within the xBio:D database. The API can respond with HTML, JSON, XML, or JSON with padding (JSONP) and accepts HTTP GET and POST requests indiscriminately. The backend of the API is written in Oracle's PL/SQL database language, which is fast but often inflexible, while a Python presentation layer mitigates request handling and authentication.

OJ_Break Version 2 is a new and improved edition of the work started in Version 1. Version 2 introduces a completely restructured and standardized data model to further enhance the functionality of the xBio:D database.

Contents

API Information and Access

This page specifies the methods and data defined by OJ_Break Version 2, more precisely those that are defined by the Occurrence data domain. To get information on any of the other data domains defined in OJ_Break Version 2, visit the See also section.

Using the OJ_Break Version 2 API requires calling methods with corresponding, method specific parameters (found on this page) and a few other required parameters. These required parameters include specifying a return format, an API access key, and a version number. 

   Example: http://osuc.biosci.ohio-state.edu/OJ_Break/getOccurrenceInfo?occurrence_id=1&format=html&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2

Notice the specification of the version parameter at the end of the example method call. With the introduction of OJ_Break Version 2, the version parameter has a default value of 2 making the specification in the example unnecessary. To read more about using the OJ_Break Version 2 API, go to OJ_Break API Access.


Occurrence Data Model

Procedural Reference

Occurrence

getOccurrenceInfo

Description
Parameters
  • occurrence_id: occurrence_id
  • format: string
  • key: string
  • version: number
Return
Example
http://osuc.biosci.ohio-state.edu/OJ_Break/getOccurrenceInfo?occurrence_id=1&format=html&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2

getOccurrencesInfo

Description
Parameters
  • occurrence_ids: array of occurrence_id
  • format: string
  • key: string
  • version: number
Return
Example
http://osuc.biosci.ohio-state.edu/OJ_Break/getOccurrencesInfo?occurrence_ids=1,2&format=html&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2

Occurrence Data Type Glossary

Classes

CollectingDate

CollectingDateRange

CollectingTime

CollectionOccurrence (realizes OccurrenceExtended)

DeterminationBasic

DeterminationExtended (extends DeterminationBasic)

NoncollectionOccurrence (realizes OccurrenceExtended)

OccurrenceAssociation (extends OccurrenceTrimmed)

OccurrenceBasic

OccurrenceExtended (extends OccurrenceBasic)

OccurrenceTrimmed (extends OccurrenceBasic)

Preparation

Sequence

SequencePrimers

  • forward: String
  • reverse: String

SpecimenGroup

Elements

alt_id

String - An alternate identifier for the specimen.

assoc_type

String - A description of the biological relationship between a specified taxon and another organism.

assoc_type_full

String - A complete description of the biological relationship between a specified taxon and another organism.

ceid

Number -

coll_date

String -

coll_date_sortable

String -

coll_id

Number -

coll_method

String

comments

String -

date_recorded

String

det_date

String

det_id

Number

det_status

String

end_date

String

end_date_sortable

String

end_time

String

enterer

String

extract_quality

String

field_code

String

guid

GUID - Globally Unique Identifier that uniquely identifies a resource.

habitat

String

lab_code

String

last_update

String

life_status

String

num_preps

Number - Number of preparations.

occurrence_coll_id

Number

occurrence_id

Number

occurrence_type

String

seq_result

String

spm_sex

String

start_time

String

pcr_result

String

prep_contents

String

prep_type

String

type_status

String

unvouchered_coll

?

updater

String

vouchered

Boolean_flag

See also

Visit any of the below links to find information about the other data domains defined by OJ_Break Version 2.

Retrieved from "https://xbiod.osu.edu/index.php?title=OJ_Break_v2_Occurrence_Reference&oldid=2062"