Top Level Ontology

Latest (June 2013) slide presentation

- https://portal.i-marine.d4science.org/group/data-e-infrastructure-gateway/workspace?itemid=55f18f59-d807-474b-aa5a-88b123d0dae8

Person responsible for editing/maintaining this page

Carlo Allocca (carlo@ics.forth.gr)

TLO-Development activity

General Description

This activity concerns with the development of a top level ontology (called MarineTLO) that will integrate the concepts currently existing in marine-domain knowledge bases (in particular FLOD and ECOSCOPE knowledge bases). The MarineTLO-development activity is dived into six sub-activities (or Tasks) and related to each other as shown in the diagram in Fig 1.

Methodology

It is based on an Iterative and Incremental development approach. As such, one iteration will involve all the above tasks that are described here http://wiki.i-marine.eu/index.php/Top_Level_Ontology. All the iterations will be accurately described and new MarineTLO version will be delivered in each iteration.

Activities scheduled with deadlines

Each iteration is planned to be monitored by opening related tickets.

Related Wiki Pages

http://wiki.i-marine.eu/index.php/XSearch

Motivation - Goal - Requirements

Describe a scenario that will justify the need for having such a MarineTLO on top of marine-domain knowledge bases.

THE MOTIVATIONS ARE BASED ON THE FACT THAT: Semantic technologies, applications and services for biodiversity mostly rely on the rise of an interconnected and shared tree-of-life like dataset scaling on the web. The various communities (including also marine one) are contributing to this joint effort aim to share domain data and their meaning, to provide a solid basis for biodiversity systems interoperability.

THE GOAL IS: Our goal in modelling and formalising a Top Level Ontology (MarineTLO) is for integrating and semantically extending the underlying models of existing marine data sources. Specifically, the MarineTLO is used on the top of a number of real and heterogeneous marine data sources, including FLOD and ECOSCOPE, as knowledge mediator to represent, manipulate and reason upon and across them.

THE REQUIREMENTS ARE: This Top Level Ontology has to focus on EAF ( Ecosystem Approach to Fisheries / Marine Resources) and should be generic enough to provide consistent abstractions or specifications of concepts included in all data models or ontologies of iMarine data sources such as ECOSCOPE, TDWG-WORMS, FLOD, AGROVOC, DwC, IBIS [Gangemi 2002], [Doerr 2003], and provide the necessary properties to make this distributed knowledge base a coherent source of facts relating observational data with the respective spatiotemporal context and categorical (systematic) domain knowledge

Related Meetings (and their slides)

Analysis, Design and Implementation

FLOD Ontological Analysis

This activity has the primary goal to provide a common understanding of the FLOD ontology network. It has been considered necessary for the development of the MarineTLO. The associated ticket is https://issue.imarine.research-infrastructures.eu/ticket/888

FLOD Ontological Analysis, 04-Dec-2012
- https://portal.i-marine.d4science.org/group/data-e-infrastructure-gateway/workspace?itemid=04d81d92-d3e3-41d9-aeaf-605bd5c4ea33

FLOD Ontological Analysis, 07-Dec-2012
- http://wiki.i-marine.eu/index.php/7.12.2012-TLO_FLOD_Ontological_Analysis

FLOD Ontological Analysis, 31-Dec-2012
- https://portal.i-marine.d4science.org/group/data-e-infrastructure-gateway/workspace?itemid=55f18f59-d807-474b-aa5a-88b123d0dae8

Ecoscope Ontological Analysis

This activity has the primary goal to provide a common understanding of the ECOSCOPE ontology network. It has been considered necessary for the development of the MarineTLO. The associated ticket is https://issue.imarine.research-infrastructures.eu/ticket/889

ECOSCOPE Ontological Analysis, 13-Dec-2012
- https://portal.i-marine.d4science.org/group/data-e-infrastructure-gateway/workspace?itemid=7414845a-942d-4c1d-b343-27caeee15053

ECOSCOPE Ontological Analysis, 11-Jan-2013, meeting, online
- https://portal.i-marine.d4science.org/group/data-e-infrastructure-gateway/workspace?itemid=fc7d36b4-96d8-4083-a524-430487ffb5fd

MarineTLO Design

The activities is related to the design of MarineTLO ontology. The associated ticket is https://issue.imarine.research-infrastructures.eu/ticket/890

Describing the MarineTLO design, 21-Dec-2012
- https://portal.i-marine.d4science.org/group/data-e-infrastructure-gateway/workspace?itemid=0233e4b5-b43b-4e0b-9754-a2c299e0cda7
Describing the MarineTLO design, 24-Dec-2012
- https://portal.i-marine.d4science.org/group/data-e-infrastructure-gateway/workspace?itemid=6fe8c22f-1152-4caf-bfbe-47d07339f905

MarineTLO Implementation

The activities is related to the implementation of MarineTLO ontology using OWL 2 language. The associated ticket is https://issue.imarine.research-infrastructures.eu/ticket/891

Please loot at http://wiki.i-marine.eu/index.php/Top_Level_Ontology#TLO_Products for the versions of the MarineTLO

SPARQL endpoints (Virtuoso and OWLIM-Lite)
- http://62.217.127.213:8890/sparql with graph name http://www.ics.forth.gr/isl/TLObasedDataWarehouse

- http://62.217.127.213:8080/openrdf-workbench/repositories/TLODataWarehouse/

Competency queries
- https://portal.i-marine.d4science.org/group/data-e-infrastructure-gateway/workspace?itemid=4700c39a-922e-48b2-ba2c-fe7e0e2074b8

MarineTLO Usage

Activities related to the usage of MarineTLO (+ references to documents/ wiki pages/ tickets). This activity is associated to the ticket https://issue.imarine.research-infrastructures.eu/ticket/900

Here, we describe possible scenarios in which MarineTLO can be evaluated. Currently, we identify the followings:

MarineTLO as meta-model for FLOD, ECOSCOPE and WoRMS
- Fact Sheets and Competence Queries

MarineTLO as knowledge model for semantic search in X-search
- Suppose that a user is looking for publications about tuna. Specifically he wants to find experiments that were applied to several species of tuna. So, he submits the query tuna and gets a sorted list of results and various categories of entities like Regional Fisheries Body, Species, FAO Country, etc. User realizes that the category Species may contain interesting entities. He notices that there is an entity with the label skipjack tuna which is a medium-sized fish in the tuna family found in tropical and warm-temperate waters. User wants to learn more information about that species. Specifically, he would like to see other species for which the skipjack tuna is predator or is prey. By clicking the icon next to the entity's name, user is able to instantly (at real-time) retrieve such information. In particular, in the back end, a SPARQL query is sent to the MarineTLO's endpoint asking for that information. Note that the 'Species' have been derived from FLOD, while the properties 'is predator of' and 'is prey of' have been derived from ECOSCOPE's knowledge base. That would be impossible without the exploitation of the MarineTLO.

MarineTLO Evaluation

This activity is related to the evaluation of the MarineTLO ontology. The associated ticket is https://issue.imarine.research-infrastructures.eu/ticket/892

A required activity for the MarineTLO evaluation is to populate it with concrete instances.

To populate just the class Species, please follow the link
- https://portal.i-marine.d4science.org/group/data-e-infrastructure-gateway/workspace?itemid=2e1a3b06-5c2d-4b96-aea0-c43dc53e670a

To populate the class Species with predator and prey relationships, please follow the link
- https://portal.i-marine.d4science.org/group/data-e-infrastructure-gateway/workspace?itemid=506fb989-7af4-492e-b654-19f4fd2113a5

Competence Queries, 22-03-2013
- https://portal.i-marine.d4science.org/group/data-e-infrastructure-gateway/workspace?itemid=c2895cc3-6a53-4ef6-ac43-b37d172324bc

MarineTLO Populating, 22-03-2013
- WoRMS-TLO: https://portal.i-marine.d4science.org/group/data-e-infrastructure-gateway/workspace?itemid=45f3b81c-b502-4345-b861-340d8e8a388c

MarineTLO Evaluation Report, 22-04-2013
- https://portal.i-marine.d4science.org/group/data-e-infrastructure-gateway/workspace?itemid=4700c39a-922e-48b2-ba2c-fe7e0e2074b8

MarineTLO-related Products

The Notion of MarineTLO Version

Each MarineTLO version consists of

A release number
An .owl file
A set of competency queries
A short description describing the changes
It could also contain a set of mappings between data source and MarineTLO, each of them described as an OWL file

TODO: We also need a document that contains the scope notes of each class

Evolution Process

Since last meeting in Rome (26-03-2013), we planned to release a new version every two months (for correcting errors, based on requirements, priorities, usage needs, etc).