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  

Nikos  Minadakis,  ESWC  2014  Summer  School,  Crete   8  

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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