Developer

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Programming with the EcoPortal API

• Using NCBO Technology In Your Project
  • Semantic resource Web Services
  • Annotator Web Service
  • Semantic resource
• Getting an API key
• NCBO Widgets
  • Types of NCBO Widgets and use cases
  • How to use NCBO Widgets
    • Term-selection field on a form
      • Hidden form elements auto-generated
      • Optional attributes
    • Semantic resource search widget
    • Semantic resource visualization widget
    • NCBO Semantic resource Tree Widget
      • Description
      • Location
      • Setup
      • Callbacks and Event Triggers
      • Public Methods

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Programming with the EcoPortal API

Documentation about how to use the EcoPortal REST API to access information is available here:

• http://ecoportal.lifewatch.eu:8080/documentation

  • Using NCBO Technology In Your Project

    There are several ways in which you can use the NCBO technology on your own Web site or in your application. For example, I can think of:

    • I have a list of terms that were used to annotate a data set, how can I see if any of these terms exist in standard semantic resources? Use the Search Web service to search for your term in all semantic resources in BioPortal. If you have a small list of terms, searching each term individually via the EcoPortal Search UI may be sufficient. Otherwise, for a long list of terms, use the Search Web service directly.

    • I would like to find all terms mapped from my semantic resource to other semantic resources in EcoPortal.
      Use the Mapping web service to find terms in other EcoPortal semantic resources similar to terms in your semantic resource. These mappings include mapping generated manually (DbXrefs) and programatically (LOOM).

    • I am the curator for a database and need to triage papers to identify which papers from DATACITE are most related to my database and a good source of new information to add to my database. Use the Annotator Web service to identify ontology terms in textual data

    • I have DATACITE abstracts and want to link information in the abstracts to my database of interest. Use the Annotator Web service. If your database of interest is included in the NCBO Resource Index you can search the database(s) for records that contain these terms. See https://github.com/lifewatch-eric/documentation/wiki/EcoTools#resource-index for more details on the Resource Index web service.

    • I have a web form with text fields I would like to populate with semantic resource terms, e.g. to select relevant terms from EcoPortal semantic resource. Use the Autocomplete widget. Select the "Get Code" button for the code and instructions on how to add this Javascript to your web form.

    • I would like to add the graph display of my semantic resource on my web site.

    • I would like to get all terms from a semantic resource and re-format the data to use in my own system.

    • I need to navigate through a semantic resource and traverse the semantic resource hierarchy for my software application, how can I use the Web services to do this?

    • How can I limit the selection of semantic resources used with the NCBO Annotator to a certain Category or Domain?

  • Getting an API key

    Use of the EcoPortal REST API requires an API key. To retrieve your API key, log into your account on the EcoPortal website. Your API key will be listed in plain text on your account page. E.g.

    

    If you don't have an account, you'll need to create one.

  • NCBO Widgets

    NCBO widgets are the HTML or Javascript code that you can put on your Web site or Web form to use EcoPortal functionality there. Using NCBO Widgets is just one of the ways in which you can use the NCBO technology directly on your Web site or in your application.

    • Types of NCBO Widgets and use cases