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API documentation

introduction

novoseek offers an API that allows the programmatic access to its functionality and information. This document supposes that you are familiar with novoseek and its use, for more information on how novoseek works and what kind of information it provides please check http://www.novoseek.com/Help.action.
With the novoseek API one can for example execute searches to obtain documents or the search profile, or get details of specific documents or biomedical entities that are available in novoseek. The API uses the REST (http://en.wikipedia.org/wiki/Restful) web services protocol that is easy to use in most standard programming languages. Calls to the API are expressed as URLs and return data in XML format that can then be processed.

Get an API Key to use the novoseek API

To use the API you need a valid key that identifies you as a user. This key is free and to obtain one please fill out the "sign up" form (on the left side under "Sign up")


What the novo|seek API can do for you

The API uses a single access point that is called "api.action". For the specific function calls the parameter "action" is used. Currently the following actions are available:

  • Search for documents:
    • Document search (action=search # parameters= query, corpus, maxElement, dateTo, dateFrom, criterion, showType, disam, annot, onlyIds)
    • Document search using database identifiers (action=searchBioentity # parameters= externalDBId, DBName, biotype, corpus, maxElement, dateTo, dateFrom, criterion, showType, disam, annot, onlyIds)
    • Document search using documents identifiers (action=searchDocuments # parameters= documentId, corpus, maxElement, dateTo, dateFrom, criterion, showType, disam, annot, onlyIds)
    • Document detail (action=documentDetail # parameters= documentId, corpus, annot )
  • Get detailed information on biomedical concepts:
    • Biomedical concept detail using external database identifier (action=bioentityDetailExt # parameters= externalDBId, DBName, bioType )
    • Biomedical concept detail using internal database identifier (action=bioentityDetailInt # parameters= entityType, internalId )
  • Generate a list of key concepts for a search:
    • Key concept for a search (action=profile # parameters= query, corpus, entityTypeProfile, bioTypeProfile, dateTo, dateFrom, maxElement, maxElementProfile, criterion, disam)
    • Key concept using database identifiers (action=profileBioentity # parameters= externalDBId, DBName, biotype, bioTypeProfile, corpus, entityTypeProfile, dateTo, dateFrom, maxElement, maxElementProfile, criterion, disam)
    • Key concept using documents identifiers (action=profileDocuments # parameters= documentId, corpus, entityTypeProfile, bioTypeProfile, dateTo, dateFrom, maxElement, maxElementProfile, criterion, disam)
  • Advanced search functionality:
    • Search detail (action=searchDetail # parameters= query )
    • Search disambiguation (action=disambiguated # parameters= query,bioType, entityType, maxElement)
    • Search disambiguation using database identifiers (action=disambiguatedExtId # parameters= externalDBId, DBName, bioType, maxElement)
  • Get information of what data is available in novo|seek:
    • List of available biomedical concept types (action=corporaList # no parameters)
    • List of available corporas (action=biomedical conceptList # no parameters )
    • List of database identifiers used in novoseek (action=externalDBIdList # no parameters)

The base URL for all calls to the novoseek API is [http://api.novoseek.com]. To construct the calls to the API use this URL and add the part that is described below in the specific sections

novo|seek API documentation for version 1.0, last updated on 2009/12/15.