Difference between revisions of "OJ Break v2 Literature 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.
Line 10: Line 10:
 
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/getLiteratureInfo?pub_id=234&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2
+
     Example: http://osuc.biosci.ohio-state.edu/OJ_Break/getLiteratureInfo?pub_id=234&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 - Literature.png|none|frame|Literature Data Model]]
  
 
== Procedural Reference ==
 
== Procedural Reference ==
Line 24: Line 27:
 
* ''version'': number
 
* ''version'': number
 
===== Return =====
 
===== Return =====
−
* LiteratureCitationBasic
+
* [[#LiteratureCitationBasic|LiteratureCitationBasic]]
 
===== Example =====
 
===== Example =====
−
http://osuc.biosci.ohio-state.edu/OJ_Break/getCitationInfo?citation_id=234&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2
+
http://osuc.biosci.ohio-state.edu/OJ_Break/getCitationInfo?citation_id=234&format=html&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2
 
==== getLiteratureInfo ====
 
==== getLiteratureInfo ====
 
===== Description =====
 
===== Description =====
 
===== Parameters =====
 
===== Parameters =====
−
* ''pub_id'': ''pub_id''
+
* ''pub_id'': ''[[#pub_id|pub_id]]''
 
* ''format'': string
 
* ''format'': string
 
* ''key'': string
 
* ''key'': string
 
* ''version'': number
 
* ''version'': number
 
===== Return =====
 
===== Return =====
−
* LiteratureExtended
+
* [[#LiteratureExtended (extends LiteratureBasic)|LiteratureExtended]]
  
 
===== Example =====
 
===== Example =====
−
http://osuc.biosci.ohio-state.edu/OJ_Break/getLiteratureInfo?pub_id=234&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2
+
http://osuc.biosci.ohio-state.edu/OJ_Break/getLiteratureInfo?pub_id=234&format=html&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2
  
 
==== getLiteratureParts ====
 
==== getLiteratureParts ====
 
===== Description =====
 
===== Description =====
 
===== Parameters =====
 
===== Parameters =====
−
* ''pub_id'': ''pub_id''
+
* ''pub_id'': ''[[#pub_id|pub_id]]''
−
* ''offset'': number (optional)
+
* ''*offset'': number
−
* ''limit'': number (optional)
+
* ''*limit'': number
 
* ''format'': string
 
* ''format'': string
 
* ''key'': string
 
* ''key'': string
 
* ''version'': number
 
* ''version'': number
 
===== Return =====
 
===== Return =====
−
* LiteratureReturnParts
+
* [[#LiteratureReturnParts (extends LiteratureReturn)|LiteratureReturnParts]]
  
 
===== Example =====
 
===== Example =====
−
http://osuc.biosci.ohio-state.edu/OJ_Break/getLiteratureParts?pub_id=234&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2
+
http://osuc.biosci.ohio-state.edu/OJ_Break/getLiteratureParts?pub_id=234&format=html&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2
  
 
==== getLiteratureTaxonCitations ====
 
==== getLiteratureTaxonCitations ====
 
===== Description =====
 
===== Description =====
 
===== Parameters =====
 
===== Parameters =====
−
* ''pub_id'': ''pub_id''
+
* ''pub_id'': ''[[#pub_id|pub_id]]''
−
* ''offset'': number (optional)
+
* ''*offset'': number
−
* ''limit'': number (optional)
+
* ''*limit'': number
 
* ''format'': string
 
* ''format'': string
 
* ''key'': string
 
* ''key'': string
 
* ''version'': number
 
* ''version'': number
 
===== Return =====
 
===== Return =====
−
* LiteratureReturnTaxonCitation
+
* [[#LiteratureReturnTaxonCitation (extends LiteratureReturn)|LiteratureReturnTaxonCitation]]
  
 
===== Example =====
 
===== Example =====
−
http://osuc.biosci.ohio-state.edu/OJ_Break/getLiteratureTaxonCitations?pub_id=234&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2
+
http://osuc.biosci.ohio-state.edu/OJ_Break/getLiteratureTaxonCitations?pub_id=234&format=html&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2
  
 
==== getLiteratureAssocCitations ====
 
==== getLiteratureAssocCitations ====
 
===== Description =====
 
===== Description =====
 
===== Parameters =====
 
===== Parameters =====
−
* ''pub_id'': ''pub_id''
+
* ''pub_id'': ''[[#pub_id|pub_id]]''
−
* ''offset'': number (optional)
+
* ''*offset'': number
−
* ''limit'': number (optional)
+
* ''*limit'': number
 
* ''format'': string
 
* ''format'': string
 
* ''key'': string
 
* ''key'': string
 
* ''version'': number
 
* ''version'': number
 +
 
===== Return =====
 
===== Return =====
−
* LiteratureReturnAssociations
+
* [[#LiteratureReturnAssociations (extends LiteratureReturn)|LiteratureReturnAssociations]]
  
 
===== Example =====
 
===== Example =====
−
http://osuc.biosci.ohio-state.edu/OJ_Break/getLiteratureAssocCitations?pub_id=234&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2
+
http://osuc.biosci.ohio-state.edu/OJ_Break/getLiteratureAssocCitations?pub_id=234&format=html&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2
 +
 
 +
== Literature Data Type Glossary ==
 +
=== Classes ===
 +
==== LiteratureArticle (realizes [[#LiteratureExtended (extends LiteratureBasic)|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
 +
 
 +
==== LiteratureAssociationCitation (extends [[#LiteratureOccurrenceCitation (extends LiteratureCitationBasic)|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 (extends LiteratureBasic)|LiteratureExtended]]) ====
 +
* ''publisher'': String
 +
* ''city'': String
 +
* ''num_pages'': String
 +
 
 +
==== LiteratureBulletin (realizes [[#LiteratureExtended (extends LiteratureBasic)|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 (extends LiteratureBasic)|LiteratureExtended]]) ====
 +
* ''book'': [[#LiteratureBook (realizes LiteratureExtended)|LiteratureBook]]
 +
* ''chap_num'': String
 +
* ''start_page'': String
 +
* ''end_page'': String
 +
 
 +
==== LiteratureContribution (realizes [[#LiteratureExtended (extends LiteratureBasic)|LiteratureExtended]]) ====
 +
* ''source'': [[#LiteratureExtended (extends LiteratureBasic)|LiteratureExtended]]
 +
 
 +
==== LiteratureCitationBasic ====
 +
* ''citation_id'': ''[[#citation_id|citation_id]]
 +
* ''pages'': array of [[#LiteraturePDFPage|LiteraturePDFPage]]
 +
 
 +
==== LiteratureCitationExtended (extends [[#LiteratureCitationBasic|LiteratureCitationBasic]]) ====
 +
* ''pub'': [[#LiteratureExtended (extends LiteratureBasic)|LiteratureExtended]]
 +
 
 +
==== LiteratureExtended (extends [[#LiteratureBasic|LiteratureBasic]]) ====
 +
* ''pub_author'': [[OJ_Break v2 Agent Reference#AgentExtended (extends AgentBasic)|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 (extends OccurrenceBasic)|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 (extends LiteratureOccurrenceCitation)|LiteratureAssociationCitation]]
 +
 
 +
==== LiteratureReturnParts (extends [[#LiteratureReturn|LiteratureReturn]]) ====
 +
* ''pub_parts'': array of [[#LiteratureExtended (extends LiteratureBasic)|LiteratureExtended]]
 +
 
 +
==== LiteratureReturnTaxonCitation (extends [[#LiteratureReturn|LiteratureReturn]]) ====
 +
* ''pub_citations'': array of [[#LiteratureTaxonCitation (extends LiteratureCitationBasic)|LiteratureTaxonCitation]]
 +
 
 +
==== LiteratureTaxonCitation (extends [[#LiteratureCitationBasic|LiteratureCitationBasic]]) ====
 +
* ''taxon'': [[OJ_Break v2 Taxon Reference#TaxonRelationship (extends TaxonExtended)|TaxonRelationship]]
 +
* ''annotation'': ''[[#annotation|annotation]]''
 +
 
 +
==== LiteratureTaxonCitationExtended (extends [[#LiteratureTaxonCitation (extends LiteratureCitationBasic)|LiteratureTaxonCitation]]) ====
 +
* ''pub'': [[#LiteratureExtended (extends LiteratureBasic)|LiteratureExtended]]
 +
 
 +
=== Elements ===
 +
==== annotation ====
 +
String - Comments associated with the journal.
 +
==== citation_id ====
 +
Number - A unique identifier given to a citation.
 +
==== doi ====
 +
DOI - The digital object identifier (DOI) assigned to a publication.
 +
==== guid ====
 +
GUID - Globablly Unique Identifier which uniquely identifies a resource.
 +
==== 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 ==
 
== See also ==
Line 93: Line 208:
 
* [[OJ_Break v2 Journal Reference|Journal]]
 
* [[OJ_Break v2 Journal Reference|Journal]]
 
* [[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]]
 
* [[OJ_Break v2 Taxon Reference|Taxon]]
 
* [[OJ_Break v2 Taxon Reference|Taxon]]

Latest revision as of 16:37, 9 June 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 Literature 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/getLiteratureInfo?pub_id=234&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.


Literature Data Model

Procedural Reference

Literature

getCitationInfo

Description
Parameters
  • citation_id: citation_id
  • format: string
  • key: string
  • version: number
Return
Example
http://osuc.biosci.ohio-state.edu/OJ_Break/getCitationInfo?citation_id=234&format=html&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2

getLiteratureInfo

Description
Parameters
  • pub_id: pub_id
  • format: string
  • key: string
  • version: number
Return
Example
http://osuc.biosci.ohio-state.edu/OJ_Break/getLiteratureInfo?pub_id=234&format=html&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2

getLiteratureParts

Description
Parameters
  • pub_id: pub_id
  • *offset: number
  • *limit: number
  • format: string
  • key: string
  • version: number
Return
Example
http://osuc.biosci.ohio-state.edu/OJ_Break/getLiteratureParts?pub_id=234&format=html&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2

getLiteratureTaxonCitations

Description
Parameters
  • pub_id: pub_id
  • *offset: number
  • *limit: number
  • format: string
  • key: string
  • version: number
Return
Example
http://osuc.biosci.ohio-state.edu/OJ_Break/getLiteratureTaxonCitations?pub_id=234&format=html&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2

getLiteratureAssocCitations

Description
Parameters
  • pub_id: pub_id
  • *offset: number
  • *limit: number
  • format: string
  • key: string
  • version: number
Return
Example
http://osuc.biosci.ohio-state.edu/OJ_Break/getLiteratureAssocCitations?pub_id=234&format=html&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2

Literature Data Type Glossary

Classes

LiteratureArticle (realizes LiteratureExtended)

  • journal_id: journal_id
  • journal: journal_name
  • series: String
  • volume: String
  • vol_num: String
  • start_page: String
  • end_page: String

LiteratureAssociationCitation (extends LiteratureOccurrenceCitation)

LiteratureBasic

LiteratureBook (realizes LiteratureExtended)

  • publisher: String
  • city: String
  • num_pages: String

LiteratureBulletin (realizes LiteratureExtended)

  • journal_id: journal_id
  • journal: journal_name
  • series: String
  • volume: String
  • vol_num: String
  • start_page: String
  • end_page: String

LiteratureChapter (realizes LiteratureExtended)

  • book: LiteratureBook
  • chap_num: String
  • start_page: String
  • end_page: String

LiteratureContribution (realizes LiteratureExtended)

LiteratureCitationBasic

LiteratureCitationExtended (extends LiteratureCitationBasic)

LiteratureExtended (extends LiteratureBasic)

LiteratureOccurrenceCitation (extends LiteratureCitationBasic)

LiteraturePDF

LiteraturePDFPage

  • page: String
  • url: URL

LiteratureReturn

LiteratureReturnAssociations (extends LiteratureReturn)

LiteratureReturnParts (extends LiteratureReturn)

LiteratureReturnTaxonCitation (extends LiteratureReturn)

LiteratureTaxonCitation (extends LiteratureCitationBasic)

LiteratureTaxonCitationExtended (extends LiteratureTaxonCitation)

Elements

annotation

String - Comments associated with the journal.

citation_id

Number - A unique identifier given to a citation.

doi

DOI - The digital object identifier (DOI) assigned to a publication.

guid

GUID - Globablly Unique Identifier which uniquely identifies a resource.

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.

Retrieved from "https://xbiod.osu.edu/index.php?title=OJ_Break_v2_Literature_Reference&oldid=2057"