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jhpoelen edited this page Nov 15, 2016 · 111 revisions

Welcome to EOL's Global Biotic Interactions (GloBI) wiki!

Build Status

Mission

The mission of this project is to find efficient ways to normalize and integrate species-interaction data. By making this data readily available, GloBI will enable researchers and enthusiasts to answer questions about localized, one-to-one species interactions and big-picture changes in species interactions over time. For example, GloBI can answer which species an Angel Shark (Squatina squatina) eats in the Gulf of Mexico, or return the results of a query for the number of Angel Sharks feeding in the Gulf of Mexico between 2005 and 2010.

FAQ

How do I . . .

... get to the interaction data?

There's many ways to access the GloBI interaction data. Please see Home#accessing-species-interaction-data for your options.

... correct taxonomic names (e.g. Homo saliens --> Homo sapiens) without changing the original data file?

See Taxonomy-Matching#submitting-name-corrections.

... contribute a new dataset?

See How to Contribute Data to Global Biotic Interactions? for a list of options on how to contribute data.

... suggest a correction to an existing dataset?

Submit an issue and describe what it is you think should be changed (see this issue for an example).

Support and Community

This project is funded by EOL's Rubenstein Fellowship Program 2013 and would not be possible without the hard work and dedication of academic, government, and citizen scientists around the world that have gathered species interaction data and shared their datasets. For more news about our efforts, please visit our blog.

Introduction

GloBI contains code to normalize and integrate existing species-interaction datasets and export the resulting integrated interaction dataset.

Taxonomy Matching

As part of the species-interaction normalization process, GloBI provides mechanisms for robust taxonomy matching. Please see Taxonomy Matching for more information.

Ontologies and Vocabularies

GloBI attempts to re-use existing Ontologies and Vocabularies to link terms used in data sources to promote the machine readability of the data and integration with other linked datasets.

Dataset Management

Most original dataset are managed in this github repository. For a step-by-step plan to update/ edit datasets, please visit Dataset Management.

Accessing Species Interaction Data

To access normalized species interaction data you can download data in bulk, use software libraries (R and javascript) or access the API directly. The table below gives an overview of ways to access the data.

Name Description Link
Web API species interaction API to help integrate interaction data into your (web) app see api wiki for some example
javascript libraries for embedding interaction data (and widgets) into your web app globi.js for widgets and globi-data.js for data api
R library for accessing GloBI data in R rglobi (github)
darwin core archive darwin core archive of species interaction data and related darwin core archive current/ stable or darwin core archive with interactions aggregated by study current/ stable
tsv single interaction table expressed in tab separated values tsv current
rdf ttl/nquads archive archive of species interaction data expressed in globi and associated ontologies in rdf/nquad format rdf/nquad archive tar ball current/ rdf/ttl stable
sparql endpoint exposing interaction data using apache jena's fuseki, an rdf store sparql console, example query that should return first ten triples in json format
neo4j graphdb archive dump of http://neo4j.org with normalized datasets neo4j graph db tar ball current/ stable
neo4j rest api execute Cypher queries or use other neo4j rest api operations Neo4j Data Browser, more examples

Generating Normalized Datasets

mvn clean install runs tests, builds the eol-globi-data tool, normalizes the imported datasets, and exports the normalized data to various data archives such as a neo4j graphdb, darwin core archive and rdf/turtle archive. This process might take awhile, depending on your network and computer configuration.

As part of this Maven build, the eol-globi-data tool is executed in module eol-globi-datasets and imports, normalizes, integrates, and exports the biotic interaction datasets.

The datasets below are (re-)created daily. A list of interaction dataset contributors can be found here.

Normalization Process

Data Flow