Difference between revisions of "Top Level Ontology"
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=== General Description === | === 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 | + | 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. |
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=== Methodology === | === 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 | + | 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 === | === Activities scheduled with deadlines === | ||
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== Motivation - Goal - Requirements == | == Motivation - Goal - Requirements == | ||
| − | Describe a scenario that will justify the need for having such a | + | 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: | THE MOTIVATIONS ARE BASED ON THE FACT THAT: | ||
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THE GOAL IS: | THE GOAL IS: | ||
| − | Our goal in modelling and formalising a Top Level Ontology ( | + | 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: | THE REQUIREMENTS ARE: | ||
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== FLOD Ontological Analysis == | == 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 | + | 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 | *'''FLOD Ontological Analysis''', 04-Dec-2012 | ||
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== Ecoscope Ontological Analysis == | == 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 | + | 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 | *'''ECOSCOPE Ontological Analysis''', 13-Dec-2012 | ||
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**https://portal.i-marine.d4science.org/group/data-e-infrastructure-gateway/workspace?itemid=fc7d36b4-96d8-4083-a524-430487ffb5fd | **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 | + | The activities is related to the design of MarineTLO ontology. The associated ticket is https://issue.imarine.research-infrastructures.eu/ticket/890 |
| − | *'''Describing the | + | *'''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 | ** https://portal.i-marine.d4science.org/group/data-e-infrastructure-gateway/workspace?itemid=0233e4b5-b43b-4e0b-9754-a2c299e0cda7 | ||
| − | *'''Describing the | + | *'''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 | **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 | + | 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 | + | * 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) | *SPARQL endpoints (Virtuoso and OWLIM-Lite) | ||
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**https://portal.i-marine.d4science.org/group/data-e-infrastructure-gateway/workspace?itemid=4700c39a-922e-48b2-ba2c-fe7e0e2074b8 | **https://portal.i-marine.d4science.org/group/data-e-infrastructure-gateway/workspace?itemid=4700c39a-922e-48b2-ba2c-fe7e0e2074b8 | ||
| − | == | + | == MarineTLO Results == |
| − | === | + | === MarineTLO Usage === |
| − | Activities related to the usage of | + | 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 | + | 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 | ** 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 | + | ** 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 | + | 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. | A required activity for the MarineTLO evaluation is to populate it with concrete instances. | ||
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**https://portal.i-marine.d4science.org/group/data-e-infrastructure-gateway/workspace?itemid=c2895cc3-6a53-4ef6-ac43-b37d172324bc | **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 | **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 | **https://portal.i-marine.d4science.org/group/data-e-infrastructure-gateway/workspace?itemid=4700c39a-922e-48b2-ba2c-fe7e0e2074b8 | ||
| − | == | + | == MarineTLO Products == |
| − | Each | + | Each MarineTLO version consists of |
* A release number | * A release number | ||
* An .owl file | * An .owl file | ||
* A set of competency queries | * A set of competency queries | ||
* A short description describing the changes | * A short description describing the changes | ||
| − | * It could also contain a set of mappings between data source and | + | * 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 | TODO: We also need a document that contains the scope notes of each class | ||
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=== Version 1.0.0 released on 26-03-2013 === | === Version 1.0.0 released on 26-03-2013 === | ||
* Release Number: 1.0.0 | * Release Number: 1.0.0 | ||
| − | * Documentation of the | + | * Documentation of the MarineTLO version 1.0.0 https://issue.imarine.research-infrastructures.eu/ticket/1764#comment:1 |
| − | * This version of the | + | * This version of the MarineTLO containing classes, properties and instances to test the MarineTLO over the fact sheet |
**https://portal.i-marine.d4science.org/group/data-e-infrastructure-gateway/workspace?itemid=1eb50637-736c-4d37-8604-7544215c989b | **https://portal.i-marine.d4science.org/group/data-e-infrastructure-gateway/workspace?itemid=1eb50637-736c-4d37-8604-7544215c989b | ||
* Competence queries covering the fact sheets | * Competence queries covering the fact sheets | ||
| Line 194: | Line 194: | ||
** e.g. http://62.217.127.128:8890/describe/?url=http%3A%2F%2Fwww.ecoscope.org%2Fontologies%2Fecosystems%23thunnus_albacares&sid=6&urilookup=1 information about thunnus albacares are returned. | ** e.g. http://62.217.127.128:8890/describe/?url=http%3A%2F%2Fwww.ecoscope.org%2Fontologies%2Fecosystems%23thunnus_albacares&sid=6&urilookup=1 information about thunnus albacares are returned. | ||
| − | == | + | == MarineTLO Related Tickets == |
=== First Iteration === | === First Iteration === | ||
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* Ecoscope Ontological Analysis: https://issue.imarine.research-infrastructures.eu/ticket/889 '''CLOSED''' | * Ecoscope Ontological Analysis: https://issue.imarine.research-infrastructures.eu/ticket/889 '''CLOSED''' | ||
| − | * | + | * MarineTLO Design: https://issue.imarine.research-infrastructures.eu/ticket/890 '''CLOSED''' |
| − | * | + | * MarineTLO Implementation: https://issue.imarine.research-infrastructures.eu/ticket/891 '''CLOSED''' |
| − | * | + | * MarineTLO Results: TLO Usage https://issue.imarine.research-infrastructures.eu/ticket/900 '''CLOSED''' |
| − | * | + | * MarineTLO Evaluation, https://issue.imarine.research-infrastructures.eu/ticket/892 '''CLOSED''' |
| − | * | + | * MarineTLO Population, https://issue.imarine.research-infrastructures.eu/ticket/1220 '''CLOSED''' |
* MarineTLO Version 2.0.0, https://issue.imarine.research-infrastructures.eu/ticket/1603 '''OPEN''' | * MarineTLO Version 2.0.0, https://issue.imarine.research-infrastructures.eu/ticket/1603 '''OPEN''' | ||
Revision as of 17:21, 2 July 2013
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
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
TCOM in Italy, 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 Belgium, 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
Semantic Cluster Meeting, online, 13.02.2013
- TLO activities
- Minutes from Leo: http://wiki.i-marine.eu/index.php/13.02.2013_Semantic_Cluster
TCOM in Italy, Pisa, 21.03.2013
- gCube and Production of RDF Data (FORTH side)
TCOM in Italy, Rome, 26.03.2013
- TLO-‐Acvity: Status, Open Issues and Next Steps
- Minutes of the Meeting, 27-03-2013:
TCOM in Greece, Skiathos, 18.06.2013
- We presented "TLO-related Activities
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
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
- FLOD Ontological Analysis, 07-Dec-2012
- FLOD Ontological Analysis, 31-Dec-2012
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
- ECOSCOPE Ontological Analysis, 11-Jan-2013, meeting, online
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
- Describing the MarineTLO design, 24-Dec-2012
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)
- Competency queries
MarineTLO Results
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
- To populate the class Species with predator and prey relationships, please follow the link
- Competence Queries, 22-03-2013
- MarineTLO Populating, 22-03-2013
- MarineTLO Evaluation Report, 22-04-2013
MarineTLO Products
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).
Version 1.0.0 released on 26-03-2013
- Release Number: 1.0.0
- Documentation of the MarineTLO version 1.0.0 https://issue.imarine.research-infrastructures.eu/ticket/1764#comment:1
- This version of the MarineTLO containing classes, properties and instances to test the MarineTLO over the fact sheet
- Competence queries covering the fact sheets
- OWL Mappings: FLOD-TLO, Ecoscope-TLO and WoRMS-TLO
Previous TLO Versions
- TLO Version 13/11/2012, https://portal.i-marine.d4science.org/group/data-e-infrastructure-gateway/workspace?itemid=832af2c7-70d2-4ac3-8985-ed1efcaa0a40
Current MarineTLO-based repository
- Virtuoso
- Browse Virtuoso MarineTLO-based repository @ http://62.217.127.128:8890/fct/
- e.g. http://62.217.127.128:8890/describe/?url=http%3A%2F%2Fwww.ecoscope.org%2Fontologies%2Fecosystems%23thunnus_albacares&sid=6&urilookup=1 information about thunnus albacares are returned.
MarineTLO 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
- MarineTLO Design: https://issue.imarine.research-infrastructures.eu/ticket/890 CLOSED
- MarineTLO Implementation: https://issue.imarine.research-infrastructures.eu/ticket/891 CLOSED
- MarineTLO Results: TLO Usage https://issue.imarine.research-infrastructures.eu/ticket/900 CLOSED
- MarineTLO Evaluation, https://issue.imarine.research-infrastructures.eu/ticket/892 CLOSED
- MarineTLO Population, https://issue.imarine.research-infrastructures.eu/ticket/1220 CLOSED
- MarineTLO Version 2.0.0, https://issue.imarine.research-infrastructures.eu/ticket/1603 OPEN
- MarineTLO Version 2.0.0 Documentation, https://issue.imarine.research-infrastructures.eu/ticket/1764 OPEN
- Documentation of the process used for creating MarineTLO-based warehouses, https://issue.imarine.research-infrastructures.eu/ticket/1848 OPEN
