Difference between revisions of "OJ Break v2 Taxon Reference"

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'''Introduction'''
 
'''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 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.
 
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.
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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.  
 
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
+
     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]].
 
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]].
 +
 +
 +
[[File:OJ_Break Data Model - Taxon.png|none|frame|Taxon Data Model]]
  
 
== Procedural Reference ==
 
== Procedural Reference ==
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* ''version'': Number
 
* ''version'': Number
 
===== Return =====
 
===== Return =====
−
* [[#TaxonComplete_.28extends_TaxonRelationship.29|TaxonComplete]]
+
* [[#TaxonComplete (extends TaxonRelationship)|TaxonComplete]]
  
 
===== Example =====
 
===== Example =====
−
http://osuc.biosci.ohio-state.edu/OJ_Break/getTaxonInfo?tnuid=30148&inst_id=1&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2
+
http://osuc.biosci.ohio-state.edu/OJ_Break/getTaxonInfo?tnuid=30148&inst_id=1&format=html&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2
  
 
==== getTaxonHierarchy ====
 
==== getTaxonHierarchy ====
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* ''version'': Number
 
* ''version'': Number
 
===== Return =====
 
===== Return =====
−
* [[#TaxonRelationship_.28extends_TaxonExtended.29|TaxonRelationship]]
+
* [[#TaxonRelationship (extends TaxonExtended)|TaxonRelationship]]
  
 
===== Example =====
 
===== Example =====
−
http://osuc.biosci.ohio-state.edu/OJ_Break/getTaxonHierarchy?tnuid=30148&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2
+
http://osuc.biosci.ohio-state.edu/OJ_Break/getTaxonHierarchy?tnuid=30148&format=html&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2
  
 
==== getTaxonIncludedTaxa ====
 
==== getTaxonIncludedTaxa ====
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* ''version'': Number
 
* ''version'': Number
 
===== Return =====
 
===== Return =====
−
* [[#TaxonReturnIncluded_.28extends_TaxonReturn.29|TaxonReturnIncluded]]
+
* [[#TaxonReturnIncluded (extends TaxonReturn)|TaxonReturnIncluded]]
  
 
===== Example =====
 
===== Example =====
−
http://osuc.biosci.ohio-state.edu/OJ_Break/getTaxonIncludedTaxa?tnuid=30148&inst_id=1&show_syns=Y&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2
+
http://osuc.biosci.ohio-state.edu/OJ_Break/getTaxonIncludedTaxa?tnuid=30148&inst_id=1&show_syns=Y&format=html&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2
  
 
==== getTaxonSynonyms ====
 
==== getTaxonSynonyms ====
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* ''version'': Number
 
* ''version'': Number
 
===== Return =====
 
===== Return =====
−
* [[#TaxonReturnSynonyms_.28extends_TaxonReturn.29|TaxonReturnSynonyms]]
+
* [[#TaxonReturnSynonyms (extends TaxonReturn)|TaxonReturnSynonyms]]
  
 
===== Example =====
 
===== Example =====
−
http://osuc.biosci.ohio-state.edu/OJ_Break/getTaxonSynonyms?tnuid=30148&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2
+
http://osuc.biosci.ohio-state.edu/OJ_Break/getTaxonSynonyms?tnuid=30148&format=html&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2
  
 
==== getTaxonAssociations ====
 
==== getTaxonAssociations ====
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===== Return =====
 
===== Return =====
−
* [[#TaxonReturnAssociations_.28extends_TaxonReturn.29|TaxonReturnAssociations]]
+
* [[#TaxonReturnAssociations (extends TaxonReturn)|TaxonReturnAssociations]]
  
 
===== Example =====
 
===== Example =====
−
http://osuc.biosci.ohio-state.edu/OJ_Break/getTaxonAssociations?tnuid=30148&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2
+
http://osuc.biosci.ohio-state.edu/OJ_Break/getTaxonAssociations?tnuid=30148&format=html&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2
  
 
==== getTaxonLiteratureCitations ====
 
==== getTaxonLiteratureCitations ====
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* ''*offset'': Number  
 
* ''*offset'': Number  
 
* ''*limit'': Number  
 
* ''*limit'': Number  
−
* ''*show_syns'': Boolean_flag
+
* ''*show_children'': Boolean_flag
 
* ''format'': String
 
* ''format'': String
 
* ''key'': String
 
* ''key'': String
 
* ''version'': Number
 
* ''version'': Number
 
===== Return =====
 
===== Return =====
−
* [[#TaxonReturnLiteratureCitations_.28extends_TaxonReturn.29|TaxonReturnLiteratureCitations]]
+
* [[#TaxonReturnLiteratureCitations (extends TaxonReturn)|TaxonReturnLiteratureCitations]]
  
 
===== Example =====
 
===== Example =====
−
http://osuc.biosci.ohio-state.edu/OJ_Break/getTaxonLiteratureCitations?tnuid=30148&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2
+
http://osuc.biosci.ohio-state.edu/OJ_Break/getTaxonLiteratureCitations?tnuid=30148&format=html&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2
  
 
==== getTaxonOccurrences ====
 
==== getTaxonOccurrences ====
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* ''version'': Number
 
* ''version'': Number
 
===== Return =====
 
===== Return =====
−
* [[#TaxonReturnOccurrences_.28extends_TaxonReturn.29|TaxonReturnOccurrences]]
+
* [[#TaxonReturnOccurrences (extends TaxonReturn)|TaxonReturnOccurrences]]
  
 
===== Example =====
 
===== Example =====
−
http://osuc.biosci.ohio-state.edu/OJ_Break/getTaxonOccurrences?tnuid=30148&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2
+
http://osuc.biosci.ohio-state.edu/OJ_Break/getTaxonOccurrences?tnuid=30148&format=html&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2
  
 
==== getTaxonTypes ====
 
==== getTaxonTypes ====
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* ''version'': Number
 
* ''version'': Number
 
===== Return =====
 
===== Return =====
−
* [[#TaxonReturnOccurrences_.28extends_TaxonReturn.29|TaxonReturnOccurrences]]
+
* [[#TaxonReturnOccurrences (extends TaxonReturn)|TaxonReturnOccurrences]]
  
 
===== Example =====
 
===== Example =====
−
http://osuc.biosci.ohio-state.edu/OJ_Break/getTaxonTypes?tnuid=30148&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2
+
http://osuc.biosci.ohio-state.edu/OJ_Break/getTaxonTypes?tnuid=30148&format=html&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2
  
 
==== getTaxonLocalities ====
 
==== getTaxonLocalities ====
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* ''version'': Number
 
* ''version'': Number
 
===== Return =====
 
===== Return =====
−
* [[#TaxonReturnLocalities_.28extends_TaxonReturn.29|TaxonReturnLocalities]]
+
* [[#TaxonReturnLocalities (extends TaxonReturn)|TaxonReturnLocalities]]
  
 
===== Example =====
 
===== Example =====
−
http://osuc.biosci.ohio-state.edu/OJ_Break/getTaxonLocalities?tnuid=30148&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2
+
http://osuc.biosci.ohio-state.edu/OJ_Break/getTaxonLocalities?tnuid=30148&format=html&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2
  
 
==== getTaxonDeterminers ====
 
==== getTaxonDeterminers ====
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* ''version'': Number
 
* ''version'': Number
 
===== Return =====
 
===== Return =====
−
* [[#TaxonReturnDeterminers_.28extends_TaxonReturn.29|TaxonReturnDeterminers]]
+
* [[#TaxonReturnDeterminers (extends TaxonReturn)|TaxonReturnDeterminers]]
  
 
===== Example =====
 
===== Example =====
−
http://osuc.biosci.ohio-state.edu/OJ_Break/getTaxonDeterminers?tnuid=30148&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2
+
http://osuc.biosci.ohio-state.edu/OJ_Break/getTaxonDeterminers?tnuid=30148&format=html&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2
  
 
==== getTaxonInstitutions ====
 
==== getTaxonInstitutions ====
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* ''version'': Number
 
* ''version'': Number
 
===== Return =====
 
===== Return =====
−
* [[#TaxonReturnInstitutions_.28extends_TaxonReturn.29|TaxonReturnInstitutions]]
+
* [[#TaxonReturnInstitutions (extends TaxonReturn)|TaxonReturnInstitutions]]
  
 
===== Example =====
 
===== Example =====
−
http://osuc.biosci.ohio-state.edu/OJ_Break/getTaxonInstitutions?tnuid=30148&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2
+
http://osuc.biosci.ohio-state.edu/OJ_Break/getTaxonInstitutions?tnuid=30148&format=html&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2
  
 
==== getTaxonHabitats ====
 
==== getTaxonHabitats ====
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* ''version'': Number
 
* ''version'': Number
 
===== Return =====
 
===== Return =====
−
* [[#TaxonReturnHabitats_.28extends_TaxonReturn.29|TaxonReturnHabitats]]
+
* [[#TaxonReturnHabitats (extends TaxonReturn)|TaxonReturnHabitats]]
  
 
===== Example =====
 
===== Example =====
−
http://osuc.biosci.ohio-state.edu/OJ_Break/getTaxonHabitats?tnuid=30148&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2
+
http://osuc.biosci.ohio-state.edu/OJ_Break/getTaxonHabitats?tnuid=30148&format=html&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2
  
 
==== getTaxonMedia ====
 
==== getTaxonMedia ====
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* ''version'': Number
 
* ''version'': Number
 
===== Return =====
 
===== Return =====
−
* [[#TaxonReturnMedia_.28extends_TaxonReturn.29|TaxonReturnMedia]]
+
* [[#TaxonReturnMedia (extends TaxonReturn)|TaxonReturnMedia]]
  
 
===== Example =====
 
===== Example =====
−
http://osuc.biosci.ohio-state.edu/OJ_Break/getTaxonMedia?tnuid=30148&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2
+
http://osuc.biosci.ohio-state.edu/OJ_Break/getTaxonMedia?tnuid=30148&format=html&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2
  
 
== Taxon Data Type Glossary ==
 
== Taxon Data Type Glossary ==
 
=== Classes ===
 
=== Classes ===
 
==== TaxonAssociation ====
 
==== TaxonAssociation ====
−
* ''assoc_taxon'': [[#TaxonRelationship_.28extends_TaxonExtended.29|TaxonRelationship]]  
+
* ''assoc_taxon'': [[#TaxonRelationship (extends TaxonExtended)|TaxonRelationship]]  
 
* ''assoc_type'': ''[[#assoc_type|assoc_type]]''  
 
* ''assoc_type'': ''[[#assoc_type|assoc_type]]''  
 
* ''assoc_type_full'': ''[[#assoc_type_full|assoc_type_full]]''
 
* ''assoc_type_full'': ''[[#assoc_type_full|assoc_type_full]]''
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==== TaxonBasic ====
 
==== TaxonBasic ====
 
* ''tnuid'': ''[[#tnuid|tnuid]]''
 
* ''tnuid'': ''[[#tnuid|tnuid]]''
 +
* ''guid'': ''[[#guid|guid]]''
 +
* ''tcid'': ''[[#tcid|tcid]]''
 
* ''taxon'': ''[[#taxon|taxon]]''
 
* ''taxon'': ''[[#taxon|taxon]]''
 
* ''taxon_author'': ''[[#taxon_author|taxon_author]]''
 
* ''taxon_author'': ''[[#taxon_author|taxon_author]]''
  
−
==== TaxonComplete (extends [[#TaxonRelationship_.28extends_TaxonExtended.29|TaxonRelationship]]) ====
+
==== TaxonComplete (extends [[#TaxonRelationship (extends TaxonExtended)|TaxonRelationship]]) ====
−
* ''stats'': [[#TaxonInfoStats_.28extends_TaxonStats.29|TaxonInfoStats]]
+
* ''stats'': [[#TaxonInfoStats (extends TaxonStats)|TaxonInfoStats]]
 
* ''contribs'': array of Contribution
 
* ''contribs'': array of Contribution
 
* ''orig_desc'': [[OJ_Break v2 Literature Reference#LiteratureExtended|LiteratureExtended]]
 
* ''orig_desc'': [[OJ_Break v2 Literature Reference#LiteratureExtended|LiteratureExtended]]
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==== TaxonHierClass ====
 
==== TaxonHierClass ====
−
* ''Class'': [[#TaxonHierUnit_.28extends_TaxonBasic.29|TaxonHierUnit]]
+
* ''Class'': [[#TaxonHierUnit (extends TaxonBasic)|TaxonHierUnit]]
  
 
==== TaxonHierCohort ====
 
==== TaxonHierCohort ====
−
* ''Cohort'': [[#TaxonHierUnit_.28extends_TaxonBasic.29|TaxonHierUnit]]
+
* ''Cohort'': [[#TaxonHierUnit (extends TaxonBasic)|TaxonHierUnit]]
  
 
==== TaxonHierDivision ====
 
==== TaxonHierDivision ====
−
* ''Division'': [[#TaxonHierUnit_.28extends_TaxonBasic.29|TaxonHierUnit]]  
+
* ''Division'': [[#TaxonHierUnit (extends TaxonBasic)|TaxonHierUnit]]  
  
 
==== TaxonHierFamily ====
 
==== TaxonHierFamily ====
−
* ''Family'': [[#TaxonHierUnit_.28extends_TaxonBasic.29|TaxonHierUnit]]
+
* ''Family'': [[#TaxonHierUnit (extends TaxonBasic)|TaxonHierUnit]]
  
 
==== TaxonHierGenus ====
 
==== TaxonHierGenus ====
−
* ''Genus'': [[#TaxonHierUnit_.28extends_TaxonBasic.29|TaxonHierUnit]]
+
* ''Genus'': [[#TaxonHierUnit (extends TaxonBasic)|TaxonHierUnit]]
  
 
==== TaxonHierInfraclass ====
 
==== TaxonHierInfraclass ====
−
* ''Infraclass'': [[#TaxonHierUnit_.28extends_TaxonBasic.29|TaxonHierUnit]]
+
* ''Infraclass'': [[#TaxonHierUnit (extends TaxonBasic)|TaxonHierUnit]]
  
 
==== TaxonHierInfraorder ====
 
==== TaxonHierInfraorder ====
−
* ''Infraorder'': [[#TaxonHierUnit_.28extends_TaxonBasic.29|TaxonHierUnit]]
+
* ''Infraorder'': [[#TaxonHierUnit (extends TaxonBasic)|TaxonHierUnit]]
  
 
==== TaxonHierKingdom ====
 
==== TaxonHierKingdom ====
−
* ''Kingdom'': [[#TaxonHierUnit_.28extends_TaxonBasic.29|TaxonHierUnit]]
+
* ''Kingdom'': [[#TaxonHierUnit (extends TaxonBasic)|TaxonHierUnit]]
  
 
==== TaxonHierOrder ====
 
==== TaxonHierOrder ====
−
* ''Order'': [[#TaxonHierUnit_.28extends_TaxonBasic.29|TaxonHierUnit]]
+
* ''Order'': [[#TaxonHierUnit (extends TaxonBasic)|TaxonHierUnit]]
  
 
==== TaxonHierPhylum ====
 
==== TaxonHierPhylum ====
−
* ''Phylum'': [[#TaxonHierUnit_.28extends_TaxonBasic.29|TaxonHierUnit]]
+
* ''Phylum'': [[#TaxonHierUnit (extends TaxonBasic)|TaxonHierUnit]]
  
 
==== TaxonHierSpecies ====
 
==== TaxonHierSpecies ====
−
* ''Species'': [[#TaxonHierUnit_.28extends_TaxonBasic.29|TaxonHierUnit]]
+
* ''Species'': [[#TaxonHierUnit (extends TaxonBasic)|TaxonHierUnit]]
  
 
==== TaxonHierSubclass ====
 
==== TaxonHierSubclass ====
−
* ''Subclass'': [[#TaxonHierUnit_.28extends_TaxonBasic.29|TaxonHierUnit]]
+
* ''Subclass'': [[#TaxonHierUnit (extends TaxonBasic)|TaxonHierUnit]]
  
 
==== TaxonHierSubcohort ====
 
==== TaxonHierSubcohort ====
−
* ''Subcohort'': [[#TaxonHierUnit_.28extends_TaxonBasic.29|TaxonHierUnit]]
+
* ''Subcohort'': [[#TaxonHierUnit (extends TaxonBasic)|TaxonHierUnit]]
  
 
==== TaxonHierSubfamily ====
 
==== TaxonHierSubfamily ====
−
* ''Subfamily'': [[#TaxonHierUnit_.28extends_TaxonBasic.29|TaxonHierUnit]]
+
* ''Subfamily'': [[#TaxonHierUnit (extends TaxonBasic)|TaxonHierUnit]]
  
 
==== TaxonHierSuborder ====
 
==== TaxonHierSuborder ====
−
* ''Suborder'': [[#TaxonHierUnit_.28extends_TaxonBasic.29|TaxonHierUnit]]
+
* ''Suborder'': [[#TaxonHierUnit (extends TaxonBasic)|TaxonHierUnit]]
  
 
==== TaxonHierSubphylum ====
 
==== TaxonHierSubphylum ====
−
* ''Subphylum'': [[#TaxonHierUnit_.28extends_TaxonBasic.29|TaxonHierUnit]]
+
* ''Subphylum'': [[#TaxonHierUnit (extends TaxonBasic)|TaxonHierUnit]]
  
 
==== TaxonHierSubspecies ====
 
==== TaxonHierSubspecies ====
−
* ''Subspecies'': [[#TaxonHierUnit_.28extends_TaxonBasic.29|TaxonHierUnit]]
+
* ''Subspecies'': [[#TaxonHierUnit (extends TaxonBasic)|TaxonHierUnit]]
  
 
==== TaxonHierSubtribe ====
 
==== TaxonHierSubtribe ====
−
* ''Subtribe'': [[#TaxonHierUnit_.28extends_TaxonBasic.29|TaxonHierUnit]]
+
* ''Subtribe'': [[#TaxonHierUnit (extends TaxonBasic)|TaxonHierUnit]]
  
 
==== TaxonHierSuperfamily ====
 
==== TaxonHierSuperfamily ====
−
* ''Superfamily'': [[#TaxonHierUnit_.28extends_TaxonBasic.29|TaxonHierUnit]]
+
* ''Superfamily'': [[#TaxonHierUnit (extends TaxonBasic)|TaxonHierUnit]]
  
 
==== TaxonHierTribe ====
 
==== TaxonHierTribe ====
−
* ''Tribe'': [[#TaxonHierUnit_.28extends_TaxonBasic.29|TaxonHierUnit]]
+
* ''Tribe'': [[#TaxonHierUnit (extends TaxonBasic)|TaxonHierUnit]]
  
 
==== TaxonHierUnit (extends [[#TaxonBasic|TaxonBasic]]) ====
 
==== TaxonHierUnit (extends [[#TaxonBasic|TaxonBasic]]) ====
Line 348: Line 353:
 
==== TaxonInfoStats (extends [[#TaxonStats|TaxonStats]]) ====
 
==== TaxonInfoStats (extends [[#TaxonStats|TaxonStats]]) ====
 
* ''child_stats'': array of [[#TaxonStats|TaxonStats]]
 
* ''child_stats'': array of [[#TaxonStats|TaxonStats]]
 +
* ''num_records'': Number
 
* ''num_spms'': Number
 
* ''num_spms'': Number
  
−
==== TaxonRelationship (extends [[#TaxonExtended_.28extends_TaxonBasic.29|TaxonExtended]]) ====
+
==== TaxonRelationship (extends [[#TaxonExtended (extends TaxonBasic)|TaxonExtended]]) ====
 
* ''rel_type'': ''[[#rel_type|rel_type]]''
 
* ''rel_type'': ''[[#rel_type|rel_type]]''
−
* ''parent_taxon'': [[#TaxonBasic|TaxonBasic]]
+
* ''parent_taxon'': [[#TaxonExtended|TaxonBasic]]
 
* ''hier'': [[#TaxonHierarchy|TaxonHierarchy]]
 
* ''hier'': [[#TaxonHierarchy|TaxonHierarchy]]
  
Line 362: Line 368:
  
 
==== TaxonReturnDeterminers (extends [[#TaxonReturn|TaxonReturn]]) ====
 
==== TaxonReturnDeterminers (extends [[#TaxonReturn|TaxonReturn]]) ====
−
* ''determiners'': array of [[#TaxonExtended_.28extends_TaxonBasic.29|AgentExtended]]
+
* ''determiners'': array of [[#TaxonExtended (extends TaxonBasic)|AgentExtended]]
  
 
==== TaxonReturnHabitats (extends [[#TaxonReturn|TaxonReturn]]) ====
 
==== TaxonReturnHabitats (extends [[#TaxonReturn|TaxonReturn]]) ====
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==== TaxonReturnIncluded (extends [[#TaxonReturn|TaxonReturn]]) ====
 
==== TaxonReturnIncluded (extends [[#TaxonReturn|TaxonReturn]]) ====
−
* ''includedTaxa'': array of [[#TaxonExtended_.28extends_TaxonBasic.29|AgentExtended]]
+
* ''includedTaxa'': array of [[#TaxonExtended (extends TaxonBasic)|TaxonExtended]]
  
 
==== TaxonReturnInstitutions (extends [[#TaxonReturn|TaxonReturn]]) ====
 
==== TaxonReturnInstitutions (extends [[#TaxonReturn|TaxonReturn]]) ====
Line 380: Line 386:
  
 
==== TaxonReturnMedia (extends [[#TaxonReturn|TaxonReturn]]) ====
 
==== TaxonReturnMedia (extends [[#TaxonReturn|TaxonReturn]]) ====
−
* ''media'': array of [[OJ_Break v2 Media Reference#MediaExtended|MediaExtended]]
+
* ''media'': array of [[OJ_Break v2 Media Reference#MediaExtended (extends MediaBasic)|MediaExtended]]
  
 
==== TaxonReturnOccurrences (extends [[#TaxonReturn|TaxonReturn]]) ====
 
==== TaxonReturnOccurrences (extends [[#TaxonReturn|TaxonReturn]]) ====
Line 386: Line 392:
  
 
==== TaxonReturnSynonyms (extends [[#TaxonReturn|TaxonReturn]]) ====
 
==== TaxonReturnSynonyms (extends [[#TaxonReturn|TaxonReturn]]) ====
−
* ''synonyms'': array of [[#TaxonRelationship_.28extends_TaxonExtended.29|TaxonRelationship]]
+
* ''synonyms'': array of [[#TaxonRelationship (extends TaxonExtended)|TaxonRelationship]]
  
 
==== TaxonSource ====
 
==== TaxonSource ====
Line 410: Line 416:
 
String - the describer(s) of a taxon.
 
String - the describer(s) of a taxon.
 
==== fossil ====
 
==== 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.  
+
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 ====
 
==== habitat ====
 
String - Description or identifier of the ecological or environmental area that a particular species is known to inhabit.  
 
String - Description or identifier of the ecological or environmental area that a particular species is known to inhabit.  
Line 420: Line 428:
 
Number - A number representing the rank of a taxon with higher numbers representing higher positions in the taxonomic hierarchy.  
 
Number - A number representing the rank of a taxon with higher numbers representing higher positions in the taxonomic hierarchy.  
 
==== rel_type ====
 
==== 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.  
+
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 ====
 
==== status ====
−
String - The nomenclatural status of a taxon name using a formalized vocabulary.  
+
String - The nomenclatural status of a taxon name using a formalized vocabulary.
 
==== taxon ====
 
==== taxon ====
−
String - A taxon name string.  
+
String - A taxon name string.
 
==== taxon_author ====
 
==== taxon_author ====
−
String - The author(s) of a taxon with parenthesis surrounding the name of the author(s) if necessary.  
+
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 ====
 
==== tnuid ====
−
Number - The taxon name use identifier which uniquely identifies a taxon.  
+
Number - The taxon name use identifier which uniquely identifies a taxon within xBio:D.  
 
==== valid ====
 
==== valid ====
 
String - A ''Valid'' or ''Invalid'' string representing the validity of a taxon name using subjective interpretations if warranted.
 
String - A ''Valid'' or ''Invalid'' string representing the validity of a taxon name using subjective interpretations if warranted.
Line 441: Line 451:
 
* [[OJ_Break v2 Literature Reference|Literature]]
 
* [[OJ_Break v2 Literature Reference|Literature]]
 
* [[OJ_Break v2 Locality Reference|Locality]]
 
* [[OJ_Break v2 Locality Reference|Locality]]
 +
* [[OJ_Break v2 Media Reference|Media]]
 
* [[OJ_Break v2 Occurrence Reference|Occurrence]]
 
* [[OJ_Break v2 Occurrence Reference|Occurrence]]
 
* [[OJ_Break v2 Search Reference|Search]]
 
* [[OJ_Break v2 Search Reference|Search]]

Latest revision as of 13:44, 25 September 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 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.

Contents

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

Description
Parameters
  • tnuid: tnuid
  • *inst_id: inst_id
  • format: String
  • key: String
  • version: Number
Return
Example
http://osuc.biosci.ohio-state.edu/OJ_Break/getTaxonInfo?tnuid=30148&inst_id=1&format=html&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2

getTaxonHierarchy

Description
Parameters
  • tnuid: tnuid
  • format: String
  • key: String
  • version: Number
Return
Example
http://osuc.biosci.ohio-state.edu/OJ_Break/getTaxonHierarchy?tnuid=30148&format=html&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2

getTaxonIncludedTaxa

Description
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
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

Description
Parameters
  • tnuid: tnuid
  • *offset: Number
  • *limit: Number
  • *show_fossils: Boolean_flag
  • format: String
  • key: String
  • version: Number
Return
Example
http://osuc.biosci.ohio-state.edu/OJ_Break/getTaxonSynonyms?tnuid=30148&format=html&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2

getTaxonAssociations

Description
Parameters
  • tnuid: tnuid
  • *offset: Number
  • *limit: Number
  • *basic_only: Boolean_flag
  • format: String
  • key: String
  • version: Number
Return
Example
http://osuc.biosci.ohio-state.edu/OJ_Break/getTaxonAssociations?tnuid=30148&format=html&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2

getTaxonLiteratureCitations

Description
Parameters
  • tnuid: tnuid
  • *offset: Number
  • *limit: Number
  • *show_children: Boolean_flag
  • format: String
  • key: String
  • version: Number
Return
Example
http://osuc.biosci.ohio-state.edu/OJ_Break/getTaxonLiteratureCitations?tnuid=30148&format=html&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2

getTaxonOccurrences

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

getTaxonTypes

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

getTaxonLocalities

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

getTaxonDeterminers

Description
Parameters
  • tnuid: tnuid
  • *inst_id: inst_id
  • *offset: Number
  • *limit: Number
  • format: String
  • key: String
  • version: Number
Return
Example
http://osuc.biosci.ohio-state.edu/OJ_Break/getTaxonDeterminers?tnuid=30148&format=html&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2

getTaxonInstitutions

Description
Parameters
  • tnuid: tnuid
  • *offset: Number
  • *limit: Number
  • format: String
  • key: String
  • version: Number
Return
Example
http://osuc.biosci.ohio-state.edu/OJ_Break/getTaxonInstitutions?tnuid=30148&format=html&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2

getTaxonHabitats

Description
Parameters
  • tnuid: tnuid
  • *offset: Number
  • *limit: Number
  • format: String
  • key: String
  • version: Number
Return
Example
http://osuc.biosci.ohio-state.edu/OJ_Break/getTaxonHabitats?tnuid=30148&format=html&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2

getTaxonMedia

Description
Parameters
  • tnuid: tnuid
  • *media_type: media_type
  • *inst_id: inst_id
  • *offset: Number
  • *limit: Number
  • format: String
  • key: String
  • version: Number
Return
Example
http://osuc.biosci.ohio-state.edu/OJ_Break/getTaxonMedia?tnuid=30148&format=html&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2

Taxon Data Type Glossary

Classes

TaxonAssociation

TaxonBasic

TaxonComplete (extends TaxonRelationship)

TaxonExtended (extends TaxonBasic)

TaxonHierarchy

Aggregate of one or more of the following classes:

TaxonHierClass

TaxonHierCohort

TaxonHierDivision

TaxonHierFamily

TaxonHierGenus

TaxonHierInfraclass

TaxonHierInfraorder

TaxonHierKingdom

TaxonHierOrder

TaxonHierPhylum

TaxonHierSpecies

TaxonHierSubclass

TaxonHierSubcohort

TaxonHierSubfamily

TaxonHierSuborder

TaxonHierSubphylum

TaxonHierSubspecies

TaxonHierSubtribe

TaxonHierSuperfamily

TaxonHierTribe

TaxonHierUnit (extends TaxonBasic)

TaxonInfoStats (extends TaxonStats)

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

TaxonRelationship (extends TaxonExtended)

TaxonReturn

TaxonReturnAssociations (extends TaxonReturn)

TaxonReturnDeterminers (extends TaxonReturn)

TaxonReturnHabitats (extends TaxonReturn)

TaxonReturnIncluded (extends TaxonReturn)

TaxonReturnInstitutions (extends TaxonReturn)

TaxonReturnLiteratureCitations (extends TaxonReturn)

TaxonReturnLocalities (extends TaxonReturn)

TaxonReturnMedia (extends TaxonReturn)

TaxonReturnOccurrences (extends TaxonReturn)

TaxonReturnSynonyms (extends TaxonReturn)

TaxonSource

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

TaxonStats

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.

Retrieved from "https://xbiod.osu.edu/index.php?title=OJ_Break_v2_Taxon_Reference&oldid=2189"