Plic2OWL: PlinianCore-to-OWL translation

The Plinian Core vocabulary is a standard data model designed to share biological species level information. It is developped as an XML schema (XSD).

The Plinian Core ontology is a representation the XSD PlinianCore data model as an OWL ontology, to be used in RDF-based knowledge graphs.

This repository is a Python application that transtlates the Plinian Core XML schema into an OWL ontology. The output format is RDF Turtle.

Current status

The documentation of the ontology is deployed on the Github pages of this repository.

The WebVOWL only interface is accessible from this page.

WARNING: this is an on-going work, the generated ontology may change at any time.

Quick start guide

This repository relies on Conda to manage the execution environment. File environment.yml defines an environment named plic2owl.

1. Install Conda
2. Set up and activate the environment:

conda env create -f environment.yml
conda activate plic2owl

3. Run the translation of the currently available Plinian Core schema:

cd app
python ./main.py \
   https://raw.githubusercontent.com/tdwg/PlinianCore/master/xsd/abstract%20models/stable%20version/PlinianCore_AbstractModel_v3.2.2.7.xsd \
   --copy schemas \
   --output ../ontology/plic_ontology.ttl

Detailed Usage

First CD to directory app. Script main.py runs the translation. It takes a local path or a URL of the XML schema to translate, for instance:

python ./main.py /home/user/plic/PlinianCore.xsd

or

python ./main.py https://myserver.org/plic/PlinianCore.xsd

At each invocation, this will download the XML schema as well as all the imported schemas. To save time and bandwidth, add option --copy to store the downloaded schemas to a local directory.

python ./main.py /home/user/plic/PlinianCore.xsd --copy schemas

At subsequent invocations, the XSD files will be read from directory schemas. You may run the same command again or keep only the base name of the schema:

python ./main.py PlinianCore.xsd --copy schemas

By default, the generated RDF triples are printed out on the standard output. You may change this with option --output:

python ./main.py PlinianCore.xsd --copy schemas --output ../ontology/ontology.ttl

Configuration

Edit file config/default_config.yml to change the default namespace of imported XSD components (used when loaded XSDs do not mention a target namespace), and the namespaces for which we want to generate RDF terms.

You may specify an alternate configuration file with option --config:

python ./main.py https://myserver.org/plic/PlinianCore.xsd --copy schemas --config ../config/config_plic.yml

File config/logging.yml configures the application logger. By default the target is the standard output, and the log level is WARNING. See the logging API documentation for customization.

Imported schemas and equivalent RDF vocabularies

	Access to Biological Collection Data (ABCD)
XSD	Namespace: http://www.tdwg.org/schemas/abcd/2.06 Source: http://rs.tdwg.org/abcd/2.06/ABCD_2.06.xsd
RDF	Namespace: http://rs.tdwg.org/abcd/terms/ Source: https://github.com/tdwg/abcd/blob/master/ontology/abcd_concepts.owl
	Darwin Core Terms (DwC) + extensions
XSD	Namespace: http://rs.tdwg.org/dwc/terms/ Source: https://raw.githubusercontent.com/tdwg/PlinianCore/master/xsd/abstract%20models/stable%20version/tdwg_dwc_extensions.xsd
RDF	Namespace: http://rs.tdwg.org/dwc/terms/ Source: http://rs.tdwg.org/dump/terms.ttl
	Dublin Core Elements
XSD	Namespace: http://purl.org/dc/elements/1.1/ Source: http://dublincore.org/schemas/xmls/qdc/dc.xsd
RDF	Namespace: http://purl.org/dc/elements/1.1/ Source: https://www.dublincore.org/specifications/dublin-core/dcmi-terms/dublin_core_elements.ttl
	Dublin Core Terms
XSD	Namespace: http://purl.org/dc/terms/ Source: http://dublincore.org/schemas/xmls/qdc/dcterms.xsd
RDF	Namespace: http://purl.org/dc/terms/ Source: https://www.dublincore.org/specifications/dublin-core/dcmi-terms/dublin_core_terms.ttl
	Ecological Metadata Language (EML)
XSD	Namespace: eml://ecoinformatics.org/eml-2.1.1 Source: https://raw.githubusercontent.com/tdwg/PlinianCore/master/xsd/abstract%20models/stable%20version/eml.xsd
RDF	none
	Encyclopedia of Life (EOL)
XSD	Namespace: http://www.eol.org/transfer/content/0.3 Source: https://raw.githubusercontent.com/tdwg/PlinianCore/master/xsd/abstract%20models/stable%20version/content_0_3.xsd
RDF	none
	GISIN
XSD	Namespace: http://www.gisin.org/gisin/SpeciesStatus Source: https://raw.githubusercontent.com/tdwg/gisin/master/xsd/SpeciesStatus.xsd
RDF	none
	Taxon Concept Schema (TCS)
XSD	Namespace: http://www.tdwg.org/schemas/tcs/1.01 Source: https://raw.githubusercontent.com/tdwg/tcs/master/TCS101/v101.xsd
RDF	none