Adding Biodiversity Datasets from Argentinian Patagonia to the Web - - PowerPoint PPT Presentation

Adding Biodiversity Datasets from Argentinian Patagonia to the Web

• f Data

Marcos Zárate, CENPAT - CONICET Germán Braun, GILIA - UNCOMA Pablo Fillottrani, DCIC - UNS

S4BioDiv 2017 – 2nd International Workshop on Semantics for Biodiversity

Motivation

• Currently there is a steadily growing wealth of

biodiversity data from a wide range of disciplines which are available from on-line information systems around the world.

• Biodiversity community has standardized shared

common vocabularies such as Darwin Core (DwC) together with platforms as the Integrated Publishing Toolkit (IPT).

Motivation

• Since 2011 CENPAT has started to publicly share

its biodiversity data under Open Data license.

• These data are available as Darwin Core Archive

(DwC-A) through IPT (http://ipt.cenpat- conicet.gob.ar:8081/)

The Problem

• IPT platform focuses on publishing content in

unstructured or semi-structured formats but reducing the possibilities to interoperate with other datasets and make them accessible for machines.

• Though the DwC is defined in an RDF document,

integration of biodiversity data in the Semantic Web (SW) is in its early stages.

Proposed Solution

• We present a transformation process to publish

biodiversity data as RDF datasets.

• This process uses OpenRefine and RDF refine for

generating RDF triples and define URIs.

• We use GraphDB for storing, browsing, accessing

and linking data with external RDF datasets.

Proposed Architecture

URI Definition

• In order to generate URI for each resource, we use

GREL (General Refine Expression Language) also provided by OpenRefine.

• The general structure of the URIs is :

▫ http://[base uri]/[DwC class]/[value]

• The resulting RDF triple for an occurrence

is:

▫ SUBJECT <base_uri/occurrence/f6bbf85d-85ea-4605-87fad81aca73a1cd > ▫ PREDICATE rdf:type ▫ OBJECT dwc:Occurrence

Exploitation: Conservation Status of

Species

• Information about the state of conservation is

missing in CENPAT datasets.

Exploitation: Occurrences by Year

• The following query allows to observe the

temporality of the occurrences and its results are visualised using R and ggplot2 package.

Exploitation: Locations of Marine Mammals

• This query retrieve the locations (latitude and

longitude) for the species Mirounga Leonina, and its results are visualized using R and ggmap package.

Results

• In this initial stage only a few datasets were

converted to RDF, our platform stored 502.00 RDF triples.

• Also for the user to be able to exploit the dataset we

define some SPARQL queries and their corresponding visualization using the statistical software R.

Future work

• As future works, we plan to automate some tasks
• f the process and interlink with more datasets.
• Providing easier SPARQL access for non-skilled

users.

• We are analyzing other ontologies such as

ENVO, NCBI and OWL Time and working on a suite of complementary ontologies for describing every aspect of semantic biodiversity.

Links of interest

• Github project

▫ https://github.com/cenpat-gilia/CENPAT-GILIA- LOD

• SPARQL Endpoint

▫ http://crowd.fi.uncoma.edu.ar:3333/repositories/ BIO_CNP_GILIA

• R scripts

▫ https://github.com/cenpat-gilia/CENPAT-GILIA- LOD/tree/master/r-scripts

Thank you for your attention