EDIT General Meeting Carvoeiro, 23-25 January 2008

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12 nov. 2013 (il y a 7 années et 10 mois)

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EDIT General Meeting

Carvoeiro, 23
-
25 January 2008


EDIT General Meeting

Carvoeiro, 23
-
25 January 2008

EDIT

(Re) Visionary Taxonomy

The Internet Platform for Cybertaxonomy

Walter Berendsohn

EDIT General Meeting

Carvoeiro, 23
-
25 January 2008

Platform for Cybertaxonomy:


Long
-
term Vision

The Platform provides taxonomists with
tailored


full & efficient
data access


IT tools facilitating
fieldwork


IT tools for
data analysis


IT tools for assembly of
treatments

and makes the generation of
reusable data


and information an integral and
non
-

obstructive part

of the taxonomic work process

EDIT General Meeting

Carvoeiro, 23
-
25 January 2008

A new architecture


Towards decoupled components


Interoperability through the use of standard interfaces


Multiple components varying in complexity according to
user needs


Components may be (desktop or web) applications for
human users or a (web) services for machines


No single user interface



Adaptation to individual institutional IT preconditions


Gradual migration of existing installations, integration of
existing and future projects


Adaptable to new challenges, e.g. Life Watch

EDIT General Meeting

Carvoeiro, 23
-
25 January 2008

x

TDWG Ontology
Unversal Biodiversity Data Bus
RDF
Common Data Model
Transfer Objects
XML
EDIT Platform Components
Fieldwork
CDM-compliant systems
Personal Components
Taxonomic
EDI-T-Editor
CDM Store
(working copy)
Descriptive
CDM-compliant systems
...
Validation services
Names
References
Geo services
Distribution Maps
Occurrence Maps
BioGeomancer
Central Components
Software Tracker
find applications & services
Experts DB
agents, tax expertise
Virtual Library
metaLib, SFX, Drupal
collectio
n
BHL,
Libraries
BioCASe/Tax
specimens,types, ...
Catalogue of Life
names & taxa
Search Feeds (e.g. RSS)
Shibboleth
Identity Provider, SSO
Community Components
webpages, forum, blog
personal mashup
literature, bookmarks
file sharing
calendar, mailinglist
CDM Store
Remote API
Sync API
OAI-PMH
Annotation
RSS change
LSID
XML
XML
Scratch-
pads
(Drupal-Sites)
Dataportal
(Drupal)


...
...
collectio
n
CDM
Stores
GBIF
Converter services
Word Doc -> CDM
TDWG RDF -> CDM
Checklist -> CDM
TaxonX -> CDM
NEXUS -> CDM
TaXMLit -> CDM
...
EDIT General Meeting

Carvoeiro, 23
-
25 January 2008

Communities


Communities delimited
by focus on taxon, geo
-
graphy or application


Consist of 1 or more
taxonomists and 0 to
many technical
collaborators


Collaborative data
management

webpages, forum, blog
personal mashup
literature, bookmarks
file sharing
calendar, mailinglist
CDM Store
Remote API
Sync API
OAI-PMH
Annotation
RSS change
LSID
Scratch-
pads
(Drupal-Sites)
Dataportal
(Drupal)
EDIT General Meeting

Carvoeiro, 23
-
25 January 2008

Common Data Model (CDM)


Semantic and technical
specification covering all
core data areas


TDWG standards


Aim: all data in highly
standardised form


EDIT Scratchpads for
communication and less
stringent data collection

webpages, forum, blog
personal mashup
literature, bookmarks
file sharing
calendar, mailinglist
CDM Store
Remote API
Sync API
OAI-PMH
Annotation
RSS change
LSID
Scratch-
pads
(Drupal-Sites)
Dataportal
(Drupal)
EDIT General Meeting

Carvoeiro, 23
-
25 January 2008

Community CDM data store


Central structured data
store for a community


CDM programming
library (Java; Hibernate
& Spring framework,
different db systems)


APIs and services to
communicate with other
programs and services

webpages, forum, blog
personal mashup
literature, bookmarks
file sharing
calendar, mailinglist
CDM Store
Remote API
Sync API
OAI-PMH
Annotation
RSS change
LSID
Scratch-
pads
(Drupal-Sites)
Dataportal
(Drupal)
EDIT General Meeting

Carvoeiro, 23
-
25 January 2008

Community Dataportal


Publishes CDM store


Allows annotations


Developed with WP6
exemplar groups

webpages, forum, blog
personal mashup
literature, bookmarks
file sharing
calendar, mailinglist
CDM Store
Remote API
Sync API
OAI-PMH
Annotation
RSS change
LSID
Scratch-
pads
(Drupal-Sites)
Dataportal
(Drupal)
EDIT General Meeting

Carvoeiro, 23
-
25 January 2008

Who does what?

WP6 / Drupal
community


WP5 with WP6
exemplar group
taxonomists

WP5 / TDWG
community

webpages, forum, blog
personal mashup
literature, bookmarks
file sharing
calendar, mailinglist
CDM Store
Remote API
Sync API
OAI-PMH
Annotation
RSS change
LSID
Scratch-
pads
(Drupal-Sites)
Dataportal
(Drupal)
EDIT General Meeting

Carvoeiro, 23
-
25 January 2008

x

TDWG Ontology
Unversal Biodiversity Data Bus
RDF
Common Data Model
Transfer Objects
XML
EDIT Platform Components
Fieldwork
CDM-compliant systems
Personal Components
Taxonomic
EDI-T-Editor
CDM Store
(working copy)
Descriptive
CDM-compliant systems
...
Validation services
Names
References
Geo services
Distribution Maps
Occurrence Maps
BioGeomancer
Central Components
Software Tracker
find applications & services
Experts DB
agents, tax expertise
Virtual Library
metaLib, SFX, Drupal
collectio
n
BHL,
Libraries
BioCASe/Tax
specimens,types, ...
Catalogue of Life
names & taxa
Search Feeds (e.g. RSS)
Shibboleth
Identity Provider, SSO
Community Components
webpages, forum, blog
personal mashup
literature, bookmarks
file sharing
calendar, mailinglist
CDM Store
Remote API
Sync API
OAI-PMH
Annotation
RSS change
LSID
XML
XML
Scratch-
pads
(Drupal-Sites)
Dataportal
(Drupal)


...
...
collectio
n
CDM
Stores
GBIF
Converter services
Word Doc -> CDM
TDWG RDF -> CDM
Checklist -> CDM
TaxonX -> CDM
NEXUS -> CDM
TaXMLit -> CDM
...
EDIT General Meeting

Carvoeiro, 23
-
25 January 2008

CDM Transfer Objects

Common Data Model
Transfer Objects
XML
Converter services
Word Doc -> CDM
TDWG RDF -> CDM
Checklist -> CDM
TaxonX -> CDM
NEXUS -> CDM
TaXMLit -> CDM
...
Communication between
components via CDM
Transfer Objects

E.g. converter services, but
also Scratchpads, data
portal, institutional
applications, etc.

Reusable!

EDIT General Meeting

Carvoeiro, 23
-
25 January 2008

Geo services


EDIT analytical map
services


Online GIS Client


Multi species


Targeted at ATBI sites


Occurrence2Distribution
transformation service


Visualisation and analysis
services for Dataportal


Use of standard services
where available

Geo services
Distribution Maps
Occurrence Maps
BioGeomancer
EDIT General Meeting

Carvoeiro, 23
-
25 January 2008

Search feeds


Search

for (e.g.):


Specimens in BioCASe/
Tax


Occurrences in GBIF


References and digital
documents in ViTaL


Taxa in Catalogue of Life


Agents in ExpertsDB


Subscribe to searches


Use any RSS client

or the Scratchpads

Experts DB
agents, tax expertise
Virtual Library
metaLib, SFX, Drupal
collectio
n
BHL,
Libraries
BioCASe/Tax
specimens,types, ...
Catalogue of Life
names & taxa
Search Feeds (e.g. RSS)
collectio
n
CDM
Stores
GBIF
EDIT General Meeting

Carvoeiro, 23
-
25 January 2008

Common security framework


Single sign
-
on for all
connected components and
services possible


Based on widely used
international standards


Secures web
-

services &
applications


Experts database (WP2)
forms part of the identity
provision


Proposal for Life Watch


Experts DB
agents, tax expertise
Shibboleth
Identity Provider, SSO
EDIT General Meeting

Carvoeiro, 23
-
25 January 2008

x

TDWG Ontology
Unversal Biodiversity Data Bus
RDF
Common Data Model
Transfer Objects
XML
EDIT Platform Components
Fieldwork
CDM-compliant systems
Personal Components
Taxonomic
EDI-T-Editor
CDM Store
(working copy)
Descriptive
CDM-compliant systems
...
Validation services
Names
References
Geo services
Distribution Maps
Occurrence Maps
BioGeomancer
Central Components
Software Tracker
find applications & services
Experts DB
agents, tax expertise
Virtual Library
metaLib, SFX, Drupal
collectio
n
BHL,
Libraries
BioCASe/Tax
specimens,types, ...
Catalogue of Life
names & taxa
Search Feeds (e.g. RSS)
Shibboleth
Identity Provider, SSO
Community Components
webpages, forum, blog
personal mashup
literature, bookmarks
file sharing
calendar, mailinglist
CDM Store
Remote API
Sync API
OAI-PMH
Annotation
RSS change
LSID
XML
XML
Scratch-
pads
(Drupal-Sites)
Dataportal
(Drupal)


...
...
collectio
n
CDM
Stores
GBIF
Converter services
Word Doc -> CDM
TDWG RDF -> CDM
Checklist -> CDM
TaxonX -> CDM
NEXUS -> CDM
TaXMLit -> CDM
...
EDIT General Meeting

Carvoeiro, 23
-
25 January 2008

Personal Components

Fieldwork
CDM-compliant systems
Taxonomic
EDI-T-Editor
CDM Store
(working copy)
Descriptive
CDM-compliant systems
...


...
...

Stand
-
alone software
applications specifically
developed for the platform


Combine ease of use with
taxonomic exactitude


Generate re
-
usable data
(CDM)


Linked to community
platform by means of
synchronisation interface

EDIT General Meeting

Carvoeiro, 23
-
25 January 2008

EDIT Taxonomic Editor software

EDIT General Meeting

Carvoeiro, 23
-
25 January 2008

EDIT Taxonomic Editor

EDIT General Meeting

Carvoeiro, 23
-
25 January 2008

EDIT Taxonomic Editor

EDIT General Meeting

Carvoeiro, 23
-
25 January 2008

EDIT Taxonomic Editor

EDIT General Meeting

Carvoeiro, 23
-
25 January 2008

Expected outcome 2010


A refined consensus Common Data Model (CDM)


Exemplar groups provide example for cybertaxonomic
work process (reusable, dynamic, standards
-
based,
community consensus)


The European Checklist databases (Fauna Europaea,
Euro+Med & ERMS) are platform based (PESI Project)
and constantly improved


Working Platform
-
based Community websites for several
taxa


A series of EDIT software products are used by
taxonomists and developers of taxonomic software

EDIT General Meeting

Carvoeiro, 23
-
25 January 2008

x

Integration

is ...

For individual contributors,

please see EDIT Website

EDIT General Meeting

Carvoeiro, 23
-
25 January 2008


.. not a piece

of cake

EDIT General Meeting

Carvoeiro, 23
-
25 January 2008

w.berendsohn@bgbm.org