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

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. 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. 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. 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. Seman$c
post-­‐processing
of
search
results
5
Applica>ons
1/3
Nikos
Minadakis,
ESWC
2014
Summer
School,
Crete
5

6. 6
Applica>ons
2/3
Fact
Sheet
Generator
Nikos
Minadakis,
ESWC
2014
Summer
School,
Crete
6

7. 7
Applica>ons
3/3
Ichthys
Nikos
Minadakis,
ESWC
2014
Summer
School,
Crete
7

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. 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. 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. 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. 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. 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. 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. 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. 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. Bibliographic Resources
Species
Bibliography
Resource
is_about_type
xsd:string
xsd:string
xsd:string
>tle
Nikos
Minadakis,
ESWC
2014
Summer
School,
Crete
17

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. 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