EDIT General Meeting Carvoeiro, 23-25 January 2008.

EDIT General MeetingCarvoeiro, 23-25 January 2008


EDIT

(Re) Visionary TaxonomyThe Internet Platform for Cybertaxonomy

Walter Berendsohn


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


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


x

TDWG OntologyUnversal Biodiversity Data Bus

RDF Common Data ModelTransfer Objects

XML

EDIT Platform Components

FieldworkCDM-compliant systems

Personal Components

TaxonomicEDI-T-Editor

CDM Store(working copy)

DescriptiveCDM-compliant systems...

Validation servicesNames

References

Geo servicesDistribution MapsOccurrence Maps

BioGeomancer

Central Components

Software Trackerfind applications & services

Experts DBagents, tax expertise

Virtual LibrarymetaLib, SFX, Drupal

collectionBHL,

Libraries

BioCASe/Taxspecimens,types, ...

Catalogue of Lifenames & taxa

Search F

eeds (e.g. RS

S)

ShibbolethIdentity Provider, SSO

Community Components

webpages, forum, blogpersonal mashupliterature, bookmarks

file sharingcalendar, mailinglist

CDM Store

Remote APISync API

OAI-PMH

AnnotationRSS change

LSID

XML

XML

Scratch-pads

(Drupal-Sites)

Dataportal(Drupal)

……

...

...

collectionCDMStores

GBIF

Converter servicesWord Doc -> CDM

TDWG RDF -> CDMChecklist -> CDMTaxonX -> CDM

NEXUS -> CDMTaXMLit -> CDM

...


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



CDM Store

Remote APISync API

OAI-PMH


LSID

Scratch-pads

(Drupal-Sites)

Dataportal(Drupal)


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



CDM Store

Remote APISync API

OAI-PMH


LSID

Scratch-pads

(Drupal-Sites)

Dataportal(Drupal)


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



CDM Store

Remote APISync API

OAI-PMH


LSID

Scratch-pads

(Drupal-Sites)

Dataportal(Drupal)


Community Dataportal

• Publishes CDM store• Allows annotations• Developed with WP6

exemplar groups



CDM Store

Remote APISync API

OAI-PMH


LSID

Scratch-pads

(Drupal-Sites)

Dataportal(Drupal)


Who does what?

WP6 / Drupal community

WP5 with WP6 exemplar group taxonomists

WP5 / TDWG community



CDM Store

Remote APISync API

OAI-PMH


LSID

Scratch-pads

(Drupal-Sites)

Dataportal(Drupal)


x



XML



Personal Components





References


BioGeomancer

Central Components




collectionBHL,

Libraries



Search F

eeds (e.g. RS

S)





CDM Store

Remote APISync API

OAI-PMH


LSID

XML

XML

Scratch-pads

(Drupal-Sites)

Dataportal(Drupal)

……

...

...

collectionCDMStores

GBIF




...


CDM Transfer Objects

Common Data ModelTransfer Objects

XML




...

Communication between components via CDM Transfer Objects

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

Reusable!


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


BioGeomancer


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



collectionBHL,

Libraries



Search F

eeds (e.g. RS

S)

collectionCDMStores

GBIF


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




x



XML



Personal Components





References


BioGeomancer

Central Components




collectionBHL,

Libraries



Search F

eeds (e.g. RS

S)





CDM Store

Remote APISync API

OAI-PMH


LSID

XML

XML

Scratch-pads

(Drupal-Sites)

Dataportal(Drupal)

……

...

...

collectionCDMStores

GBIF




...


Personal Components





……

...

...

• 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 Taxonomic Editor software


EDIT Taxonomic Editor


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


x

Integration is ...

For individual contributors, please see EDIT Website


.. not a piece of cake


[email protected]

EDIT General Meeting Carvoeiro, 23-25 January 2008.

Documents

Transcript of EDIT General Meeting Carvoeiro, 23-25 January 2008.