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Querying a Marine Data Warehouse Using SPARQL
ESWC 4th Summer School
Crete, September 2014
Presenter: Nikos Minadakis Ins$tute of Computer Science -‐ FORTH
Informa$on Systems Laboratory
Nikos Minadakis, ESWC 2014 Summer School, Crete 1
– Top-‐level ontology for the marine domain (also applicable to the terrestrial domain)
– Created in the content of the iMarine project to tackle the need for integra$ng sets of facts about marine species, and thus to assist research about species and biodiversity.
– Provides a unified and coherent core model for schema mapping which enables formula$ng and answering queries that cannot be answered by any individual source.
MarineTLO
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V1 V2 V3 V4
– MarineTLO Version 2.0.0
– Water Areas – Species -‐> Water Areas – Countries – Countries -‐ > Water
Areas – Species -‐> Countries – Ecosystems – Ecosystems -‐> Countries – Species -‐> Ecosystems – Exclusive Economical
Zones – Fishing Gears – Fishing Vessels – Common Names of
Species
– MarineTLO Version 3.0.0 – Capture (Catch and
ByCatch) – Catch – Biological Parameters
– Longevity, size, weight
– Sta$s$cal Indicators – Publica$ons – Species -‐> Publica$ons
– MarineTLO Version 1.0.0
– Compe$tors – Species Codes – Images – References
– Species – Predators – Classifica$on – Scien$fic
Names
MarineTLO Concepts
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MarineTLO Warehouse Contents
5.5M Triples 53,797 Species 53,797 Scientific Names 12,752 Authorships 155,510 Common Names
2,054 Predators
853 Ecosystems 47 Water Areas 294 Countries 160 EEZ
90 Vessel Types 112 Gear Types
13,131 Bibliography resources 3,206 Statistic Indicators
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Seman$c post-‐processing of search results
Applica>ons 1/3
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Fact Sheet Generator
Applica>ons 2/3
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Ichthys
Applica>ons 3/3
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• MatWare • h`p://www.ics.forth.gr/isl/MatWare/
• MarineTLO • h`p://www.ics.forth.gr/isl/MarineTLO/
• TripleStores – MarineTLO-‐Warehouse: h`p://virtuoso.i-‐marine.d4science.org:8890/sparql
– also browsable through: h`p://virtuoso.i-‐marine.d4science.org:8890/fct
Links
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Related Publica>ons • Y. Tzitzikas, N. Minadakis, Y. Marketakis, P. Fafalios, C. Alloca, M. Mountantonakis, I. Zidianaki.
MatWare: Constructing and Exploiting Domain Specific Warehouses by Aggregating Semantic Data. In 11th Extended Semantic Web Conference (ESWC'14), Anissaras, Crete, Greece, May 2014.
• M. Mountantonakis, C. Allocca, P. Fafalios, N. Minadakis, Y. Marketakis, C. Lantzaki, Y. Tzitzikas. Extending VoID for Expressing the Connectivity Metrics of a Semantic Warehouse, In 1st International Workshop on Dataset PROFILing & fEderated Search for Linked Data (PROFILES'14), co-located with ESWC'14, Anissaras, Crete, Greece, May 2014.
• Y. Tzitzikas, N. Minadakis, Y. Marketakis, P. Fafalios, C. Alloca, and M. Mountantonakis. Quantifying the Connectivity of a Semantic Warehouse. In procs of the 4th International Workshop on Linked Web Data Management (LWDM 2014) March, 2014.
• Y. Tzitzikas, C. Allocca, C. Bekiari, Y. Marketakis, P. Fafalios and N. Minadakis, Ontology-based Integration of Heterogeneous and Distributed Information of the Marine Domain, ERCIM News vol. 96, Special Theme on Linked Open Data, January 2014.
• Y. Tzitzikas, C. Allocca, C. Bekiari, Y. Marketakis, P. Fafalios, M. Doerr, N. Minadakis, T. Patkos and L. Candela , “Integrating Heterogeneous and Distributed Information about Marine Species through a Top Level Ontology”, 7th Metadata and Semantics Research Conference, MTSR 2013, Thessaloniki, Greece, November 2013.
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Triples: 58,278 Main Concepts: Ecosystems, Predators Graph: h"p://eswc/summerschool/Ecoscope
Triples: 676,480 Main Concepts: Scien$fic Names Graph: h"p://eswc/summerschool/DBpedia
Triples: 2,249,035 Main Concepts: Habitats, CommonNames, Bibliography References Graph: h"p://eswc/summerschool/Fishbase
Schema: 1,582 triples Graph:h"p://eswc/summerschool/Schema
Marine Data
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Simplified Data Schema
Species
Scien>fic_Name_Assignment
assignedDate
xsd:string
xsd:string
xsd:dateTime
Actor name
Ecosystem_ Environment
is_introduc
ed_at
Water_Area
Country is_bio>cally_related_to
CommonName name xsd:string
is_used_in xsd:string
Bibliography Resource
xsd:string
xsd:string
xsd:string
authorName
>tle hasLanguage
Ecosystem_Type
has_type
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Simplified Data Schema
tloCore: BT27_Species
tloCore: LT5_usually_is_predator_of
tloCore: BC46_1_Scien>fic_Name_Assignment
tloimarine :assignedDate
xsd:string
xsd:string
xsd:dateTime
tloCore: BC8:Actor
tloimarine: name
tloCore: BC14_Ecosystem_ Environment tloim
arine:
LX14_is_int
roduced_at
tloCore: BC15_Water_Area
tloCore: BC4_2_Country
tloimarine: LX10_is_bio>cally_related_to
tloimarine: CommonName
tloimarine :name xsd:string
tloimarine :is_used_in
xsd:string
tloimarine: Bibliography Resource
xsd:string
xsd:string
xsd:string
tloimarine:authorN
ame
tloimarine:>tle tloimarine:hasLanguage
tloCore: BT7_Ecosystem_Type
tloCore:LX3_has_type
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Naming
Species
usually_is_predator_of Scien>fic_Name_Assignment
assignedDate
xsd:string
xsd:string
xsd:dateTime
Actor name
Country is_bio>cally_related_to
CommonName name
xsd:string
is_used_in hasLa
nguage xsd:string
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Example Query “Find the common names of thunnus albacares” define input:inference 'h`p://eswc/summerschool/Schema' prefix tloimarine: <h`p://www.ics.forth.gr/isl/MarineTLO/v4/marinetloimarine.owl#> prefix tloCore: <h`p://www.ics.forth.gr/isl/MarineTLO/v4/marinetlo.owl#> SELECT ?commonName WHERE { <h`p://www.fishbase.org/en$ty#thunnus_albacares> tloCore: LX4_has_appella$on> ?x . ?x rdf:type tloimarine:CommonName . ?x tloimarine:name ?commonName . }
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Example Query: Results commonName
A'ahi
A'ahi hae
A'ahi mapepe
A'ahi maueue
A'ahi 'oputea
A'ahi 'opu$'i
A'ahi patao
A'ahi tari'a'uri
A'ahi tatumu
A'ahi teaamu
A'ahi $amatau
A'ahi vere
Ahi
Albakor
Albakora
Albakora
Albacor
Albacora
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Species DistribuDon and Predators
Species
usually_is_predator_of
Ecosystem_ Environment
is_introduced_at
Water_Area
Country
Ecosystem_Type
has_type
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Bibliographic Resources
Species Bibliography Resource
is_about_type
xsd:string
xsd:string
xsd:string
>tle
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Queries 1-‐13 1. Return all the species
2. Return 17 predators
3. Return the species that are predators or preys
4.* Return all the informa$on for Thunnus Albacares and the graph that contains it
5.* Select the full scien$fic name (name,authorship,date) of Thunnus Albacares
6. Return the total number of species
7. Retrieve the graph of the pairs of species that are predators of the same prey and create the graph using tloCore:usually_is_compe$tor_of predicate 8. Retrieve the graph of the actors that discovered species and the discovery dates. Create the graph using tloimarine:was_discovered_by and tloimarine:was_discovered_on predicates. 9. Return the number of predators of each species
10. Return the species that have more than 10 predators and sort the results according to the predators number. 11. Return the species that are not predators
12. Return the ecosystems and ecosystem types that each species lives in
13.* Return the wateareas that thunnus albacares is a na$ve species
* Use the URI: <h`p://www.fishbase.org/en$ty#thunnus_albacares> ** Use the URI: <h`p://www.fishbase.org/en$ty#Japan>
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Queries 14-‐21 14.** Does Thunnus albacares live in Japan?
15.* Return the common names of Thunnus albacares and the language they are expressed in. Return also the countries where those names are used if this informa$on is available 16. Return the species men$oned in bibliographic entries of author ‘Fahay M.”. Return the exact name of the authos, the $tle of the entry, the language of it as well as the related species 17. Select the all the greek common names
18. Select the species that contain the word salmon or thunnus in their scien$fic name (use 2 alterna$ve ways of expressing the query) 19. Return all the species that were discovered by “Temminck” and “Schlegel”
20.* Return all the species that are preys or predators of Thunnus albacares and the common names of them if they exist 21. Describe the URIS of Species that live in Greece and contain the word “yellow” in their common names. * Use the URI: <h`p://www.fishbase.org/en$ty#thunnus_albacares> ** use the URI: <h`p://www.fishbase.org/en$ty#Japan>
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