Difference between revisions of "OJ Break v2 Occurrence Reference"
| Line 93: | Line 93: | ||
* ''unvouchered'': ''[[#unvouchered|unvouchered]]'' | * ''unvouchered'': ''[[#unvouchered|unvouchered]]'' | ||
==== OccurrenceExtended ==== | ==== OccurrenceExtended ==== | ||
| − | * ''locality'': [[OJ_Break v2 Locality Reference | + | * ''locality'': [[OJ_Break v2 Locality Reference#LocalityExtended_.28extends_LocalityBasic.29|LocalityExtended]] |
* ''coll_date'': [[#CollectingDate|CollectingDate]] | * ''coll_date'': [[#CollectingDate|CollectingDate]] | ||
* ''coll_method'': [[#coll_method|coll_method]] | * ''coll_method'': [[#coll_method|coll_method]] | ||
| Line 128: | Line 128: | ||
* ''spm_sex'': ''[[#spm_sex|spm_sex]]'' | * ''spm_sex'': ''[[#spm_sex|spm_sex]]'' | ||
* ''life_status'': ''[[#life_status|life_status]]'' | * ''life_status'': ''[[#life_status|life_status]]'' | ||
| − | * ''preparations'': array of [[# | + | * ''preparations'': array of [[#Preparation|Preparation]] |
=== Elements === | === Elements === | ||
Revision as of 20:58, 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.
Contents
- 1 API Information and Access
- 2 Procedural Reference
- 3 Occurrence Data Type Glossary
- 3.1 Classes
- 3.1.1 CollectingDate
- 3.1.2 CollectingDateRange
- 3.1.3 CollectingTime
- 3.1.4 CollectionOccurrence (realizes OccurrenceExtended)
- 3.1.5 DeterminationBasic
- 3.1.6 DeterminationExtended
- 3.1.7 NoncollectionOccurrence
- 3.1.8 OccurrenceAssociation
- 3.1.9 OccurrenceBasic
- 3.1.10 OccurrenceExtended
- 3.1.11 OccurrenceTrimmed
- 3.1.12 Preparation
- 3.1.13 Sequence
- 3.1.14 SequencePrimers
- 3.1.15 SpecimenGroup
- 3.2 Elements
- 3.1 Classes
- 4 See also
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
getOccurrencesInfo
Description
Parameters
- occurrence_ids: array of occurrence_id
- format: string
- key: string
- version: number
Return
- array of OccurrenceExtended
Example
Occurrence Data Type Glossary
Classes
CollectingDate
- coll_date: coll_date
- coll_date_sortable: coll_date_sortable
- coll_date_type: coll_date_type
- coll_date_range: CollectingDateRange
CollectingDateRange
- start_date: start_date
- start_date_sortable: start_date_sortable
- end_date: end_date
- end_date_sortable: end_date_sortable
CollectingTime
- start_time: start_time
- end_time: end_time
CollectionOccurrence (realizes OccurrenceExtended)
- occurrence_type: occurrence_type
- alt_ids: array of alt_id
- institution: InstitutionBasic
- spm_groups: array of SpecimenGroup
- ceid: ceid
- coll_time: CollectingTime
- field_code: field_code
- determinations: array of DeterminationExtended
- media: array of MediaExtended
- sequences: array of Sequence
- date_recorded: date_recorded
- updater: updater
DeterminationBasic
- taxon: TaxonRelationship
- determiner: AgentExtended
DeterminationExtended
- det_id: det_id
- det_date: det_date
- det_status: det_status
- type_status: type_status
- occurrence_coll_id: occurrence_coll_id
- coll_id: coll_id
NoncollectionOccurrence
- num_spms: Number
- determination: DeterminationBasic
OccurrenceAssociation
- assoc_type: assoc_type'
- assoc_type_full: assoc_type_full
OccurrenceBasic
- occurrence_id: occurrence_id
- guid: guid
- vouchered: vouchered
- unvouchered: unvouchered
OccurrenceExtended
- locality: LocalityExtended
- coll_date: CollectingDate
- coll_method: coll_method
- collector: AgentExtended
- habitat: habitat
- associations: array of OccurrenceAssociation
- comments: comments
- orig_citation: LiteratureCitationExtended
- enterer: enterer
- last_update: last_update
OccurrenceTrimmed
- alt_ids: array of alt_id
- institution: InstitutionBasic
- determination: DeterminationBasic
Preparation
- prep_type: prep_type
- prep_contents: prep_contents
- num_preps: num_preps
Sequence
- lab_code: lab_code
- gene: String
- primers: SequencePrimers
- sequence: String
- seq_result: seq_result
- pcr_result: pcr_result
- pcr_notes: String
- extract_quality: extract_quality
- extract_notes: String
SequencePrimers
- forward: String
- reverse: String
SpecimenGroup
- num_spms: Number
- spm_sex: spm_sex
- life_status: life_status
- preparations: array of Preparation
Elements
See also
Visit any of the below links to find information about the other data domains defined by OJ_Break Version 2.
