On the 22 July 2014, OpenChannels.org and the EBM Tools Network, two of the premier sources of information about coastal and marine planning and management tools in the United States and internationally, hosted the iMarine webinar: iMarine Data e-Infrastructure Initiative for Fisheries Management and Conservation of Marine Living Resources. The webinar focused on the presentation of the iMarine initiative and its powerful data e-infrastructures and services, followed by a presentation of a set of use cases related to Geospatial Analysis, Ecology, Biodiversity and Life History Traits. The presentations were given by Pasquale Pagano, CNR-ISTI and iMarine Technical Director and Gianpaolo Coro, CNR-ISTI. Watch the video of the webinar here https://www.youtube.com/watch?v=lgf30BPyBbk

1. iMarine
Data
e-­‐Infrastructure
Ini$a$ve
for
Fisheries
Management
and
Conserva$on
of
Marine
Living
Resources
Data access, harmonization, analysis, and
management platform
Pasquale
Pagano
(CNR)
iMarine
Technical
Director
pasquale.pagano@is$.cnr.it
22
July
2014
Open
Channel
Webinar
Gianpaolo
Coro
(CNR)
iMarine
Data
Analyst
gianpaolo.coro@is$.cnr.it

2. Pasquale
Pagano
• Master
Degree
in
Computer
Science
• Ph.D
in
Informa$on
Engineering
on
Distributed
Systems
• it.linkedin.com/in/pasqualepagano/
Gianpaolo
Coro
• Master
Degree
in
Physics
-­‐
Cyberne$cs
• Ph.D
in
Computer
Science
• it.linkedin.com/pub/gianpaolo-­‐coro/16/665/b5a
2
iMarine
-­‐
Just
an
overview

3. Concepts
iMarine
-­‐
Just
an
overview
The
ini=a=ve
(the
visionary
leadership)
The
e-­‐infrastructure
(the
opera$onal
plaUorm)
The
system
(the
enabling
sw
system)
3

4. THE
INITIATIVE
Distinguishing capabilities of the iMarine initiative
iMarine
-­‐
Just
an
overview
4

5. iMarine
Objec$ve
5
iMarine
-­‐
Just
an
overview
Launch
an
Ini$a$ve
aimed
at
establishing
and
opera$ng
a
data
Infrastructure
suppor$ng
the
principles
of
the
Ecosystem
Approach
to
Fisheries
Management
and
Conserva=on
of
Marine
Living
Resources
Nov
2011
Sept
2014
Apr
2016

6. Address
system
harmoniza$on
6
iMarine
-­‐
Just
an
overview
VLIZ
IOC
FIN
CRIA
IRD
FAO
T2
MyOcean
SeaDatanet
Other
sources
FIGIS
Fisheries
Ocean
environment
Biodiversity
ESTAT
DG-­‐MARE
Na$onal
DOF
Ecoscope
ICES
RDB
Taxonomy
Emodnet
Biology
WORMS
OBIS
Aquamaps
Niche
modelling
algorithms
Open
Source
so^ware
Open
SDMX
-­‐
CLM
SDMX
GBIF
EoL
NEAFC
FishBase
Courtesy
by
Marc
Taconet
(FAO)

7. Role
of
the
iMarine
Board
• Mobilize
user
community
– Core
set
of
influen$al
partners
mobilized
to
work
on
two
main
business
cases:
Support
to
implementa=on
of
the
EU
Common
Fishery
Policy
Support
to
FAO’s
deep
seas
fisheries
programme
• Develop
governance
model
– Public
partnerships
– Policies
–
data
sharing
–
so^ware
sharing
• Address
systems’
harmoniza$on
– Ra$onalize
solu$ons
among
partners
(cost
efficiency)
– Agree
on
“iMarine”
standards
iMarine
-­‐
Just
an
overview
•
FAO
•
DG
MARE
•
Eurostat
•
NEAFC
•
MEDDE/DOF
•
IRD
•
ICES
•
IOC/OBIS
•
FIN
•
CRIA
•
VLIZ
•
T2/GENESI-­‐DEC
Environment
Biodiversity
Fisheries
7

8. THE
INFRASTRUCTURE
Distinguishing capabilities of the iMarine e-
infrastructure and its enabling software
iMarine
-­‐
Just
an
overview
8

9. Concepts
and
Defini$ons
iMarine
-­‐
Just
an
overview
9

10. The
D4Science
infrastructure
iMarine
is
exploi$ng
a
Hybrid
Data
Infrastructure
combining
over
500
so^ware
components
into
a
coherent
and
centrally
managed
system
of
hardware,
so^ware,
and
data
resources.
iMarine
-­‐
Just
an
overview
10

11. Born
from
the
user
needs
11
iMarine
-­‐
Just
an
overview
I
need
to
host
my
applica$ons
in
a
secure
and
scalable
environment
I
need
to
maintain
my
database
I
need
to
backup
my
data
I
need
to
securely
delivery
my
data
to
a
set
of
known
people
I
want
to
offer
a
flexible
sharing,
storage,
repor$ng,
search
and
retrieval
tool

12. Born
from
the
user
needs
12
iMarine
-­‐
Just
an
overview
I
need
to
manage
and
analyze
biological
and
ecological
data
I
need
to
manage
the
full
data
life-­‐cycle
from
import
to
valida$on,
cura$on,
harmoniza$on
and
publica$on
I
need
to
offer
to
my
team
a
powerful
tool
to
manage
code-­‐lists
I
need
to
store
and
analyze
geospa$al
explicit
informa$on
I
need
to
reduce
the
costs
of
data
maintenance
of
my
dept.

13. Born
from
the
user
needs
13
iMarine
-­‐
Just
an
overview
I
need
to
access
authorita$ve
biological
and
ecological
data
I
need
to
simplify
the
access
to
my
geospa$al
data
I
need
to
mash-­‐up
sta$s$cal
and
biodiversity
data
I
need
to
validate
my
datasets
and
provide
a
standard
access
to
them
I
need
to
analyse
my
big
datasets

14. User
Needs
Analysis
14
iMarine
-­‐
Just
an
overview
• Needs
– Not
isolated
– Not
disconnected
– Not
trivial
• Solu$ons
– Actual
and
with
an
eye
to
the
future
– Designed
for
individuals
and
looking
at
the
community

15. iMarine
e-­‐infrastructure
iMarine
is
exploi$ng
D4Science.org
iMarine
-­‐
Just
an
overview
15
Geographically
Distributed
Compu$ng
Infrastructure
Across
administra$ve
boundaries
Across
private
and
commercial
providers
Service
Alloca$ons,
Deployment,
Monitoring,
and
Opera$on
Uniform
resource
and
data
access
Opera$on
Built
on
SLAs
Support
monitoring,
audi$ng,
repor$ng,
and
no$fica$on
Trust
Privacy,
governance,
and
apribu$on
Security,
trusted
network

16. Infrastructure:
key
characteris$cs
• Efficient
and
tailored
storage
technologies
• Computa=onal
environments
dealing
with
the
volume
of
the
data
• Elas=c
management
of
the
resources,
monitoring,
aler$ng,
recovery
• Collabora=ve
environment
to
support
scien$fic
communi$es
• Rich
porQolio
of
applica=ons
to
perform
access,
valida$on,
enriching,
processing,
sharing,
and
mash-­‐up
of
data
iMarine
-­‐
Just
an
overview
16

17. Capaci$es:
Storage
as
Service
17
iMarine
-­‐
Just
an
overview
to
host
and
maintain
data
Database
High-­‐availability
Standard
Ready-­‐to-­‐use
Cloud
Storage
Scalable
Reliable
Secure
Geographical
DB
Scalable
OGC
Standard
Privacy
and
AEribuFon

18. Capaci$es:
Compu$ng
as
Service
18
iMarine
-­‐
Just
an
overview
to
process
and
extract
knowledge
Scalable
Easy
to
Manage
Across
Boundaries
Tailored
Elas<c
Assignment
of
CompuFng
Assignment
of
Processors
Virtual
Research
Environment
Rich
and
Heterogeneous
High
Throughput
Map-­‐Reduce
Parallel
R

19. Applica$ons
as
a
Service
19
iMarine
-­‐
Just
an
overview
to
curate
and
manage
data
Metadata
Genera<on
GeospaFal
Data
Biodiversity
Data
StaFsFcal
Data
Harmoniza<on
Disambiguate
Validate
Integrate
and
Consistency
Check
Data
Exchange
OGC
protocols
DarwinCore
SDMX

20. THE
APPLICATIONS
CATALOGUE
Distinguishing capabilities of the iMarine catalogue
of applications
iMarine
-­‐
Just
an
overview
20

21. Management
and
interpreta$on
of
biological
and
ecological
data
in
the
environment
Complete
full
life-­‐cycle
data
framework,
from
observa$onal
data
to
aggregated
data
repositories
enriched
with
valida$on
and
analy$cal
tools
Storage
and
interpreta$on
of
geospa$al
explicit
informa$on,
including
WPS
processing
Flexible
sharing,
storage,
repor$ng,
search
and
retrieval,
aggrega$on
and
projec$on
facili$es
Applica$ons
as
a
Service
iMarine
-­‐
Just
an
overview
A
BUNDLE
is
a
set
of
services
and
technologies
grouped
according
to
a
family
of
related
tasks
for
achieving
a
common
objec$ve
21

22. Occurrence
and
Taxonomic
Data
Discovery
Occurrence
Data
Processing
Species
Distribu=on
Modeling
Species
Distribu=on
Maps
Discovery
Taxonomic
Data
Comparison
Taxonomic
Data
Matching
Code
List
Discovery
Code
List
Management
Sta=s=cal
Engine
Tabular
Data
Discovery
Tabular
Data
Enrichment
Tabular
Data
Management
Tabular
Data
Processing
Geospa=al
Data
Discovery
Geospa=al
Data
Processing
Enhanced
Documents
Management
Fact-­‐sheets
Management
Informa=on
Object
Discovery
Messaging
Shared
Workspace
Social
Networking
Facili=es
Applica$ons
as
a
Service
22
iMarine
-­‐
Just
an
overview
A
BUNDLE
is
a
set
of
services
and
technologies
grouped
according
to
a
family
of
related
tasks
for
achieving
a
common
objec$ve

23. THE
DATA
CATALOGUE
Distinguishing capabilities of the iMarine catalogue
of applications
iMarine
-­‐
Just
an
overview
23

24. iMarine
OBIS
WoR
MS
WoR
DS
GBIF
CoL
ITIS
IRMN
G
NCBI
MyOc
ean
WOA
EuroS
tat
Data.
FAO
…
Data
24
iMarine
-­‐
Just
an
overview
iMarine
Registries
Valida=on
Enriching
Processing
Sharing

25. Data
Ontologies
and
Data
Warehouses
Biological
and
Ecological
Data
GeoSpa$al
Data
Sta$s$cal
Data
Documents
iMarine
-­‐
Just
an
overview
DarwinCore
/
ISO19139
>35
M
Observa$ons
(OBIS)
≈
120
K
Observed
Species
(OBIS)
≈
500
K
Taxa
(WoRMS)
>600
K
Scien$fic
Names
(ITIS)
>12
K
Species
Maps
(AquaMaps)
≈
600
Species
Extent
(FAO)
…
FishBase,
SeaLifeBase
…
CoL,
GBIF
SDMX
*
Ø FAO
CodeLists
Ø IRD
CodeLists
Ø FAO
datasets
Ø Eurostat
Ø …
ISO19139
(OGC
W*S)
Ø 15
years
Chemical
and
Physical
variables
in
2D
space
Ø Ice
concentra$on
and
velocity,
Chlorophyll,
Oxygen,
Nitrate,
Phosphate,
Phytoplankton
as
carbon,
Salinity,
Temperature,
…
Ø On-­‐demand
Chemical
and
Physical
variables
in
3D
space
Ø Apparent
Oxygen
U$liza$on,
Dissolved
Oxygen,
Salinity,
Temperature,
…
>
450
variables
25
OAI-­‐PMH,
OpenSearch
Ø FAO
Facksheets
Ø Aqua$c
Commons
Ø Bioline
Interna$onal
Ø Biodiversity
Heritage
Ø OceanDocs
Ø Nature,
PenSo^
Journals
Ø …
RDF,
OWL
Ø FAO
FLOD
Ø Marine
Top
Level
Ontology
Ø IRD
Ecoscope
Ø FactForge,
Yago2
Ø …

26. THE
COLLABORATIVE
ENVIRONMENT
Distinguishing capabilities of the iMarine
collaborative environment
iMarine
-­‐
Just
an
overview
26

27. Is
this
enough?
• An
ecosystem
of
par$cipatory
data
e-­‐
Infrastructures
• Regulated
by
policies
• Enabled
by
standards
• Promo$ng
not
only
access
but
mash-­‐up
of
heterogeneous
data
iMarine
-­‐
Just
an
overview
User
centric
27

28. Virtual
Research
Environment
iMarine
is
user-­‐centric
and
workflow-­‐oriented
thanks
to
the
gCube
VRE
technology
Virtual
Research
Environment
(VRE)
is
• a
distributed
and
dynamically
created
environment
• where
subset
of
data,
services,
computa$onal,
and
storage
resources
• regulated
by
tailored
policies
• are
assigned
to
a
subset
of
users
via
interfaces
• for
a
limited
=meframe
• at
li_le
or
no
cost
for
the
providers
of
the
par$cipatory
data
e-­‐infrastructures
iMarine
-­‐
Just
an
overview
L.
Candela,
D.
Castelli,
P.
Pagano
(2013)
Virtual
Research
Environments:
An
Overview
and
a
Research
Agenda.
Data
Science
Journal,
Vol.
12
28
e-­‐Infrastructure
VRE
VRE
VRE

29. Virtual
Research
Environment
29
iMarine
-­‐
Just
an
overview
to
share
and
collaborate
Share
Database
Tables
Workflow
Files
Communicate
Post
Favourite
ConnecFon
Organize
Dynamic
VRE
CreaFon
Secure
Policy
Control

30. Infrastructure:
Collabora$ve
Environment
iMarine
-­‐
Just
an
overview
A
single
place
to
• Get
status
and
updates
from
applica$ons
and
other
users
they
are
interested
in;
• Get
no$fica$ons
about
messages,
jobs
comple$on,
new
generated
products,
etc.
30
Share
Updates
User
news
feed
VREs
user
is
member
of

31. Infrastructure:
Collabora$ve
Environment
iMarine
-­‐
Just
an
overview
A
single
place
to
• Get
status
and
updates
from
applica$ons
and
other
users
they
are
interested
in;
• Get
no$fica$ons
about
messages,
jobs
comple$on,
new
generated
products,
etc.
Feeds from
Applications
FeedfromUsers
31

32. Infrastructure:
Collabora$ve
Environment
iMarine
-­‐
Just
an
overview
A
single
place
to
• Manage
data,
store
and
preserve
them
• Share
data
32

33. THE
SOFTWARE
Distinguishing capabilities of gCube software
iMarine
-­‐
Just
an
overview
33

34. iMarine
Technology
• iMarine
is
powered
by
gCube
iMarine
-­‐
Just
an
overview
34
openhub.net

35. USE
CASES
Few examples of the analytics capabilities
iMarine
-­‐
Just
an
overview
35

36. Geospa$al
Analysis
Ecology
Biodiversity
Life
History
Traits
Prac$cal
Examples
iMarine
-­‐
Just
an
overview
36

37. Geospa$al
Analysis
iMarine
-­‐
Just
an
overview
37

38. Rasteriza$on
A
polygonal
map
is
transformed
into
a
raster
map
or
into
a
point
map
iMarine
-­‐
Just
an
overview
38

39. Maps
Comparison
compare
Compares
:
• Species
Distribu$on
maps
• Environmental
layers
• SAR
Images
iMarine
-­‐
Just
an
overview
39

40. Periodicity
and
Seasonality
Periodicity:
12
months
Extrac=on
Tools
Fourier
Analysis
iMarine
-­‐
Just
an
overview
40

41. Environmental
Signal
Processing
Resampling
Spectrogram
iMarine
-­‐
Just
an
overview
41

42. WaterHeight
Column
Given
a
layer
containing
3D
environmental
informa$on
• Extract
the
environmental
informa$on
along
Z
given
X,Y,T
at
resolu$on
R
• Produce
charts
and
ranges
iMarine
-­‐
Just
an
overview
42

43. iMarine
-­‐
Just
an
overview
43
Ecology

44. Niche
Modelling
• AquaMaps
–
Suitable
Habitat
• AquaMaps
–
Na$ve
Habitat
• AquaMaps
for
2050
Scenario
• Ar$ficial
Neural
Networks
Gadus
morhua
AquaMaps
-­‐
Suitable
Habitat
iMarine
-­‐
Just
an
overview
44

45. Outliers
Detec$on
Presence
Points
Density-­‐based
Clustering
and
Outliers
detec$on
Distance
Based
Clustering
K-­‐Means
X-­‐Means
DBScan
Cetorhinus
maximus
iMarine
-­‐
Just
an
overview
45

46. iMarine
-­‐
Just
an
overview
46
Biodiversity

47. Climate
Changes
Effects
on
Species
Es$mated
impact
of
climate
changes
over
20
years
on
11549
species.
Pseudanthias
evansi
The
occupancy
by
the
Pseudanthias
evansi
decreases
in
Area
71
but
increases
in
Area
77
Bioclimate
HSpec
Overall
occupancy
in
=me
iMarine
-­‐
Just
an
overview
47

48. Similarity
between
habitats
Habitat
Representa$veness
Score:
1. Measures
the
similarity
between
the
environmental
features
of
two
areas
2. Assesses
the
quality
of
models
and
environmental
features
HRS=10.5
Habitat
Representa$veness
Score
La$meria
chalumnae
iMarine
-­‐
Just
an
overview
48

49. Occurrence
Data
from
GBIF
Occurrence
Data
from
Obis
∩
Intersec=on
-­‐
Difference
ᴜ
Union
A
x,y
Event
Date
Modif
Date
Author
Species
Scien=fic
Name
Occurrence
Points
B
x,y
Event
Date
Modif
Date
Author
Species
Scien=fic
Name
Records
Similarity
DD
Duplicates
Dele=on
iMarine
-­‐
Just
an
overview
49

50. BiOnym
A
flexible
workflow
approach
to
taxon
name
matching
Accounts
for:
• Varia$ons
in
the
spelling
and
interpreta$on
of
taxonomic
names
• Combina$on
of
data
from
different
sources
• Harmoniza$on
and
reconcilia$on
of
Taxa
names
Raw
Input
String
Gadus
morua
Lineus
1758
Correct
Transcrip$on:
Gadus
morhua
(Linnaeus,
1758)
Preprocessing
And
Parsing
Taxon
name
Matcher
1
Taxon
name
Matcher
2
Taxon
name
Matcher
n
PostProcessing
Reference
Source
(ASFIS)
Reference
Source
(FISHBASE)
Reference
Source
(WoRMS)
Reference
Source
(Other
in
DwC-­‐A)
iMarine
-­‐
Just
an
overview
50

51. Trendylyzer
-­‐
Recognize
Big
Changes
in
Species
Presence
• Fill
some
knowledge
gaps
on
marine
species
• Account
for
sampling
biases
• Define
trends
for
common
species
Plankton regime shift
Herring recovered after the fish ban
iMarine
-­‐
Just
an
overview
51

52. iMarine
-­‐
Just
an
overview
52
Life
History
Traits

53. 𝑊= 𝑎​ 𝐿↑𝑏
Calculate
the
a
and
b
parameters
for
14
230
species
by
means
of
Bayesian
Methods
Length-­‐Weight
Rela$onships
Approach:
Ø Collabora$ve
development
with
the
final
user
Ø Integra$on
of
user’s
R
Scripts
Ø Usage
of
parallel
processing
for
R
Scripts
Ø Periodic
runs
bluewatermag.com.au
Ø The
por$ng
to
the
D4Science
Sta$s$cal
Manager
allowed
to
run
the
scripts
in
distributed
fashion
Ø The
$me
reduc$on
was
from
20
days
to
11
hours!
95.4%
reduc=on
iMarine
-­‐
Just
an
overview
53

54. Safe
Biological
Limits
of
Large
Stocks
Re-­‐es$mated
SSB
limit
Re-­‐es$mated
HS
Rule-­‐
based
HS
Re-­‐es$mated
precau$onary
limit
Es=mate
biological
limits
for
50
Northeast
Atlan=c
fish
stocks
Ø Use
real
measures
Ø Rely
on
previous
expert
knowledge
Ø Use
Bayesian
models
to
combine
informa$on
iMarine
-­‐
Just
an
overview
54

55. Resilience
vs
Produc$vity
of
a
Species
Best
Resilience
and
Produc$vity
pair
for
the
species
iMarine
-­‐
Just
an
overview
55

56. THE
WAY
TO
USE
IT
Distinguishing capabilities of the exploitation
models
iMarine
-­‐
Just
an
overview
56

57. Mul$-­‐tenant
Delivery
Model
Infrastructure
as
a
Service
• Dynamic
deployment
• Hos$ng
• Resource
Lifecycle
• Monitoring
• Accoun$ng
• Security
So^ware
as
a
Service
• BiolCube
• ConnectCube
• GeosCube
• StatsCube
PlaUorm
as
a
Service
• FeatherWeightStack
• SmartGears
• Applica$onSupportLayer
• SOA3
iMarine
-­‐
Just
an
overview
57

58. Landscape
D4Science
e-­‐Infrastructure
gCube
Framework
gCube
Apps
Discussion
www.i-­‐marine.eu
i-­‐marine.d4science.org
www.openhub.net/p/gCube
info@i-­‐marine.eu
iMarine
-­‐
Just
an
overview
58

59. Google
Analy$cs
iMarine
portal
iMarine
-­‐
Just
an
overview
59