Difference between revisions of "OJ Break v2 Occurrence Reference"

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* ''end_time'': ''[[#end_time|end_time]]''
 
* ''end_time'': ''[[#end_time|end_time]]''
 
==== CollectionOccurrence (realizes [[OccurrenceExtended_.28extends_OccurrenceBasic.29|OccurrenceExtended]]) ====
 
==== CollectionOccurrence (realizes [[OccurrenceExtended_.28extends_OccurrenceBasic.29|OccurrenceExtended]]) ====
 +
* ''occurrence_type'': ''[[#occurrence_type|occurrence_type]]''
 +
* ''alt_ids'': array of ''[[#alt_id|alt_id]]''
 +
* ''institution'': [[OJ_Break v2 Institution Reference#InstitutionBasic|InstitutionBasic]]
 +
* ''spm_groups'': array of [[#SpecimenGroup|SpecimenGroup]]
 +
* ''ceid'': ''[[#ceid|ceid]]''
 +
* ''coll_time'': ''[[#CollectingTime|CollectingTime]]
 +
* ''field_code'': ''[[#field_code|field_code]]''
 +
* ''determinations'': array of [[#DeterminationExtended_.28extends_DeterminationBasic.29|DeterminationExtended]]
 +
* ''media'': array of [[#MediaExtended|MediaExtended]]
 +
* ''sequences'': array of [[#Sequence|Sequence]]
 +
* ''date_recorded'': ''[[#date_recorded|date_recorded]]''
 +
* ''updater'': ''[[#updater|updater]]
 +
 
==== DeterminationBasic ====
 
==== DeterminationBasic ====
 +
* ''taxon'': [[OJ_Break v2 Taxon Reference#TaxonRelationship|TaxonRelationship]]
 +
* ''determiner'': [[#OJ_Break v2 Agent Reference#AgentExtended_.28extends_AgentBasic.29|AgentExtended]]
 
==== DeterminationExtended ====
 
==== DeterminationExtended ====
 +
* ''det_id'': ''[[#det_id|det_id]]''
 +
* ''det_date'': ''[[#det_date|det_date]]''
 +
* ''det_status'': ''[[#det_status|det_status]]''
 +
* ''type_status'': ''[[#type_status|type_status]]''
 +
* ''occurrence_coll_id'': ''[[#occurrence_coll_id|occurrence_coll_id]]''
 +
* ''coll_id'': ''[[#coll_id|coll_id]]''
 
==== NoncollectionOccurrence ====
 
==== NoncollectionOccurrence ====
 +
* ''num_spms'': Number
 +
* ''determination'': [[#DeterminationBasic|DeterminationBasic]]
 
==== OccurrenceAssociation ====
 
==== OccurrenceAssociation ====
 +
* ''assoc_type'': ''[[#assoc_type|assoc_type']]''
 +
* ''assoc_type_full'': ''[[#assoc_type_full|assoc_type_full]]''
 
==== OccurrenceBasic ====
 
==== OccurrenceBasic ====
 +
* ''occurrence_id'': ''[[#occurrence_id|occurrence_id]]''
 +
* ''guid'': ''[[#guid|guid]]''
 +
* ''vouchered'': ''[[#vouchered|vouchered]]''
 +
* ''unvouchered'': ''[[#unvouchered|unvouchered]]''
 
==== OccurrenceExtended ====
 
==== OccurrenceExtended ====
 +
* ''locality'': [[OJ_Break v2 Locality Reference|#LocalityExtended_.28extends_LocalityBasic.29|LocalityExtended]]
 +
* ''coll_date'': [[#CollectingDate|CollectingDate]]
 +
* ''coll_method'': [[#coll_method|coll_method]]
 +
* ''collector'': [[OJ_Break v2 Agent Reference#AgentExtended_.28extends_AgentBasic.29|AgentExtended]]
 +
* ''habitat'': ''[[#habitat|habitat]]''
 +
* ''associations'': array of [[#OccurrenceAssociation|OccurrenceAssociation]]
 +
* ''comments'': ''[[#comments|comments]]''
 +
* ''orig_citation'': [[OJ_Break v2 LiteratureCitationExtended_.28extends_LiteratureCitationBasic.29#LiteratureCitationExtended|LiteratureCitationExtended]]
 +
* ''enterer'': ''[[#enterer|enterer]]''
 +
* ''last_update'': ''[[#last_update|last_update]]''
 
==== OccurrenceTrimmed ====
 
==== OccurrenceTrimmed ====
 +
* ''alt_ids'': array of ''alt_id''
 +
* ''institution'': [[InstitutionBasic]]
 +
* ''determination'': [[#DeterminationBasic|DeterminationBasic]]
 
==== Preparation ====
 
==== Preparation ====
 +
* ''prep_type'': ''[[#prep_type|prep_type]]''
 +
* ''prep_contents'': ''[[#prep_contents|prep_contents]]''
 +
* ''num_preps'': ''[[#num_preps|num_preps]]''
 
==== Sequence ====
 
==== Sequence ====
 +
* ''lab_code'': ''[[#lab_code|lab_code]]''
 +
* ''gene'': String
 +
* ''primers'': ''[[#SequencePrimers|SequencePrimers]]''
 +
* ''sequence'': String
 +
* ''seq_result'': ''[[#seq_result|seq_result]]''
 +
* ''pcr_result'': ''[[#pcr_result|pcr_result]]''
 +
* ''pcr_notes'': String
 +
* ''extract_quality'': ''[[#extract_quality|extract_quality]]''
 +
* ''extract_notes'': String
 
==== SequencePrimers ====
 
==== SequencePrimers ====
 +
* ''forward'': String
 +
* ''reverse'': String
 
==== SpecimenGroup ====
 
==== SpecimenGroup ====
 +
* ''num_spms'': Number
 +
* ''spm_sex'': ''[[#spm_sex|spm_sex]]''
 +
* ''life_status'': ''[[#life_status|life_status]]''
 +
* ''preparations'': array of [[#Preparations|Preparations]]
  
 
=== Elements ===
 
=== Elements ===

Revision as of 20:56, 11 March 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 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 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.

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=json&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.

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=json&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=json&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2

Occurrence Data Type Glossary

Classes

CollectingDate

CollectingDateRange

CollectingTime

CollectionOccurrence (realizes OccurrenceExtended)

DeterminationBasic

DeterminationExtended

NoncollectionOccurrence

OccurrenceAssociation

OccurrenceBasic

OccurrenceExtended

OccurrenceTrimmed

Preparation

Sequence

SequencePrimers

  • forward: String
  • reverse: String

SpecimenGroup

Elements

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=1877"