Infrastructure

How GBIF works as a global informatics infrastructure

GBIF Tools Overview

GBIF makes available several free to use, open-source tools and services. The table below lists GBIF's most widely used and talked-about tools. They span several categories of use, such as data assessment, data cleaning, data publishing, data visualization, and metadata authoring. A longer list of tools can be found on http://tools.gbif.org/.

Name Categories of use Short Description Demo site Project site Mailing list
Integrated Publishing Toolkit (IPT) Data publishing, Metadata authoring, Data discovery Publishes primary occurrence data, species checklists and taxonomies, and general metadata about data sources. It can also serve as a repository for data referenced in an article. Link Link Link
Nodes Portal Toolkit (NPT) Startup Data discovery Enables participants to establish a simple, GBIF-compliant web presence Link Link Link
Darwin Core Archive Validator Data assessment Validates that a Darwin Core Archive complies with the Darwin Core Text Guidelines Link Link
Name Parser Data cleaning Atomizes scientific names, and validates that a scientific name is a well-formed 3-part name Link Link

Nodes Portal Toolkit (NPT) Startup

See also

NPT Startup is a tool that targets GBIF Participants who have limited web presence. It helps establish the Node’s identity on the web, manage biodiversity information at the country/thematic level, and engage local and global communities in bringing up the relevance of biodiversity information.

NPT Startup is one of the outcomes of the Nodes Portal Toolkit project (NPT), which identifies the need for facilitating the development of national and thematic biodiversity portals with reusable biodiversity informatics components. NPT Startup is built with Drupal content management framework backed by a strong, fast-growing, open-source community. Collaborating together with ViBRANT and INBio, NPT Startup is a proof-of-concept of joint development.

By deploying NPT Startup, a website will be ready for you with initial national checklist derived from GBIF mediated data and species contents (descriptions, images and videos) from the Encyclopedia of Life. Common website features like news and RSS feeds will available for you too. There are thousands of features from the Drupal community, so you can easily extend and customise NPT Startup to serve your needs.

The following video presents the NPT Startup in more detail.

Darwin Core Archive Validator

See also

Helps you validate that a Darwin Core Archive complies with the Darwin Core Text Guidelines. It validates that the metadata file complies with the GBIF Metadata Profile and the Ecological Markup Language (EML). It also inspects the mapped concepts against the extensions registered with GBIF, identifying unknown or required concepts that are missing.

It doesn’t perform any data assessment (i.e. taxonomic or geospatial assessments), however, it does visualize the first 100 rows, helping you identify bad mappings or missing data.

Try it out now online, or by playing with its web services.

Please note that this will likely be included in the GBIF API in future versions.

Name Parser

See also

Helps you atomize scientific names, and validate that a scientific name is a well-formed 3-part name. The parser is based on regular expressions to dissect a name string into its components.

Try it out now online, or by playing with its web services.

Please note that this will likely be included in the GBIF API in future versions.