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21 Οκτ 2013 (πριν από 3 χρόνια και 5 μήνες)

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Urmas

Kõljalg
: Data sources (WP1)

Task 1.1 Assessment and evaluation of biodiversity data sources

Lead UTARTU;
MfN
, UEF, UFZ, SGN, HCMR, BGBM, UCPH, MRAC,
Plazi
, NRM,IBSAS, EBCC,
NBIC, WCMC;

The evaluation will assess important data characteristics, such as
coverage, accessibility, quality, and format. Targeted data types 1) remote
sensing data (incl. derived products e.g. vegetation and habitat maps,
habitat classification schemes); 3) taxonomic backbone data; 4) ecological
data; 5) specimen data from scientific collections; 6) species profile data,
including descriptions and functional traits, conservation status,
distribution and abundance data; 7) DNA sequence data.

Urmas

Kõljalg
: Data sources (WP1)

Task 1.2 Harmonization of European taxonomic backbone and


analysis of taxonomic coverage

Lead BGBM;
MfN
, UTARTU, UEF, UFZ, SGN, FIN, HCMR, UCPH, MRAC,
Plazi
, NRM,
IBSAS, NBIC

A unified taxonomic backbone will be built on the Pan
-
European Species directories
Infrastructure (PESI, www.eu
-
nomen.eu), and harmonized with ongoing attempts towards
a global Catalogue of Life (
CoL
). This task will integrate the Fauna
Europaea

and
Euro+Med

PlantBase

databases into the EDIT Platform for
Cybertaxonomy
, set up a mechanism for
regular updates, develop a full set of GEO BON and
LifeWatch

compliant services for
integration of taxonomic backbone data into the overall EU BON framework, and integrate
these services with INSPIRE conformant national data sources that include taxonomic
names.

Urmas

Kõljalg
: Data sources (WP1)

Task 1.3 Gap analysis of available biodiversity information sources and


identifying priorities

Lead
MfN
; UTARTU, GBIF, FIN, BGBM, MRAC, WCMC

Based on the assessments of data sources undertaken for task 1.1. and the review of
policy requirements in WP6 (task 6.1.), identified gaps in data coverage and quality for
different information layers will be evaluated against scientific interests and capacities in
the biodiversity information stakeholder communities, focusing at the European level.
Taxonomic, geographic, thematic, and other areas of bias will be analyzed in assessed
datasets and priority levels for closing gaps will be provided, also comparing European to
global level coverage.

Urmas

Kõljalg
: Data sources (WP1)

Task 1.4 Integrated approaches for focused biodiversity data mobilization

Lead NRM; UTARTU,
Pensoft
, BGBM, UCPH, MRAC,
Plazi
,
GlueCAD
, IBSAS, NBIC;

With this task, EU BON will advance data mobilization efforts targeting collection
-
based
and molecular data. In particular, three activities will be pursued:
i
) Through the open
-
source DINA initiative led by NRM to develop a web
-
based collection management
system, an integrated solution for digitizing, managing and mobilizing specimen data in
natural history collections will be developed. ii) The open access system JACQ (Virtual
Herbaria) for capturing botanical data will be integrated with other web services, to allow
increased participation of a significant number of European herbaria to feed their data
into GBIF,
BioCASE
, and other networks relevant for GEO BON. iii) For DNA and genomic
datasets, a set of web
-
based services, integrating distributional and molecular information
will be provided, also linking to molecular identification
.

Urmas

Kõljalg
: Data sources (WP1)

Task 1.5 Exploring citizen science


based approaches for mobilizing and


generating biodiversity data

Lead UTARTU;
MfN
,
Pensoft
, FIN, HCMR, UCPH,
Plazi
,
GlueCAD
, NRM, IBSAS, NBIC;

This task will explore the potentials of citizen science based approaches for biodiversity
assessment and monitoring, particularly for achieving more comprehensive data
coverage and towards future GEO BON developments. Using highly successful
technology
-
based citizen science recording schemes from EU BON partners and
associates, the status of citizen science and its links to curricula and environmental
education will be evaluated for best practice examples from at least five EU countries.
Elements for an action plan for pan
-
European citizen science networking for biodiversity
information will be developed, including supporting an education network that will
provide links to international and global initiatives and programs.

Data Integration and Interoperability

WP2

Hannu Saarenmaa

Objectives


Establish
an
information architecture
for the EU BON project that will be
compatible with the global GEO
BON, INSPIRE
, other European projects,
and the
LifeWatch

research infrastructure


Develop
data integration and interoperability between the various
networks, and with new generation of
data sharing
tools enhance linking
between
observational data, ecosystem monitoring data, and remote
sensing data


Develop
new web service interfaces for data holdings using state
-
of
-
the
-
art standards and protocols.
Register the
networks on the
GEOSS Common
Infrastructure

(GCI) using
harmonised

metadata


Develop
a new
portal

to enable fast access to EU BON integrated data and
products by researchers,
decision
makers
and other stakeholders


Ensure
global coordination
of development efforts through an
international data interoperability task force
and adoption
of the results
through helpdesk and a comprehensive training
programme

Backdrop:
GEO BON wants to achieve
an operational system by 2015


What do we mean by “operational”?


data flow from observations through various
aggregation and processing services,

end
-
to
-
end to Essential Biodiversity Variables
(EBV) and indicators;


automated and streamlined, as appropriate;


using a plug
-
and
-
play service
-
oriented approach;


coordinated through the GEO BON registry system
and linked to the GEOSS Common Infrastructure;


transparent to users through portals.


Occurr
ence

Analysable
dataset

Obser
-

vation

Specimen

Taxonomy

Eco
-
logical

Analysable
dataset

Plot

Individual

Measurem
ent

Geo
-
spatial

Analysable
dataset

Scenarios

Remote
sensing

In Situ

Eco
-
System
Services

Analysable
dataset

Surveys

Spatial
data

National

Statistics

EBV
-
1

EBV
-
2

EBV
-
x

Indicator
-
1

Indicator
-
2

Processing
service
-
1

Processing
service
-
3

GEOSS &

GEO BON

Registries

Processing
service
-
2

Other

inputs

Streamlined data flow, end
-
to
-
end

Integration

EU BON WP2 Deliverables

1.
Review (January 2014)


Design of information architecture


Review of data standards

2.
New data sharing tools (2014/2015)

3.
Registry and metadata catalogue
(2014/2015)

4.
Portal (2015/2016)

5.
A
ssessment
of training
activities (2016)

EU BON WP2 Milestones in year 1


A global Informatics Task force


Invited (March)


First meeting (May/June)


Helpdesk opened (April)


Review


Draft outlines (May)


Deliverable (January 2014)


Initial informatics workshop (May/June)


Specifications for data sharing tools (January)


First training workshop (January)

GEOSS

Clearinghouses

GEO

Web Portals

GEOSS Common

Infrastructure

Components

& Services

Standards and

Interoperability

Best Practices

Wiki

User
Requirements

Registries

Main GEO

Web Site

Registered Community
Resources

Community

Portals

Client

Applications

Client Tier

Mediation Tier

Community

Catalogues

Alert

Servers

Workflow

Management

Processing

Servers

Access Tier

GEONETCast

Product Access

Servers

Sensor Web

Servers

Model Access

Servers

Test

Facility

Mediation

Servers

CSW

WMS

CSW

W*S

WMS

WFS

WFS

SOS

SAS

SPS

W*S

CSW

WPS

CSW

WMS

CSW

GEOSS
Infrastructure Components

Task 2.1 Design of information
architecture for EU BON


Starting
from the information architectures of relevant infrastructures,
i.e., GBIF, LTER, GEOSS, GEO BON
,
LifeWatch
, and INSPIRE,
adopt a
coherent architecture

that will guide the development, integration
and
interoperability
efforts within the EU BON project.


The
architecture will highlight the
relevant
components
of
registry, portal,
semantic mediation, workflows, and e
-
services as envisaged in the GEO
BON
Detailed Implementation
Plan and open access as recommended by
the GEOSS Data Sharing Principles.


Link
to
, and
adopt informatics components and approaches of other
relevant EU projects.


The
task will
address heterogeneity
of projects and networks by ensuring
that the developments of EU BON can be
migrated
to permanent
infrastructures
.


In
particular, the architecture will map GCI components to European and
global
biodiversity infrastructure.


(
Lead CSIC; UTARTU, UEF, GBIF, MRAC,
GlueCAD
, IBSAS, NBIC,
TerraData
;
Months
4
-
14)

Task 2.2 Improving data standards and
interoperability


Starting
from the GEO BON Detailed Implementation Plan and the
architecture (task 2.1) as well as
relevant European
projects
(
ALTERNet
, EBONE,
LifeWatch
),
review the state
-
of
-
the
-
art
and
needs for
improvement of
the current data standards of TDWG,
OGC,
BioCASE
, GBIF, LTER
-
Europe, PESI, and INSPIRE.


Consider how
the available protocols and mechanisms for
interoperability can be best used for
integrating

different data
layers (i.e., genetic data, primary occurrence data, monitoring data,
ecological measurements,
remote sensing
data) in the European
context.


Consider
reasons for
heterogeneity

of biodiversity information and
make recommendations
for use of standards by the various
networks.


(
Lead GBIF; UTARTU, UEF, CSIC,
Pensoft
,
MRAC
,
Plazi
,
GlueCAD
,
INPA, IBSAS, NBIC,
TerraData
;
Months
4
-
51)

Task 2.3 Tools for data sharing


This
task will work with international partners (task 2.7) to
scope
the requirements and build new releases
of data
sharing tools for
relevant data providers.


These
open source tools implement the selected
interoperability
mechanisms
(task 2.2) and data publishing mechanisms (task 8.5)
for use by the relevant networks, and
provide registration
and
query functions towards the GCI.


As
the basis of development,
existing tools
for
metadata,
occurrence
data and ecological data from GBIF and LTER will be
used.


New
tools for sharing
habitat data
will
be investigated
.


A
model for distributed development will be adopted.


(
Lead MRAC; UTARTU, UEF, GBIF,
Pensoft
,
Plazi
,
GlueCAD
, INPA,
IBSAS; Months 9
-
51)

Task 2.4 Metadata registry and
catalogue


Building
on the existing GBIF and LTER registry and metadata
catalogues, an
enhanced and
integrated metadata
system
will be
developed for EU BON.


The
various entities such as networks, projects, sites,
and datasets
identified in the analysis and
mobilization

efforts of WP1 will be
described in the new registry/catalogue.


The entity descriptions should include
web service interfaces
or
other access points, and will also
be registered
at the GCI and other
indexing services.


In
order to overcome heterogeneity of data,
accommodate
multilingualism
, enhance discoverability and interoperability, and
facilitate querying in portals, the use
of
Knowledge
Organisations

Systems

(KOS; e.g., thesauri) will be explored.


(
Lead GBIF; UEF, CSIC,
Pensoft
, MRAC
, INPA, IBSAS; Months 9
-
51)

Task 2.5 European Biodiversity Portal


A
European Biodiversity Portal (EBP) will be developed as the main GEO
BON
information hub
.


It
will link
to relevant
databases and information systems, policy contacts
and recommendations, and structured
advice for
assessing relevant
distributed information/datasets for different user groups, including
contributions
from citizen
science data gathering gateways.


The
EBP will technically integrate the various data sources under
one
search
facility

and spatially/temporally oriented user interface.


The
portal will build on the tools developed
by task
2.3, functions
developed by task 2.4.


It
will provide
access

to full detailed data, geographic
visualisation
, and
remotely sensed data. It will be closely linked to the GCI and GEO Portal,
and access layers and data
from GEOSS
sources.


The
portal would also act as
showcase for the products
from the
analytical and
modelling

activities
of other WPs and
support workflows
for building such products using the registered e
-
services.


The portal
will also serve general dissemination functions for WP8.


(
Lead CSIC; UEF, GBIF,
UnivLeeds
,
Pensoft
,
FIN
, MRAC,
Plazi
,
GlueCAD
,
NBIC; Months 1
-
54)

Task 2.6 Technical support and
helpdesk


This
task will set up a
technical coordination unit
and helpdesk for
European networks and for global outreach
as envisaged
in the GEO BON
Detailed Implementation Plan.


The
helpdesk will also support developments in
other WPs
, and will play a
key role in reviewing all design documents, testing the developments and
giving
feedback to
developers.


The
helpdesk will actively promote and assist national BONs and other
users in installing
and using
the tools that enable the interoperability
mechanisms (task 2.3).


It
will promote open access and
assist in
registering EU BON services at
the GCI, and help populating the portal with content from other WPs
and
partners
.


The
helpdesk facility will be set in place in collaboration and synergy with
the common
Helpdesk platform
of the MRAC, which is currently active for
six projects.


(
Lead MRAC; UEF,
Pensoft
; Months 4
-
54)

Task 2.8 Training programme


This
task will develop and operate a training

programme

in data and
metadata integration strategies, use
of standards
, and use of data tools,
within the EU BON consortium and beyond, thereby contributing also to
WP8 and
the long term impact of the project.


The
training events
will start with introduction courses and will first
target
the
consortium members.

As
the project evolves and the tools become
available the trainings will target
also external
users.
The
plan is to invite
stakeholders from and beyond Europe. We target an audience up to
25
participants
per event
.


The
training
programme

will be organized
in collaboration with the DEST
(the
Distributed European
School of Taxonomy) set up under the European
project EDIT and currently maintained by RBINS
, MRAC
and NBGB.
Initially
mainly dedicated to taxonomy courses, the scope has now been
broadened to
other biodiversity
and environment related training
activities (http://www.taxonomytraining.eu/).


(
Lead MRAC; UEF
,
Pensoft
; Months 4
-
54)

Task 2.7 Informatics task force and
global cooperation


In
order to ensure integration of the various initiatives and
reduction of heterogeneity of biodiversity information
, EU
BON will
need to
liaise broadly
on technical issues.


In
this task an informatics and data standards
task force
and
advisory board will be organized and operated.


In
particular, the task will cooperate with, and
build on
technical
solutions developed by the
LifeWatch

infrastructure and several FP7
infrastructure projects
for biodiversity
.


Close
and
regular contact with the GEOSS Infrastructure
Implementation Board

and the GEO
BON Steering
Committee will
be ensured.


It
will also be necessary to link to and cooperate with related
initiatives in
other parts of the world
, such as ALA,
DataOne
,
regional BONs, etc), and help to ensure their compatibility.


(Lead UEF;
MfN
, GBIF, CSIC, MRAC, IBSAS, NBIC; Months 4
-
54)

Summary


EU BON WP2 aligns very closely to GEO BON
WG8


global task force will ensure this


We have a lot to learn on how to be part of
the GEOSS Common Infrastructure


We need to pilot structure and function for
LifeWatch


We will need to build on tools already being
worked on in the community


LifeWatch

Component Architecture

Some Generic Data Standards,
Interoperability Requirements, and Tools

XYZ, t, P

XY,

t
,

P

XYZ
,

t
, P/ B

NetCDF

S
-
DB

O&M

MetaCat

NetCDF

WFS, WMS, …

SOS

EML, CSV

XYZ, t, P/ B


Multi
-
dimensional

Traditional Spatial

Signals

Ecosystem

GBIF IPT

EML,
DwC

XYZ, T, Tx


Occurrence

GenBank

FTP/ ASN.1

XYZ, T, Al


Genome

EML

ISO 19115/p2

FGDC

Meta
-
Data Landscape

Dublin Core

Darwin Core

OPeNDAP
/

NetCDF
/ HDF
-
5

Semantic Web / Linked Open Data

What is the role of a portal in a

Service Oriented Architecture?

Project
-
ware

Pre
-
GBIF

SOA

LifeWatch
, GEOSS, SEIS

EAI

GBIF


and in distributed communities?

source:Sam Gentile

Service Architecture

Service

Service

Service

Service

Ecosystem Services

Remote sensing

Ecological measurements

Occurrence

Service virtualizes how that capability is
performed, and where and by whom the
resources are provided, enabling multiple
providers and consumers to participate
together in shared business activities.

Multiple Service Consumers

Multiple Business Processes

Multiple Discrete Resources

Multiple Service Providers

source:TietoEnator AB, Kurts
Bilder

Biodiversity science

SOA structures the business and its systems as a set
of capabilities that are offered

as Services, organized into a Service Architecture

Shared

Services

A Service Centric Portal