Sustainability of EDIT Informatics Activities
Jan 11, 2016
Sustainability of EDIT Informatics Activities
BoD working group on sustainability
Executive Summary, 20th July 2009:
“… set of themes we are sure we want to have sustainability ...
Science (e-science) […] e-infrastructure ISTC (core)Elements of the Cyber platform (core) but depends on
decision on platform (use by the community)CDM data store & portal: Supported for 5 years.Scratchpads: will continue (project funding ?). EDIT could part
support it.” [agenda point 4f]
EDIT’s Information Science and Technology Committee (ISTC)
Information Science and Technology Committee
The short and medium term goals of the ISTC (until 2011) are to:
1. Define the key areas for integration that will assist EDIT researchers and developers in creating a [cyber]taxonomic platform.
2. Participate in establishing an integrated platform by changing or adapting resources in order to reach a common goal.
3. Advise on the annual revision of the WP5 work plan.
The new ISTC
The purpose of the ISTC is to:Further cross-institutional integration through formal
agreements on sharing hardware and other basic infrastructure joint software development joint development of web services
Exchange information with regard to participants’ IST projects Identify opportunities for collaboration with “external” IST-
projects Joint applicationsSupport standardisation efforts
The new ISTC
MoU revision cycles: June 20: MoU Draft
submitted to EDIT Coordinator and Network Steering Committee
July 20: Comments, received, integrated in new Draft; circulate draft to BoD, CETAF, ISTC for comment
November 30: Comments discussed and integrated; circulation of MoU to EDIT and CETAF directors for signature.
The EDIT Platform for Cybertaxonomy (and the Common Data Model – CDM)
EDIT’s Biodiversity Informatics Strategy
Scope: from data discovery to web and print publicationof monographs, floras, faunas and checklistsIndividuals, institutions, collaborative groups and networks
The EDIT Platform for Cybertaxonomy• A data quality-oriented software environment
supporting the entire taxonomic workflow.• Based on the Common Data Model (EDIT CDM), with
an extendible open-source Java programming library. EDIT Scratchpads
• User-defined web publication, communication and integration of multiple information sources.
• Based on a hosted multi-site open source content management system (Drupal).
The EDIT Common Data Model (CDM)
Core of the EDIT Platform for CybertaxonomyCovering the entire taxonomic data domainBased on existing standards / models / exchange formats
The CDM Programming Library
The EDITor (EDIT Taxonomic Editor)
A new editor for the new data modelOffers CDM Library import/export functionality to end users.A key tool for data integration.
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Data Entry & Import/Export
EDITor
CDM
Excel
Structured Descriptive Data (TDWG standard)
Access to Biological Collection Data (TDWG st.)
RIS Reference Format
Apps: community, EDIT, commercial, individual
Access to GBIF occurrence data (Specimens & Observations)Based on BioCASE/ SYNTHESYS portal softwareConfigurable query expansion using taxonomic checklists
Search results can be imported into the CDM
EDIT Specimen & Observation Explorer
• Application of Drupal Content Management System
• Feature-rich• Integrated with existing
biodiversity infrastructure• Configurable through
administrative interface• Customizable through Drupal
interface templates (“themes”)
CDM Dataportal
Web Publishing
Software Download Site
wp5.e-taxonomy.eu/cdm-setups/
Ongoing Software Development Work
Generic print publication serviceIntegration of descriptive informationFull support for structured specimen dataPoint map support Integration with the Biodiversity Heritage
LibraryTo be finalised by the end of the EDIT Project
Pan European Species Inventories (PESI)
Anton Gürntsch, BGBM Berlin-Dahlem
CATE (Creating a Taxonomic e-Science)
Two exemplar web-revisions: Araceae Juss. – Aroid Lillies
~ 3,500 taxaLed by Simon Mayo, RBG Kew
Sphingidae Latreille, 1802 – Hawkmoths~ 2,000 taxaLed by Ian Kitching,
NHM London
Fully CDM-based Integrates key-generation
softwareScratchpad for
communicationsBen Clark, RBG Kew
Further Project Support for the Platform
PESIBHL EuropeSYNTHESYS 2ViBRANTi4Life(e-Monocots)LifeWatch (!)
Why collaborating in IT developments?
Taxonomic domain is highly collaborative Example: Flora projects, Checklists, Digitisation efforts
Previous domain-specific efforts in biodiversity informatics Numerous individual and some institutional implementations Few working software products, only covering parts of the domain Investments: 100’s of million Euro world-wide
Joint modelling and standard-building Efforts for 20 years now Excellent knowledge of the information structures
New Investment EDIT, EDIT-spin-offs, CATE etc. already represent new soft money
commitments of about 11 Mio Euro from EU- and national sources Aiming at a sustainable, collaborative, comprehensive solution We all face similar problems in taxonomic computing