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 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 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.

Procedural Reference

Literature

getCitationInfo

Parameters

• citation_id: citation_id
• format: string
• key: string
• version: number

Return

• LiteratureCitationBasic

Example

http://osuc.biosci.ohio-state.edu/OJ_Break/getCitationInfo?citation_id=234&format=html&key=FBF57A9F7A666FC0E0430100007F0CDC&version=2

getLiteratureInfo

Parameters

• pub_id: pub_id
• format: string
• key: string
• version: number

Return

• LiteratureExtended

Example

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

getLiteratureParts

Parameters

• pub_id: pub_id
• *offset: number
• *limit: number
• format: string
• key: string
• version: number

Return

• LiteratureReturnParts

Example

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

getLiteratureTaxonCitations

Parameters

• pub_id: pub_id
• *offset: number
• *limit: number
• format: string
• key: string
• version: number

Return

• LiteratureReturnTaxonCitation

Example

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

getLiteratureAssocCitations

Parameters

• pub_id: pub_id
• *offset: number
• *limit: number
• format: string
• key: string
• version: number

Return

• LiteratureReturnAssociations

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)

• assoc_type: assoc_type
• assoc_type_full: assoc_type_full

LiteratureBasic

• pub_id: pub_id
• guid: guid
• pub_type: pub_type
• pub_year: pub_year
• pub_month: pub_month

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)

• source: LiteratureExtended

LiteratureCitationBasic

• citation_id: citation_id
• pages: array of LiteraturePDFPage

LiteratureCitationExtended (extends LiteratureCitationBasic)

• pub: LiteratureExtended

LiteratureExtended (extends LiteratureBasic)

• pub_author: AgentExtended
• pub_title: pub_title
• doi: doi
• pub_pdf: LiteraturePDF

LiteratureOccurrenceCitation (extends LiteratureCitationBasic)

• occurrence: OccurrenceExtended

LiteraturePDF

• url: URL
• filesize: String
• public: public
• pages: array of LiteraturePDFPage

LiteraturePDFPage

• page: String
• url: URL

LiteratureReturn

• general: LiteratureBasic

LiteratureReturnAssociations (extends LiteratureReturn)

• assoc_citations: array of LiteratureAssociationCitation

LiteratureReturnParts (extends LiteratureReturn)

• pub_parts: array of LiteratureExtended

LiteratureReturnTaxonCitation (extends LiteratureReturn)

• pub_citations: array of LiteratureTaxonCitation

LiteratureTaxonCitation (extends LiteratureCitationBasic)

• taxon: TaxonRelationship
• annotation: annotation

LiteratureTaxonCitationExtended (extends LiteratureTaxonCitation)

• pub: 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.

• Agent
• Geographic Place
• Institution
• Journal
• Locality
• Media
• Occurrence
• Search
• Taxon