View source for OJ Break v2 Literature 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.

== 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 '''Literature''' data domain. To get information on any of the other data domains defined in OJ_Break Version 2, visit the [[#See_also|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/getLiteratureInfo?pub_id=234&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 ==
=== Literature ===
==== getCitationInfo ====
===== Description =====
===== Parameters =====
* ''citation_id'': ''[[#citation_id|citation_id]]''
* ''format'': string
* ''key'': string
* ''version'': number
===== Return =====
* [[#LiteratureCitationBasic|LiteratureCitationBasic]]
===== Example =====
http://osuc.biosci.ohio-state.edu/OJ_Break/getCitationInfo?citation_id=234&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2
==== getLiteratureInfo ====
===== Description =====
===== Parameters =====
* ''pub_id'': ''[[#pub_id|pub_id]]''
* ''format'': string
* ''key'': string
* ''version'': number
===== Return =====
* [[#LiteratureExtended_.28extends_LiteratureBasic.29|LiteratureExtended]]

===== Example =====
http://osuc.biosci.ohio-state.edu/OJ_Break/getLiteratureInfo?pub_id=234&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2

==== getLiteratureParts ====
===== Description =====
===== Parameters =====
* ''pub_id'': ''[[#pub_id|pub_id]]''
* ''*offset'': number
* ''*limit'': number
* ''format'': string
* ''key'': string
* ''version'': number
===== Return =====
* [[#LiteratureReturnParts_.28extends_LiteratureReturn.29|LiteratureReturnParts]]

===== Example =====
http://osuc.biosci.ohio-state.edu/OJ_Break/getLiteratureParts?pub_id=234&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2

==== getLiteratureTaxonCitations ====
===== Description =====
===== Parameters =====
* ''pub_id'': ''[[#pub_id|pub_id]]''
* ''*offset'': number
* ''*limit'': number
* ''format'': string
* ''key'': string
* ''version'': number
===== Return =====
* [[#LiteratureReturnTaxonCitation_.28extends_LiteratureReturn.29|LiteratureReturnTaxonCitation]]

===== Example =====
http://osuc.biosci.ohio-state.edu/OJ_Break/getLiteratureTaxonCitations?pub_id=234&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2

==== getLiteratureAssocCitations ====
===== Description =====
===== Parameters =====
* ''pub_id'': ''[[#pub_id|pub_id]]''
* ''*offset'': number
* ''*limit'': number
* ''format'': string
* ''key'': string
* ''version'': number

===== Return =====
* [[#LiteratureReturnAssociations_.28extends_LiteratureReturn.29|LiteratureReturnAssociations]]

===== Example =====
http://osuc.biosci.ohio-state.edu/OJ_Break/getLiteratureAssocCitations?pub_id=234&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2

== Literature Data Type Glossary ==
=== Classes ===
==== LiteratureArticle (realizes [[#LiteratureExtended_.28extends_LiteratureBasic.29|LiteratureExtended]]) ====
* ''journal_id'': ''[[OJ_Break v2 Journal Reference#journal_id|journal_id]]''
* ''journal'': ''journal''
* ''series'': String
* ''volume'': String
* ''vol_num'': String
* ''start_page'': String
* ''end_page'': String

==== LiteratureAssociationCitation (extends [[#LiteratureOccurrenceCitation_.28extends_LiteratureCitationBasic.29|LiteratureOccurrenceCitation]]) ====
* ''assoc_type'': ''[[OJ_Break v2 Taxon Reference#assoc_type|assoc_type]]''
* ''assoc_type_full'': ''[[OJ_Break v2 Taxon Reference#assoc_type_full|assoc_type_full]]''

==== LiteratureBasic ====
* ''pub_id'': ''[[#pub_id|pub_id]]''
* ''guid'': ''[[#guid|guid]]''
* ''pub_type'': ''[[#pub_type|pub_type]]''
* ''pub_year'': ''[[#pub_year|pub_year]]''
* ''pub_month'': ''[[#pub_month|pub_month]]''

==== LiteratureBook (realizes [[#LiteratureExtended_.28extends_LiteratureBasic.29|LiteratureExtended]]) ====
* ''publisher'': String
* ''city'': String
* ''num_pages'': String

==== LiteratureBulletin (realizes [[#LiteratureExtended_.28extends_LiteratureBasic.29|LiteratureExtended]]) ====
* ''journal_id'': ''[[OJ_Break v2 Journal Reference#journal_id|journal_id]]''
* ''journal'': ''[[OJ_Break v2 Journal Reference#journal_name|journal_name]]''
* ''series'': String
* ''volume'': String
* ''vol_num'': String
* ''start_page'': String
* ''end_page'': String

==== LiteratureChapter (realizes [[#LiteratureExtended_.28extends_LiteratureBasic.29|LiteratureExtended]]) ====
* ''book'': [[#LiteratureBook_.28realizes_LiteratureExtended.29|LiteratureBook]]
* ''chap_num'': String
* ''start_page'': String
* ''end_page'': String

==== LiteratureContribution (realizes [[#LiteratureExtended_.28extends_LiteratureBasic.29|LiteratureExtended]]) ====
* ''source'': [[#LiteratureExtended_.28extends_LiteratureBasic.29|LiteratureExtended]]

==== LiteratureCitationBasic ====
* ''citation_id'': ''[[#citation_id|citation_id]]
* ''pages'': array of [[#LiteraturePDFPage|LiteraturePDFPage]]

==== LiteratureCitationExtended (extends [[#LiteratureCitationBasic|LiteratureCitationBasic]]) ====
* ''pub'': [[#LiteratureExtended_.28extends_LiteratureBasic.29|LiteratureExtended]]

==== LiteratureExtended (extends [[#LiteratureBasic|LiteratureBasic]]) ====
* ''pub_author'': [[OJ_Break v2 Agent Reference#AgentExtended_.28extends_AgentBasic.29|AgentExtended]]
* ''pub_title'': ''[[#pub_title|pub_title]]''
* ''doi'': ''[[#doi|doi]]''
* ''pub_pdf'': [[#LiteraturePDF|LiteraturePDF]]

==== LiteratureOccurrenceCitation (extends [[#LiteratureCitationBasic|LiteratureCitationBasic]]) ====
* ''occurrence'': [[OJ_Break v2 Occurrence Reference#OccurrenceExtended_.28extends_OccurrenceBasic.29|OccurrenceExtended]]

==== LiteraturePDF ====
* ''url'': URL
* ''filesize'': String
* ''public'': public
* ''pages'': array of [[#LiteraturePDFPage|LiteraturePDFPage]]

==== LiteraturePDFPage ====
* ''page'': String
* ''url'': URL

==== LiteratureReturn ====
* ''general'': [[#LiteratureBasic|LiteratureBasic]]

==== LiteratureReturnAssociations (extends [[#LiteratureReturn|LiteratureReturn]]) ====
* ''assoc_citations'': array of [[#LiteratureAssociationCitation_.28extends_LiteratureOccurrenceCitation.29|LiteratureAssociationCitation]]

==== LiteratureReturnParts (extends [[#LiteratureReturn|LiteratureReturn]]) ====
* ''pub_parts'': array of [[#LiteratureExtended_.28extends_LiteratureBasic.29|LiteratureExtended]]

==== LiteratureReturnTaxonCitation (extends [[#LiteratureReturn|LiteratureReturn]]) ====
* ''pub_citations'': array of [[#LiteratureTaxonCitation_.28extends_LiteratureCitationBasic.29|LiteratureTaxonCitation]]

==== LiteratureTaxonCitation (extends [[#LiteratureCitationBasic|LiteratureCitationBasic]]) ====
* ''taxon'': [[OJ_Break v2 Taxon Reference#TaxonRelationship_.28extends_TaxonExtended.29|TaxonRelationship]]
* ''annotation'': ''[[#annotation|annotation]]''

==== LiteratureTaxonCitationExtended (extends [[#LiteratureTaxonCitation_.28extends_LiteratureCitationBasic.29|LiteratureTaxonCitation]]) ====
* ''pub'': [[#LiteratureExtended_.28extends_LiteratureBasic.29|LiteratureExtended]]

=== Elements ===
==== annotation ====
String -
==== citation_id ====
Number - 
==== doi ====
DOI - The digital object identifier (DOI) assigned to a publication.
==== pub_id ====
Number - The publication identifier which uniquely identifies a publication. 
==== pub_type ====
String - The type of format in which this piece of literature was published. 
==== pub_year ====
Number - The year the publication was published.
==== pub_month =====
Number - The month the publication was published.
==== public ====
Boolean_flag - A Y or N indicator that signifies whether a journal is made public or not.

== See also ==
Visit any of the below links to find information about the other data domains defined by OJ_Break Version 2.

* [[OJ_Break v2 Agent Reference|Agent]]
* [[OJ_Break v2 Geographic Place Reference|Geographic Place]]
* [[OJ_Break v2 Institution Reference|Institution]]
* [[OJ_Break v2 Journal Reference|Journal]]
* [[OJ_Break v2 Locality Reference|Locality]]
* [[OJ_Break v2 Occurrence Reference|Occurrence]]
* [[OJ_Break v2 Search Reference|Search]]
* [[OJ_Break v2 Taxon Reference|Taxon]]