Querying a Marine Data 
Warehouse Using SPARQL 
ESWC 4th Summer School 
Crete, September 2014 
Presenter: 
Nikos 
Minadaki...
MarineTLO 
– Top-­‐level 
ontology 
for 
the 
marine 
domain 
(also 
applicable 
to 
the 
terrestrial 
domain) 
– Created ...
MarineTLO 
Concepts 
V1 
V2 
V3 
V4 
– MarineTLO 
Version 
2.0.0 
– Water 
Areas 
– Species 
-­‐> 
Water 
Areas 
– Countri...
MarineTLO Warehouse 
Contents 
5.5M Triples 53,797 Species 53,797 Scientific Names 
12,752 Authorships 
155,510 Common Nam...
Seman$c 
post-­‐processing 
of 
search 
results 
5 
Applica>ons 
1/3 
Nikos 
Minadakis, 
ESWC 
2014 
Summer 
School, 
Cret...
6 
Applica>ons 
2/3 
Fact 
Sheet 
Generator 
Nikos 
Minadakis, 
ESWC 
2014 
Summer 
School, 
Crete 
6
7 
Applica>ons 
3/3 
Ichthys 
Nikos 
Minadakis, 
ESWC 
2014 
Summer 
School, 
Crete 
7
8 
• MatWare 
• h`p://www.ics.forth.gr/isl/MatWare/ 
• MarineTLO 
• h`p://www.ics.forth.gr/isl/MarineTLO/ 
• TripleStores ...
Related 
Publica>ons 
• Y. Tzitzikas, N. Minadakis, Y. Marketakis, P. Fafalios, C. Alloca, M. Mountantonakis, I. Zidianaki...
Triples: 
58,278 
Main 
Concepts: 
Ecosystems, 
Predators 
Graph: 
h"p://eswc/summerschool/Ecoscope 
Triples: 
676,480 
Ma...
Simplified Data Schema 
Species 
Scien>fic_Name 
_Assignment 
assignedDate 
xsd:string 
xsd:string 
xsd:dateTime 
Actor 
n...
Simplified Data Schema 
tloCore: 
LT5_usually_is_predator_of 
tloCore: 
BT27_Species 
tloCore: 
BC46_1_Scien>fic_ 
Name_As...
Naming 
usually_is_predator_of 
Species 
Scien>fic_Name 
_Assignment 
assignedDate 
xsd:string 
xsd:string 
xsd:dateTime 
...
Example Query 
“Find 
the 
common 
names 
of 
thunnus 
albacares” 
define 
input:inference 
'h`p://eswc/summerschool/Schem...
Example Query: Results 
commonName 
A'ahi 
A'ahi 
hae 
A'ahi 
mapepe 
A'ahi 
maueue 
A'ahi 
'oputea 
A'ahi 
'opu$'i 
A'ahi...
Species DistribuDon and Predators 
usually_is_predator_of 
Species 
Ecosystem_ 
Environment 
is_introduced_at 
Water_Area ...
Bibliographic Resources 
Species 
Bibliography 
Resource 
is_about_type 
xsd:string 
xsd:string 
xsd:string 
>tle 
Nikos 
...
Queries 
1-­‐13 
1. 
Return 
all 
the 
species 
2. 
Return 
17 
predators 
3. 
Return 
the 
species 
that 
are 
predators ...
Queries 
14-­‐21 
14.** 
Does 
Thunnus 
albacares 
live 
in 
Japan? 
15.* 
Return 
the 
common 
names 
of 
Thunnus 
albaca...
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Tutorial: Querying a Marine Data Warehouse Using SPARQL - I.Fundulaki - ESWC SS 2014

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Tutorial: Querying a Marine Data Warehouse Using SPARQL - I.Fundulaki - ESWC SS 2014

  1. 1. 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
  2. 2. MarineTLO – 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. Nikos Minadakis, ESWC 2014 Summer School, Crete 2
  3. 3. MarineTLO Concepts 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$fic Names Nikos Minadakis, ESWC 2014 Summer School, Crete 3
  4. 4. MarineTLO Warehouse Contents 5.5M Triples 53,797 Species 53,797 Scientific Names 12,752 Authorships 155,510 Common Names 2,054 Predators 853 Ecosystems 47 Water Areas 294 Countries 160 EEZ 90 Vessel Types 112 Gear Types 13,131 Bibliography resources 3,206 Statistic Indicators Nikos Minadakis, ESWC 2014 Summer School, Crete 4
  5. 5. Seman$c post-­‐processing of search results 5 Applica>ons 1/3 Nikos Minadakis, ESWC 2014 Summer School, Crete 5
  6. 6. 6 Applica>ons 2/3 Fact Sheet Generator Nikos Minadakis, ESWC 2014 Summer School, Crete 6
  7. 7. 7 Applica>ons 3/3 Ichthys Nikos Minadakis, ESWC 2014 Summer School, Crete 7
  8. 8. 8 • 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 Nikos Minadakis, ESWC 2014 Summer School, Crete 8
  9. 9. 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. Nikos Minadakis, ESWC 2014 Summer School, Crete 9
  10. 10. 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 Nikos Minadakis, ESWC 2014 Summer School, Crete 10
  11. 11. Simplified Data Schema Species Scien>fic_Name _Assignment assignedDate xsd:string xsd:string xsd:dateTime Actor name Ecosystem_ Environment is_introduced_at Water_Area is_bio>cally_related_to Country CommonName name xsd:string is_used_in xsd:string Bibliography Resource xsd:string xsd:string xsd:string authorName >tle hasLanguage Ecosystem_Typ e has_type Nikos Minadakis, ESWC 2014 Summer School, Crete 11
  12. 12. Simplified Data Schema tloCore: LT5_usually_is_predator_of tloCore: BT27_Species tloCore: BC46_1_Scien>fic_ Name_Assignment tloimarine :assignedDate xsd:string xsd:string xsd:dateTime tloCore: BC8:Actor tloimarine: name tloCore: BC14_Ecosystem_ Environment tloimarine: LX14_is_introduced_at tloCore: BC15_Water_Area tloCore: BC4_2_Country tloimarine: LX10_is_bio>cally_related_to tloimarine: CommonName tloimarine :name xsd:stri ng tloimarine :is _used_in xsd:stri ng tloimarine: Bibliography Resource xsd:string xsd:string xsd:string tloimarine:authorName tloimarine:>tle tloimarine:hasLanguage tloCore: BT7_Ecosystem_Type tloCore:LX3_has_type Nikos Minadakis, ESWC 2014 Summer School, Crete 12
  13. 13. Naming usually_is_predator_of Species Scien>fic_Name _Assignment assignedDate xsd:string xsd:string xsd:dateTime Actor name is_bio>cally_related_to Country CommonName name xsd:string is_used_in hasLanguage xsd:string Nikos Minadakis, ESWC 2014 Summer School, Crete 13
  14. 14. 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$on> ?x . ?x rdf:type tloimarine:CommonName . ?x tloimarine:name ?commonName . } Nikos Minadakis, ESWC 2014 Summer School, Crete 14
  15. 15. Example Query: Results commonName A'ahi A'ahi hae A'ahi mapepe A'ahi maueue A'ahi 'oputea A'ahi 'opu$'i A'ahi patao A'ahi tari'a'uri A'ahi tatumu A'ahi teaamu A'ahi $amatau A'ahi vere Ahi Albakor Albakora Albakora Albacor Albacora Nikos Minadakis, ESWC 2014 Summer School, Crete 15
  16. 16. Species DistribuDon and Predators usually_is_predator_of Species Ecosystem_ Environment is_introduced_at Water_Area Country Ecosystem_Typ e has_type Nikos Minadakis, ESWC 2014 Summer School, Crete 16
  17. 17. Bibliographic Resources Species Bibliography Resource is_about_type xsd:string xsd:string xsd:string >tle Nikos Minadakis, ESWC 2014 Summer School, Crete 17
  18. 18. Queries 1-­‐13 1. Return all the species 2. Return 17 predators 3. Return the species that are predators or preys 4.* Return all the informa$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$ty#Japan> Nikos Minadakis, ESWC 2014 Summer School, Crete 18
  19. 19. Queries 14-­‐21 14.** Does Thunnus albacares live in Japan? 15.* Return the common names of Thunnus albacares and the language they are expressed in. Return also the countries where those names are used if this informa$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> Nikos Minadakis, ESWC 2014 Summer School, Crete 19

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