Consolidated ViBRANT Project Final Review Presentations

Meeting agenda
Wednesday 29th Jan. 2014
EC premises (Room 0/S5)
Avenue de Beaulieu 25
1160 Brussels

9.30 Welcome and introduction of participants
9.35 Overview of results & achievements, incl. a summary of budget & resources V. Smith
RESEARCH ACTIVITIES
10.05 WP2: Technical architecture
10.25 WP7: Biodiversity literature access and data mining
NETWORKING ACTIVITIES
10.45 WP3: Training, outreach and community support
11.05 COFFEE BREAK
11.30 WP4: Standardisation
11.50 WP8: Ecological and conservation data mobilisation
SERVICE ACTIVITIES
12.10 WP5: Interaction and services
12.30 WP6: Scholarly publishing
12.50 LUNCH
MANAGEMENT & IMPACT
14.00 ViBRANT impact and product sustainability
14.20 WP1: Management and Financial matters
14.50 Additional discussion (if necessary)
15.10 Reviewers meeting with Project Officer Reviewers and PO
15.30 Quick feedback from reviewers
15.45 Contingency (in case of over run)
End of review for the consortium
16.00 Preparation of review report Reviewers and PO

S. Rycroft (NHM)
D. Morse (OU)

T. Backeljau (RBINS)
Y. de Jong (RBINS)
C. Arvanitidis (HCMR)

N. Caithness (UOXF.E9)
L. Penev (PENSOFT)

V. Smith
V. Smith
All
All

Overview of results &
achievements
Vincent Smith
Natural History Museum London

ViBRANT Project Year 3/Final Review Meeting – Brussels 29-01-2014

Overview of results & achievements

The Project ID
Project coordinator
Vincent Smith

Project number: 261532
Start date: 01 Dec 2010
End date: 30 Nov 2013

WP Leaders
1: Dave Roberts
2: Simon Rycroft
3: Thierry Backeljau
4: Yde de Jong/Wouter Los
5: Neil Caithness
6: Lyubomir Penev
7: David Morse
8: Christos Arvanitidis

NHM, UK

NHM, UK
RBINS, BE
RBINS, BE/UvA, NL
UOXF.E9, UK
Pensoft, BG
OU, UK
HMCR, GR


Overview of results & chievements
17 partners in 9 countries
(universities, museums & 2 SMEs)



Project’s concept and objectives
Vision
Connecting the people, data & science of
biodiversity

Position
Open & sustainable development of a federated
network of biodiversity informatics infrastructures

Mission
Facilitate the mobilisation, sharing, reuse and
publication of biodiversity data



Project’s concept and objectives
1.

2.
3.
4.

5.
6.

provide sustainable services in data
mobilisation, integration, publication, sharing,
use and reuse to research communities and the
European public
connect end users of biodiversity data to
networks of primary producers
provide means to establish and document the
state of the art in biodiversity research
identify research and development needs and
gaps in the provision of support to biodiversity
researchers
provide an information centre for biodiversity
research results
defragment access to biodiversity data



Interconnecting nodes in an federated network that retain operational autonomy


Our Products for
Promoting open access publishing and literature mining
Biodiversity data Journal
Novel open access journal for data publication
65,000 unique visits within three months

Pensoft Writing Tool
Integrated online manuscript-authoring platform
50 manuscript submissions within first month

Bibliography of Life
Freely accessible bibliographic citations
Over 215,000 references


Our Products for
Enabling data visualisation and computation
OBOE

GeoCAT

Web-based platform for
computing applications

Rapid geospatial
conservation assessments

13 computational
tools

1000 assessments in
2012

CartoDB

Ikey+ / Mkey+

Open source
visualisation platform

Online services for
identification keys

26,000 subscribed
users

Over 250 uses
per month



Our Products for
efficient interoperability
Knowledge Organisation System
Controlled vocabularies for data
mobilisation and aggregation

Platform for Cybertaxonomy
Effective links with Scratchpads
for major European checklists



Our Products for
facilitating community support & participation
COMBER
Citizen science project for divers and
snorkelers
5,650 marine species observations by citizen
scientists

Training and Outreach
Support and train users - enable community grow
38 training courses
453 participants
20 Scratchpad ambassadors
New scratchpads.eu portal



The ViBRANT Network hub

Enter, structure, curate, link and publish biodiversity data online
7000 active users in 630 vibrant communities
Over 260 citations in peer reviewed papers


Scratchpads case studies | 4 out of 630 communities
Solanaceae source

Sampled Red List Index for Plants

Agriculture - Horticulture
African Ichthyology Portal

Animal Biodiversity

Plants Conservation
Diatoms online

Citizen Science


Publications
62 scientific papers (59 open access)
with a rate of c. 2 every month
Incl. Nature , PLoS One, BMC Informatics, BMC
Ecology, ZooKeys & Biodiversity Data Journal

Selected publications
Three special issues
Zookeys vols 150, 209 & 365

The white paper
Hardisty, A., Roberts D. and The Biodiversity Informatics
Community. “A Decadal View of Biodiversity
Informatics: Challenges and Priorities.” BMC
Ecology 13 (2013)


Conference presentations
105 conference presentations
reach out to more than 10,000 people
(incl. researchers, policy makers and the public)

Meetings/workshops
• Biodiversity Informatics Horizons 2013
in Rome, Italy
• 96 workshops with more than 4,000
participants (incl. 38 Scratchpads
training courses)


ViBRANT brochure
Presenting the major ViBRANT products
Structured to address a wider audience
32 pages full colour

Scratchpads brochure
Presenting Scratchpads functionality
through several successful case studies by
several biodiversity communities
24 pages full colour



Year 2 review feedback
Strengthen integration and clarify the main end products of the project
 Year 3 was focused on integration activities and promoting main ViBRANT products
Attribute more emphasis on dissemination and hands-on training, including the organisation of final
event and widening user communities.
 More training and dissemination activities than year 1 & 2. Online & on-site training, ambassadors
activities, brochures

Prepare by 31st March 2013 a note outlining the activities and tasks to be accomplished in the last
year, indicating the priority and time by which they are targeted to be achieved.
 Prepared and submitted
Prepare by 31st March 2013 a note summarising the changes brought to the DoW to date, and
introduce subsequently a request for contract amendment, including contractual modifications and
the updated DoW.
 Prepared and submitted
Deliverables should be more substantial content-wise and respect FP7 guidelines for project reports.
In particular the final report should present clearly project results and their applicability, added value
and impact.
 Included in the final report

 all completed
 on time
 on line

Year 3 deliverables
D1.1 - Overall Management
Report on the project overall management procedures

D2.3 - Financial sustainability
Project’s financial sustainability model

D2.4 - Unit testing
Distributed and automated unit testing mechanism for Scratchpad code

D3.3 - Community delivery and evaluation
Assessment of a self supporting open source community for sustainable implementation

D4.3 - Design of robust services
Develop robust services, based on usage statistics and user feedback

D5.3 - Sustainable software services
Refined and sustainable software services available for public use

D6.3 - Data publication workflow
Description of workflows and tools developed or upgraded by Pensoft in the course of the ViBRANT project

D7.3 - Literature search
Develop the literature search software

D8.3 - A start-up portal for discovery of GBIF mediated data
Delivery of a Scratchpad based start-up portal for discovery of GBIF mediated data


Budget breakdown for the project

REDACTED



Type of Position (paid by the project positions)

Number of people

Scientific Coordinator

1

Work package leaders

8

Experienced researchers

44

PhD Students

9

Technical staff

34



Sustainability outlook
• 8,500 active users (7,000 in
Scratchpads)
• 630 Scratchpads communities
• More than 1.5 million unique visitors to
ViBRANT tools and services over the
three-years (1.2 million to Scratchpad
sites)
• NERC funding
e-monocot
• Marie Curie Grant (IIF)
Starting mid-2014

• US-NSF Grants
• Major community databases to be
migrated to Scratchpads

Spin-off activities
Promote links to EU projects BioVeL,
agInfra, BioSOS, EU-BON, GIGESMED
Identify opportunities in H2020 to
capitalise on current investments and
minimise future redundant activities


WP2: Technical
architecture
Simon Rycroft


WP2: Technical architecture

Research activities

Description & Objectives
WP Description

To develop and deliver the technical architecture required to host,
integrate and sustain the Scratchpad framework within the ViBRANT
consortium. This moves the Scratchpad prototype into a sustainable
open-source, enterprise-level system.

WP partners

WP Objectives

• Develop and deliver an enhanced technical framework for hosting
the Scratchpad infrastructure.
• Distribute the Scratchpad server so that other institutions can
independently host Scratchpads.
• Develop new functionality for Scratchpads, including human
interfaces and APIs.
• Develop a financial model for sustainable delivery of service.

Year three effort

52.61 PM



Research activities

Activities
Year three deliverables

D2.3 – Financial sustainability
Report on options for the
ViBRANT financial sustainability
model including selection of
preferred model and
accompanying Service Level
Agreements (SLA's).



Research activities

Activities

D2.4 – Unit testing
Distributed and automated unit testing
mechanism for Scratchpad code
completed and available. This will operate
in conjunction with the Scratchpad
Sandbox to ensure that the latest version
of the software is available for testing.
Other year three activities

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Data search portal providing a single point of entry to all Scratchpad data
Report on the options for a biodiversity data citation metric
Additional module development as highlighted by M2.20
Integration of products from other WPs, including the PWT, OBOE, RefBank,
Vocabularies services, CDM and GeoCAT.



Research activities

Foreground

Scratchpads
Description

Scratchpads is an open source and
free to use platform that enables
you to work in a collaborative online
environment. With a Scratchpad
you can easily create your own
website to structure, manage, link
and publish biodiversity data.



Research activities

Follow up activities

Key Highlights
• All Scratchpads 1 sites have now been migrated to Scratchpads 2
• The Scratchpads are now hosted on a stable platform with failover and
mirroring capabilities
• Completely redesigned Scratchpads homepage
• Many new features have been added to the Scratchpads, including import from
Excel, export to DwC-A, content citation, integration with Lucid & BRAHMS,
integration with the PWT…



Research activities

Scratchpads
KPI – Impact - Sustainability

• Numbers of users and sites is increasing at a consistent rate.
• The number of views of Scratchpads data is increasing, although we only
started measuring the numbers of views in a reliable way within the last year.
• The quantity of content is increasing, and if it were possible to measure the
quality of the content, that too is improving.



Research activities


• Scratchpads integrating ViBRANT products with BioVeL (pilot project on killerwhales)
• Integration of agricultural VREs – agriDrupal in association with agInfra project
and FAO
• Project proposal to integrate ISA Tools, BioVeL and Scratchpads into a single
virtual research environment
• New projects to migrate existing online biodiversity databases to Scratchpads
(e.g. H&M World’s Birds Checklist, Flora of Zimbabwe, MycoNet project)


WP7: Biodiversity literature
access and data mining
David Morse
Open University


WP7: Biodiversity literature access and data mining

Research activities

WP Description

To facilitate the recovery of key content types (e.g. taxonomic names)
and underpinning data from published documents, and the
integration of those documents into the Scratchpad framework to
meet the needs of Scratchpad users.

WP partners

WP Objectives

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Community contributed bibliography
Identification and mark-up of elements within documents
Disambiguation and annotation of mark-up
Web service for search and information retrieval

Year three effort

43.63 PM



Research activities

Activities

D7.3 - Literature search

The deliverable is branded as ReFindit,
which with RefBank achieves our goal of a
Bibliography of Life.


• ViBRANT corpus, to support future
NLP research
• RefConcile, to de-duplicate
bibliographic references
• Support for
• OBOE-Scratchpad integration
• audience analysis


Research activities

Foreground

Description

A freely accessible bibliography of
every taxonomic paper ever
published.
Draws on references in Scratchpads
and other targeted resources
making it easier for researchers to
produce accurate references for
their citations.



Research activities

RefBank
A network of servers to store, de-duplicate
and parse bibliographic references into
which users can load, edit and delete
references, to provide a curated set of
references.

ReFindit
A tool to discover and download
bibliographic references from a wide range
of open access on-line bibliographies,
including RefBank.



Research activities


• More than 220,000 references loaded before
launch 3Q 2013.
• All references loaded into Scratchpads are
automatically harvested.
• Used seamlessly by authors in PWT when
searching for references.
• Will be supported and used by Plazi and
Pensoft after ViBRANT.
• The underlying tools are being adopted by
the Global Names Architecture project, and
being investigated by two EU FP7 projects,
agINFRA and pro-iBiosphere.



Research activities


• Use of the Bibliography of Life within
related projects.
• More RefBank nodes planned.
• Take up of ViBRANT technology within the
Global Names Architecture project,
including a reworked RefBank as
BionomialBank.
• Continued collaboration between VU and
OU analysing the audience of
e-infrastructure users.
• Project proposals submitted based on
analysing content of RefBank.
• Project proposals submitted based on
ViBRANT’s NLP tools used in preparing the
Corpus, and extend to identify images.

WP3: Training, outreach
and community support
Thierry Backeljau
Institut Royal des Sciences Naturelles de Belgique


WP3: Training, outreach & community support
Click to enter WP[x]: Title of WP

Network activities

WP Description

Empower and enable biodiversity scientists to use ViBRANT tools to
strengthen community collaboration. In particular to enhance the
development of Scratchpads and to support and extend the user
communities, leading to increased production of digital biodiversity
information.

WP partners

WP Objectives

• Organisation and delivery of ViBRANT training courses
• Implementation of network activities to extend the ViBRANT
community and to foster its long-term stability
• Conducting user studies
• Providing community support for the use of ViBRANT services

Year three effort

29.23 PM

Year 3/Final Review Meeting – Brussels 29-01-2014


Network activities

Activities

D3.3 Community delivery and evaluation
Structuring the necessary support
mechanisms, crowdsourcing the support,
maximizing its efficiency and assessment
of the user base needs nurture a
community based model and keep the
open source community alive!

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International training: on-site & online
Wiki-based documentation system
Open source bug/issues tracker
Global network of Ambassadors
ViBRANT’s audience classifier tool
Funder and output analysis tool


Network activities

Foreground

Training
International training sessions, given online
and on-site play an important role in
assisting both new and existing Scratchpad
users.

Support
A wiki-based documentation system and an
open source bug/issues tracker play a vital
role in connecting Scratchpads users with
the Scratchpads developers.



Network activities

Foreground

Ambassadors
A global network of experienced
Scratchpads users support their local user
community, linking the Scratchpads
support team with the user base.

Sociological studies of use
In a series of studies, use and users were
identified, in order to learn about impact
and possible future actions to improve
Scratchpads’ impact.



Network activities

Training, outreach & support
Description

Large part of effort is invested in
training. A mediawiki provides the
basis for online and printed training
manuals, a FAQ and videos. Redmine
tracks all bug reports, feature
requests and support queries from
users. A worldwide Ambassadors
network supports local Scratchpads
communities and promotes
Scratchpads use.

Training organised by Ambassador in Lviv, May 2013



Network activities

Sociological studies
Description

How can impact of Scratchpads be
evaluated? What is the disciplinary
landscape in which Scratchpads
are and can be used? Who are the
scholarly and non-scholarly users
and does this change over time?
Do Scratchpads create a new
collaborative environment? What
strategies may lead to a larger
uptake?

Co-author network of a Scratchpad

Knowledge flows in the
journal citation network



Network activities

Training, outreach & support

• Over 450 participants have attended 38
international on-site & online training.
• A total of 2,907 issues submitted to the
Redmine system have been tracked: > 2,500
have been successfully resolved.
• The help wiki has had 129,000 views since its
creation in March 2012.
• Twenty users from 16 different countries
signed up for the Ambassadors scheme.
• Training, support and outreach, along with
sociological studies performed on the userbase, nurtured the creation of a community
contribution business model that safeguards
the long-term sustainability for most of the
project’s products.


Network activities

Sociological studies

Several publications are in different stages of
finalisation. Some findings:
• Increased use, main users in higher education
and research organizations. Small numbers of
other user types suggest societal use (and
possibilities for new outreach).
• Scratchpads membership also includes nonresearchers, and generally members were
previously not collaborating. So Scratchpads
do organise taxonomists.
• Sustainability and impact may require
strategies to involve communities in research
infrastructures, next to individuals.
• Collaboration between different relevant
disciplines is important.


Network activities


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Promotion of Scratchpads via the Distributed European School of Taxonomy
Scratchpads training is part of the DEST training curriculum
Training and support is sustained by NHM London
Continued Scratchpads promotion and support by Ambassadors
Use of Scratchpads as project website promoted in project proposals
Studies on use and users will be continued, leading to further insights in
strategies to involve researchers and research communities, including citizen
scientists.
• Work on methods for measuring impact to be continued, also in related
projects.


WP4: Standardisation
Yde de Jong
Institut Royal des Sciences Naturelles de Belgique


WP4: Standardisation Title of WP
Click to enter WP[x]:

Network activities

WP Description

Ensure compatibility and interoperability of all data within ViBRANT
and to other research and publishing infrastructures and services.

WP partners

Enforce or facilitate the use of externally standardised ontologies or
when no adequate standards exist, enable ViBRANT users to develop,
document, and voluntarily share new ontologies.
WP Objectives

• Facilitate integration and harmonisation of distributed data-sets.

• Provide management and dissemination facilities for the
necessary ontologies by:
o
o

Providing access to external services based on these ontologies and APIs.
Developing APIs building on standard ontologies and protocols.

Year three effort

44.8 PM

• Provide biologists with the necessary flexibility to express their
knowledge regardless of whether the terminology has been
standardised.


Network activities

Activities

D4.3 – Design of robust services
Continuing improvements and extensions
on establishing cross-platform integration
and further 'Ontology Platform’
advancements.

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Workflow optimised services on ViBRANT
index
KOS integration into Scratchpads
Xper2 and EDIT Platforms publishing
capability on Mediawiki
Xper2 (further) integration into CDM
Fauna Europaea data papers & migration
Global Names Europe H2020 preparations


Network activities

GBIF Knowledge Organization System (KOS)
Description

Offers a set of Vocabulary Tools and
Services providing routines and
mechanisms to build, manage and
exchange (controlled) vocabularies,
including:
• Term Forum (Semantic Media Wiki)
• Term Browser
• Vocabulary Server
• Resource Repository



Network activities

EDIT Platform for Cybertaxonomy
Description

• Offers a virtual common access
point, optimising data exchange
and management for taxonomists
and supporting the treatment of
descriptive data.
• Interoperate with the Scratchpads,
KOS, Pensoft and Xper2 platforms.
• Hosts various taxonomic data sets
and backbones (like CoL & PESI).



Network activities

Foreground

ViBRANT index publishing platform
Offers a common searching index and
access service for ViBRANT and CDM data,
optimised for e-Science workflow
application (via the BiodiversityCatalogue),
using the CDM web-service layer.

ViBRANT Single Access Key Service
Offers a web service for biological key
generation, based on the Xper2 platform
features, helping building a
consistent descriptive system for use in
multi-access keys or descriptive items.


Network activities

Foreground

KOS – Scratchpads integration module
Offers a feature replacing vocabularies in
Scratchpads by controlled vocabularies
from the GBIF Resources Repository,
including (potential) updates of GBIF KOS
terms.

Global Names Europe - assay
Offers a contribution to the Global Names
Architecture preparations as a necessary
component of Research Data eInfrastructures: Framework for Action in
H2020


Network activities

Foreground

MediaWiki publishing platform
Offers enhancements on the publishing
capability of the Semantic MediaWiki for
use in KOS for vocabulary management.
Also for the Xper2 and EDIT Platforms this
Mediawiki features were investigated.

Pensoft publishing platform
Offers the preparation of data papers using
the PWT following the launch of the BDJ as
a next generation platform for publishing
biodiversity science and data.
ZooKeys special issue on Fauna Europaea.


Network activities

ViBRANT WP4 products & services

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67 Scratchpads harvested/published into the
ViBRANT index, including 262,664 taxa.
Two GBIF KOS vocabulary instances imported
into the Scratchpads.

CDM data set (Flora of Cyprus) imported into a
(test) Scratchpad.
Effective employment of the MediaWiki as a
publishing platform for e-Taxonomy.
TDWG VoMaG task group established for KOS
governance.
Active GN-EU outreach in initiatives like RDA,
Coopeus, BIH/LifeWatch, TDWG, and EUDAT.
57 Fauna Europaea data papers manuscripts in
preparation in the PWT.
Xper² (full) integration into the CDM Taxonomic
Editor.


Network activities


• Import of additional KOS vocabularies into the Scratchpads.
• Implementation of BDJ as a tool triggering community participation for
taxonomic indexing/editing and validation for taxonomic standardisation.
• Further employment of CDM for the hosting and integrated access of
biodiversity data (EU BON) and descriptive data treatments (pro-iBiosphere).
• Description of GN-EU as an European contribution to the Global Names
Architecture and the initiation of H2020 bids as part of a collaborative
(LifeWatch) Taxonomic Roadmap plan.
• Continuation of VoMaG task group activities.



Network activities

ViBRANT WP4 working meeting, Berlin, 8-9 October 2012

WP8: Ecological and
conservation data mobilisation
Christos Arvanitidis
Hellenic Centre for Marine Research


WP8: Ecological & conservation data mobilisation

Network activities

WP Description

The primary objective was to extend the capacity of the Scratchpads
(in collaboration with WP2, WP4, and WP5) into ecology and
conservation science. This has been proved to be particularly
important for the sustainability of the project since its products are
now being used by communities which are not traditionally included
in the taxonomists

WP partners

WP Objectives
i. facilitate naturalist citizen scientists to contribute their observational information to the eInfrastructure.
ii. improve data quality of information present in thematic and global biodiversity databases;
iii. boost GBIF network expansion at national and regional scales;
iv. integrate data from various biodiversity sources for ecological and biodiversity assessment and,
v. facilitate the Red List assessment processes for endangered species by IUCN and other
stakeholders.

Year three effort

45.7 PM




Network activities

Activities
D8.3 - A start-up portal for discovery of GBIF mediated data

M8.18 - Scratchpads module for data recording (Citizen Science) Alpha version
M8.23 - Integration of the 3D morphological and anatomical data
in Scratchpads
M8.24 - Scientific document with the results from the COMBER
data
M8.20 - Ecological and conservation applications implemented as
a service
M8.21 - Integration of visualization applications with Scratchpads

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Implementation (expansion of COMBER to
the Aegean and Ionian Seas)
Dissemination (e.g. IPC, Sydney, AU;
BIH2020, Roma, IT)
Impact and sustainability (GBIF NPT,
COMBER, BICT, GeoCAT, CartoDB)
Publication of pioneering scientific
documents

WP8: Ecological & conservationTitle mobilisation
Click to enter WP[x]: data of WP

Network activities

Foreground

COMBER
COMBER is a citizen science project for
divers and snorkelers to collect information
on marine species and contribute to
biodiversity monitoring. The software
serves as a platform for similar citizen
science projects.



Network activities

Foreground

GeoCAT
GeoCAT simplifies the process of Red
Listing and helps to identify threatened
species. GeoCAT is an open source,
browser-based tool that performs rapid
geospatial analysis for Red List assessment.



Network activities

Foreground

NPT Start-up
The Nodes Portal Toolkit start-up is an
open source tool that provides
biodiversity information web presence
for GBIF Participants. The toolkit
supports countries by highlighting the
available national biodiversity species
data for the benefit of science and
society.

BICT
The Biological Index Calculation Tool
(BICT) is an online tool available via
OBOE. BICT calculates up to eleven
different biodiversity indices on data
submitted by the user and returns
calculated data as well as a graphical
report.



Network activities

COMBER
Description
The module is now fully integrated in Scratchpads2
and consequently in the ViBRANT e-Infrastructure
with a different, but fully functional and userfriendly, interface that can be searched in many
ways.
The philosophy for the Alpha version of the COMBER
tool is that it is not restricted to fish species but can
include any species found in the Mediterranean,
even species detected for the first time in this
regional sea. Furthermore, it is not directed
exclusively to the SCUBA divers joining the diving
clubs but can be operated by any diver or snorkeler
throughout his/her diving/ snorkeling/ sailing
activity. These features provide the tool with the
potential to be adopted by many more user groups
and applied in a more independent and automated
way. It can also be readily customized to
accommodate the needs of almost any citizenscientists project.
Finally, the data sets produced by the pilot have been
analyzed and presented in a scientific document,
testing a formal scientific hypothesis.


Network activities

COMBER

The COMBER module has already been adopted
by three Consortia:
i. EU BON, a recently started international
project, funded by the EU in the context of
the 7th RTD FP3. The decision for the Greek
study site (Amvrakikos) was made during the
kick-off meeting of the project in Berlin, 1214/02/2013.
ii. CIGESMED is a project which runs under the
SeasERA ERAnet (EU funded) in the
Mediterranean Sea.
iii. LifeWatchGreece, which is the national hub to
the ESFRI Infrastructure.



Network activities

GeoCAT
Description
Over the past year, the tool GeoCAT was
extended to make easier its integration with
Scratchpads2. GeoCAT had already the
possibility of opening files in various formats,
created by Scratchpads, like for example CSV,
but those formats did not contain semantics
on the information content. Therefore,
Scratchpads2 implemented the TDWG
Standard Darwin Core Archives (DWC-A), so
that an observation, or a specimen in a
collection, could be exported under this
format.



Network activities

GeoCAT
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GeoCAT has been further supported by one EU Consortium and a
UK call for grants. The tool is maintained by the IUCN and is
already part of the IUCN daily workflows for many scientists
doing conservation assessments. The IUCN is also using GeoCAT
in its training courses and maintaining the user community.
For the continuation of GeoCAT’s development the EU project EU
BON is extending functionality to support a larger amount of
data and integration with other geospatial platforms.
Finally NERC (UK Natural Environment Research Council) through
the call on “Environmental Big Data Capital” call is funding in
2014 the development of additional functionality for GeoCAT to
add multispecies support and deeper integration with CartoDB.
GeoCAT has already had an impact on large user groups and this
is reflected by the impressive number of users as well as by the
number of citations GeoCAT is picking up in scientific peerreviewed publications and the wider media.



Network activities

NPT Start-up
Description
The tool helps GBIF Participants to set up a national
biodiversity information website that includes an
initial species country checklist and static maps of
species occurrence data published through GBIF.
It also provides species contents (descriptions,
functional traits, images and videos) from the
Encyclopedia of Life, as well as basic features to run
the website as a communication portal.
The product helps establish the Node’s identity on
the web, manage biodiversity information at the
country/thematic level and engage local and global
communities with the relevance of biodiversity
information.
NPT Start-up was developed in Drupal because this
content management system has a very strong open
source community behind it. There are numerous
biodiversity information related projects that make
use of Drupal as a development framework, so
extensive functionality relevant to biodiversity
information is already available and this is likely to be
maintained and extended in the future.



Network activities

NPT Start-up
A review of the first version of the NPT Start-up was conducted
from 9 April to 20 May 2013 amongst all GBIF Node Managers
and Nodes staff. Fifty percent of the forty GBIF Participant
Nodes responding to the questionnaire indicated an interest in
using the first version of the NPT Start-up in its current form.
The majority of the responding Nodes considered the first
version of the NPT Start-up as either “very useful” or
“extremely useful”. Half of the respondents (20 GBIF Participant
Nodes) of the NPT start-up review indicated the desire to use
the tool in its initial form.
TaiBIF has contributed by translating the installation procedure
in traditional Chinese. GBIF Participant Nodes in Argentina,
ASEAN Centre for Biodiversity, Belgium, Chinese Taipei, Costa
Rica, Indonesia, Kenya, Madagascar, Norway, Portugal, and
South Africa have tried installing the tool and have provided
invaluable suggestions to the development and the
documentation.
Currently, a group of around 10 GBIF Participant Nodes have
indicated the interest in becoming part of an early adoption
program.


Network activities

BICT
Description

The indices calculated by the module
are those most frequently used in
ecological, conservation and
environmental health assessment
studies.
The three last indices, BQI, AMBI and
BENTIX, are largely used during the
implementation of the EU Water
Framework Directive (WFD) and in
the context of the Marine Strategy
Framework Directive (MSFD).



Network activities

BICT

i.

ii.

The BICT module has already been adopted
by EMBOS (European Marine Biodiversity
Information System), a Consortium
developing a network of permanent marine
biodiversity monitoring stations from the
Arctic to the Mediterranean and the Black
Seas, as their main tool for the assessment
of the benthic quality. EMBOS is funded by
the EU COST instrument and it's running for
four years: 2011-2015. This issue was
discussed during the last meeting of the
Consortium in Riga 15-17/10/2013.
BICT will be further developed and made
available in the context of the
LifeWatchGreece (ESFRI) Infrastructure.


Network activities


• LifeWatch will make available most of the products developed by ViBRANT
(WP8)
• Some EU projects and Consortia have already adopted the services of the
project as part of their hard-core operational system (e.g. EMBOS, MAPMED,
EU BON, CIGESMED)
• There has been a growing interest in communities for the services and
products of ViBRANT, which has overcome any of the initial anticipation or
assessment, especially in the cases of GeoCAT, CartoDB, and NPT start-up
• Some of these products have already initiated the development of spin-off
schemes (Vizzuality)
• The WP8 is well involved in the proposals under development in the context of
the HORIZONS 2020




Network activities

Our mottos: (a) team work; (b) just DO IT!

WP5: Interaction and
services
Neil Caithness
University of Oxford


WP5: Data Interaction and Services

Service activities

WP Description

To provide seamless integration of relevant external computing
services for biodiversity researchers and Scratchpad users

WP partners

WP Objectives

•
•
•
•
•
•

Stable middle-ware and backend infrastructure
Clean and attractive web-based user interface
Extensible palette of services with server-side post processing
Fully documented machine API for task submission
Loosely coupled architecture for maximum maintainability
Usage tracking by number of tasks, users, and location

Year three effort

37 PM



Service activities

Activities

D5.3
Refined and sustainable software services
available for public use with mechanisms
to measure usage rates


• IKey+ MKey+ (UPMC, ULR, JKI)
• CartoDB (VIZZ)



Service activities

Foreground

OBOE
The purpose of OBOE is to provide easy
access to computing services.



Service activities

Foreground

IKey+ / Mkey+
Single- and multi-access identification keys,
delivered on-demand, via web-services.



Service activities

Foreground

CartoDB
A cloud based mapping, analysis and
visualization engine that lets users build
spatial applications for mobile devices and
the web.



Service activities

OBOE
Description

OBOE is a science gateway to
research computing:
• new methods for developers to
deploy their applications in the
cloud
• easy access for users with no
need for technical knowledge of
cloud computing



Service activities

OBOE

•
•
•
•
•

~200 users
~1000 tasks
Still growing …
… unsolicited new users
Links with Manchester HTC centre

(anticipated soon)

• Support from Microsoft Research
• Migration to Windows Azure



Service activities

IKey+ / MKey+
Description

Online services for identification
using structured descriptive data
(SDD)
• single-access keys (IKey+)
• multi-access keys (MKey+)



Service activities

IKey+ / MKey+

Recently introduced services that are expected
to grow quickly:
• >350 IKey+ keys in Oct & Nov 2013
• >150 MKey+ keys in Oct & Nov 2013



Service activities

CartoDB
Description

CartoDB was launched in April 2012,
version 2.0 was released in Nov 2012.
The platform is already being used by
major news organizations, research
institutions, non-profits, and geospatial
application developers the world
throughout.



Service activities

CartoDB
The latest CartoDB release allows anyone to
create geo-temporal maps directly from their
browser. To make this possible, the CartoDB
team has been quietly perfecting a new
technology over the past few months. CartoDB
is already being used by the UN, US National
Park Service, Twitter, The Guardian and the
World Resources Institute.



Service activities


IEEE/ACM CCGrid 2014
14th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing
May 26-29, 2014 -- Chicago, IL, USA

Microsoft Research Awards
~40K


WP6: Scholarly
publishing
Lyubomir Penev
Pensoft Publishers


WP6: Scholarly Publishing

Service activities

WP Description

Develop novel tools and workflows to streamline the publication
process at all stages, starting from authoring, through peer-review
and editing, to publishing and dissemination. Develop and promote
XML tagging and semantic Web publishing in the biodiversity
domain. Establish a novel data publishing platform.

WP partners

WP Objectives

• Automated submission, review and publication from Scratchpads
and GBIF
• New methods of XML tagging
• Streamline the scholarly publication process
• Automated deposition of taxon descriptions
• Highly automated data publishing workflow
• Semantic enhancements to biodiversity publications

Year three effort

14.6 PM



Service activities

Activities
D6.3 Data publication workflow
Biodiversity Data Journal and Pensoft Writing Tool:

• a next-generation, narrative (text) and data

integrated, publishing workflow
• authoring, peer review and publication
within a single platform, for the first time
• community peer review

•
•
•
•
•

ReFindit tool
Bibliography of Life, RefBank and ReFindit
interface design
Five research papers
ViBRANT special issue published
Another ViBRANT special issue assembled


Service activities

Foreground

Pensoft Writing Tool (PWT)
An entirely XML-based, manuscript
authoring, online, collaborative platform,
integrated with peer-review, editorial,
publishing and dissemination tools.

Biodiversity Data Journal (BDJ)
Novel, community peer-reviewed, openaccess journal, launched to accelerate
mobilisation, dissemination and sharing of
biodiversity-related data through the act of
scholarly publishing.


Service activities

Pensoft Writing Tool (PWT)
Description
• Full article life cycle, from writing to
publication and dissemination
• Upfront XML markup
• Submit at the click of a button
• Import Darwin Core and other data into text
• Automated import of manuscripts
generated in various platforms
• A set of pre-defined article templates
• Easy online collaborative editing by coauthors and peers
• No layout stage, reduced publication costs!



Service activities

Biodiversity Data Journal (BDJ)
Description
• Making “small” data “big”!
• No lower/upper limit of manuscript size
• Articles structured and stored as DATA
• Community ownership of data
• Download data straight from the text
• A novel community-based peer-review
• Easy online collaborative revisions
• Post-publication peer-review
• Free to publish for now
• Low page charges in future affordable by all



Service activities

Flying start and increasing usage of PWT/BDJ Workflow
PWT Usage Monthly Stats
Authorships

Manuscripts

1/14

12/13

11/13

10/13

9/13

8/13

7/13

6/13

5/13

4/13

3/13

2/13

1/13

1400
1200
1000
800
600
400
200
0

BDJ Usage Monthly Stats
Authors

Papers

140
120
100
80
60
40

• Innovative, XML-based publishing workflows,
proven successful; currently a model for
other publishers to follow
• Increased dissemination and re-use of
published content
• “Small” data publishing in BDJ: a globally
unique and viable data mobilisation tool
• Educational and sociological impact of data
publishing and sharing
• Low production costs will ensure reduced
page charges and facilitate sustainability
• The PWT/BDJ workflow has potential to
expand in other domains

20
0
9/2013

10/2013

11/2013

12/2013

1/2014



Service activities


• Expansion of the PWT/BDJ workflow in other domains, in first place
Genomics, Biomedicine, Agricuture, etc.
• Launch of industry standard, XML-based data publishing platform as a service
for other journals or publishers
• Further promotion and increased number of users of PWT/BDJ
• Adoption of XML markup and semantic enhancements by other journals
• Further automation of input and output data publishing formats
• Closer integration with Scratchpads, GBIF, and other data suppliers
• Possible solution for the “dark” taxa problem
• Re-publishing and databasing of historical literature



Service activities

Welcome aboard!

ViBRANT Impact and
Product Sustainability
Vincent Smith


Impact and Product Sustainability

KPIs / Scientific Impact
Product

Usage

Scratchpads

7,000 active users 1.5m* visitors

OBOE

1,000 job
submissions

BDJ/PWT

22,000 unique
visitors/3 months
47 articles since
launch

GeoCAT

1,000 assessments
5 official IUCN
assessments

COMBER

409 activities - 5,600
observations

Scratchpads visitors

Ikey+/Mkey+

500 keys produced

* 1.2m during ViBRANT




62 Scientific publications in 20 international
scientific journals from 97 different authors
Three special issues (one more in preparation)
Zookeys v.150: e-Infrastructures for data publishing in
biodiversity science
Zookeys v.209: No specimen left behind: mass digitization of
natural history collections
Zookeys v.365: DNA barcoding: a practical tool for
fundamental and applied biodiversity research

Selected publications:
5%

•

•
•
OA
95%

not OA

•

Hardisty A., Roberts D & The Biodiversity Informatics Community.
A decadal view of biodiversity informatics: challenges and
priorities. BMC Ecology 13 (2013)
Duin D. et al. Identifying audiences of e-infrastructures – Tools
for measuring impact. PLoS ONE 7 (2012)
Smith et al. Collaborative electronic infrastructures to accelerate
taxonomic research. ZooKeys 150 (2011)
Harfoot M, Roberts D. Data would help ecosystem models.
Nature (2014)


Impact of Scratchpad communities to the
wider scientific community

Citations to Scratchpad communities

Average of > 100 citations per year (2012)
in scientific Journals to Scratchpads
communities and the Scratchpads project

Citations to the Scratchpad project



105 Conference presentations in 23 countries
(Europe, America, Asia, Africa & Oceania)
96 workshops and training courses in 24 Countries
Marie Curie fellowship (IIF) – ViBRANT-BioVeL
Biodiversity Informatics Horizons 2013, Rome
200 participants – 6 organising, 17 participating EU FP7 projects
Spin-off: h2020.myspecies.info for coalescing community activities
and support future joined actions



D2.3: Financial Sustainability
A service will be considered
sustainable if it is both available and
continues to be used on an
open-ended basis

A federated network of compatible
services with no single point of failure


D2.3 Financial Sustainability
Scratchpads

Status: secure

Platform for Cybertaxonomy

Status: secure

Biowikifarm

Status: secure

PWT & Scratchpad publication tool

Status: secure

Nodes Portal Toolkit Startup

Status: secure

OBOE

Status: uncertain

RefBank

Status: reasonably secure

GoldenGATE


Xper2

Status: secure

GeoCAT

Status: secure

CartoDB

Status: secure

COMBER




A successful hybrid sustainability model

Anchoring to core funding
•
•

Society

Generate compelling use cases to enable
support by associated institutions
Develop towards mutually established goals
(e.g. ESFRI objectives, EU objectives)

Community

Institution

+
Investment in Crowdsourcing
• Nurture a community based
sustainability model
• Minimise support and development
costs by outsourcing to the end user
communities

Confidence

Agility

Marketing


Drupal CMS
git repository
Modularity

Scratchpads portal

Ambassadors scheme
Co-learning environment

Issues queue

Wiki based documentation
Train the trainers effort

Self-learning (e.g. sandbox)


Identifying common goals
Investigation of the interaction area with
other EU funded projects, tools and
services
BIH 2013 Conference
200 participants – 17 supporting projects
The White paper
"A decadal view of biodiversity informatics:
challenges and priorities." BMC
ecology (2013)
Interactions with
BioVeL, agInfra, ISA-tools, CIGESMED, EUBON

135 registered users from 28 countries



Future plans
• Sustain the existing tools and services
• Capitalise on ViBRANT’s successful products
and promote Innovation for future scientific
application scenarios
• Identify potential convergence with other EU
initiatives

Work towards supporting
the data to model the Biosphere

WP1: Management and
Financial Matters
Vincent Smith / Dave Roberts


WP1: Management & Financial Matters

Service activities

WP Description

Workpackage 1 provides the consortium financial management
required by the Commission and integration of the activities
undertaken within the consortium

WP partners
The logos of the
partners will be
included at the final
stage of merging all
the presentations –
Do not fill this in

WP Objectives

• Project management
• Consortium coordination
• Financial administration

Year three effort



D1.1: Overall management
Agile Management

Properties of Agile management

• More efficient and responsive
management model
• Re-direction of some aspects of
project to better integrate with the
other elements and create a better
product (e.g. WP7)
• Our user-centric focus required a
easily adaptable management model



Project agile management

Year 1
Prototyping

Year 2

Year 3

Operation

Integration



Project management elements
Management committee

Project Reporting
Management of resources
Advisory Board
Consortium members
Interactions with other projects



Digital Project management
Project structure
DoW and modifications
Deadline monitoring

Project outputs
Scientific papers, Deliverables &
Milestones, Presentations, Reports
Effective communication
Forums for WP, Administration and
Researchers with more than 1100
registered posts
Open access
Scratchpads based website



Outputs
•
•
•

•

Deliverables all completed on time
164 Milestones
3
Annual consolidated reports
1
Final report
23



Management Committee
• 12 meetings (7 through teleconferencing)
• Open proceedings (Agenda & Minutes)
• Management by consensus (no voting
necessary)

Project reporting
• In each annual review new milestones for
the next year
• Single narrative reports drafted
• All reporting documents online



Year 3 financial breakdown
Budgeted spend

REDACTED



Year 3 financial breakdown

REDACTED



Project financial breakdown
Budgeted spend

REDACTED




REDACTED



Community Contribution

REDACTED


Wednesday 29th January 2014
EC premises (Room 0/S5)
Avenue de Beaulieu 25
1160 Brussels

Final review meeting

Consolidated ViBRANT Project Final Review Presentations

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