OJ Break v2 Occurrence Reference

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.

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.

Procedural Reference

Occurrence

getOccurrenceInfo

Parameters

• occurrence_id: occurrence_id
• format: string
• key: string
• version: number

Return

• OccurrenceExtended

Example

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

getOccurrencesInfo

Parameters

• occurrence_ids: array of occurrence_id
• format: string
• key: string
• version: number

Return

• array of OccurrenceExtended

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

• 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 (extends DeterminationBasic)

• 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 (realizes OccurrenceExtended)

• num_spms: Number
• determination: DeterminationBasic

OccurrenceAssociation (extends OccurrenceTrimmed)

• assoc_type: assoc_type
• assoc_type_full: assoc_type_full

OccurrenceBasic

• occurrence_id: occurrence_id
• guid: guid
• vouchered: vouchered
• unvouchered: unvouchered

OccurrenceExtended (extends OccurrenceBasic)

• 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 (extends OccurrenceBasic)

• 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

alt_id

String - An alternate identifier for the specimen.

assoc_type

String - A description of the biological relationship between two organisms.

assoc_type_full

String - A full description of the biological relationship between two organisms.

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.

• Agent
• Geographic Place
• Institution
• Journal
• Literature
• Locality
• Media
• Search
• Taxon