OJ Break v2 Taxon 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 Taxon 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/getTaxonInfo?tnuid=30148&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.

Taxon Data Model

Procedural Reference

Taxon

getTaxonInfo

Parameters

• tnuid: tnuid
• *inst_id: inst_id
• format: String
• key: String
• version: Number

Return

• TaxonComplete

Example

http://osuc.biosci.ohio-state.edu/OJ_Break/getTaxonInfo?tnuid=30148&inst_id=1&format=html&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2

getTaxonHierarchy

Parameters

• tnuid: tnuid
• format: String
• key: String
• version: Number

Return

• TaxonRelationship

Example

http://osuc.biosci.ohio-state.edu/OJ_Break/getTaxonHierarchy?tnuid=30148&format=html&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2

getTaxonIncludedTaxa

Parameters

• tnuid: tnuid
• *inst_id: inst_id
• *rank: rank
• *offset: Number
• *limit: Number
• *show_syns: Boolean_flag
• *show_fossils: Boolean_flag
• *types_only: Boolean_flag
• format: String
• key: String
• version: Number

Return

• TaxonReturnIncluded

Example

http://osuc.biosci.ohio-state.edu/OJ_Break/getTaxonIncludedTaxa?tnuid=30148&inst_id=1&show_syns=Y&format=html&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2

getTaxonSynonyms

Parameters

• tnuid: tnuid
• *offset: Number
• *limit: Number
• *show_fossils: Boolean_flag
• format: String
• key: String
• version: Number

Return

• TaxonReturnSynonyms

Example

http://osuc.biosci.ohio-state.edu/OJ_Break/getTaxonSynonyms?tnuid=30148&format=html&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2

getTaxonAssociations

Parameters

• tnuid: tnuid
• *offset: Number
• *limit: Number
• *basic_only: Boolean_flag
• format: String
• key: String
• version: Number

Return

• TaxonReturnAssociations

Example

http://osuc.biosci.ohio-state.edu/OJ_Break/getTaxonAssociations?tnuid=30148&format=html&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2

getTaxonLiteratureCitations

Parameters

• tnuid: tnuid
• *offset: Number
• *limit: Number
• *show_children: Boolean_flag
• format: String
• key: String
• version: Number

Return

• TaxonReturnLiteratureCitations

Example

http://osuc.biosci.ohio-state.edu/OJ_Break/getTaxonLiteratureCitations?tnuid=30148&format=html&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2

getTaxonOccurrences

Parameters

• tnuid: tnuid
• *inst_id: inst_id
• *place_id: place_id
• *offset: Number
• *limit: Number
• *show_children: Boolean_flag
• *basic_only: Boolean_flag
• format: String
• key: String
• version: Number

Return

• TaxonReturnOccurrences

Example

http://osuc.biosci.ohio-state.edu/OJ_Break/getTaxonOccurrences?tnuid=30148&format=html&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2

getTaxonTypes

Parameters

• tnuid: tnuid
• *inst_id: inst_id
• *offset: Number
• *limit: Number
• *basic_only: Boolean_flag
• *show_children: Boolean_flag
• *primary_only: Boolean_flag
• format: String
• key: String
• version: Number

Return

• TaxonReturnOccurrences

Example

http://osuc.biosci.ohio-state.edu/OJ_Break/getTaxonTypes?tnuid=30148&format=html&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2

getTaxonLocalities

Parameters

• tnuid: tnuid
• *inst_id: inst_id
• *place_id: place_id
• *offset: Number
• *limit: Number
• *show_children: Boolean_flag
• format: String
• key: String
• version: Number

Return

• TaxonReturnLocalities

Example

http://osuc.biosci.ohio-state.edu/OJ_Break/getTaxonLocalities?tnuid=30148&format=html&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2

getTaxonDeterminers

Parameters

• tnuid: tnuid
• *inst_id: inst_id
• *offset: Number
• *limit: Number
• format: String
• key: String
• version: Number

Return

• TaxonReturnDeterminers

Example

http://osuc.biosci.ohio-state.edu/OJ_Break/getTaxonDeterminers?tnuid=30148&format=html&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2

getTaxonInstitutions

Parameters

• tnuid: tnuid
• *offset: Number
• *limit: Number
• format: String
• key: String
• version: Number

Return

• TaxonReturnInstitutions

Example

http://osuc.biosci.ohio-state.edu/OJ_Break/getTaxonInstitutions?tnuid=30148&format=html&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2

getTaxonHabitats

Parameters

• tnuid: tnuid
• *offset: Number
• *limit: Number
• format: String
• key: String
• version: Number

Return

• TaxonReturnHabitats

Example

http://osuc.biosci.ohio-state.edu/OJ_Break/getTaxonHabitats?tnuid=30148&format=html&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2

getTaxonMedia

Parameters

• tnuid: tnuid
• *media_type: media_type
• *inst_id: inst_id
• *offset: Number
• *limit: Number
• format: String
• key: String
• version: Number

Return

• TaxonReturnMedia

Example

http://osuc.biosci.ohio-state.edu/OJ_Break/getTaxonMedia?tnuid=30148&format=html&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2

Taxon Data Type Glossary

Classes

TaxonAssociation

• assoc_taxon: TaxonRelationship
• assoc_type: assoc_type
• assoc_type_full: assoc_type_full
• assoc_occurrences: array of OccurrenceBasic

TaxonBasic

• tnuid: tnuid
• guid: guid
• tcid: tcid
• taxon: taxon
• taxon_author: taxon_author

TaxonComplete (extends TaxonRelationship)

• stats: TaxonInfoStats
• contribs: array of Contribution
• orig_desc: LiteratureExtended

TaxonExtended (extends TaxonBasic)

• describer: describer
• status: status
• valid: valid
• rank: rank
• valid_taxon: TaxonBasic
• fossil: fossil
• homonym: homonym
• common_names: array of common_name
• source: TaxonSource

TaxonHierarchy

Aggregate of one or more of the following classes:

• TaxonHierKingdom (1)
• TaxonHierPhylum (0 or 1)
• TaxonHierDivision (0 or 1)
• TaxonHierSubphylum (0 or 1)
• TaxonHierClass (0 or 1)
• TaxonHierSubclass (0 or 1)
• TaxonHierInfraclass (0 or 1)
• TaxonHierOrder (0 or 1)
• TaxonHierSuborder (0 or 1)
• TaxonHierInfraorder (0 or 1)
• TaxonHierCohort (0 or 1)
• TaxonHierSubcohort (0 or 1)
• TaxonHierSuperfamily (0 or 1)
• TaxonHierFamily (0 or 1)
• TaxonHierSubfamily (0 or 1)
• TaxonHierTribe (0 or 1)
• TaxonHierSubtribe (0 or 1)
• TaxonHierGenus (0 or 1)
• TaxonHierSpecies (0 or 1)
• TaxonHierSubspecies (0 or 1)

TaxonHierClass

• Class: TaxonHierUnit

TaxonHierCohort

• Cohort: TaxonHierUnit

TaxonHierDivision

• Division: TaxonHierUnit

TaxonHierFamily

• Family: TaxonHierUnit

TaxonHierGenus

• Genus: TaxonHierUnit

TaxonHierInfraclass

• Infraclass: TaxonHierUnit

TaxonHierInfraorder

• Infraorder: TaxonHierUnit

TaxonHierKingdom

• Kingdom: TaxonHierUnit

TaxonHierOrder

• Order: TaxonHierUnit

TaxonHierPhylum

• Phylum: TaxonHierUnit

TaxonHierSpecies

• Species: TaxonHierUnit

TaxonHierSubclass

• Subclass: TaxonHierUnit

TaxonHierSubcohort

• Subcohort: TaxonHierUnit

TaxonHierSubfamily

• Subfamily: TaxonHierUnit

TaxonHierSuborder

• Suborder: TaxonHierUnit

TaxonHierSubphylum

• Subphylum: TaxonHierUnit

TaxonHierSubspecies

• Subspecies: TaxonHierUnit

TaxonHierSubtribe

• Subtribe: TaxonHierUnit

TaxonHierSuperfamily

• Superfamily: TaxonHierUnit

TaxonHierTribe

• Tribe: TaxonHierUnit

TaxonHierUnit (extends TaxonBasic)

• next: rank

TaxonInfoStats (extends TaxonStats)

• child_stats: array of TaxonStats
• num_records: Number
• num_spms: Number

TaxonRelationship (extends TaxonExtended)

• rel_type: rel_type
• parent_taxon: TaxonBasic
• hier: TaxonHierarchy

TaxonReturn

• general: TaxonBasic

TaxonReturnAssociations (extends TaxonReturn)

• associations: array of TaxonAssociation

TaxonReturnDeterminers (extends TaxonReturn)

• determiners: array of AgentExtended

TaxonReturnHabitats (extends TaxonReturn)

• hatitats: array of habitat

TaxonReturnIncluded (extends TaxonReturn)

• includedTaxa: array of TaxonExtended

TaxonReturnInstitutions (extends TaxonReturn)

• institutions: array of InstitutionBasic

TaxonReturnLiteratureCitations (extends TaxonReturn)

• pub_citations: array of LiteratureTaxonCitationExtended

TaxonReturnLocalities (extends TaxonReturn)

• localities: array of LocalityExtended

TaxonReturnMedia (extends TaxonReturn)

• media: array of MediaExtended

TaxonReturnOccurrences (extends TaxonReturn)

• occurrences: array of OccurrenceExtended

TaxonReturnSynonyms (extends TaxonReturn)

• synonyms: array of TaxonRelationship

TaxonSource

• id: Number
• name: String
• logo: URL
• url: URL
• query: URL

TaxonStats

• rank: rank
• rank_value: rank_value
• num_taxa: Number

Elements

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.

common_name

String - A common name for a taxon that can be included as a taxon name string but is never valid.

describer

String - the describer(s) of a taxon.

fossil

String - A modified boolean_flag, either Y, N or B, representing whether a taxon name is a extinct fossil, exclusively extant, or present today and in fossils.

guid

String - A globally unique identifier for an xBio:D domain resource in the form of a stable URI dereferenced by the bioguid.osu.edu domain.

habitat

String - Description or identifier of the ecological or environmental area that a particular species is known to inhabit.

homonym

Boolean_flag - Boolean_flag indicating whether or not the determination was a homonym

rank

String - The taxonomic (hierarchical) rank of a taxon name.

rank_value

Number - A number representing the rank of a taxon with higher numbers representing higher positions in the taxonomic hierarchy.

rel_type

String - The taxonomic (hierarchical) relationship between the taxonomic concept indicated by the taxon name and its parent taxonomic concept. Can be Member, Junior synonym, etc.

status

String - The nomenclatural status of a taxon name using a formalized vocabulary.

taxon

String - A taxon name string.

taxon_author

String - The author(s) of a taxon with parenthesis surrounding the name of the author(s) if necessary.

tcid

Number - The taxonomic concept identifier which uniquely identifies a taxon concept, which may have many name uses, within xBio:D.

tnuid

Number - The taxon name use identifier which uniquely identifies a taxon within xBio:D.

valid

String - A Valid or Invalid string representing the validity of a taxon name using subjective interpretations if warranted.

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
• Occurrence
• Search