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 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
- 2.1 Taxon
- 2.1.1 getTaxonInfo
- 2.1.2 getTaxonHierarchy
- 2.1.3 getTaxonIncludedTaxa
- 2.1.4 getTaxonSynonyms
- 2.1.5 getTaxonAssociations
- 2.1.6 getTaxonLiteratureCitations
- 2.1.7 getTaxonOccurrences
- 2.1.8 getTaxonTypes
- 2.1.9 getTaxonLocalities
- 2.1.10 getTaxonDeterminers
- 2.1.11 getTaxonInstitutions
- 2.1.12 getTaxonHabitats
- 2.1.13 getTaxonMedia
- 2.1 Taxon
- 3 Taxon Data Type Glossary
- 3.1 Classes
- 3.1.1 TaxonAssociation
- 3.1.2 TaxonBasic
- 3.1.3 TaxonComplete (extends TaxonRelationship)
- 3.1.4 TaxonExtended (extends TaxonBasic)
- 3.1.5 TaxonHierarchy
- 3.1.6 TaxonHierClass
- 3.1.7 TaxonHierCohort
- 3.1.8 TaxonHierDivision
- 3.1.9 TaxonHierFamily
- 3.1.10 TaxonHierGenus
- 3.1.11 TaxonHierInfraclass
- 3.1.12 TaxonHierInfraorder
- 3.1.13 TaxonHierKingdom
- 3.1.14 TaxonHierOrder
- 3.1.15 TaxonHierPhylum
- 3.1.16 TaxonHierSpecies
- 3.1.17 TaxonHierSubclass
- 3.1.18 TaxonHierSubcohort
- 3.1.19 TaxonHierSubfamily
- 3.1.20 TaxonHierSuborder
- 3.1.21 TaxonHierSubphylum
- 3.1.22 TaxonHierSubspecies
- 3.1.23 TaxonHierSubtribe
- 3.1.24 TaxonHierSuperfamily
- 3.1.25 TaxonHierTribe
- 3.1.26 TaxonHierUnit (extends TaxonBasic)
- 3.1.27 TaxonInfoStats (extends TaxonStats)
- 3.1.28 TaxonRelationship (extends TaxonExtended)
- 3.1.29 TaxonReturn
- 3.1.30 TaxonReturnAssociations (extends TaxonReturn)
- 3.1.31 TaxonReturnDeterminers (extends TaxonReturn)
- 3.1.32 TaxonReturnHabitats (extends TaxonReturn)
- 3.1.33 TaxonReturnIncluded (extends TaxonReturn)
- 3.1.34 TaxonReturnInstitutions (extends TaxonReturn)
- 3.1.35 TaxonReturnLiteratureCitations (extends TaxonReturn)
- 3.1.36 TaxonReturnLocalities (extends TaxonReturn)
- 3.1.37 TaxonReturnMedia (extends TaxonReturn)
- 3.1.38 TaxonReturnOccurrences (extends TaxonReturn)
- 3.1.39 TaxonReturnSynonyms (extends TaxonReturn)
- 3.1.40 TaxonSource
- 3.1.41 TaxonStats
- 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 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=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
Taxon
getTaxonInfo
Description
Parameters
Return
Example
getTaxonHierarchy
Description
Parameters
- tnuid: tnuid
- format: String
- key: String
- version: Number
Return
Example
getTaxonIncludedTaxa
Description
Parameters
- tnuid: tnuid
- inst_id: inst_id (optional)
- rank: rank (optional)
- offset: Number (optional)
- limit: Number (optional)
- show_syns: Boolean_flag (optional)
- show_fossils: Boolean_flag (optional)
- types_only: Boolean_flag (optional)
- format: String
- key: String
- version: Number
Return
Example
getTaxonSynonyms
Description
Parameters
- tnuid: tnuid
- offset: Number (optional)
- limit: Number (optional)
- show_fossils: Boolean_flag (optional)
- format: String
- key: String
- version: Number
Return
Example
getTaxonAssociations
Description
Parameters
- tnuid: tnuid
- offset: Number (optional)
- limit: Number (optional)
- basic_only: Boolean_flag (optional)
- format: String
- key: String
- version: Number
Return
Example
getTaxonLiteratureCitations
Description
Parameters
- tnuid: tnuid
- offset: Number (optional)
- limit: Number (optional)
- show_syns: Boolean_flag (optional)
- format: String
- key: String
- version: Number
Return
Example
getTaxonOccurrences
Description
Parameters
- tnuid: tnuid
- inst_id: inst_id (optional)
- place_id: place_id (optional)
- offset: Number (optional)
- limit: Number (optional)
- show_children: Boolean_flag (optional)
- basic_only: Boolean_flag (optional)
- format: String
- key: String
- version: Number
Return
Example
getTaxonTypes
Description
Parameters
- tnuid: tnuid
- inst_id: inst_id (optional)
- offset: Number (optional)
- limit: Number (optional)
- basic_only: Boolean_flag (optional)
- show_children: Boolean_flag (optional)
- primary_only: Boolean_flag (optional)
- limit: Number (optional)
- offset: Number (optional)
- format: String
- key: String
- version: Number
Return
Example
getTaxonLocalities
Description
Parameters
- tnuid: tnuid
- inst_id: inst_id (optional)
- place_id: place_id (optional)
- offset: Number (optional)
- limit: Number (optional)
- show_children: Boolean_flag (optional)
- format: String
- key: String
- version: Number
Return
Example
getTaxonDeterminers
Description
Parameters
- tnuid: tnuid
- inst_id: inst_id (optional)
- offset: Number (optional)
- limit: Number (optional)
- format: String
- key: String
- version: Number
Return
Example
getTaxonInstitutions
Description
Parameters
- tnuid: tnuid
- offset: Number (optional)
- limit: Number (optional)
- format: String
- key: String
- version: Number
Return
Example
getTaxonHabitats
Description
Parameters
- tnuid: tnuid
- offset: Number (optional)
- limit: Number (optional)
- format: String
- key: String
- version: Number
Return
Example
getTaxonMedia
Description
Parameters
- tnuid: tnuid
- media_type: media_type (optional)
- inst_id: inst_id (optional)
- offset: Number (optional)
- limit: Number (optional)
- format: String
- key: String
- version: Number
Return
Example
Taxon Data Type Glossary
Classes
TaxonAssociation
- assoc_taxon: TaxonRelationship class
- assoc_type: assoc_type element
- assoc_type_full: assoc_type_full element
- assoc_occurrences: array of OccurrenceBasic class
TaxonBasic
- tnuid: tnuid element
- taxon: taxon element
- taxon_author: taxon_author element
TaxonComplete (extends TaxonRelationship)
- stats: TaxonInfoStats class
- contribs: array of Contribution class
- orig_desc: LiteratureExtended class
TaxonExtended (extends TaxonBasic)
- describer: describer element
- status: status element
- valid: valid element
- rank: rank element
- valid_taxon: TaxonBasic class
- fossil: fossil element
- homonym: homonym element
- common_names': array of common_name element
- source: TaxonSource class
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 class
TaxonHierCohort
- Cohort: TaxonHierUnit class
TaxonHierDivision
- Division: TaxonHierUnit class
TaxonHierFamily
- Family: TaxonHierUnit class
TaxonHierGenus
- Genus: TaxonHierUnit class
TaxonHierInfraclass
- Infraclass: TaxonHierUnit class
TaxonHierInfraorder
- Infraorder: TaxonHierUnit class
TaxonHierKingdom
- Kingdom: TaxonHierUnit class
TaxonHierOrder
- Order: TaxonHierUnit class
TaxonHierPhylum
- Phylum: TaxonHierUnit class
TaxonHierSpecies
- Species: TaxonHierUnit class
TaxonHierSubclass
- Subclass: TaxonHierUnit class
TaxonHierSubcohort
- Subcohort: TaxonHierUnit class
TaxonHierSubfamily
- Subfamily: TaxonHierUnit class
TaxonHierSuborder
- Suborder: TaxonHierUnit class
TaxonHierSubphylum
- Subphylum: TaxonHierUnit class
TaxonHierSubspecies
- Subspecies: TaxonHierUnit class
TaxonHierSubtribe
- Subtribe: TaxonHierUnit class
TaxonHierSuperfamily
- Superfamily: TaxonHierUnit class
TaxonHierTribe
- Tribe: TaxonHierUnit class
TaxonHierUnit (extends TaxonBasic)
- next: rank element
TaxonInfoStats (extends TaxonStats)
- child_stats: array of TaxonStats
- num_spms: Number
TaxonRelationship (extends TaxonExtended)
- rel_type: rel_type element
- parent_taxon: TaxonBasic class
- hier: TaxonHierarchy class
TaxonReturn
- general: TaxonBasic class
TaxonReturnAssociations (extends TaxonReturn)
- associations: array of TaxonAssociation class
TaxonReturnDeterminers (extends TaxonReturn)
- determiners: array of AgentExtended class
TaxonReturnHabitats (extends TaxonReturn)
- hatitats: array of habitat element
TaxonReturnIncluded (extends TaxonReturn)
- includedTaxa: array of AgentExtended class
TaxonReturnInstitutions (extends TaxonReturn)
- institutions: array of InstitutionBasic class
TaxonReturnLiteratureCitations (extends TaxonReturn)
- pub_citations: array of LiteratureTaxonCitationExtended class
TaxonReturnLocalities (extends TaxonReturn)
- localities: array of LocalityExtended class
TaxonReturnMedia (extends TaxonReturn)
- media: array of MediaExtended class
TaxonReturnOccurrences (extends TaxonReturn)
- occurrences: array of OccurrenceExtended class
TaxonReturnSynonyms (extends TaxonReturn)
- synonyms: array of TaxonRelationship class
TaxonSource
- id: Number
- name: String
- logo: URL
- url: URL
- query: URL
TaxonStats
- rank: rank element
- rank_value: rank_value element
- 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.
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.
tnuid
Number - The taxon name use identifier which uniquely identifies a taxon.
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.
