View source for Top Level Ontology

== 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 (for short TLO) that will integrate the concepts currently existing in marine-domain knowledge bases (in particular FLOD and ECOSCOPE knowledge bases).  The TLO-Development activity is dived into six sub-activities (or Tasks) and related to each other as shown in the diagram in Fig 1. 



[[File:Pic1.png|center]]

=== 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 TLO Modules/ Versions will be delivered in each iteration ready to be used.

=== Activities scheduled with deadlines ===

At least two iterations are needed to complete the TLO-Development activity with deadlines December 2012 and January 2013, respectively.  Each iteration is planned to be monitored by opening related tickets. And, as in January there is going to be the next meeting, we (Claudio, Julien and Carlo) will discuss if we need a third or more iterations. 


== Related Cluster ==
http://wiki.i-marine.eu/index.php/Semantic_cluster_achievements

== Related Wiki Pages ==
http://wiki.i-marine.eu/index.php/XSearch

== Meeting In Progress ==

===Meeting In Rome, 03.11.2012 ===
http://wiki.i-marine.eu/index.php/03.11.2012.MeetingInRome

=== Meeting on "FLOD Ontological Analysis: First Iteration", 7.12.2012 ===
For the details of the first meeting, please follow the link
http://wiki.i-marine.eu/index.php/7.12.2012-TLO_FLOD_Ontological_Analysis. This meeting is related to the ticket https://issue.imarine.research-infrastructures.eu/ticket/224#comment:15

=== TCOM In Ostende, 29.01.2013  ===

* Agenda and Presentation, please follow the link https://portal.i-marine.d4science.org/group/data-e-infrastructure-gateway/workspace?itemid=dd36ba2b-f2fa-46ae-b5d0-1b6e2616f995

<!-- * For the details of the Semantic Cluster, Minutes of the TLO-Activity at the 4th TCOM imarine in Ostende on 29 Jan 2013: Julien’s Scenario and TLO-Instantiating Plan/Discussion, please follow the link http://bscw.research-infrastructures.eu/bscw/bscw.cgi/d276309/Semantic%20Cluster%20and%20TLO%20ActivitiesVer1.docx -->

=== Meeting Tconf of the Semantic Cluster, 13.02.2013  ===

* The proposed TLO activities https://portal.i-marine.d4science.org/group/data-e-infrastructure-gateway/workspace?itemid=70ef515b-2d2a-4258-a78c-9a1931d6ad3b A new version: https://portal.i-marine.d4science.org/group/data-e-infrastructure-gateway/workspace?itemid=cf9341d0-f234-4dc4-96a3-be62fc247b75

* Minutes from Leo: http://wiki.i-marine.eu/index.php/13.02.2013_Semantic_Cluster

=== TCOM In Pisa, 21.03.2013  ===

* We presented: gCube and Production of RDF Data  (FORTH side)
please follow the link https://portal.i-marine.d4science.org/group/data-e-infrastructure-gateway/workspace?itemid=11fd7b11-7056-4985-b562-8570adbf9fdc

=== TCOM in Rome, 26.03.2013 ===

* We presented: TLO-‐Acvity: Status, Open Issues and Next Steps
  http://bscw.research-infrastructures.eu/bscw/bscw.cgi/d279129/Tcom5-SemanticCluster-TLO_Activities.pdf

* Minutes of the Meeting in Rome, FAO 27-03-2013:
 http://bscw.research-infrastructures.eu/bscw/bscw.cgi/d279249/Minutes%20of%20the%20Meeting%20in%20Rome%2027%2003%202013.docx

== Motivation - Goal - Requirements ==
Describe a scenario that will justify the need for having such a TLO 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 (TLO) is for '''integrating''' and '''semantically extending''' the underlying models of existing marine data sources. Specifically, the TLO 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

== FLOD Ontological Analysis ==
The ontological analysis of FLOD (+ references to documents/ wiki pages/ tickets). This activity is associated to the ticket https://issue.imarine.research-infrastructures.eu/ticket/888

This sub-activity, with the first iteration, has the primary goal to provide a common understanding of the FLOD ontology network. It has been considered necessary for the development of the TLO.

The '''first draft (04-Dec-2012)''' describing the '''FLOD Ontological Analysis at the first iteration''' can be found here  http://bscw.research-infrastructures.eu/bscw/bscw.cgi/d260861/FLOD%20analysis%20First%20Iteration.pdf

The '''first (07-Dec-2012)''' '''Tconf''' on the '''FLOD Ontological Analysis at the first iteration''' can be found here http://wiki.i-marine.eu/index.php/7.12.2012-TLO_FLOD_Ontological_Analysis

The '''second draft (31-Dec-2012)''' describing the '''FLOD Ontological Analysis at the first iteration''' can be found here  http://bscw.research-infrastructures.eu/bscw/bscw.cgi/d273954/FLOD31122012.pdf

== Ecoscope Ontological Analysis ==
The ontological analysis of Ecoscope (+ references to documents/ wiki pages/ tickets). This activity is associated to the ticket https://issue.imarine.research-infrastructures.eu/ticket/889

This sub-activity, with the first iteration, has the primary goal to provide a common understanding of the ECOSCOPE ontology network. It has been considered necessary for the development of the TLO.

The '''first draft (13-Dec-2012)''' describing the '''ECOSCOPE Ontological Analysis''' at the first iteration can be found here http://bscw.research-infrastructures.eu/bscw/bscw.cgi/d261574/MainECOSCOPE.pdf


The '''first (11-Jan-2013) Tconf''' on the ECOSCOPE Ontological Analysis at the first iteration can be found here http://bscw.research-infrastructures.eu/bscw/bscw.cgi/d274281/ECOSCOPEmeetingWithJulien10012013.docx

== TLO Design ==
The activities carried out towards the design of TLO (+ references to documents / wiki pages/ tickets). This activity is associated to the ticket https://issue.imarine.research-infrastructures.eu/ticket/890

The '''first draft (21-Dec-2012)''' describing the TLO design at the first iteration can be found here http://bscw.research-infrastructures.eu/bscw/bscw.cgi/261904

The '''second draft (24-Dec-2012)''' describing the TLO design at the first iteration can be found here http://bscw.research-infrastructures.eu/bscw/bscw.cgi/d261983/TLO_draft(0.2).doc

== TLO Implementation ==
The activities carried out for the implementation of TLO (+ references to documents/ wiki pages/ tickets). This activity is associated to the ticket https://issue.imarine.research-infrastructures.eu/ticket/891

A SPARQL endpoint has been set at the following address http://139.91.183.78:8890/sparql. Based on this, it is possible to run the set of queries available here http://bscw.research-infrastructures.eu/bscw/bscw.cgi/d261933/TLO-Set%20of%20Queries%20firt%20iteration.pdf

== TLO Results ==

=== TLO Usage ===
Activities related to the usage of TLO (+ 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 TLO can be evaluated. Currently, we identify the followings:

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

* TLO 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 TLO'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 TLO.

=== TLO Evaluation ===
Activities related to the evaluation of TLO (+ references to documents/ wiki pages/ tickets). This activity is associated to the ticket https://issue.imarine.research-infrastructures.eu/ticket/892


Currently, we are working on TLO-Populating activity. To give a support to this activity, I started to design the OWL output structure of the information we need according to the current version of the TLO. Below you can find two links:

1) To populate just the class Species, please follow the link http://bscw.research-infrastructures.eu/bscw/bscw.cgi/d275986/OutputStructureToPopulateTLO-Species.rtf  

2) To populate the class Species with predator and prey relationships, please follow the link http://bscw.research-infrastructures.eu/bscw/bscw.cgi/d275990/OutputStructureToPopulateTLO-SpeciesWithPredatorAndPrey.rtf

3) I am willing to discuss about other type of outputs depending on the data you can provide.

* Competence Queries, 22-03-2013
** http://bscw.research-infrastructures.eu/bscw/bscw.cgi/d278201/Competency%20queries%20TLOVer1.0.0.docx

* TLO Populating, 22-03-2013 
** WoRMS-TLO : http://bscw.research-infrastructures.eu/bscw/bscw.cgi/d278205/description%20of%20WoRMS-TLO%20processVer1.docx

* TLO Evaluation Report, 22-04-2013 
**http://bscw.research-infrastructures.eu/bscw/bscw.cgi/d280005/TLOVer1.0.0%20Evaluation22042013%20.docx

== TLO Products ==
Each TLO 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 TLO, 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). 

=== Version 1.0.0 released on 26-03-2013 ===
* Release Number: 1.0.0
* Documentation of the TLO version 1.0.0 https://issue.imarine.research-infrastructures.eu/ticket/1764#comment:1
* This version of the TLO containing classes, properties and instances to test the TLO over the fact sheet 
  http://bscw.research-infrastructures.eu/bscw/bscw.cgi/d278160/TLO.zip
*Proposed a set  of competence queries covering the fact sheets
  http://bscw.research-infrastructures.eu/bscw/bscw.cgi/d278201/Competency%20queries%20TLOVer1.0.0.docx
* OWL Mappings: FLOD-TLO, Ecoscope-TLO and WoRMS-TLO
**  http://bscw.research-infrastructures.eu/bscw/bscw.cgi/d278164/Mappings.zip
**  http://bscw.research-infrastructures.eu/bscw/bscw.cgi/d282801/iMarine%20Mapping%20Descriptions.pdf

=== Previous TLO Versions ===
* TLO Version 13/11/2012, http://bscw.research-infrastructures.eu/bscw/bscw.cgi/d260671/TLO-Ontology_20121113.owl

== TLO Related Tickets ==

=== First Iteration ===
* FLOD Ontological Analysis: https://issue.imarine.research-infrastructures.eu/ticket/888 '''CLOSED'''

* Ecoscope Ontological Analysis: https://issue.imarine.research-infrastructures.eu/ticket/889 '''CLOSED'''

* TLO Design: https://issue.imarine.research-infrastructures.eu/ticket/890 '''CLOSED'''

* TLO Implementation: https://issue.imarine.research-infrastructures.eu/ticket/891 '''CLOSED'''

* TLO Results: TLO Usage https://issue.imarine.research-infrastructures.eu/ticket/900 '''CLOSED''' 

* TLO Evaluation, https://issue.imarine.research-infrastructures.eu/ticket/892 '''CLOSED'''

* TLO Instatiation, https://issue.imarine.research-infrastructures.eu/ticket/1220 '''OPEN'''