pro-iBiosphere

The pro-iBiosphere project will soon come to an end

Wed, 20 Aug 2014 10:35:00 +0300

The Coordination and Support Action pro-iBiosphere will come to an end by the 31^st of August 2014. The project was launched for two years to investigate ways to increase the accessibility of biodiversity data, improve the efficiency of its curation and increase the user base of biodiversity data consumers and applications. Ten of its key major outcomes have been summarised in the "pro-iBiosphere final brochure".

The project delivered a series of recommendations on various pressing topics to the wider biodiversity informatics community, for instance, on how to improve the use of digital infrastructures among taxonomists, on how to addresses barriers to the open exchange of biodiversity knowledge that arise from European laws, in particular European legislation on copyright and database protection rights. The recommendations have been documented in various pro-iBiosphere deliverables (here available).

The project conducted 5 pilots and organised a total of seven meetings. The enthusiasm, involvement and breadth of the community participation to these meetings was very impressive!. The pro-iBiosphere final event took place from the 10^th - 12th of June 2014 at the Bouchout Castle (Botanic Garden Meise, Belgium). An audience consisting of more than 75 persons participated in the event. Activities organised during the event included a Workshop on the Biodiversity Catalogue, Demonstrations on the project pilots, Demonstrations on the outcomes of the Data Enrichment Hackathon, a Training on WikiMedia, a Poster session and the Final Conference.

A major highlight of the Final conference was the official launch and ceremony of the Bouchout Declaration for Open Biodiversity Knowledge Management. At present (August 2014) more than 170 institutions and 90 organisations have signed the Declaration. For more information please see the news items "The Bouchout Declaration: A commitment to open science for better management of nature" (published below on page # and "The Bouchout Declaration: A contribution from the biodiversity community to Open Digital Science" (published on the Digital Agenda for Europe website).

The conference proceedings, including an event report (detailing the statistics and outputs of the Final Conference), a Storify (i.e. a collection of tweets and pictures) and pictures, are available here.

It has been a pleasure working with all of you!

Soraya Sierra

pro-iBiosphere Project Leader

Scaling in ecology and biodiversity conservation explained in a book and an online tool

Mon, 04 Aug 2014 18:14:00 +0300

The 5-year EU project Securing the Conservation of biodiversity across Administrative Levels and spatial, temporal, and Ecological Scales (SCALES) has come to an end in July 2014 resulting in a first of its kind description of challenges that arise in protecting biodiversity across different scales.

A wide range of practical methods and recommendations to improve conservation at regional, national and supranational scales are included in a book published as a synthesis of project outcomes. The book "Scaling in Ecology and Biodiversity Conservation" was published in advanced open access via Pensoft Publisher's Advanced Books platform. This innovative format aimed at accelerating data publishing, mining, sharing and reuse, offers a range of semantic enhancements to book contents, including external sources.

Results are also presented in an easy to use interactive SCALETOOL, specifically developed for the needs of policy and decision-makers. The tool also provides access to a range of biodiversity data and driver maps compiled or created in the project.

Human actions, motivated by social and economic driving forces, generate various pressures on biodiversity, such as habitat loss and fragmentation, climate change, land use related disturbance patterns, or species invasions that have an impact on biodiversity.

Each of these factors acts at characteristic scales, and the scales of social and economic demands, of environmental pressures, of biodiversity impacts, of scientific analysis, and of governmental responses do not necessarily match. However, management of the living world will be effective only if we understand how problems and solutions change with scale.

'The book and the tool are the first of their kind and would be of great help to everyone concerned with the conservation of biodiversity. They provide ideas of how to handle complex issues of scaling in applied and theoretical environmental studies' says the chief editor Prof. Klaus Henle.

The book aims to bundle the main results of SCALES in a comprehensive manner and present it in a way that is usable not only for scientists but also for people making decisions in administration, management, policy or even business and NGOs; to people who are more interested in the "practical" side of this issue.

Guidelines, practical solutions and special tools are also presented as a special web based portal, SCALETOOL, which puts together scientific outcomes widely spread over the scientific literature.

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Original Source:

Henle K, Potts S, Kunin W, Matsinos Y, Simila J, Pantis J, Grobelnik V, Penev L, Settele J (Eds) (2014) Scaling in Ecology and Biodiversity Conservation. Advanced Books: e1169. doi: 10.3897/ab.e1169

Creative Commons Signs the Bouchout Declaration

Fri, 18 Jul 2014 12:16:19 +0300

Creative Commons, a nonprofit organization that enables the sharing and use of creativity and knowledge through free legal tools, just signed the Bouchout Declaration in line with its vision and commitment to open science Data.

Creator and steward of the legal and technical infrastructure that allows open licensing of content, the non profit organization entirely supports the Declaration which exhorts the use of licenses or waivers to grant all users a free right to copy, use, distribute, transmit and display the work publicly, as well as to build on the work and to make derivative works, subject to proper attribution consistent with community practices.

Creative Commons, which has participated in the activities that led to the Joint Declaration of the Data Citation Principles and advocates the use of persistent identifiers to allow discovery and attribution of resources, encourages the Declaration to promote tracking the use of identifiers in links and citations. This methods ensures that sources and suppliers of data are assigned credit for their contributions and Persistent identifiers for data objects and physical objects such as specimens, images and taxonomic treatments with standard mechanisms to take users directly to content and data.

Creative Commons, which works assiduously on fostering the promulgation of open policies and practices, naturally encourages the declaration calls for Policy developments to foster free and open access to biodiversity data.

If you too believe that open biodiversity information is crucial for science and society, join the movement and sign the Bouchout Declaration!

BioVeL meeting "In Practice and in future" to be hosted in Paris, France on November 13, 2014

Tue, 15 Jul 2014 10:30:51 +0300

The next BioVel meeting will take place in Paris, France on November 13, 2014.

This one-day event, entitled "BioVeL : In Practice and in future" aims at presenting the achievments, experiences gained and lesson learnt from the BioVel initiative which has been working on building a virtual laboratory for biodiversity research. This event will also provide an opportunity to introduce BioVel plans for the future.

BioVeL is a pilot implementation of some of the core ideas from the LifeWatch Preparatory Phase. In the past three years the project has been working with the biodiversity research community to construct, test, and revise some essential elements of a robust e-infrastructure for biodiversity and ecosystem research.

The event will be structured around the 3 key goals that encapsulate the BIH2013 initiative.

• Integration: Making better use of existing data and tools.
• Cooperation: Working together towards a global biosphere model.
• Promotion: Informatics leadership to serve the needs of science and policy.

For more information and registration, click here.

For any additional information, please contact: elisabeth.paymal@fondationbiodiversite.fr.

Find out more on the BioVel project a www.biovel.eu.

The Bouchout Declaration highlighted by the European Commission via the EC Digital Agenda website

Tue, 08 Jul 2014 18:38:38 +0300

The article published on July 7, 2014 on the European Commission Digital Agenda website presents the Bouchout Declaration launched by the project on June 12, 2014 like a major contribution from the biodiversity community to Open Digital Science.

The article stresses that only three weeks after being launched, this unprecedented declaration have already been endorsed by more than 70 institutions and 140 individuals from 40 countries around the Globe. A total success!

With their signature, the management of the organizations and individuals encourage an overarching approach to Biodiversity Knowledge Management based on the principles of Open Access, the use of unique stable identifiers for data objects, resolution mechanisms that take users directly to content and data, registries that allow discovering, access and re-use of the data as well as fostering an ongoing dialogue to refine the concept of Open Biodiversity Knowledge Management.

The Bouchout Declaration has been translated into 8 languages available online on the Bouchout Declaration website.

Follow the Bouchout Declaration on twitter @bouchoutdec

Read the full article by the European Commission online at www.ec.europa.eu/digital-agenda

Successful outputs of the pro-iBiosphere Final Conference held in Meise

Thu, 26 Jun 2014 18:20:56 +0300

The pro-iBiosphere Final Conference successfully took place in Meise on June 12, 2014 at the Bouchout Castle in the Botanic Garden Meise in the North of Brussels. More than 75 participants from the biodiversity and/or e-Infrastructures community joined the active discussions while (i) reviewing project results and the key areas of improvement in the design and implementation of an OBKMS and (ii) providing recommendations on future research needs for the preparation of the next WP 2016-2017 of EU Horizon 2020 Framework Programme for Research and Innovation.

On this occasion, one of the major highlight of the conference has been the official launch ceremony of the Bouchout Declaration on Open Biodiversity Knowledge Management System (OBKMS) in which key biodiversity institutions officially signed it together and the release of the Bouchout Declaration website. Following the event, a total of 66 organizations and 116 individuals endorsed the Declaration. The Declaration has been translated into 8 languages available online on the dedicated website.

The Final Conference has been the last meeting organised among a series of activities, so-called pro-iBiosphere Final event, including (i) MS24 - Model Evaluation Workshop held on June 9-10, (ii) Training on Wikimedia, (iii) Biodiversity Catalogue (BioVeL) Workshop, (iv) Demonstrations on project pilots, (v) Demonstrations on outcomes of pro-iBiosphere Data Enrichment Hackathon and a Poster session organised during coffee breaks on June 11.

The proceedings of the Final Conference (updated agenda with presentations, final attendee list and pictures) with conclusions of each session are available on the wiki page.

An event report has also been produced and is available here detailing the Final Conference objectives, programme, promotion, audience and outputs.

For any additional information, please contact us at info@pro-ibiosphere.eu.

ICT Proposers' Day 2014 - Registration is open

Tue, 24 Jun 2014 11:19:53 +0300

The ICT Proposers' day 2014 (#ICTpropday) is a networking event organised by the European Commission and will be held in Florence, Italy on the 9th and 10th of October 2014.

This event is specifically dedicated to networking and promoting research and innovation in the field of Information and Communication Technologies. It will focus on networking for the Horizon 2020 Work Programme 2015.

It is free of charge and offers an exceptional occasion to build quality partnerships as it will connect academia, research institutes, industrial stakeholders, SMEs and government actors from all over Europe. The registration to attend the event is now open.

Find out more on ICT Proposers’ Day website. Register now here.

The 5th BioVeL project newsletter released

Thu, 19 Jun 2014 09:57:35 +0300

The BioVeL project, supporting research on biodiversity by offering computerized tools ("workflows") to process large amounts of data from cross-disciplinary sources is proud to announce the release of its Spring 2014 newsletter.

The 5th BioVeL newsletter focuses on the latest developments with the e-laboratory, especially with its new portal. It also addresses the sustainability of the project.

pro-iBiosphere and the BioVeL project have been in close contact in the past months while pro-iBiosphere became a " BioVeL friend ", supporting the objectives of the BioVeL project and the BioVeL project participated in the pro-iBiosphere Final Event while organising a Workshop on Biodiversity Catalogue on June 11, 2014 and financially sponsoring catering and lunch on that day.

The Spring 2014 BioVeL newsletter is available online here.

The Bouchout Declaration: A commitment to open science for better management of nature

Thu, 12 Jun 2014 16:42:00 +0300

The Bouchout Declaration targets the need for data to be openly accessible, so that scientists can use the information for new types of research and to provide better advice. Currently, data may be prevented from becoming open or usable because of copyright оr concerns of institutions that hold the data, or because it is not in a form that can be easily managed by computers. The Declaration identifies mechanisms to structure open data so that they can be drawn together, queried and analysed on a much larger scale than was previously possible.

The Bouchout Declaration allows the community to demonstrate its support for data to be openly available. It extends previous efforts, like the Berlin Declaration, to the biodiversity sciences. The objective is to promote free and open access to data and information about biodiversity by people and computers. This will help to bring about an inclusive and shared knowledge management infrastructure that will inform our decisions so that we respond more effectively to the challenges of the present and future.

"Biodiversity research is painstakingly built up from the study of billions of specimens over hundreds of years from every region of the Earth. We are now in a position to share this hard-won knowledge freely with everyone who wishes to read, extend, interconnect, or apply it. We should do so as soon as humanly possible. If we do, we will not only make biodiversity research more accessible, discoverable, retrievable, and useful. We will make it more useful for the critical purpose of preserving biodiversity itself," comments Peter Suber from the Harvard Open Access Project on the significance of the declaration.

International initiatives like the Global Biodiversity Information Facility (GBIF) support science and society by gathering and helping scientists to analyse knowledge acquired by past generations and from streams new observations and technologies. The GBIF's Executive Secretary Donald Hobern commented: "This knowledge cannot be recreated and needs to be used and reinterpreted over time. We need to manage it as a precious resource of value to the whole human race. This is why Open Biodiversity Knowledge Management matters."

The Bouchout Declaration emerged from the pro-iBiosphere project (a Coordination and Support Action funded through the European Union's Seventh Framework Programme (FP7/2007-2013) under Grant Agreement №312848 ) as a reaction to the need of better access to biodiversity information. The inaugural ceremony of the Bouchout Declaration (including official launch of the website) will take place on the 12th of June 2014 during the final event of the project.

"Museum collections around the world hold invaluable biodiversity information that are often hidden in dark rooms. Digitalizing and providing free and open access to these resources through an Open Biodiversity Knowledge Management System in Europe is crucial for the advancement of biodiversity research and better management of nature for a sustainable future. We are happy to be one of the first institutions which endorsed the Declaration" concluded Prof. Johannes Vogel, Director General of the Museum für Naturkunde, Berlin.

Universities, research institutions, funding agencies, foundations, publishers, libraries, museums, archives, learned societies, professional associations and individuals who share the vision of the Bouchout Declaration are invited to join the signatories. If you wish to join the list of signatories or would like to receive additional information please email bouchout@plazi.org.

Among the initial signatories are some of the world's leading natural history museums, botanical gardens, and scientific networks.

Official launch of the Bouchout Declaration for Open Biodiversity Knowledge Management

Thu, 12 Jun 2014 16:32:04 +0300

The Bouchout Declaration is a major output from the pro-iBiosphere project.

The Bouchout Declaration is an opportunity for those organizations, initiatives and individuals who create, manage and use biodiversity information, and who believe in the opportunities and potential of the big data world, to declare their support of the Open Access agenda.

By endorsing the principles of Open Access and discoverability of data, the signatories strengthen the arguments that will be put to governments and funding bodies, and will accelerate the maturation and evolution of Open Biodiversity Knowledge Management, making biodiversity sciences more relevant, innovative, and responsive to societal needs.

As of to-date, 73 signatories from 26 countries share the vision expressed in the Bouchout Declaration.

The Bouchout Declaration official launch took place today during the pro-iBiosphere Final Conference at Bouchout Castle, Botanic Garden Meise in Belgium. The offical Website (bouchout-declaration.org) has been unveiled on this occasion.

If you also share the vision of the Bouchout Declaration, we invite you to sign this document here.

Classical monographs re-published in advanced open access

Wed, 11 Jun 2014 15:45:00 +0300

The new Advanced Books platform of Pensoft opens new horizons for semantic book publishing

Easy access to legacy data collected over hundreds-of-years of exploration of nature from the convenience of people's own computers for anyone all over the world? It may sound futuristic but a brand new pilot showcases how this is possible here and now.

The new workflow demonstrates a re-publication of a volume of Flora Malesiana in a semantically enriched HTML edition available on the newly launched, Advanced Books publishing platform. The platform was demonstrated today at the EU funded pro-iBiosphere project which supported, in part, the re-publication of Flora Malesiana.

When Linnaeus was laying the foundations of taxonomy as a science in his Species Plantarum and Systema Naturae books he probably did not imagine that his methods of publication of natural history data would remain almost unchanged for more than 270 years! The bulk of the information on the living World is still closed in paper-based legacy literature, especially in fundamental regional treatises such as Flora, Fauna and Mycota series, hardly accessible for readers, despite the dramatic changes in the publishing technologies that have taken place over the last decade.

The new pilot, developed by Pensoft Publishers in a cooperation with the Naturalis Biodiversity Center, Plazi, and Botanischer Garten und Botanisches Museum Berlin-Dahlem (BGBM), demonstrates how a fundamental book in natural history can start a new life with Advanced Books. Re-publication of the Flora of Northumberland & Durham, published in 1838, will be the next to appear as a result of a collaboration between the Botanical Garden Meise National Botanic Garden of Belgium and Pensoft.

Flora Malesiana is a systematic account of the flora of Malesia, the plant-geographical unit spanning six countries in Southeast Asia: Indonesia, Malaysia, Singapore, Brunei Darussalam, the Philippines, and Papua New Guinea. The plant treatments are not published in a systematic order but as they come about by the scientific efforts of some 100 collaborators all over the world.

With the new platform, such scientifically important historical monographs, enriched with additional information from up-to-date external sources related to organisms' names, species treatments, information on their ecology, distribution and conservation value, morphological characters, etc., become freely usable for anyone at any place in the world.

The re-publication in advanced open access comes with the many other benefits of the digitization and markup efforts such as data extraction and collation, distribution and re-use of content, archiving of different data elements in relevant repositories and so on.

"Advanced Books will bring many outstanding scientific monographs to a new life, however the platform is not only restricted to e-publish our legacy literature." commented Prof. Lyubomir Penev, Managing Director of Pensoft. "New books are mostly welcome on the platform, joining their historical predecessors in an open, common, human- and machine-readable, data space for the benefit of future researchers and the society in general" concluded Prof. Penev.

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Original Source:

de Wilde W (2014) Flora Malesiana. Series I - Seed Plants, Volume 14. Myristicaceae. Advanced Books: e1141. doi: 10.3897/ab.e1141

Open exchange of scientific knowledge and European copyright: The case of biodiversity information

Sun, 08 Jun 2014 17:23:00 +0300

As a part of the series of final project utputs a new pro-iBiosphere article published in the open access journal ZooKeys assesses the need and future for building an Open Biodiversity Knowledge Management System (OBKMS) - the infrastructure for a system that will intelligently manage and integrate digital biodiversity information.

Background. The 7th Framework Programme for Research and Technological Development is helping the European to prepare for an integrative system for intelligent management of biodiversity knowledge. The infrastructure that is envisaged and that will be further developed within the Programme "Horizon 2020" aims to provide open and free access to taxonomic information to anyone with a requirement for biodiversity data, without the need for individual consent of other persons or institutions. Open and free access to information will foster the re-use and improve the quality of data, will accelerate research, and will promote new types of research. Progress towards the goal of free and open access to content is hampered by numerous technical, economic, sociological, legal, and other factors. The present article addresses barriers to the open exchange of biodiversity knowledge that arise from European laws, in particular European legislation on copyright and database protection rights.

We present a legal point of view as to what will be needed to bring distributed information together and facilitate its re-use by data mining, integration into semantic knowledge systems, and similar techniques. We address exceptions and limitations of copyright or database protection within Europe, and we point to the importance of data use agreements. We illustrate how exceptions and limitations have been transformed into national legislations within some European states to create inconsistencies that impede access to biodiversity information.

Conclusions. The legal situation within the EU is unsatisfactory because there are inconsistencies among states that hamper the deployment of an open biodiversity knowledge management system. Scientists within the EU who work with copyright protected works or with protected databases have to be aware of regulations that vary from country to country. This is a major stumbling block to international collaboration and is an impediment to the open exchange of biodiversity knowledge. Such differences should be removed by unifying exceptions and limitations for research purposes in a binding, Europe-wide regulation.

Original Source:

Egloff W, Patterson DJ, Agosti D, Hagedorn G (2014) Open exchange of scientific knowledge and European copyright: The case of biodiversity information. ZooKeys 414: 109–135. doi: 10.3897/zookeys.414.7717

Last days to register for the pro-iBiosphere Final Event (held on June 10-12 in Meise)

Wed, 04 Jun 2014 17:02:17 +0300

Do not miss this unique opportunity and join us in Meise (Brussels) from June 10-12 to participate in this major event devoted to making fundamental biodiversity data digital, open and re-usable (organized by the pro-iBiosphere project funded by the European Commission DG Connect)!

This pro-iBiosphere Final Event is taking place at a crucial time for the development of new instruments for the future needs of biodiversity research through the preparation of the next WP 2016-2017 of EU Horizon 2020 Framework Programme for Research and Innovation.

Within this context, one of the main highlights of the conference will be to provide key recommendations and inputs from biodiversity experts to the European Commission.

In this context, if you plan to attend and have not yet registered, please do it here (free of charge).

Follow and contribute to the Final Event discussions while tweeting using the following hashtag: #pibmei !

For further information on this event please visit the dedicated wiki page here or contact us at final-event@pro-ibiosphere.eu.

Register now to the pro-iBiosphere Final series of events in Brussels!

Wed, 30 Apr 2014 09:42:00 +0300

by Stephanie Morales

The pro-iBiosphere project supported by the European Commission (DG CONNECT) through its FP7 research funding programme has the pleasure to invite you to join its Final Event.

During its two-year duration, pro-iBiosphere contributed to making fundamental biodiversity data digital, open and re-usable. The achievements of the project will be presented in a series of activities (workshops, trainings, demonstrations and a Final Conference) that will take place from Tuesday the 10th to Thursday the 12th of June 2014 at the Bouchout Castle in the Botanic Garden Meise, in Meise (Brussels), Belgium.

The event wiki page here has been recently updated with additional information on the different series of activities organised and the Final Conference agenda now comprises worldwide high-level speakers, including (i) officials from the European Commission DG Connect, the US National Academy of Sciences, (ii) representatives from botanic gardens, natural museums, other biodiversity initiatives and (iii) experts or (iv) researchers specialized in biodiversity informatics, environmental/natural science.

One of the key objectives of these series of events is to provide key recommendations and inputs from biodiversity experts for the preparation of the next WP 2016-2017 as specifically asked by the European Commission.

The number of registered attendees has already reached a good level of participation, in this context, if you plan to attend and have not yet registered, we can only recommend you do to it as soon as possible here (due to room capacity constraints).

For further information on this event (agenda, concept & objectives, registration) please visit the Event wiki page or contact us at final-event@pro-ibiosphere.eu.

pro-iBiosphere project demonstrates its pilots at the final conference in Meise (Brussels)

Tue, 29 Apr 2014 15:51:00 +0300

The pro-iBiosphere Final Event will take place on 9 – 13 June 2014 at the Bouchout Castle of the Botanic Garden Meise, Brussels. During the third day of the meeting a special event is designated for the demonstration of the pro-iBiosphere pilots.

During this session, the task and pilot leaders will demonstrate the tools and workflows developed or improved in the course of the project. The demonstration will be interactive and will allow for discussions, real-time tests and consultations on possible implementations by the interested stakeholders. The pilots and demos planned until now are:

Interoperability of taxon treatments

In the past, taxonomic information has been published in numerous scattered outlets and in different formats. The production of a taxonomic revision or such as a flora or fauna required that the appropriate text was discovered, and retyped manually. The current pilot demonstrates a greatly accelerated workflow that takes advantage of the informatics developments of pro-iBiosphere. The workflow locates, identifies, and enhances data included in treatments from both legacy and newly published taxonomic literature, facilitating discovery, analysis, and reuse through the Plazi Treatment Repository (PTR).

The workflow includes the following steps:

Step 1: Convert printed taxonomic articles/monographs to digital text format.
Step 2a: Mark up generic document features and domain-specific information (taxon treatments) and store the results at Plazi; and also
Step 2b: Export of newly published treatments marked up during the editorial process (for example in the journals ZooKeys, PhytoKeys and Mycokeys)
Step 3: Browse, search, export and re-use treatments coming from different sources.

Streamlining automated registration of taxon names between publishers and registries

The pre-publication registration of taxonomic and nomenclatural acts with registries such as the International Plat Name Index (IPNI), Index Fungorum, MycoBank, and ZooBank involves two main classes of actors: (1) publishers, and (2) registry curators. The publisher takes the responsibility for initiating the registration of nomenclatural acts so that the workﬂow can be performed following a common stepwise model:

Step 1. XML message from the publisher to the registry on acceptance of the manuscript containing the type of act, taxon names, and preliminary bibliographic metadata; the registry will store the data but not make these publicly available before the ﬁnal publication date.
Step 2a. Response XML report containing the unique identiﬁed of the act as supplied by the registry and/or any relevant error messages.
Step 2b. Error correction and d-duplication performed manually: human intervention at either registry’s or publisher’s side (or at both).
Step 3. Inclusion of registry supplied identiﬁers in the published treatments (protologues, nomenclatural acts).
Step 4. Making the information in the registry publicly accessible upon publication, providing a link from the registry record to the artice.

Improved cooperation and interoperability of e-infrastructures

Challenges related to the technical interoperability of biodiversity data present themselves in competing standards, ambiguous, poor or absent documentation, lack of stable identifier systems and the absence of semantic interoperability. For improving the interoperability between e-infrastructures, stable identifiers for biodiversity collection objects and a global service registry were identified as the two major achievables for progress. The use of state-of-the-art digitisation software & tools for literature markup is another important factor.

Steps forward 1: Implementation of HTTP-URIs by 8 major institutions for their collection objects by October 2013 and recommendations for further topics to be explored in detail.
Steps forward 2: Agreement on the BiodiversityCatalogue as a global registry for biodiversity related services. Improvement recommendations for it to be able to fill this role even better, registration of services available now.
Steps forward 3: Workflow improvement between the Plazi document registry and the Common Data Model (CDM)-based EDIT Platform for Cybertaxonomy (http://wiki.pro-ibiosphere.eu/wiki/Pilot_3 ). In the course of this a markup granularity table evolved. The pro-iBiosphere pilot portals visualize the data results at different stages and show the possibilities for scientists willing to mark up their data. The markup granularity table explains in detail work load and connected output gain.

Workshop on mark-up of biodiversity literature

Sat, 26 Apr 2014 16:20:00 +0300

Daniel Mietchen (Museum für Naturkunde Berlin)

For two days in February 2014, a pro-iBiosphere workshop on mark-up of biodiversity literature brought together a group of 20 participants at the Museum für Naturkunde in Berlin. In an introductory talk, Rod Page of the University of Glasgow presented the idea of a biodiversity knowledge graph that interlinks the biodiversity literature with the wider biodiversity information landscape. He then discussed a number of use cases for mark-up - namely for archiving, display and citation linking - and questioned whether it was actually necessary for identifying nodes and extracting edges of the knowledge graph, which could be achieved by simple indexing. He also discussed collaborative editing and version control with regards to mark-up.

With this introductory presentation having set the stage for discussing mark-up of the biodiversity literature in general terms and from a long-term perspective, the following presentations looked at specific subsets of that literature corpus, at specific use cases, at specific approaches to mark-up, and at workflows and business models around that. For example, Dimitris Koureas of the Natural History Museum in London discussed how the mark-up of specimen records in the literature could help with the digitization of specimen labels (which are often transcribed in systematic reviews of taxa or collections), and how the tracking of specimen citations in the literature could allow to assess the impact of collections on current and past research. Another perspective was provided by William Ullate of the Biodiversity Heritage Library, who described how BHL is ramping up its efforts on mark-up, including through gamification.

Throughout the workshop, there was a lively discussion, and the individual talks were given not according to a fixed schedule but when the respective topic came up in the discussion. All presentations are linked from the workshop page on the pro-iBiosphere wiki.

Figure 1: The Biodiversity Knowledge Graph. By Roderic Page.

The 2014 Biodiversity Data Enrichment Hackathon in a nutshell

Sat, 26 Apr 2014 16:08:00 +0300

Soraya Sierra*, Rutger Vos* (Naturalis Biodiversity Center)

*soraya.sierra@naturalis.nl, rutger.vos@naturalis.nl

From 17 – 21 March 2014, software developers and taxonomists came together in Leiden, the Netherlands, to address the challenges, and highlight the opportunities, in the enrichment of biodiversity data by engaging in intensive, collaborative software development: The Biodiversity Data Enrichment Hackathon. The event had two goals:

To facilitate re-use and enhancement of biodiversity knowledge by a broad range of stakeholders, such as ecologists and niche modelers.
To foster a community of experts in biodiversity informatics and to build human links between research projects and institutions.

The Hackathon brought together 37 participants (including developers and taxonomists, i.e. scientific professionals that gather, identify, name and classify species) from 10 countries: Belgium, Bulgaria, Canada, Finland, Germany, Italy, the Netherlands, New Zealand, the UK, and the US. The participants brought expertise in processing structured data, text mining, development of ontologies, digital identification keys, geographic information systems, niche modeling, natural language processing, provenance annotation, semantic integration, taxonomic name resolution, web service interfaces, workflow tools, and visualization.

The Biodiversity Data Enrichment Hackathon followed a use-case-driven model, i.e. a model where effort during the Hackathon was prioritized on the basis of compelling end user scenarios that could be enabled by the combined contributions of people that otherwise, outside of the Hackathon, do not collaborate. Most use cases and exemplar data were provided by taxonomists. The suggested use cases resulted in nine breakout groups addressing three main themes: (i) mobilizing heritage biodiversity knowledge; (ii) formalizing and linking concepts; and (iii) interoperability between service platforms.

Beyond deriving prototype solutions for each use case, areas of insufficiency were discussed and are being pursued further. It was striking how many possible applications for biodiversity data there were and how quickly solutions could be put together when the normal constraints to collaboration were broken down for a week. Conversely, mobilizing biodiversity knowledge from their silos in heritage literature and natural history collections will continue to require formalization of the concepts (and the links between them) that define our research domain as well as increased interoperability between the software platforms that operate on these concepts.

The tangible outcomes of the Hackathon are finding sustainable homes in the appropriate code bases (e.g. the code bases for CDM platform, the Plazi server, the BHL server) and registries and repositories (e.g. the BiodiversityCatalogue, the Pypi index, the NCBO BioPortal), or form the basis of proofs-of-concept for scientific publications and project proposals. The main intangible outcomes of the event are turning out to be the fostering of a community of experts in biodiversity informatics and the strengthened human links between research projects and institutions. The event also demonstrated both the ongoing need for data normalization and integration, e.g. through the application of ontologies, as well as the opportunities for innovative research such integration will afford.

Additional information of the Hackathon is available here. The outcomes of the Hackathon will be reported in the Biodiversity Data Journal (May 2014 issue) and presented during the pro-iBiosphere final event.

The Final Link between Legacy Literature and Bioclimatic Modelling

Fri, 25 Apr 2014 16:08:00 +0300

Patricia Kelbert1 and Quentin Groom2

1. Botanischer Garten und Botanisches Museum Berlin-Dahlem, Freie Universität Berlin, Germany

2. Botanic Garden Meise, Belgium

The EDIT Platform for Cybertaxonomy is a convenient tool for managing and editing details of specimens and observations. Also, the BioVel workflows for data refinement and niche modelling provide a powerful means to clean up and analyse the distributions of organisms. A way to join these seamlessly together was lacking so that, at the one end of the workflow, a researcher can manage their data in a user friendly interface, and at the other, sophisticated models of distributions can be generated. This problem was tackled by a task group at the recent pro-iBiosphere Hackathon.

One of the pro-iBiosphere pilots was to use legacy literature as a source of data on the historical changes to the distribution of Chenopodium vulvaria. Details of over 2000 observations and specimens were imported into the Common Data Model (CDM) database administered with the Taxonomic EDITor. Many of these data were extracted from legacy literature through a process of digitization and mark-up. These were imported as a whole into the CDM and are a valuable test dataset for bioclimatic niche modelling. In this way, heterogeneous data was homogenised to make it tractable to statistical analysis.

Until now, the link between database and workflow could only be performed by experienced users, who would need directly access to the database. During the hackathon the task group developed a new Java web-service within the CDM-library. This web-service takes the identifier of a taxon as input and returns a list of specimens or observation details. The precise fields returned were based on the prerequisites for reusing in the BioVel refinement workflow, but also contained other fields that might be useful in the future. In this manner we have completed the final link in a workflow that starts with 16th century botanists and ending with 21st century bioclimatic modelling.

Figure 1. A schema showing the flow of data from legacy publications to modelling workflows. The red arrow shows the additional link in the chain.

Merging, extracting, and annotating biodiversity data with rich semantics using NeXML

Fri, 25 Apr 2014 11:33:00 +0300

Bachir Balech (Institute of Biomembranes and Bioenergetics -
Italian National Research Center), Christian Brenninkmeijer (University of Manchester), Hannes Hettling (Naturalis Biodiversity Center), Rutger Vos (Naturalis Biodiversity Center)

Biodiversity phylogenetics' analysis workflows usually involve various software tools connected in series and depend on different sources and types of data. The proliferation of different, mutually incompatible and poorly defined data syntax standards poses significant challenges both for software developers and end users of such workflows. Recent years have seen the development and adoption of a new, expressive, and easy to process data standard that intends to remedy this issue: NeXML.

NeXML is an XML standard that supports the representation of (among others) taxa, character-state matrices and phylogenetic trees as well as semantic annotations (using RDFa) within one single document and is therefore specifically tailored to ease the interplay of different tools in evolutionary comparative and biodiversity analysis.

Since XML documents are generally intended to be handled by software rather than by users directly, a software tool to easily manipulate NeXML files appears desirable. To this end, participants of the biodiversity data enrichment hackathon (Leiden, the Netherlands, 17 – 21 March 2014) developed web services that can (i) construct NeXML documents from data encoded in commonly-used phylogenetic file formats or add metadata to an existing NeXML document, and (ii) extract information identified by the user from a given NeXML file and represent it in a variety of output formats.

To make the NeXML merger- and extractor tools easily accessible for the biodiversity research community and to enable their integration into existing workflows, they are implemented as RESTful web services, to be hosted by Naturalis Biodiversity Center and made available in the BiodiversityCatalogue. Clients that use these services can be implemented in a variety of ways; proofs-of-concept demonstrate that this is trivially done using the popular workflow management tool Taverna, such that these data merger and extractor facilities are available to the users of, inter alia, BioVeL workflows. Preliminary tests of NeXML merger and extractor have been conducted using data inputs and outputs used by the phylogenetic service set of BioVeL (https://www.biodiversitycatalogue.org/services/31/service_endpoint); while, NeXML extractor output has been tested, visualizing a phylogenetic tree with its taxa associated metadata, by implementing ITOL (http://itol.embl.de/) tool wraper within a taverna workflow.

For more information, visit the project wiki: http://wiki.pro-ibiosphere.eu/wiki/NeXML_Services

Extracting trait information from digitized floras

Thu, 24 Apr 2014 17:16:00 +0300

Robert Hoehndorf (Aberystwyth University), Quentin Groom (Botanic Garden Meise), George Gosline (Royal Botanic Gardens Kew), Claus Weiland (Biodiversity and Climate Research Centre / Senckenberg), Thomas Hamann (Naturalis Biodiversity Center)

The aim of the Traits task group at the recent pro-iBiosphere Biodiversity Data Enrichment Hackathon was to extract plant trait data from digitized Floras (i.e. a book that describes the plant life occurring in a particular region or time). We wanted to demonstrate the feasibility of using an ontology-based approach for extracting and integrating trait information from digitized Floras, even when the Floras are available in different languages. To tackle our main aim, we addressed two main questions: (1) Can we automatically extract trait and phenotype information from Flora descriptions written in multiple languages (English and French)?, and (2) Can we represent and integrate the extracted trait and phenotype information semantically using an ontology-based approach?

Extracting structured information about traits and phenotypes from natural language descriptions is a common problem in mobilizing legacy biodiversity data. One tool that has been developed for this purpose is the CharaParser [1], which is applied in the Phenoscape project [2] and integrated in the Phenex tool [3]. As the flora descriptions in our use cases were written in both on English and French language, and CharaParser primarily supports English language descriptions, we have chosen not to use CharaParser during the Hackathon. Instead we followed a simple text matching approach applicable to multiple languages. In particular, we identified mentions of plant anatomical entities (taken from the Plant Ontology [4]) and mentions of trait or phenotype terms (from the PATO ontology [5]) in the Flora descriptions. We used a dictionary to translate French and English terms referring to plant anatomy or plant traits. In the future, we plan to use more complex approaches such as CharaParser to provide a more complete and accurate mark-up of anatomy and phenotype terms in Flora descriptions.

To semantically describe traits, we follow the Entity-Quality (EQ) approach [6] that has been widely applied to semantically characterize model organism [7] and disease phenotypes [8]. Using the EQ model, a trait is characterized by an entity (E) of which a trait is observed, and the quality (Q) that characterizes the trait. The characterize identity can be an anatomical entity (from the Plant Ontology), or a biological process or function (from the Gene Ontology). The Phenotypic Attribute and Trait Ontology (PATO) contains a rich classification of widely applicable traits. A phenotype is described in a similar way using the EQ pattern, but the quality has a specific value and is a subclass of the trait. For example, the trait "flower color" will be described using the entity "flower" (from Plant Ontology) and the trait "color" (from PATO). The phenotype "flower red" is described using the entity "flower" (from Plant Ontology) and the quality "red" (from PATO), where "red" is a subclass of "color" in PATO.

We then used a data-driven approach to build a flora phenotype ontology (FLOPO) from the EQ statements we identified in the Flora descriptions. FLOPO is an ontology of over 25,000 trait and phenotype terms, all of which have at least one taxon annotation in one of the Floras we processed. The draft of FLOPO is available in BioPortal (http://bioportal.bioontology.org/ontologies/FLOPO), and the source code we produced and the data we used is available from http://wiki.pro-ibiosphere.e/wiki/Traits_Task_Group.

We have also started to generate further resources that we plan to use in the future. In particular, we have started to add environmental terms to the Environment Ontology [9] that will allow us to extract parts of the environmental conditions in which taxa are found, we collected vocabulary and glossary terms that need to be incorporated into FLOPO. We have also experimented with using an RDF store that contains the FLOPO and its taxon annotations.

[1] Cui, H. (2012). CharaParser for fine-grained semantic annotation of organism morphological descriptions. Journal of American Society of Information Science and Technology. 63(4) DOI: 10.1002/asi.22618 http://onlinelibrary.wiley.com/doi/10.1002/asi.22618/pdf
[2] http://phenoscape.org/
[3] http://phenoscape.org/wiki/Phenex
[4] http://www.plantontology.org
[5] http://obofoundry.org/wiki/index.php/PATO:Main_Page
[6] Gkoutos, G. V., Green, E. C., Mallon, A.-M. M., Hancock, J. M., and Davidson, D. (2005) Using ontologies to describe mouse phenotypes. Genome biology, 6(1).
[7] Mungall, C., Gkoutos, G., Smith, C., Haendel, M., Lewis, S., and Ashburner, M. (2010) Integrating phenotype ontologies across multiple species. Genome Biology, 11(1), R2+.
[8] Robinson, P. N. et al. (2008) The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease. American journal of human genetics, 83(5), 610–615.
[9] http://www.jbiomedsem.com/content/4/1/43

For more information, please contact Robert Hoehndorf: leechuck@leechuck.de

SWeDe (Scientific Web-service Description) - an XML Schema Definition for describing Web Services in the scientific domain

Thu, 24 Apr 2014 16:33:00 +0300

Niall Beard (University of Manchester), Patricia Kelbert (FUB-BGBM), Bachir Balech (Institute of Biomembranes and Bioenergetics - Italian National Research Center)

At the Biodiversity Data Enrichment Hackathon in Leiden we created an XML Schema Definition for describing Web services in the scientific domain called SWeDe (Scientific Web-service Description).

A web service provider wishing to propagate their web service will upload descriptive information on catalogue sites such as the Biodiversity Catalogue, the Tools Registry or any other relevant catalogue. This information should include a textual description of how to use the service as well as usage conditions such as licensing and restrictions, and other useful annotations.

The purpose of SWeDe is to allow web service providers to maintain just one document describing their web services rather than maintaining documentation over several different catalogues.

Hence, if a provider is required to change some information about their service, they can do so once - in their SWeDe document. Participating catalogues can then both periodically or in real-time, download and parse the SWeDe file and display its contents within their site. They can then update their databases with any alterations accordingly.

The SWeDe Schema was designed by scientists and developers to cover as many aspects of scientific web services as possible. These include attributes such as the scientific category, technological category, projects (ie. funding), contact information (ie. institutions, persons) , intellectual property rights (IPR) and citations. The SWeDe schema re-uses several components from the Access to Biological Collections Data (ABCD) Schema. It can be used to describe services of both the two most predominant service types, REST and SOAP.

In addition to the schema, a rudimentary form to create your own SWeDe document (code-named the "SWeDe farmer") was also produced which can be found at http://swede-farmer.herokuapp.com

Further steps involve collaborating with Biodiversity Catalogue to parse SWeDe schemas, to improve the SWeDe Farmer, and to disseminate SWeDe to the scientific community.

The full XSD schema can be found in its GitHub Repository and further reading about SWeDe can be found on the pro-iBioshpere wiki.

https://github.com/njall/XS-SWeDe

http://wiki.pro-ibiosphere.eu/wiki/The_SWeDe_Project

http://swede-farmer.herokuapp.com/

For more information please contact support@mygrid.org.uk

The running of Taverna Workflows within an IPython Notebook

Wed, 23 Apr 2014 16:58:00 +0300

Alan Williams (University of Manchester, Aleksandra Pawlik (Software Sustainability Institute), Youri Lammers (Naturalis), Ross Mounce (University of Bath)

During the recent pro-iBiosphere Data Enrichment Hackathon, a prototype Taverna Player Client Python package was developed for IPython Notebook. The package allows the listing of workflows available on a Taverna Portal, selection of a workflow and the running of the workflow within the Notebook. Data from the Python environment can be used as inputs to the workflow, and the results of the workflow run are available for further manipulation in the notebook. User can interact with the running of the workflow using the Taverna Player and interaction services.

IPython Notebook [1]provides an interactive computational environment within a web browser. Users can write and execute Python code. This code may be combined with text, mathematical and statistical calculations, production of plots and HTML display to produce shareable and re-usable notebooks. These notebooks can be shared on the IPython Notebook Viewer[2].

Taverna[3] provides a suite of tools for workflow design, editing and execution. This includes the Taverna Workbench, the main creation tool for workflows, and the Taverna Server. Taverna Server enables you to set up a dedicated server for executing workflows remotely and it can be accessed by a WSDL or a REST API.

Instances of a Taverna Portal can be used to host, share and execute Taverna Workflows. The execution takes place on a Taverna Server and is exposed within the portal using a Taverna Player. The Taverna Player can also be accessed by a REST API.

Following discussions with the developers of IPython Notebook, the exciting potential of running Taverna Workflows from within an IPython Notebook was realized.

Figure 1: Running a workflow in IPython Notebook

The Taverna Player Client can be used to chain together workflows, using the outputs from one workflow run as the inputs to another. The capabilities of IPython Notebook can be used to generate documentation of the overall experiment; the templating mechanisms of jinja2 prove extremely useful for this.

The code for the Taverna Player Client is hosted on github[4] and a description of its current classes is available[5]. An example notebook has been uploaded to the Notebook Viewer [6].

Further work on the Taverna Player Client is planned, including meetings, both remote and face-to-face with the developers of IPython Notebook. The Client has been demonstrated to members of the BioVeL[7] and SCAPE[8] projects and colleagues at the University of Leiden.

We wish to thank the developers of IPython Notebook and Taverna Player, especially for their online support during the recent hackathon.

For more information, contact support@mygrid.org.uk

[1] http://ipython.org/notebook.html

[2] http://nbviewer.ipython.org/

[3] http://www.taverna.org.uk

[4] https://github.com/myGrid/DataHackLeiden

[5] http://dev.mygrid.org.uk/wiki/download/attachments/18972939/tavernaPlayerClient.html

[6]http://nbviewer.ipython.org/urls/raw.githubusercontent.com/myGrid/DataHackLeiden/alan/Player_example.ipynb?create=1

[7] http://www.biovel.eu

[8] http://www.scape-project.eu/

Hacking OCR for pro-iBiosphere

Tue, 22 Apr 2014 13:47:00 +0300

* by David P. Shorthouse, Rod Page, Kevin Richards, Marko Tähtinen

Taking his own lead from a pitch he delivered to an audience of receptive biodiversity informaticians at the outset of the March 17-21, 2014 pro-iBiosphere hackathon, Rod Page (University of Glasgow) fashioned an engaging interface to edit the OCR text from scanned pages in the Biodiversity Heritage Library (BHL). He wooed David P. Shorthouse (Canadensys), Kevin Richards (ex Landcare Research New Zealand) and Marko Tähtinen (University of Eastern Finland, BioVeL) away from eight other competing task groups, each of which issued products in a remarkably short amount of time.

The purpose of the pro-iBiosphere hackathon was to "enrich structured biodiversity input data with semantic links to related resources and concepts". The OCR task group led by Rod had a distinctly different starting point, one that is no less important to the semantic linking of biodiversity resources. The unstructured data in the BHL is arguably the richest source of freely accessible information for taxonomists and biodiversity enthusiasts that can be mined into structured data. However, the quality of its OCR output suffers from variable typefaces, layouts, page contrasts and page bleeding, artifacts and other issues that occasionally bewilder its OCR engine. As a result, data mining and indexing routines that lift scientific names, place names, and other entities in support of semantic linking are not always successful. The browsing interface in the BHL could be made more engaging if visitors had an opportunity to rapidly correct the OCR text while viewing the original scanned image, thus enriching search and discovery for future visitors. Indeed, BHL and its partners were recently awarded a "Digging Into Data Challenge" grant (see http://blog.biodiversitylibrary.org/2014/03/first-meeting-of-mining-biodiversity.html), part of which will employ automated text-cleaning methodologies developed by its Canadian collaborators. An OCR editor might complement their funded work. Likewise, the Finnish National Library has developed its own OCR editor interface (see http://blogs.helsinki.fi/fennougrica/2014/02/21/ocr-text-editor/). Unlike the Finnish editor that uses ALTO XML as its source documents, the OCR editing interface developed during this hackathon uses BHL’s DjVu XML documents as its source, rendered as HTML5.

The OCR Task Group had one aim: provide a simple interface for interactive editing of text, as well as tools to make inferences from the edits. After four solid days of hacking, the team completed this aim and integrated value-added features to engage users and to boost developer confidence in reuse of the code. The underlying document store is the cloud-based CouchDB (on Cloudant) and the team is confident that the proof-of-concept can be made to scale. The capabilities of the software are:

An in-place panel shows the exact line in the original scanned image while the user edits a single line of OCR text at a time (Figure 1)
Global Names scientific name-finding is integrated in real-time when a user completes a line edit, giving feedback if a scientific name is newly recognized (Figure 2)
Authentication uses the facile https://oauth.io/ such that all edits are tied to users’ OAuth2-provider accounts (eg Google, Twitter, GitHub)
Frequencies of common edits are summarized in real-time and other words that may benefit from similar edits are highlighted for users
Batch processes collapse all user edits and text files are recreated for possible re-introduction into data mining routines
Unit and integration tests are included

Figure 1. The OCR Editing interface rendered as HTML5, illustrating the original line of text as a clipped image under the line being edited, a scrolling tally of user edits, lines that have been previously edited (yellow highlight) and words that share strings of characters that match previous edits elsewhere on the page (mauve highlight).

Figure 2. Tooltip showing a scientific name newly recognized by the Global Names Recognition and Discovery service when a user completes an edit.

A proof-of-concept can be examined at http://bionames.org/~rpage/ocr-correction/ and the MIT-licensed code can be obtained from https://github.com/rdmpage/ocr-correction. The team will follow-up with the BHL to share what was accomplished and to discuss how this could be integrated in their web-based interface.

The team spent the last day of the hackathon investigating the production of DjVu XML files from scanned specimen labels. Although investigations are still underway, this particular outcome would be an excellent enhancement to the workflow at the Université de Montréal Biodiversity Centre (David P. Shorthouse) and useful for other members of the Canadensys network. The OCR editing interface may also be useful for the multi-national Notes From Nature crowd-sourcing initiative, http://www.notesfromnature.org/ as well as other national, regional, and local specimen label digitizing efforts throughout the world.

Rutger Vos and Soraya Sierra (Naturalis, co-organizers) received abundant praise by all participants at the completion of the hackathon, and rightly so. The hackathon was exceptionally well organized, developer team sizes were perfect for each of the nine task groups, each participant’s work ethic was remarkable, facilities were well provisioned, and nibbles and luncheons were delectable. We look forward to the reactions of pro-iBiosphere members at the final event in Meise, Brussels.

Contact:

David P. Shorthouse

Université de Montréal Biodiversity Centre / Canadensys, Montréal, QC CANADA

Email: david.shorthouse@umontreal.ca

Important principles of identification and web integration: Identifier and Resolution

Tue, 22 Apr 2014 12:29:00 +0300

by Kevin Richards, email: richardsk777@gmail.com

The topic of "stable unique identifiers" in the biodiversity informatics community has had quite a varied history in recent years. With the fast changing world of technology, information and the latest approaches to deal with information storage and access, several changes in direction have taken place.

In these changing times it seems that trying to stick to basic technologies, especially those that work with standard internet protocols, is the way to go. However, it is important to emphasise the two major components of identifiers: the IDENTIFIER and the RESOLUTION. These important principles of identification and web integration were put to use at the recent Biodiversity Enrichment Hackathon that took place on 17-21 March 2014 in Leiden. The importance of identification and resolution is obvious when attempting to link various data sets and information sources in the Biodiversity domain.

IDENTIFIER for the data

The first issue for any user of data is the need to identify that particular piece of data. This has traditionally been done using fairly local identifiers such as a number counter (i.e. 1,2,3...). With the need to integrate and access data globally, other mechanisms have been required. The simplest approach to this is called Universally Unique Identifier (UUID). UUIDs are hard to read and quite unappealing to look at, for example "1696AC49-548F-404D-9DEA-8A1C4DDA37F4" but are still a good mechanism for identifying data in a computer system, and hence, work well for computer needs.

RESOLUTION of data by their identifiers

With the increasing demand to have data accessible and linked on the web other identifier mechanisms are required to allow data to be fetched via their identifiers. Within the biodiversity community several approaches have been taken. Originally LSID (Life Science IDentifiers) were promoted as they had several appealing features, namely, a degree of indirection from the domain name associated with the data host and a defined protocol for accessing the data and metadata for a particular object. Other identifier systems were also considered such as DOI, PURL and Handles. The main benefit of all these identifier systems is that the data is then accessible over the web using web technologies.

Then came along the semantic web with some really cool ideas about linking data together in a meaningful way and building a reusable, re-purposeable giant set of data. This has become really appealing to biodiversity informaticians and has consequently resulted in some interesting hurdles to jump to achieve these attractive ambitions. Firstly semantic web technologies highly depend on automation and basic web protocols for harvesting and linking data. So any identifier system that doesn't work well with basic HTTP web protocols is difficult to integrate. This meant that LSIDs have become unfavourable due to their reasonably complex resolution protocol. Instead basic stable permanent URLs have been promoted.

A good approach to using these type of identifiers is to first pick a very agnostic domain name, ie not an institution or university name, but perhaps a "project" name. A good example of this is the International Plant Names Index project – also known as IPNI (its data system is hosted by the Royal Botanic Gardens Kew, London). Then a locally unique identifier portion is attached to the chosen domain name. An example of this combination is Zoobank with their zoobank.org domain name and an identifier for a particular piece of data they host, eg http://zoobank.org/NomenclaturalActs/8BDC0735-FEA4-4298-83FA-D04F67C3FBEC is a resolvable identifier for the zoobank record for the taxon "Chromis abyssus".

The pro-iBiosphere project has created a Best Practices page for stable URIs that outlines some good approaches to creating identifiers for your data with consideration of semantic web requirements and the latest ideas on identification.

Data visualisation task for pro-iBiosphere

Tue, 22 Apr 2014 09:35:00 +0300

by David King* (Open University), Jeremy Miller (Naturalis), Guido Sautter (Plazi), Serrano Pereira (Naturalis)

* david.king@open.ac.uk

Inspired by Pensoft's development in electronic publishing workflows, in combination with marked-up texts generated using GoldenGATE, Jeremy Miller (Naturalis) devised the design for a dashboard to visualise treatment data with the aim of better understanding that data and assisting with its quality control. Ultimately, Jeremy's vision would make it be possible to offer a kind of reverse Biodiversity Data Journal, resurrecting primary data from marked-up legacy literature for aggregation and re-analysis. Our challenge in the recent pro-iBiosphere hackathon, excellently hosted by Naturalis, was to craft a prototype to extract and display the data for Jeremy's dashboard.

Working with GoldenGATE's author, Guido Sautter, enabled us to immediately refine one weakness of the original design: rather than process exported GoldenGATE marked-up text to extract statistical data, we could have GoldenGATE extract it for us and make that data available for export. Hence, GoldenGATE's functionality was extended and a new API service made freely available at http://plazi.cs.umb.edu/GgServer/srsStats for us to use, and for anyone else to use who wishes to explore this statistical data. Some solid visualisation work by Serrano Pereira, a recent recruit to Naturalis, using the established frameworks jQuery, jqPlot and jVectorMap saw the exported data rendered into the form Jeremy envisaged.

A version of the demonstrator produced during the hackathon is currently available at http://plazi.byobu.info/, courtesy of Plazi, a pro-iBiosphere partner. We look forward to refining and enhancing the existing demonstrator in-line with feedback from Jeremy and other users, and from its presentation at pro-iBiosphere's final event in June.

Jeremy's original concept for the dashboard is available from https://github.com/Dauvit/Data_enrichment/tree/master/data_visualisation/use_case.

The code for GoldenGATE can be downloaded from https://code.google.com/p/goldengate-tools/.

The documentation for GoldenGATE's statistical export service is available from https://github.com/Dauvit/Data_enrichment/blob/master/data_visualisation/Stats_queries_HOWTO.md.

The code for the demonstrator dashboard can be downloaded from https://github.com/Dauvit/Data_enrichment/tree/master/data_visualisation.

The pro-iBiosphere Final Event on very promising tracks

Tue, 15 Apr 2014 10:16:25 +0300

The event wiki page here has been recently updated with additional information on the different series of activities organised (workshops, trainings and demonstrations) and the Final Conference agenda now comprises worldwide high-level speakers, including (i) officials from the European Commission DG Connect, the US National Academy of Sciences, (ii) representatives from botanic gardens, natural museums, other biodiversity initiatives and (iii) experts or (iv) researchers specialized in biodiversity informatics, environmental/natural science.

One of the key objectives of these series of events will be to ensure the Final event will provide key recommendations and inputs from biodiversity experts for the preparation of the next WP 2016-2017 as specifically asked by the European Commission.

The number of registered attendees has already reached a good level of participation to insure a thorough exchange of information and experience between stakeholders interested in making fundamental biodiversity data digital, open and re-usable. Visit the different activities pages to find out more on the attendance status.

In this context, if you plan to attend and have not yet registered, we can only recommend you do to it as soon as possible here (due to room capacity constraints).

For further information on this event (agenda, concept & objectives, registration) please visit the Event wiki page or contact us at final-event@pro-ibiosphere.eu.

Despatch from the field: New species discovery, description and data sharing in less than 30 days

Thu, 27 Mar 2014 15:37:00 +0200

Researchers and the public can now have immediate access to data underlying discovery of new species of life on Earth, under a new streamlined system linking taxonomic research with open data publication.

The partnership paves the way for unlocking and preserving a wealth of 'small data' backing up research conclusions, which often become lost within a few years of an article's publication in an academic journal.

In the first example of the new collaboration in action, the Biodiversity Data Journal carries a peer-reviewed description of a new species of spider discovered during a field course in Borneo just one month ago. At the same time, the data showing location of the spider's occurrence in nature are automatically harvested by the Global Biodiversity Information Facility (GBIF), and richer data such as images and the species description are exported to the Encyclopedia of Life (EOL).

This contrasts with an average 'shelf life' of twenty-one years between field discovery of a new species and its formal description and naming, according to a recent study in Current Biology.

A group of scientists and students discovered the new species of spider during a field course in Borneo, supervised by Jeremy Miller and Menno Schilthuizen from the Naturalis Biodiversity Center, based in Leiden, the Netherlands. The species was described and submitted online from the field to the Biodiversity Data Journal through a satellite internet connection, along with the underlying data . The manuscript was peer-reviewed and published within two weeks of submission. On the day of publication, GBIF and EOL have harvested and included the data in their respective platforms.

The new workflow established between GBIF, EOL and Pensoft Publishers' Biodiversity Data Journal, with the support of the Swiss NGO Plazi, automatically exports treatment and occurrence data into a Darwin Core Archive, a standard format used by GBIF and other networks to share data from many different sources. This means GBIF can extract these data on the day of the article's publication, making them immediately available to science and the public through its portal and web services, further enriching the biodiversity data already freely accessible through the GBIF network. Similarly, the information and multimedia resources become accessible via EOL's species pages.

One of the main purposes of the partnership is to ensure that such data remain accessible for future use in research. A recent study published in Current Biology found that 80 % of scientific data are lost in less than 10 years following their creation.

Donald Hobern, GBIF's Executive Secretary, commented: "A great volume of extremely important information about the world's species is effectively inaccessible, scattered across thousands of small datasets carefully curated by taxonomic researchers. I find it very exciting that this new workflow will help preserve these 'small data' and make them immediately available for re-use through our networks."

"Re-use of data published on paper or in PDF format is a huge challenge in all branches of science", said Prof. Lyubomir Penev, managing director of Pensoft and founder of the Biodiversity Data Journal. "This problem has been tackled firstly by our partners from Plazi who created a workflow to extract data from legacy literature and submit it to GBIF. The workflow currently launched by GBIF, EOL and the Biodiversity Data Journal radically shortens the way from publication of data to their sharing and re-use and makes the whole process cost efficient", added Prof. Penev.

The elaboration of the workflow from BDJ and Plazi to GBIF through Darwin Core Archive was supported by the EU-funded project EU BON (Building the European Biodiversity Observation Network, grant No 308454). The basic concept has been initially discussed and outlined in the course of the pro-iBiosphere project (Coordination and policy development in preparation for a European Open Biodiversity Knowledge Management System, addressing Acquisition, Curation, Synthesis, Interoperability and Dissemination, grant No 312848).

Original source:

Miller J, Schilthuizen M, Burmester J, van der Graaf L, Merckx V, Jocqué M, Kessler P, Fayle T, Breeschoten T, Broeren R, Bouman R, Chua W, Feijen F, Fermont T, Groen K, Groen M, Kil N, de Laat H, Moerland M, Moncoquet C, Panjang E, Philip A, Roca-Eriksen R, Rooduijn B, van Santen M, Swakman V, Evans M, Evans L, Love K, Joscelyne S, Tober A, Wilson H, Ambu L, Goossens B (2014) Dispatch from the field: ecology of micro web-building spiders with description of a new species. Biodiversity Data Journal 2: e1076. DOI: 10.3897/BDJ.2.e1076

Outcomes of the pro-iBiosphere Workshop on Sustainable Business Models

Wed, 26 Mar 2014 16:39:00 +0200

Charlotte Johns, Kew Royal Botanic Gardens, Email: c.johns@kew.org

A workshop dedicated to sustainable business models was held during the 5th pro-iBiosphere project meeting on the 11th and 12th of February 2014, at the Museum für Naturkunde (MfN) in Berlin, Germany. It was attended by consortium members and eight external participants with experience in strategic business and finance.

The workshop was planned to split into 4 sessions. The first session looked to agree the scope of a future "iBiosphere", to decide which products and services will be included as part of the Open Biodiversity Knowledge Management System (OBKMS). This session was followed by a number of talks given by the external participants, who shared their experience on the sustainability of their projects. Session three looked at enabling factors contributing towards the OBKMS, including open access, data and technology and communication. The final session concentrated upon sustainability and governance and how the management of iBiosphere should be structured.

The main outcome of the workshop was agreement on a list of core products and services which the OBKMS will provide, and an agreement on the core functionality. Information gathered through this milestone also helped to create the draft sustainability model for the OBKMS, which highlights gaps in our present knowledge and helps to decide upon future work which needs to be completed. These workshop outcomes, along with suggestions as to how the OBKMS will be governed and a list of challenges and solutions for a number of enabling functions, can be found within D6.4.2 the ‘Draft Sustainability Report’. The information collected through the workshop will also aid future reports including D6.1.2 ‘Report on Costs’, D6.4.3 ‘Summary of model evaluations’ and D6.4.4 ‘Sustainability recommendations’, to be made available here.

We would like to again thank all the participants for the success of the workshop and who contributed valuable information that will help shape our future pro-iBiosphere sustainability deliverables.

REGISTER NOW: pro-iBiosphere Final Event in Meise (Brussels) - June 10-12, 2014

Tue, 18 Mar 2014 16:58:23 +0200

The pro-iBiosphere Final Event will take place on June 10-12 2014, at the Bouchout Castle – Meise in Belgium (Agentschap Plententuin Meise, also known as Botanic Garden Meise).

The aim of these series of activities is to present the achievements of the project and its sustainability perspectives.

The week agenda comprises:

Tuesday June 10 (PM)
Workshop on Model Evaluation

Wednesday June 11 (all day)
Demonstrations on pro-iBiosphere pilots
Demonstrations on outcomes of pro-iBiosphere Data Enrichment Hackathon
Workshop on Biodiversity Catalogue
Training on WikiMedia
Poster session

Thursday June 12 (all day)
Final Conference
Networking Cocktail

Do not miss this unique opportunity and join us in Meise (Brussels)!.

Registration is free of charge but compulsory due to room capacity constraints. You can register by filling out the online registration form at http://tiny.cc/pib-final-event.

For complementary information on the Final Event (background, registration, logistics), please visit the dedicated wiki page at http://tiny.cc/wiki_pib_final_event or contact us at final-event@pro-ibiosphere.eu.

iMarine Catalogue of Applications

Mon, 17 Mar 2014 10:45:43 +0200

The iMarine initiative provides a data infrastructure aimed at facilitating open access, the sharing of data, collaborative analysis, processing and mining processing, as well as the dissemination of newly generated knowledge. The iMarine data infrastructure is developed to support decision making in high-level challenges that require policy decisions typical of the ecosystem approach.

iMarine has developed a series of applications which can be clustered in four main thematic domains (the so called Application Bundles, set of services and technologies grouped according to a family of related tasks for achieving a common objective).

More information on the iMarine Catalogue of Applications here.

In just a couple of weeks : the release of BioVeL Portal !

Mon, 10 Mar 2014 10:38:05 +0200

BioVeL announces the upcoming release of the BioVeL Portal. Designed in response to scientists' needs through a continuous cycle of requests and feedback, the portal will be robust and scalable for handling greater workloads.

An important feature of the Portal will be the ability to do "data sweeps"– that is, to initiate multiple runs of the same workflow, each with different input conditions. Other neat points are the organisation of the workflows by categories with "facetted browsing" for easier search, and a complete history of all your own workflow runs. Also through the Portal you can share workflows and results between collaborators. And as always with BioVeL tools, the codebase used for the portal benefits from being used across multiple projects.

Access BioVeL Portal here.

Please do not hesitate to provide your comments to contact@biovel.eu

pro-iBiosphere’s series of workshops held in Berlin

Mon, 10 Feb 2014 14:55:51 +0200

The pro-iBiosphere project organied 2 workshops between February 10-12 in Berlin:

February 10: MS12 - Workshop on mark-up of biodiversity literature
February 11: MS12 - Workshop on mark-up of biodiversity literature and MS23 - Workshop on alternative business models
February 12: MS23 - Workshop on alternative business models

The workshops took place at the Museum für Naturkunde Berlin (MFN) located 43 Invalidenstraße in Berlin.

For complementary information on these events (concept, objectives and outcomes), please visit the dedicated project wiki page here or contact us: info@pro-ibiosphere.eu.

Commission launches pilot to open up publicly funded research data

Mon, 16 Dec 2013 18:15:00 +0200

Today, 16/12/2013, the European Commission announced the launch of a new Pilot on Open Research Data in Horizon 2020, to ensure that valuable information produced by researchers in many EU-funded projects will be shared freely. Researchers in projects participating in the pilot are asked to make the underlying data needed to validate the results presented in scientific publications and other scientific information available for use by other researchers, innovative industries and citizens. This will lead to better and more efficient science and improved transparency for citizens and society. It will also contribute to economic growth through open innovation. For 2014-2015, topic areas participating in the Open Research Data Pilot will receive funding of around €3 billion.

The Commission recognises that research data is as important as publications. It therefore announced in 2012 that it would experiment with open access to research data (see IP/12/790). The Pilot on Open Research Data in Horizon 2020 does for scientific information what the Open Data Strategy does for public sector information: it aims to improve and maximise access to and re-use of research data generated by projects for the benefit of society and the economy.

The Pilot involves key areas of Horizon 2020:

Future and Emerging Technologies
Research infrastructures – part e-Infrastructures
Leadership in enabling and industrial technologies – Information and Communication Technologies
Societal Challenge: Secure, Clean and Efficient Energy – part Smart cities and communities
Societal Challenge: Climate Action, Environment, Resource Efficiency and Raw materials – with the exception of topics in the area of raw materials
Societal Challenge: Europe in a changing world – inclusive, innovative and reflective Societies
Science with and for Society

Neelie Kroes, Vice-President of the European Commission for the Digital Agenda said "We know that sharing and re-using research data holds huge potential for science, society and the economy. This Pilot is an opportunity to see how different disciplines share data in practice and to understand remaining obstacles."

Commissioner Máire Geoghegan-Quinn said: "This pilot is part of our commitment to openness in Horizon 2020. I look forward to seeing the first results, which will be used to help set the course for the future."

Projects may opt out of the pilot to allow for the protection of intellectual property or personal data; in view of security concerns; or should the main objective of their research be compromised by making data openly accessible.

The Pilot will give the Commission a better understanding of what supporting infrastructure is needed and of the impact of limiting factors such as security, privacy or data protection or other reasons for projects opting out of sharing. It will also contribute insights in how best to create incentives for researchers to manage and share their research data.

The Pilot will be monitored throughout Horizon 2020 with a view to developing future Commission policy and EU research funding programmes.

The pro-iBiosphere project highlighted at the 6th EU-AU Cooperation Forum on ICT in Addis Ababa

Fri, 13 Dec 2013 17:17:34 +0200

The 6th Africa-EU Cooperation Forum on ICT took place on December 2-3 2013 at the African Union Conference Center in Addis Ababa, Ethiopia under the aegis of the European Commission and the African Union Commission.

The event was organised by the EU EuroAfrica-P8 project on the occasion of the 50th anniversary of the African Union among the African ICT week.

During 20 sessions, 300 participants had the opportunity to share knowledge and explore the possibilities for cooperation in the framework of the Joint Africa-EU Strategic Partnership (JAES).

This meeting offered opportunities to the pro-iBiosphere project to promote its activities through the dissemination of project brochures and to network with potential stakeholders from Africa such as representatives from the Ethiopian agriculture portal on the occasion of the session on ICT for Agriculture on December 3.

Working, not drinking, at the Taverna

Tue, 10 Dec 2013 17:21:00 +0200

Data analysis is a complicated and time-consuming process. Like a craftsman, you require a set of tools that source, reformat, merge and analyse data. Using these tools manually in a workflow can take weeks. Then, when you finally get the workflow working, you often need to run it again with a new set of inputs and parameters. What if there were a piece of software that could couple all these tools together and then run it all over again at a click of a button?. This is what Taverna Workbench does. Taverna, changes a time-consuming job with multiple tools into a single machine that does all the work seamlessly.

Taverna Workbench is one of the tools that supports the BioVel project with their stated aim of creating a "virtual e-laboratory that supports research on biodiversity issues". Taverna, by itself, is like a conductor without an orchestra. The power of Taverna is in the flexible coupling together of web-services, scripts and all kinds of processing engines to create workflows. For example, an obvious use case is the coupling together of the webservice from GBIF with a niche model engine and rerunning of the workflow using different projections of future climate change. However, Taverna can be used to simplify the processing of practically any digital data. Many ecologists use R as their primary statistical software. R can be run from within Taverna, but Taverna helps you couple its running to pre- and post-processing so that it can be run more easily.

Taverna is widely used among phylogeneticists and bioinformaticians, but other disciplines are rapidly adopting it. Another, unique and powerful feature of Taverna is that people can share, distribute, and collaborate on their workflows. On the website myExperiment.org scientists post their workflows for others to use, critisise and improve upon. The website works like a social network, enabling users to create groups, "like" favorite workflows and exchange ideas. You could spend the time to program your own links between services, but Taverna lets you do this easily without sacrificing innovation and adaptability.

One of the important features of Taverna is the seamless way it allows users to use webservices. There is a growing list of webservices for biodiversity from organisations such as GBIF, EOL and EU-Brazil OpenBio. One of the big issues with webservices is that they are, almost by definition, invisible to human users. Therefore, how do you find out that they exist?. This is where biodiversitycatalogue.org comes in. It allows scientists to discover webservices, but also describes how they work and their input and output formats. The pro-iBiosphere project has helped to improve the catalogue and will help to set priorities for future development. It now recommends the use of the Biodiversity Catalogue as central service registration facility for a future Open Biodiversity Knowledge Management System.

Taverna is a relatively new system to the Biodiversity community and through the BioVeL project its user-base is growing rapidly. Furthermore, people are finding new uses for it all the time.

On 5th December 2013, BioVel organised a workshop on Taverna at which pro-iBiosphere was represented. One potential use-case that is of interest to pro-iBiosphere is in the automated markup of text. Some aspects of automated markup are common to many texts, such as the identification of scientific names. On the other-hand there are other aspects that are specific to particular texts, such as the identification of treatment boundaries and language specific features. Taverna may be used to link generic services with custom scripts to significantly reduce the time it takes to markup text. Workflows could be created for one particular publication and then tweaked to work for another.

The possibilities of Taverna are almost limitless. It is just the glue, and you decide what you stick together. You might think the Taverna sounds like a quiet place for a drink, whereas, it is really the factory floor of data processing.

By Quentin Groom (National Botanic Garden of Belgium)

Outcomes of the pro-iBiosphere workshop 4 on Business Models

Tue, 10 Dec 2013 16:43:19 +0200

A pro-iBiosphere workshop on evaluation of business models took place on the 10th of October 2013 at the Botanischer Garten und Botanisches Museum (FUB-BGBM) in Berlin, Germany. It was attended by project partners and four external experts. The workshop was split into two sessions, each divided into smaller working groups. In the first session, a prioritised list of the partners' current products and services was drawn up, and the opportunities for, and threats to these were assessed. In the second session, the participants focussed on the services and activities that would comprise a future OBKMS (Open Biodiversity Knowledge Management System) and documented the constraints that might prevent the projected benefits of OBKMS from being realised.

The sessions have been very fruitful in terms of content (more than 20 matrix were made) and all participants (including external participants) have been very active during the whole day. Having external participants represented a real asset as they helped shaping the project vision more precisely while also demonstrating and confirming their interest in the OBKMS. Partners found these exercises very productive while taking time to step back and envision the future of the Consortium all together. This workshop is not the end of the exercise but only a milestone to agree on the various concepts, methodology and tools to be used to envision project sustainability and allow discussions among the partners. All in all, workshop objectives have been achieved.

The next steps of this workshop will be the release of an event report detailing the event outputs in presenting the project exploitation potential. We will keep you updated on the development of these activities.

For complementary information on the workshop (concept & objectives, agenda, participants list and presentations), visit the dedicated wiki page here.

pro-iBiosphere Meeting 4: Evaluation of the meeting

Thu, 05 Dec 2013 17:14:00 +0200

From Oct 8-10th 2013 the 4^th pro-iBiosphere meeting took place at the Botanic Garden and Botanical Museum Berlin-Dahlem. In total, 87 participants from 15 countries attended the 4 workshops held on:

1. 8 Oct Workshop 1 (M4.1): How to improve technical cooperation and interoperability at the e-infrastructure level (FUB-BGBM). For results from the workshop, see here.

2. 8 Oct Workshop 2 (M4.2): How to promote and foster the development & adoption of common mark-up standards & interoperability between schemas (PLAZI)

3. 9 Oct Workshop 3 (M6.2.2): Workshop on user engagement and benefits (RBGK)

4. 10 Oct Workshop 4 (M6.3.2): Towards sustainability towards service: Meeting to evaluate business models currently in use by partners and relevant non-partners (SIGMA)

Networking

A questionnaire was sent to the participants of the meeting. A total of 87 persons answered the questionnaire. The meeting received an overall positive feedback. The agendas of the workshop and the possibility to network were the strongest attractions for attending. Half of the delegates were able to establish or strengthen 5-10 contacts during the event (see Figure 1). Delegates appreciated the discussions and welcoming atmosphere. Despite that, they mentioned that there could have been more time allocated for each workshop and each break for discussions.

Workshops

Participants expressed their preference to work in small groups with well-defined targets. The need for presentations was very low, provided that the workshops are well focused and give ample time for discussion.

30% of the participants judged the quality of the workshop as high, 31% as very good, 13% as acceptable and 1% as below expectations (see Figure 2). 50% of the participants are interested in attending other pro-iBiosphere events in the future and 64 out of 87 persons would recommend them to colleagues.

Caption: Contacts established by participants during the pro-iBiosphere meeting (first column; clockwise: 38% of the participants were able to make between 5 and 10 contacts, second column: 14% of the participants were able to establish less than 5 contacts, third column: 4% of the participants were not able to establish any contacts, fourth column: 9% of the participants were able to establish more than 10 contacts).

Improving the technical cooperation and interoperability at the e-infrastructure level

Thu, 05 Dec 2013 17:11:00 +0200

A pro-iBiosphere workshop on "How to improve technical cooperation and interoperability at the e-infrastructure level" was held at the Botanic Garden and Botanical Museum Berlin-Dahlem (BGBM) on October 8 2013. A total of 22 participants were invited to attend the workshop, representing a wide range of international biodiversity-related institutions and e-infrastructures. The workshop focused on the establishment of two highly relevant interoperability aspects of: (i) a consistent space of stable identifiers for collection objects across European taxonomic institutions; and (ii) a central registry for biodiversity-related services.

In the workshop 8 different implementations of stable http-URI-based identifier systems in European- and US-based taxonomic institutions where positively evaluated. These implementations are an important outcome of the fruitful collaboration between pro-iBiosphere and the Information Science and Technology Commission (ISTC) of the Consortium of European Taxonomic Facilities (CETAF).

In addition, the workshop conducted a thorough analysis of the BiodiversityCatalogue (https://www.biodiversitycatalogue.org/) developed by the University of Manchester in the context of the EU 7^th Framework project BioVeL. As a result, a detailed list of recommended improvements of the Catalogue was compiled and agreed on. The University of Manchester will use these recommendations for setting priorities when further developing the Catalogue. Detailed results from the workshop are available here.

Authors: Anton Güntsch, Sabrina Eckert (FUB-BGBM)

pro-iBiosphere project highlighted at the ICT2013 event

Tue, 03 Dec 2013 16:14:15 +0200

The most visible forum for ICT research and innovation in Europe "ICT2013: Create, Connect and Grow", took place on the 6-8th of November 2013 in Vilnius (Lithuania). The event consisted of c.250 sessions and 200 exhibitors; and brought together lead thinkers and people driving European ICT research and innovation. A total of 6.000 persons participated in the event, including researchers, innovators, entrepreneurs, industry representatives, and politicians.

ICT 2013 allowed participants to share best practices and experiences in big data management, and provided them an excellent opportunity to learn about the current state of ICT research in Europe and the new Horizon2020 Framework programme for Research and Innovation.

The pro-iBiosphere project was strongly represented during the event by means of an exhibition booth and a networking session co-organised with other EC-funded projects (i.e. ei4Africa, Chain-reds, e-Science Talk). The exhibition booth entitled ‘e-Infrastructures at work and the future of research' showcased information from these four projects. Potential contacts were made with 20 stakeholders comprising projects on biodiversity data, EC-funded projects managing big data infrastructures (i.e. platforms, storage); and engineers specialised in semantic integration, enhancement, oncology, and autonomics.

The networking session on ‘What does the future hold for e-Science and Big Data?' brought together researchers, data owners and service providers (including SMEs) to explore the future for e-science and how to deliver open access to data through Horizon2020. During this session, the pro-iBiosphere project (represented by Plazi) presented its vision and potential impact to the biodiversity community and beyond. The networking session led to better understanding of how e-infrastructures can solve scientific challenges. Additional information is available here.

Vibrant workshop

Wed, 27 Nov 2013 17:36:24 +0200

Vibrant workshop for users of the EDIT Platform for Cybertaxonomy

The Vibrant workshop for users of the EDIT Platform for Cybertaxonomy was held from 11-13 November at the Botanic Garden and Botanical Museum Berlin-Dahlem (FUB-BGBM). The aim of the workshop was to explain the new Taxonomic Editor, the Data Portals and other components of the Platform to users, as well as to give an introduction to the software for structured taxonomic descriptions and keys, Xper2. The meeting brought together 40 participants representing a wide range of international biodiversity-related institutions and e-infrastructures (Euro+Med Plantbase, e-Floras, German Red Data Book editors, Pensoft publishers, Chinese Virtual Herbaria, Atlas Florae Europaeae and more).

The workshop was split into two parts, 1.5 days for the EDITor and the data portals, 0.5 days for Xper2. For the EDITor and data portal workshop, 3 parallel working groups (1 in German and 2 in English language) were led by two developers and one or two taxonomists from the FUB-BGBM. One group was solely formed by Euro+Med Plantbase family editors and taxonomic experts. For Xper2 two parallel groups were led by four colleagues from Paris. To explain the new Taxonomic EDITor two virtual box images where created (the images had the software - data Portal, Taxonomic Editor and cdmserver preinstalled). One image included a simple dataset with 10 taxa and factual data from the Compositae tribe Cichorieae. The other image included a more complex dataset from Euro+MedPlantBase, to give the editors the opportunity to do the hands-on training with the data they are handling in the framework of this project.

All three groups were able to get extensive hands-on experience with the Taxonomic EDITor and to observe the direct interaction of the EDITor with the data portals. Feedback from the users was generally positive. Some of them expressed the need of a "light" version of the EDITor which makes it easier to use for less experienced users. Constructive criticism from the participants will help to improve functionalities of the EDITor, and a part of them will use the EDIT platform in the future for their projects. The introduction and hands-on training on Xper2 was also well received by the audience and yielded some fruitful feedback for the presenters of that part of the workshop.

http://cybertaxonomy.eu/

Novel ideas and tools from pro-iBiosphere presented at the TDWG 2013 Conference

Wed, 27 Nov 2013 11:13:00 +0200

Lyubomir Penev, Gregor Hagedorn, Soraya Sierra

The latest Biodiversity Information Standards (TDWG) conference took place in Florence, Italy on October 28 – November 1, 2013. The pro-iBiosphere project was well represented in the conference with 8 participants. Consortium members contributed especially to the discussions about:

the future use of identifiers
re-establishing the Structured Descriptive Data standard in Semantic Web compatible RDF Format
future developments in DarwinCore

Presentations given by consortium members during the meeting are available here.

In order to make fundamental biodiversity data digital, open and re-usable, the pro-iBiosphere project has the vision of implementing an Open Knowledge Biodiversity System (OBKMS). The strong general current towards semantic technologies observed at the meeting, confirmed the need for this vision.

The conference is also to be remembered with the launch of the common automated registration model for higher plants, fungi and animals (one of the four pilots being conducted by the pro-iBiosphere project). Currently registration of new taxa is being conducted "by hand" by the authors, journals or registries. Pensoft journals were first to develop and offer this new service, in a collaboration with the International Plant name Index (IPNI), ZooBank and Index Fungorum. Detailed information on the automated registration pilot is available here.

Preceding the TDWG conference, Pensoft and ZooBank organised a hackathon in Sofia (Bulgaria). The hackathon resulted in several, real-time tests of the pilot, based on the TaxPub XML schema.

After the hackathon, the teams of IPNI, Index Fungorum, ZooBank, Pensoft and Plazi came together at a brief workshop to discuss the potential of the Taxonomic Concept Schema (TCS) as a possible basic model that may be used in the future for registration of taxa in the three organismic domains.

The consortium strives towards having a more open pilot registration system available by the end of the pro-iBiosphere project. At present, IPNI is having discussions with other key partners such as the IAPT committee on registration on how to open up the automated registration model.

The pro-iBiosphere project announces its final event

Wed, 27 Nov 2013 10:27:16 +0200

Please mark your calendar for the pro-iBiosphere final event!

The final meeting will take place on the 10-12th of June 2014 in Belgium.

The National Botanic Garden of Belgium (NBGB) will be host to this meeting and has opened the doors of the Bouchout Castle for this event.

During the meeting you will have the opportunity to learn about outcomes of the project, be informed about relevant topics presented by invited speakers, follow training on state-of-the art tools, and do networking with colleagues.

We will keep you updated as our preparations develop.

In case of further questions please do not hesitate to contact us at pro-ibiosphere@sigma-orionis.com.

We look forward to seeing you in June!

EUBrazilOpenBio final newsletter is now available

Tue, 26 Nov 2013 14:05:00 +0200

The final EUBrazilOpenBio newsletter for November 2013 is now available. The newsletter presents the final press release showcasing the main results of 2 year collaborative work, namely: the innovative, web-based working environment designed to serve biodiversity scenarios; the new version of the Catalogue of Life cross-mapping tool developed in the i4Life project; the provision of the Ecological Niche Modelling tool as a service through the openModeller extended web service, and its application in collaboration with BioVeL; the EUBrazilOpenBio Joint Action Plan.

This newsletter highlights:

EUBrazilOpenBio Joint Action Plan - drawing on policy strategies, analysing current progress in contributing to international targets and defining actions for future collaborative research. It defines common actions with the aim of contributing to relevant Aichi Targets in the years ahead.
EGI federatec use case on ecology - Over the last two years, BioVeL and EUBrazilOpenBio have joined forces to make openModeller ready for cloud deployment. Work within the EGI Federated Cloud Task Force has led to considerable success in enabling the openModeller service on the EGI Federated Cloud.
EUBrazilOpenBio results - EUBrazilOpenBio Technical developments, training materials and sessions, publications and papers, media spotlights and policy results all collected in one page.
A vision from the Experts - "The Crossmapper itself is a great tool, and an ideal way to identify errors and updates". Dr Christina Flann is one of the experts providing their vision on EUBrazilOpenBio story.

You can find an online version of the final EUBrazilOpenBio newsletter here.

TESS, a forerunner to pro-iBiosphere

Mon, 11 Nov 2013 10:37:00 +0200

Prof. Robert E. Kenward [1]

A project to design a Transactional Environmental Support System (www.tess-project.eu) preceded pro-iBiosphere during 2008-1011. TESS, of which partners were mostly linked to the Sustainable Use and Livelihoods Group of IUCN (www.iucn.org/SULi), recognised the need for information on species and habitats to inform policy, but also at local level for management of land and sustainable use. TESS surveyed information needs at EU level, national governments, local communities at lowest government administrative level and stakeholders. The surveys not only showed biodiversity information requirements in detail, but also found a "decision density" five magnitudes higher for local managers of land and species (in farms, forests, fisheries, hunting areas and nature reserves) than for statutory environmental assessments (SEA+EIA).

To make decisions that are good for nature, there is scope for internet exchange (transaction) of science-based decision support (from high level) for the detailed data needed to make those local decisions (but also needed for policy-making at higher level). For effective exchange, data needs to be open access, standardised in format and highly detailed (accurate and at high resolution), i.e. aspirations of pro-iBiosphere. Case studies showed that local communities were highly capable of collecting appropriate data, but that thousands of models for science-based decision support included only 10 suitable for local use, at most in two languages!

This information was of special relevance for one of the pro-iBiosphere workshops in October 2013, Workshop on User Engagement and Benefits, showing in particular the importance of delivering Faunas, Floras and Mycotas for local people to record biodiversity. Identifying and reporting species needs to be made simple and multilingual for users other than experts, which could involve smart-phone apps for image-recognition and database-linking.

As part of its surveys, TESS established a portal (www.naturalliance.eu) to signpost relevant information and encourage collection by local interests. Naturalliance is advised by major international NGOs at European and Global level, is now in 23 languages and, to encourage sustainable use of land and biodiversity, and is working with national governments on a new system to encourage systematic local participation in data exchange. Experience with funding these systems, which could signpost a one-stop-shop for identification/reporting apps, or even host the downloading, was shared during the meeting on 10 October 2013 to evaluate business models currently in use by partners and relevant non-partners.

[1] Vice-chair (Europe) of IUCN Sustainable Use and Livelihoods Specialist Group

Toward best practices for sharing and maintaining biodiversity data - GBIF Finland (FinBIF)

Wed, 06 Nov 2013 10:19:00 +0200

Hanna Koivula[1]

The Finnish Museum of Natural History is a focal point for GBIF Finland (FinBIF). For the past few years we have been constructing a national research infrastructure to serve not only data needs of biodiversity researchers, but also environmental services. The aim is to fulfill many different data requirements for various kinds of surveys and assessments concerning biodiversity. Most of our data are openly available to anyone, but technically many data users have not been able to use our web services for retrieving the data they need. The main obstacle is that the services are very new and the awareness about exchange protocols and standards of the data is poor. This is why most of the data shared by FinBIF are still extracted manually upon request. Hence, one (still unreached) goal is to name and establish best practices for sharing and maintaining biodiversity data. This is done by applying selected parts, especially for logical architecture and communication, from Enterprise architecture. The method enables us to capture essential information of our research infrastructure under construction.

Building a research infrastructure in an extremely heterogeneous "funding environment" has set some serious impediments along the way. On the other hand, it has allowed us to play with quite adventurous architectural structures and innovative pilot cases. One of these new approaches is the use of semantic web features for making data storage more flexible and data themselves better discoverable.

Participating in the pro-iBiosphere workshop on "How to improve technical cooperation and interoperability at the e-infrastructure level" that took place on the 8th of October 2013, in Berlin, gave me a good insight into existing European open biodiversity data and related services. Hands-on experience of listing our web services to the Biodiversity Catalogue triggered useful conversations on how to improve the interoperability and discoverability of the services, and gave participants take-home ideas. In the break-out discussion group we assessed the present set of metadata elements used in the Biodiversity Catalogue for describing individual services. Based on that evaluation, we made recommendations for additional elements. I also obtained many good ideas for further developing the FinBIF services.

[1] Finnish Museum of Natural History - IT Specialist GBIF Node Manager for Finland, Email: hanna.koivula@helsinki.fi

Flora of the Guianas: Toward an Online Platform

Wed, 06 Nov 2013 09:59:00 +0200

Sylvia Mota de Oliveira[1]

The three countries forming the Guianas - Guyana, Suriname and French Guiana - have more than 80% of their political territories covered by pristine Amazon forest. The Flora of the Guianas book series provides taxonomic treatments and associated data on plant species occurring in the region. At present, the published fascicles cover around 25% of the total of species recorded in the Guianas, with a total of 2294 species treated only in series A: Phanerogams and around 1000 species in other series, covering Ferns and Fern allies, Bryophytes and Fungi. Beyond taxonomy, the Flora is a rich and well curated source of primary biodiversity data. To efficiently use this source and build it further, we want to move towards an online platform, where:

Data extracted from other literature sources (Flora of Suriname, for instance) can be incorporated in a database and used as a basis for upcoming taxa treatments, increasing the rate of species descriptions;
Data gathered in the Flora fascicles can be disclosed and made available in a structured and searchable manner, openly accessible to end-users;
Interaction between Flora contributors, specialists and citizen scientists is promoted;
Links between elements of the Flora and external content, such as collection and molecular databases, can be easily enabled;
Updates of the taxonomic data can guarantee the quality and usability of the Flora in several other research fields.

To achieve these goals, the transference of the data from the printed copies of the Flora of the Guianas to such an online platform requires mark-up of text. The new workflow is being tested in a Pilot study within the pro-iBiosphere project, which will hopefully support the planning of a longer-term strategy for the complete Flora.

The first results of the pilot were presented and discussed during the pro-iBiosphere workshop on "How to promote and foster the development & adoption of common mark-up standards & interoperability between schemas" that took place on the 8th of October 2013, in Berlin. The workshop was very instructive and useful for the future strategy of the Flora of the Guianas. In this workshop, participants shared their experiences, and discussed together the most important issues/challenges that they have encountered while working on text mark-up. The heterogeneity of the group added to the discussion because participants were confronted with different levels of: 1) experience with mark-up tools; 2) data granularity; 3) consistency in the format of the content to be marked-up. Relevant topics discussed included the scaling of the mark-up activities using different tools, the costs and possible incentives for such an activity, the desired level of granularity of the mark-up, and best practices to be adopted by taxonomists and bioinformaticians.

[1] Editor of Flora of the. Guianas, Naturalis Biodiversity Center, the Netherlands. Contact: Sylvia.MotaDeOliveira@naturalis.nl

Next-generation global e-infrastructure for taxon names registry

Mon, 04 Nov 2013 17:53:00 +0200

Zookeys, the first zoological journal to introduce automatic registration in ZooBank

The latest issue of ZooKeys - no. 346 - has been automatically registered in ZooBank on its day of publication last Friday. This marks the successful deployment of an automated registration-to-publication pipeline for taxonomic names for animals. The innovative workflow was jointly funded by the EU FP7 funded project pro-iBiosphere and a U.S. National Science Foundation project to develop the Global Names Architecture (DBI-1062441).

The process of post-publication recording and indexing of species names has a long tradition, in some cases dating as far back as the middle of 19th century. But now in the 21st century with the advance of modern technologies and the opportunity to publish taxonomic novelties online, the process of post-publication recording brought into focus the concept of automated pre-publication registration.

Why is this important? The proportion of 'turbo-taxonomic' papers describing hundreds of new species increases. Registration of hundreds of new species is an issue, however it is even more important that the final publication data of the pre-registered names are reported back to ZooBank on the day of publication.

Launched as an open access peer reviewed journal in 2008, to coincide and adopt from inception the International Code of Zoological Nomenclature changes for electronic publications, ZooKeys was the first journal to provide a mandatory in-house registration in ZooBank. Since 2008, it has contributed about one third of all names currently registered in ZooBank. With the adoption of the automated ZooBank registration, ZooKeys continues its mission to set novel trends in biodiversity publishing.

Implementation of automated workflows and invention of XML-based tools will facilitate the process of publication and dissemination of biodiversity information. It will pave the way for unification and streamlining the registration process, even more to building the next-generation e-infrastructure for a common global taxon names registry. Within the pro-iBiosphere project and in cooperation with Plazi that have created the TaxPub XML schema, an automated registration workflow for plants has already been established between the International Plant Names Index (IPNI) and the PhytoKeys journal, to be applied soon also for fungi between Index Fungorum and the journal MycoKeys.

The cyber-centipede: From Linnaeus to big data

Tue, 29 Oct 2013 13:42:00 +0200

Taxonomic descriptions, introduced by Linnaeus in 1735, are designed to allow scientists to tell one species from another. Now there is a new futuristic method for describing new species that goes far beyond the tradition. The new approach combines several techniques, including next generation molecular methods, barcoding, and novel computing and imaging technologies, that will test the model for big data collection, storage and management in biology. The study has just been published in the Biodiversity Data Journal.

While 13,494 new animal species were discovered by taxonomists in 2012, animal diversity on the planet continues to decline with unprecedented speed. Concerned with the rapid disappearance rates scientists have been forced towards a so called 'turbo taxonomy' approach, where rapid species description is needed to manage conservation.

While acknowledging the necessity of fast descriptions, the authors of the new study present the other 'extreme' for taxonomic description: "a new species of the future". An international team of scientists from Bulgaria, Croatia, China, UK, Denmark, France, Italy, Greece and Germany illustrated a holistic approach to the description of the new cave dwelling centipede species Eupolybothrus cavernicolus, recently discovered in a remote karst region of Croatia. The project was a collaboration between GigaScience, China National GeneBank, BGI-Shenzhen and Pensoft Publishers.

Eupolybothrus cavernicolus has become the first eukaryotic species for which, in addition to the traditional morphological description, scientists have provided a transcriptomic profile, DNA barcoding data, detailed anatomical X-ray microtomography (micro-CT), and a movie of the living specimen to document important traits of its behaviour. By employing micro-CT scanning in a new species, for the first time a high-resolution morphological and anatomical dataset is created - the 'cybertype' giving everyone virtual access to the specimen.

This, most data-rich species description, represents also the first biodiversity project that joins the ISA (Investigation-Study-Assay) Commons, that is an approach created by the genomic and molecular biology communities to store and describe different data types collected in the course of a multidisciplinary study.

"Communicating the results of next generation sequencing effectively requires the next generation of data publishing" says Prof. Lyubomir Penev, Managing director of Pensoft Publishers. "It is not sufficient just to collect 'big' data. The real challenge comes at the point when data should be managed, stored, handled, peer-reviewed, published and distributed in a way that allows for re-use in the coming big data world", concluded Prof. Penev.

"Next generation sequencing is moving beyond piecing together a species genetic blueprint to areas such as biodiversity research, with mass collections of species in "metabarcoding" surveys bringing genomics, monitoring of ecosystems and species-discovery closer together. This example attempts to integrate data from these different sources, and through curation in BGI and GigaScience's GigaDB database to make it interoperable and much more usable," says Dr Scott Edmunds from BGI and Executive Editor of GigaScience.

Additional information:

Pensoft and the Natural History Museum London have received financial support by the EU FP7 projects ViBRANT and pro-iBiosphere. The China National GeneBank (CNGB) and GigaScience teams have received support from the BGI. The DNA barcodes were obtained through the International Barcode of Life Project supported by grants from NSERC and from the government of Canada through Genome Canada and the Ontario Genomics Institute.

Original Sources:

Stoev P, Komerički A, Akkari N, Shanlin Liu, Xin Zhou, Weigand AM, Hostens J, Hunter CI, Edmunds SC, Porco D, Zapparoli M, Georgiev T, Mietchen D, Roberts D, Faulwetter S, Smith V, Penev L (2013) Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data. Biodiversity Data Journal 1: e1013. DOI: 10.3897/BDJ.1.e1013

Edmunds SC, Hunter CI, Smith V, Stoev P, Penev L (2013) Biodiversity research in the "big data" era: GigaScience and Pensoft work together to publish the most data-rich species description. GigaScience 2:14 doi:10.1186/2047-217X-2-14

Watch the 3D cybertype video: http://www.youtube.com/watch?v=vqPuwKG8hE4&feature=em-upload_owner

Advanced Open Access publishing model

Thu, 24 Oct 2013 14:39:00 +0300

The Biodiversity Data Journal goes beyond the basics of the Gold Open Access

There are two main modes of open access publishing – Green Open Access, where the author has the right to provide free access to the article outside the publisher's web site in a repository or on his/her own website, and Gold Open Access, where articles are available for free download directly from the publisher on the day of publication.

Opening of content and data, however does not necessarily mean "easy to discover and re-use". The Biodiversity Data Journal proposed the term "Advanced Open Access" to describe an integrated, narrative (text) and data publishing model where the main goal is to make content "re-usable" and "interoperable" for both humans and computers.

To publish effectively in open access, it is not sufficient simply to provide PDF or HTML files online. It is crucial to put these under a reuse-friendly license and to implement technologies that allow machine-readable content and data to be harvested and collated into a big data pool.

The Advanced Open Access means:

Free to read
Free to re-use, revise, remix, redistribute
Easy to discover and harvest
Content automatically summarised by aggregators
Data and narrative integrated to the widest extent possible
Human- and computer-readable formats
Community-based, pre- and post-publication peer-review
Community ownership of data
Free to publish or at low cost affordable by all

BDJ shortens the distance between "narrative" (text) and "data" publishing. Many data types, such as species occurrences, checklists, measurements and others, are converted into text from spreadsheets for better readability by humans. Conversely, text from an article can be downloaded as structured data or harvested by computers for further analysis.

"Open access is definitely one of the greatest steps in scientific communication comparable to the invention of the printing technology or the peer-review system. Great but not sufficient!" said Prof. Lyubomir Penev, founder of Pensoft Publishers and the Biodiversity Data Journal. "We need to switch the focus already from making content 'available for free download' to being discoverable and extractable. Such re-usability multiplies society's investment in science".

###

Additional information:

The Biodiversity Data Journal is designed by Pensoft Publishers and was funded in part by the European Union's Seventh Framework Program (FP7) project ViBRANT.

Source: Smith V, Georgiev T, Stoev P, Biserkov J, Miller J, Livermore L, Baker E, Mietchen D, Couvreur T, Mueller G, Dikow T, Helgen K, Frank J, Agosti D, Roberts D, Penev L (2013) Beyond dead trees: integrating the scientific process in the Biodiversity Data Journal. Biodiversity Data Journal 1: e995. DOI: 10.3897/BDJ.1.e995

Horizon 2020: A call to forge biodiversity links

Thu, 10 Oct 2013 16:48:00 +0300

A correspondence item, published today, 10 Oct 2013, in Nature focuses on the upcoming calls for Horizon 2020 research funding. The European Commission has said that it would prefer bids from open, collaborative consortia rather than the competitive bids seen in previous funding programmes. The authors call for an effort to forge interdisciplinary links in biodiversity research, and ask readers to contribute to discussions on project ideas.

For more information read the full correspondence item in Nature: http://www.nature.com/nature/journal/v502/n7470/full/502171d.html

Meet the pro-iBiosphere Partnership at ICT2013!

Thu, 03 Oct 2013 16:49:44 +0300

Europe’s most visible forum for ICT research and innovation, ICT2013, will take place from 6-8 November 2013 in Vilnius, Lithuania.

The ICT 2013 event will be the first opportunity to learn the details of research funding for ICT-related projects under Horizon 2020, the EU’s new research program for 2014-2020. ICT2013 will also offer participants opportunities to showcase their most advanced research, ICT products and most innovative creations and to meet delegates with common or similar topical interests with whom they could collaborate in the future.

The pro-iBiosphere partnership will be represented at the ICT2013 event with a networking session and an exhibition booth, co-organised with other three EC-funded projects: the European Grid Infrastructure (EGI), ei4Africa and CHAIN-REDS.

The networking session on ‘What does the future hold for e-Science and Big Data?’ is taking place on Nov. 6, 2013 (16:00-16:45). This session will bring together researchers, data owners and service providers (including SMEs) to explore the future for e-science and how to deliver open access to data through Horizon2020. Participation will lead to better awareness of e-infrastructures and their potential for universal access to big data and a closer understanding of how they solve scientific challenges, including supporting science’s ‘long tail’. More…

The exhibition booth ‘e-Infrastructures at work and the future of research’ will showcase demonstrations from the four EC-funded projects running the booth. Members of the four projects will be on hand to fully engage with visitors and to present several demonstrators. There will also be supporting information and materials such as posters and leaflets.

We would be glad to meet you to discuss future collaboration opportunities in the fields of open access to data and linking litterature and data: if you would like to arrange a meeting with us, please contact us!

How to find us
The networking session will be organised in the Room H1C, located in the Hal 1. The exhibition booth (n. 4B24) will be located in the Hal 4: see map below.

New framework to deliver biodiversity knowledge

Wed, 02 Oct 2013 13:28:00 +0300

Global Biodiversity Informatics Outlook sets out key steps to harness IT and open data to inform better decisions

Copenhagen, Denmark – A new initiative launched today (2 Oct) aims to coordinate global efforts and funding to deliver the best possible information about life on Earth, and our impacts upon it.

The Global Biodiversity Informatics Outlook sets out a framework to harness the immense power of information technology and an open data culture to gather unprecedented evidence about biodiversity and to inform better decisions.

The framework is outlined in a document and website entitled Delivering Biodiversity Knowledge in the Information Age, inviting policy makers, funders, researchers, informatics specialists, data holders and others to unite around four key focus areas where progress is needed.

The focus areas, each consisting of several specific components, are:

Culture – promoting practices and infrastructure for sharing data, using common standards and persistent archives, backed up by strong policy incentives and a community of willing specialists;
Data – addressing the need to transform all data about species, past and present, into usable and accessible digital formats; from historic collections and literature to citizen science observations, remote sensors and gene sequencing;
Evidence – organizing and assessing data from all sources to provide clear, consistent views giving them context; including taxonomic organization, integrated occurrences in time and space, capturing information about species interactions, and improving data quality through collaborative curation; and
Understanding – building models from recorded measurements and observations to support data-driven research and evidence-based planning, including predictive tools, better visualization and feedbacks to prioritize new data capture.

The document is being promoted through a number of upcoming events this month, including the Governing Board of the Global Biodiversity Information Facility and the Subsidiary Body on Scientific, Technical and Technological Advice of the Convention on Biological Diversity (CBD SBSTTA) where it forms part of the discussion on meeting global targets to end biodiversity loss.

The framework arose from the Global Biodiversity Informatics Conference which gathered around 100 experts in Copenhagen in July, 2012, to identify critical questions relating to biodiversity and tools needed answer them. Workshop leaders at that conference went on to draw up and author the current document.

The Global Biodiversity Informatics Outlook includes examples of projects and initiatives contributing to its objectives, and the accompanying website www.biodiversityinformatics.org invites feedback from others wishing to align their own activities to the framework.

A deck of slides for presentations about GBIO is available at http://www.slideshare.net/GBIF/global-biodiversity-informatics-outlook

pro-iBiosphere will organise a series of workshops in Berlin

Thu, 26 Sep 2013 17:41:31 +0300

The pro-iBiosphere project is organising 4 workshops to be held on October 8 -10, 2013 in Berlin:

8 Oct. - Workshop 1: How to improve technical cooperation and interoperability at the e-infrastructure level
8 Oct. - Workshop 2: How to promote and foster the development & adoption of common mark-up standards & interoperability between schemas
9 Oct. - Workshop 3: Workshop on user engagement and benefits
10 Oct. - Workshop 4: Towards sustainability towards service: Meeting to evaluate business models currently in use by partners and relevant non-partners

The workshops will take place at the Berlin Botanical Garden and Museum, Königin-Luise Straße 6-7, Berlin-Dahlem.

For complementary information on these events (concept and objectives, accommodation and transportation), please visit the dedicated project wiki page here or contact us: info@pro-ibiosphere.eu.

You are invited to follow and/or participate in the discussions on Twitter by using the hashtag #pibber !  

The Biodiversity Data Journal: Readable by humans and machines

Tue, 17 Sep 2013 15:54:00 +0300

The Biodiversity Data Journal (BDJ) and the associated Pensoft Writing Tool (PWT), launched on 16th of September 2013, offer several innovations - some of them unique - at every stage of the publishing process. The workflow allows for authoring, peer-review and dissemination to take place within the same online, collaborative platform.

Open access to content and data is quickly becoming the prevailing model in academic publishing, resulting in part from changes to policies of governments and funding agencies and in part from scientist's desire to get their work more widely read and used. Open access benefits scientists with greater dissemination and citation of their work, and provides society as a whole access to the latest research.

To publish effectively in open access, it is not sufficient simply to provide PDF files online. It is crucial to put them under a reuse-friendly license and to implement technologies that allow machine-readable content and data to be harvested by computers that can collate small scattered data into a big pool. Analyses and modelling of community-owned big data are the only way to confront environmental challenges to society, such as climate change, ecosystems destruction, biodiversity loss and others.

Manuscripts are not submitted to BDJ in the usual way, as word processor files, but are written in the online, collaborative Pensoft Writing Tool (PWT), that provides a set of pre-defined, but flexible article templates. Authors may work on a manuscript and invite external contributors, such as mentors, potential reviewers, linguistic and copy editors, and colleagues, who may read and comment on the text before submission. When a manuscript is completed, it is submitted to the journal with a simple click of a button. The tool also allows automated import of manuscripts from data management platforms, such as Scratchpads.

"This is the first workflow ever to support the full life cycle of a manuscript, from initial drafting through submission, community peer-review, publication and dissemination within a single, online, collaborative platform. By publishing papers in all branches of biodiversity science, including novel article types, such as data papers and software descriptions, BDJ becomes a gateway for either large or small data into the emerging world of "big data", said Prof. Lyubomir Penev, managing director and founder of Pensoft Publishers.

BDJ shortens the distance between "narrative (text)" and "data" publishing. Many data types, such as species occurrences, checklists, measurements and others, are converted into text from spreadsheets into a human-readable format. Conversely text from an article can be downloaded as structured data or harvested by computers for further use.

A novel community-based peer-review provides the opportunity for a large number of specialists in the field to review a manuscript. Authors may also opt for an entirely public peer-review process. Reviewers may opt to be anonymous or to disclose their names. Editors no longer need to check different reviewers' and author's versions of a manuscript because all versions can be consolidated into a single online document, again at the click of a button.

"The Biodiversity Data Journal is not just a journal, not even a data journal in the conventional sense. It is a completely novel workflow and infrastructure to mobilise, review, publish, store, disseminate, make interoperable, collate and re-use data through the act of scholarly publishing!" concluded Dr Vincent Smith from the Natural History Museum in London, the journal's Editor-in-Chief.

The platform has been designed by Pensoft Publishers and was funded in part by the European Union's Seventh Framework Program (FP7) project ViBRANT.

###

Original Source

Smith V, Georgiev T, Stoev P, Biserkov J, Miller J, Livermore L, Baker E, Mietchen D, Couvreur T, Mueller G, Dikow T, Helgen K, Frank J, Agosti D, Roberts D, Penev L (2013) Beyond dead trees: integrating the scientific process in the Biodiversity Data Journal. Biodiversity Data Journal 1: e995. DOI: 10.3897/BDJ.1.e995

Apply until 15 October for the EU Prize for Women Innovators!

Fri, 13 Sep 2013 13:09:00 +0300

After a successful first edition in 2011, the European Commission has launched the second edition of the EU Prize for Women Innovators to reward three women who have developed outstanding innovations and brought them to market.

The contest is open until 15 October 2013, 5:00 pm (Brussels time) to all women who have founded or co-founded their own company and who have at some point in their career benefited from the EU's research framework programmes or the Competitiveness and Innovation framework programme.

The first prize is EUR 100,000, second prize EUR 50,000 and the third prize EUR 25,000.

With this Prize, the European Commission aims to raise awareness about the contribution, potential and importance of Women researchers to entrepreneurship and to encourage women to exploit the commercial and business opportunities offered by their research projects and become entrepreneurs.

Compete and tell your story now to inspire other women to follow in your footsteps!

Applications can be submitted via the competition website until 15 October 2013 (5 p.m. Brussels time): www.ec.europa.eu/women-innovators

The future of biodiversity publishing

Tue, 03 Sep 2013 18:35:00 +0300

The traditional audience for books and scientific papers in which scientists report their findings has been the human reader. Now we can enhance publications by attaching to them many different kinds of digital objects (such as the sounds made by birds, maps that show where they occur, or images and videos) or by adding computer-readable sections and terms that allow computers to extract information for re-use. We refer to these enriched and marked-up documents as 'enhanced'.

While the technology is available, only a tiny proportion of scientific publications are enhanced. Without enhancement, the research that is reported in the biosystematic (= taxonomic) literature cannot participate quickly and easily in the big data world.

The EU e-Infrastructure coordination project "pro-iBiosphere", targeting the preparation of the European Open Biodiversity Knowledge Management System, makes thirteen recommendations to enhance the publication process in order to to make biodiversity data accessible, computable and re-usable. These recommendations are a plea for a major change in how we publish biodiversity research. If adopted, they have the potential to transform the role of scientific publications. The recommendations include the need to make all biosystematic literature "openly and freely accessible to the maximum extent possible and for it to be marked up with computer-legible terms from an open, platform-independent XML or similar language. Mark-up allows computers to understand what is in a document, and to extract content for use elsewhere. The complete list of recommendations is available on "The State and Quality of Biosystematics Documents and Survey Reports". Inputs are welcomed on proi-Biosphere's Google +, LinkedIn or Facebook.

The reports are based on two workshops in Leiden (February 2013) and Berlin (May 2013) organised by the project with 100 and 45 participants, respectively; a questionnaire answered by 60 persons including taxonomists and related professionals; literature review and conversations with taxonomists.

" I think pro-iBiosphere has the best sense of how to prepare for a future of biodiversity science. e-Flora, e-Faunas, e-Mycotas, e-Protistas, etc. are merely conduits for semantically ready biodiversity information to flow to end users"

"I really enjoyed the morning workshop sessions and think that the results from these morning sessions have great potential for helping shape how we best carry out biodiversity research in the future and reach our users most effectively"

said two participants of the May 2013 pro-iBiosphere workshop.

The report demonstrates that publishers and scientists are not using new technologies to their full potential. The process of publication has historically targeted scientific articles that are suited to human readership. Nowadays, articles can also be used as vehicles for data that can be extracted and then re-used by others. This process does not reduce the value of articles for people, but creates a richer and more valuable resource at a very small additional cost

The authors of the report recognise that the community must build an infrastructure that can capture and manage the rich supply of re-usable data, and make it available to other users, for example through the Linked Open Data Cloud. Only through this process, can the very rich corpus of data and its underlying sources in the published record be linked to the huge production of born-digital genomic data. With developments such as this, biologists will be better placed to rise to the grander challenges, such as understanding how the natural world will respond to a warming world.

By Donat Agosti, PLAZI

Recommendations on how to move the naming of organisms from paper and on to the Internet

Tue, 03 Sep 2013 18:32:00 +0300

"Well, I suppose I'd better start finding names for things…" was the first thing said by the ill-fated sperm whale (Physeter macrocephalus Linnaeus, 1758) in Douglas Adam's Hitchhikers Guide to the Galaxy. Such is the richness of life that, unlike that whale, mankind is still naming things. Without commonly accepted names there would be no way to communicate research about life and it is the profession of taxonomists to put names on organisms and describe the different forms of life on Earth.

The EU e-Infrastructure coordination project "pro-iBiosphere", targeting the preparation of the European Open Biodiversity Knowledge Management System, makes ten recommendations to increase the adoption of digital workflows in the biodiversity domain. The recommendations include a "focus on usability and interoperability of software, not just functionality; fostering openness with research data"; and aim at giving further stimuli to the engagement of taxonomists with digital technology. The complete list is available in the report "The use of e-tools among producers of taxonomic knowledge". The document is based on a workshop and training organised by the project with 100 participants, a questionnaire answered by 220 persons including taxonomists and related professionals, literature review and conversations with taxonomists.

One of the attendees at the pro-iBiosphere workshops said "pro-iBiosphere is helping to close the gap between technology and taxonomists". Thibaut DeMeulemeester, Postdoctoral researcher (Naturalis Biodiversity Center, Leiden, the Netherlands).

Taxonomy has traditionally been a paper-based occupation and due to the rules on naming priority it relies heavily on the vast corpus of literature that has accumulated since the works of Carl Linnaeus. Yet, other scientists, conservationists and resource managers are crying out for a more transparent, stable, available and linked system of names. This can only be achieved digitally, openly and on the internet.

The need for a digital system of taxonomy is higher than ever. Modern metagenomic methods have been developed that can extract DNA sequence from 'soup' containing hundreds of species, many of which that cannot be linked to known species and some of which may in fact be new species to science. This is an exciting new technique with the potential to teach us much about microbial ecology, evolution and diversity. Yet it presents a challenge to taxonomy. The potential for generating thousands of DNA sequence from hitherto unrecognized species means that our ability to connect the genetic and biological data with their names will be severely tested. Only a digital online system of taxonomy can hope to keep up with these exciting developments.

pro-iBiosphere aims at binding together the disparate disciplines of the life sciences and envisages the digital-taxonomist providing the names that glue it all together.

Your feedback and suggestions are welcomed on pro-iBiosphere's Google +, LinkedIn or Facebook.

By Quentin Groom, NBGB

Recommendations for removing copyright hurdles to scientific research

Tue, 03 Sep 2013 18:27:00 +0300

The EU e-infrastructure coordination pro-iBiosphere project is preparing the ground for the pursuit of biological research in the digital age. In its "Draft policy for Open Access to data and information" scientists and lawyers recommend that hurdles posed by copyright and database protection should be removed by establishing exceptions for research in a new binding, Europe-wide regulation. This report opens a consultation process that will last until December 2013. Input is welcomed on pro-iBiosphere's Google+ , LinkedIn or Facebook.

At present, national provisions on copyright and database protection regarding exceptions and limitations for research purposes differ both in detail and substance. Scientists within the EU working with copyright protected works or with protected databases have to be aware that regulations may vary considerably from country to country. This can be a major stumbling block to international collaboration in science.

The document addresses legal issues that hamper an integrative system for managing biodiversity knowledge in Europe. It describes the importance for scientists to have access to documents and data in order to synthesize disparate information and to facilitate data mining (or similar research techniques). It explores some aspects of copyright and database protection that influence access to and re-use of biodiversity data and information and refers to exceptions and limitations of copyright or database protection provided for within the relevant EU Directives.

The scientists also suggest that publicly funded institutions should refrain from claiming intellectual property rights for biodiversity data and information published or made accessible by them. Re-use of biodiversity data and information for research purposes should be allowed without any form of authorization. The only claims that publicly funded institutions should make are to ensure users fully acknowledge the sources of information that they rely on.

The report concludes that the legal situation within the EU is unsatisfactory and, hence, the creation of a much-needed integrative system for biodiversity knowledge will be hampered by copyright or by database protection. The scientific community recommends that these hurdles should be removed by unifying the terms that relate to research needs in a binding, Europe-wide regulation.

The vision pro-iBiosphere is to prepare the ground for an integrating global system for the intelligent management of biodiversity knowledge (i-Biosphere). Such system will:

Offer a robust service-oriented architecture for distributed taxon-level information
Include a central registry of sources and services, with documentation, so that they can be discovered
Provide open and free access to all names and taxonomic information from a single source to all persons who need biodiversity data, without legal barriers, copyright and database protection rights, nor requiring the consent of other individuals or institutions
Facilitate the re-use of biodiversity data and information
Be interoperable with closely related initiatives
Be fully aware of user requirements so that it serves the community as a whole
Have a solid long term sustainability plan to maintain the infrastructure and the services

In order to fulfil this vision, technical and semantic interoperability challenges need to be addressed; user requirements need to be known; sustainability plans need to be developed; and basic requirements like allowing open and free access to data and information and re-usability for legitimate purposes need to be in place. At present, these basic requirements are hampered by numerous factual, technical, economic, sociological and other factors as well as by putative or real legal barriers, in particular, copyright and database protection rights.

By Willi Egloff, PLAZI

ORCID: disambiguating authors of science

Wed, 07 Aug 2013 11:34:45 +0300

Two of the biggest challenges of aggregating data and giving credit to the sources are duplication and ambiguity. The easiest way to resolve this is through unique persistent identifiers to objects, events and people. In pro-iBiosphere we have discussed at length identifiers for specimens (http://wiki.pro-ibiosphere.eu/wiki/Best_practices_for_stable_URIs). However; a solution already exists for people. ORCID is an open, non-profit, community-driven organization that provides a registry of unique and persistent researcher identifiers.

ORCID is a hub that connects researchers and their professional activities through the embedding of ORCID iDs in key research workflows, data systems and other identifier systems. ORCID is unique in its ability to reach across disciplines, research sectors and national boundaries and in its cooperation with other identifier systems. The ORCID iD is a key component that supports system interoperability.

ORCID improves discoverability and reduces repetitive data entry.
ORCID reduces activity reporting, eases staff burden, and simplifies the manuscript submission processes.
ORCID iDs overcome name ambiguity, distinguishing researchers and ensuring work is correctly attributed.
ORCID supports a more comprehensive understanding of global research, investment and impact.

Working in collaboration with others in the research community — universities, research organizations, funders, publishers and professional associations — the embedding of ORCID iDs is widespread and includes integration in researcher profile systems, manuscript submission processes, HR systems, grant applications, and in linkages with repositories and other researcher identifier systems. ORCID benefits the entire research community, and relies upon its organizational members for support.

Registration is free for researchers, and they control the privacy of their ORCID record. It only takes seconds to register — visit ORCID today.

Quentin Groom (http://orcid.org/0000-0002-0596-5376)
Rebecca Bryant (http://orcid.org/0000-0002-2753-3881)

EC Public consultation on open research data

Thu, 04 Jul 2013 12:00:00 +0300

On the 2^nd July 2013, I attended the EC Public consultation on open research data.

The EU has already a commitment to open publication of publicly funded research, but this was a consultation on the policy for the openness of data. The European Commission recognizes that openness of data is better for scientific advancement, it promotes innovation and it is also good for the citizen. It means that scientific research will be more verifiable and it will promote acceptance of research.

There were five topics for consultation:-

1. What types of data should be open and how do you define what research data is?

2. What restrictions should be placed on openness and when?

3. Where should open data be stored and made accessible?

4. How can a culture of openness be promoted?

5. How can issues related to re-use, such as citation, be addressed?

There were many perspectives at the meeting, from industry, medical research, particle physics, publishers, research funders, librarians, etc. However, from a Biodiversity perspective I came away with several points that I thought worth sharing.

1. Biodiversity researchers are much better placed than many other fields to move towards openness. We are not often restricted by issues of personal privacy and commercially sensitive data.

2. Being open with data will cost money. It is still not easy for the majority of biodiversity scientists to get their data in a format that they can deposit in a central repository. This will require investment in software and training.

3. Well maintained central repositories are essential for the storage, dissemination and citation of open data.

4. Unique identifiers of people (e.g. ORCID), publications (e.g. DOI) and data are essential for a culture of openness.

5. Data management plans are likely to be required in Horizon 2020 proposals, either in the proposal or as a first deliverable. Data management plans are now becoming essential at national and institutional level.

We have a long way to go in the promotion of openness in the Biodiversity community. Other scientific communities are well ahead of us. Yet there are good reasons to be optimistic, particularly with the progress of open publication. A change to a culture of sharing will develop if issues of citability of data can be resolved and if institutions give recognition to researchers for being open with their data.

Can I suggest you register for an ORCID today? It will help you get credit for your work and move us towards more open science.

CC-BY

Article by Quentin Groom (NBGB)

Biodiversity Informatics Horizons 2013

Wed, 03 Jul 2013 09:47:00 +0300

Second anouncement of the BIH2013 meeting

The conference Biodiversity Informatics Horizons 2013 (BIH2013) is part of a continuing process to structure and organise the biodiversity informatics community at the European level and beyond.

BIH2013, organised by several EU projects[1], will take place over 3 full days, from lunchtime on Tuesday 3rd September to lunchtime Friday 6th, with workshops and training events on Tuesday Morning and Friday morning. The venue will be in Sapienza University, Rome (venue waiting to be confirmed).

The intention behind the meeting is to explore options for H2020 funding in this domain. The European Commission would like to see a greater level of cooperation, so less direct competition, in the responses to H2020 calls.

Invited speakers will review challenging areas and promising technologies in biodiversity informatics, pathways to sustainable implementation and changing the community culture in the context of the LifeWatch vision, decadal priorities for biodiversity informatics, and the EC roadmap workshop on biodiversity infrastructures.

Demonstration and training activities will demonstrate some of the new and exciting infrastructure building blocks that will come together to deliver the LifeWatch vision. A panel discussion with experts from regions of the world beyond Europe will explore opportunities for international cooperation that lead towards a sustainable global infrastructure. There will also be a plenary discussion on working together towards building a more sustainable future, informed by networking opportunities throughout the conference.

The conference website is: http://conference.lifewatch.unisalento.it/index.php/EBIC/BIH2013

A demonstration session is available for persons wanting to show a software product or poster and we invite anyone to contact Dr Aaike De Wever <aaike.dewever_at_naturalsciences.be> to book a space before 12th August.

Alex Hardisty, Dave Roberts and Alberto Basset
(on behalf of the organising committee)

[1] BIH2013 is sponsored by BioVel, ViBRANT, LifeWatch, EUBrazilOpenBio and pro-iBiosphere. It has been organised with help from agINFRA, BioFresh, BIO_SOS, CReATIVE-B, e-Monocot, ENVRI, EU-BON, iMarine, Lifewatch, Natural Europe, OpenUp! and PESI.

Stable identifiers for specimens – A CETAF ISTC initiative supported by pro-iBiosphere

Mon, 01 Jul 2013 09:36:00 +0300

A recent initiative of the CETAF ISTC (Consortium of European Taxonomic Facilities – Information Science and Technology Committee) aims to implement a consistent identifier system for biological collections. This could be an important contribution to the formation of an international system of stable identifiers for the realm of biodiversity data.

The desire to participate in the Semantic Web and Linked Open Data has caused new interest in modern alternative identifiers for natural history collection specimens. In 2012, the Royal Botanic Garden Edinburgh (RBGE) published a paper (Hyam et al.[1]); see also Stable Citations for Herbarium Specimens on the internet) on using the Linked Data principles to issue HTTP URIs (URLs) for their specimens. The CETAF ISTC initiative mentioned was triggered by the RBGE paper. Other important proponents include P. DeVries (see e.g. his 2012 presentation on Linked open Data).

The pro-iBiosphere project was instrumental in furthering this discussion by addressing the issue in depth during both the Leiden (2013-02) and Berlin (2013-05) workshops. Significant progress was made in reaching improved understanding of the problems of LSIDs, DOIs, and Semantic Web stable HTTP URIs; see the pro-iBiosphere report on "Towards Best Practices Guide on Editorial Policies". Additionally, a pro-iBiosphere best practices document for choosing stable URI patterns was developed.

The proposed system allows the implementation of a consistent identifier system for, for example, collections held by CETAF institutions. It is based on HTTP URIs and allows a clear distinction between physical collection objects and their associated metadata. It can provide both human and machine readable object representations.

In a "stable identifier hackathon" in June 2013 in Edinburgh, five CETAF institutions (Royal Botanical Garden Edinburgh, Museum für Naturkunde in Berlin, Royal Botanic Garden Kew, National Museum of National History Paris and Botanical Museum Berlin-Dahlem) committed to a rapid pilot implementation of the system. Naturalis Biodiversity Center in the Netherlands also plans to join this effort.

The identifier implementations of the five institutions will be reviewed during the planned pro-iBiosphere workshop on "Improving technical cooperation and interoperability at the e-infrastructure level", to be held in the week of the 8th to 11th October 2013. The workshop will also discuss the application of the technology on object types other than specimens. Furthermore a demonstration on applications to show how the system can be used will be organised.

As we demonstrate the value in this way of working, the pro-iBiosphere consortium aims to encourage other institutions to adopt HTTP URIs for their specimens. The annual meeting of TDWG Biodiversity Information Standards that will take place in Florence in November 2013 and future pro-iBiosphere workshops will be used for this purpose.

The URI approach will be expanded to other domains like treatments or images within the pro-iBiosphere pilot studies (Task 4.2). Separately, a dialogue between DataCite and our community on creating a subdomain of DOIs for observation data is being pursued.

Already Zoobank has committed to offer this approach as an alternative to its present LSID-based system. We expect other institutions in the biodiversity domain to follow and hope that the system can serve as a blueprint for additional biodiversity informatics object types beyond collections.

Article by Anton Güntsch and Gregor Hagedorn

[1] Hyam, R., Drinkwater R. E. & Harris, D. J. (2012) Stable citations for herbarium specimens on the internet: an illustration from a taxonomic revision of Duboscia (Malvaceae). Phytotaxa 73: 17–30

ICT 2013 - Conference programme announced - Have a look!

Thu, 27 Jun 2013 12:43:35 +0300

The Vice President of the European Commission, Neelie Kroes and the President of the Republic of Lithuania, Dalia Grybauskaitė will open the conference.

Speakers from across the ICT sector will address a range of issues from cloud computing, broadband, ICT infrastructures, ICT skills, cyber security, long term visions on the future and much more.

Experts will present details on how to participate in the next EU's Research Programme - Horizon 2020.

Three thematic plenaries and three parts focusing on different themes of ICT research:
• ICT for Excellent science;
• ICT for Industrial Leadership;
• ICT for Societal challenges.

A special focus wil be on Digital Futures - a journey into 2050's futures and policy challenges.

More than 4000 researchers, innovators, entrepreneurs, industry representatives, young people and politicians are expected in Vilnius.

Visit ICT2013 website here to find out more on the conference programme.

Excavating observational data buried in botanical literature

Fri, 21 Jun 2013 15:56:00 +0300

It can be surprisingly hard to map the global distribution of a species and even harder to understand how it has changed with time. Even though many millions of observations are available on the Global Biodiversity Information Facility, many more are buried in books, papers, on specimens and in databases. What if all these observations were available to us, wouldn’t this help reveal species distributions and their change?

In order to address interoperability issues, the pro-iBiosphere project is conducting various pilots. One of these pilots is testing ways in which information from legacy texts can be digitized to consolidate data. We plan to use these data to reveal how the distribution of one particular plant species has changed over time: i.e., Chenopodium vulvaria L., a small annual weed commonly associated with man-made disturbance. Due to its striking smell of rotten fish, C. vulvaria (also known as "Stinking Goosefoot") is easily identified and unlikely to be confused with any other plant.

While, in California (USA) and Victoria (Australia) it is considered an invasive weed, in northern Europe it is a declining species and has been included on the Red Lists of several countries. No one knows why this species is decreasing in some places and increasing in others. Indeed, we don’t even really know what its complete distribution is, let alone the rates of spread and decline.

To convert all the paper records of Chenopodium vulvaria into data, we first need to convert them to digital text. Sometimes, this can be done with Optical Character Recognition (OCR), but in cases were old fashioned fonts have been used, transcription can be done in Wikisource, which is more reliable, but slower than OCR. Once we have the digital text, we mark it up using the GoldenGate Editor. This tool allows us to semantically markup the text so that its meaning is explicit. These data can then be loaded into a database, georeferenced and studied.

Records of biodiversity are, by nature, patchy and biased both spatially and temporally. They are fortuitous accounts of species collected by many different individuals over long periods for a multitude of reasons. Just like fossil hunters, we only get snippets of information from different places and times. Using these pieces of evidence we can reconstruct the situation of the past through statistical techniques. Undoubtedly, the more information we can gather the more reliable our reconstructions will be. So far, we have gathered over 2000 dated observations of Chenopodium vulvaria from hundreds of books, databases and herbaria. Ultimately, we aim to have the best possible set of observations for this species.

The website of the pilot project is a portal to all the data we have gathered so far on Chenopodium. It is a work in progress, so please do not be surprise when you find gaps in the information. If you happen to have information on Chenopodium, we hope you might consider contributing it.

Article written by Quentin Groom (National Botanic Garden, Belgium)

Also collaborating on the pilot project are Patricia Kelbert, Sabrina Eckert & Susy Fuentes (Botanischer Garten und Botanisches Museum Berlin-Dahlem)

Biodiversity Informatics Horizons 2013

Thu, 20 Jun 2013 09:37:42 +0300

Biodiversity Informatics Horizons 2013 (BIH2013) is part of a continuing process to structure and organise the biodiversity informatics community at the European level and beyond.

BIH2013, organised by several European Union projects[1], will take place over 3 full days, from lunchtime on Tuesday 3rd September to lunchtime Friday 6th, with workshops and training events on the mornings of Tuesday and Friday. The meeting will take place in central Rome and the venue will be confirmed at a later time.

The intention of the meeting is to bring together those likely to form consortia for Horizon 2020 (H2020) funding in this domain. H2020 workplans should be accessible by September to allow the forming of consortia.

Invited speakers will review challenging areas and promising technologies on the subject of biodiversity informatics, pathways to sustainable implementation and changing the community culture in the context of the LifeWatch vision, decadal priorities for biodiversity informatics, and the European Comission roadmap workshop on biodiversity infrastructures.

The conference website can be accessed here.

Please register before 31 July for early registration conference fee.

A demonstration session is available for persons wanting to show a software product or poster, please contact Dr Aaike De Wever: aaike.dewever[at]naturalsciences.be to book a space before 12th August.

---

[1] BIH2013 is sponsored by BioVel, ViBRANT, LifeWatch, EUBrazilOpenBio and pro-iBiosphere. It has been organised with the help of agINFRA, BioFresh, BIO_SOS, CReATIVE-B, e-Monocot, ENVRI, EU-BON, iMarine, Lifewatch, Natural Europe, OpenUp! and PESI.

Moving forward to the Flora of Brazil Online

Wed, 19 Jun 2013 16:55:00 +0300

Eduardo Dalcin [1]

In order to attend to Target 1 of the Global Strategy for plant Conservation (GSPC), adopted by the parties in the Convention on Biological Diversity (CDB) of 2002, a Brazilian initiative coordinated by the Rio de Janeiro Botanical Garden (Rio BG) began in late 2008. The purpose of this initiative was to assemble and review the existing data on Brazilian plants, algae and fungi, and to deliver a complete list of known species by 2010. [2]

The Rio BG and Centro de Referência em Informação Ambiental (CRIA) developed a database and a web interface to support the project. The compiled data were reviewed and refined online by a network of 413 taxonomists during 2009. This remarkably comprehensive and rapid collaboration was made possible only through advances in information and communication technology as well as the increased page load speed. The increase of the speed of the website has allowed many people to work remotely and simultaneously. Finally, the list was released online in May 2010 and was published in The Brazilian Catalogue of Plants and Fungi. The resulting list that documented 40,989 species of Brazilian algae, land plants, and fungi, of which 18,932 (46.2%) are endemic to the country. [3]

In 2010, the Rio BG received a new mission from the National Research Council (CNPq) to build up a "Virtual Herbarium of Repatriated Plants" (VHRP) - The REFLORA Program. The Brazilian government signed a Memorandum of Cooperation (MoC) with Royal Botanic Gardens Kew (RBGk) and the National Museum of Natural History, Paris (MNHN) in order to make possible the "repatriation" of the high resolution digital images of the herbarium vouchers of Brazilian plants collected in Brazilian territory that are kept in their collections.

The VHRP and National Plants Checklist; other initiatives, such as National Endangered Plants Assessment (also coordinated by the Rio BG and the National Center of Flora Conservation (CNC Flora)) and a new GSPC Target for 2020 - "World Flora Online" led to a necessity of a new information system architecture, integrating all the related systems around a taxonomic and nomenclatural backbone. Thus, in a partnership with the Federal University of Rio de Janeiro / Systems Engineering and Computing Program (PESC/ COPPE/ UFRJ), in 2010, the Rio BG starts to develop a new institutional scientific information system, integrating all related initiatives of scientific collections, references, images and maps. The new version of the "List of Species of the Brazilian Flora" (part of this integrated system), was launched in February 2013. It was well received by the scientific community.

At the end of year 2013, the VHRP will be launched. This project will link vouchers from RBGK, MNHN and Rio BG, promoting the digital environment in which taxonomists and experts can discuss the material that is available, suggest names, point out duplicates and improve data quality.

In the period between 2014 and 2017, the Rio BG is planning to integrate the CNC Flora’s information system and also start the evolution of the "List of Species of the Brazilian Flora" system toward the "Flora of Brazil Online".

Considering all the activities and responsibilities of biodiversity information management in Brazil, I was invited to attend the pro-iBiosphere meetings in Berlin (21 - 23 May 2013). This meeting provided me an excellent opportunity to be in touch with leading institutions and researchers from Europe and abroad and share experiences and approaches related to the management of biodiversity information. I have learned new information and made valuable contacts.

[1] Coordinator of the Scientific Computing Center at the Rio de Janeiro Botanical Garden - Brazil

[2] Forzza, Rafaela C., et al. 2012. New Brazilian floristic list highlights conservation challenges. BioScience 62.1: 39-45.

[3] Ibid; The list was published in Forzza, Rafaela C. 2010. Catálogo de plantas e fungos do Brasil. Vol. 1. Jardim Botânico do Rio de Janeir

Herbaria@home: an innovative digitalized herbarium now drawing a web of links among botanists

Tue, 18 Jun 2013 17:18:00 +0300

When Herbaria@home started in 2006, it was a ground-breaking approach to digitise and document the archives/material of the United Kingdom's herbaria. The website provides a web-based method for documenting herbarium sheets so that they can be accessed by anyone with internet connection.

The United Kingdom has the world's largest and oldest collections of herbarium specimens held in trust by museums and universities. Documenting large herbarium collections is an extremely labour-intensive task and most museum collections are woefully under-funded as a consequence of which most of the specimens are undocumented and unavailable. Through the efforts of a small army of amateur botanists, the plant biodiversity of the United Kingdom is the most studied and recorded in the world. This project aims to apply some of that effort to making the wealth of information from historical collections widely accessible and available.

The latest innovation of the project focuses on visualizations. These are produced to identify collaboration networks between botanists during different periods based on synthesized data from Herbaria@home. The author of these visualizations is Dr. Quentin Groom (Botany and Information Technology), National Botanic Garden of Belgium.

Participation in the project is welcomed and anyone who is interested can get involved. All participants are kept informed with regular updates, and the specimens documented are immediately made available and searchable on the web.

EUBrazilOpenBio announcing two new training resources on ecological niche modelling and cross-mapping available online

Mon, 17 Jun 2013 16:03:00 +0300

EUBrazilOpenBio invites pro-iBiosphere members and biodiversity stakeholders to access two new training exercises on ecological niche modelling and cross-mapping on their website.

The objective of the new exercise on ecological niche modelling is to study Adenocalymma dichilum A.H. Gentry. This species is endemic for Brazil. According to the Official List of Threatened Brazilian Plant Species, its conservation status is "Data Deficient". A reliable distribution model would help to decide whether the distribution is poorly known or restricted in a well-delimitated region in Brazil. This exercise goes through various steps, such as, retrieving occurance points and creating models, analysing the results of the models, projecting the models under exisiting conditions, etc. For more information on this exercise please click here.

The cross-mapping tool focuses on obtaining the list of taxa present in the family Passifloraceae that is in the List of Species of the Brazilian Flora (Brazilian Flora: LSBF) but not in the Catalogue of Life (CoL). The exercise goes through various steps, such as getting the Darwincore files with taxonomic checklists, running the cross-map algorithm, checking and exporting results, etc. For more information about this tool please click here.

Linking ecophysiology to vegetation modeling and pro-iBiosphere

Mon, 17 Jun 2013 14:02:00 +0300

Shuangxi Zhou[1]

My research project aims to establish a synthesis of field experimental data on the response of different plant functions to environmental changes and to study the relationships between plant traits, processes and key environmental factors. By incorporating recent advances in plant ecophysiology and biophysics and rapid accumulation of quantitative data on plant functional traits into current vegetation dynamics models, the project can contribute greatly to the evaluation and improvement of dynamic global vegetation models. The first paper, "How should we model plant responses to drought? An analysis of stomatal and non-stomatal responses to water stress", is in press now in the Agricultural and Forest Meteorology. Two glasshouse drought experiments in Sydney and Barcelona, and two transect field projects in south Australia and southwest China will be completed this year (for more details please click here).

As the only research student attendant, it has been a great pleasure to participate in the pro-iBiosphere meeting held in Berlin on 21st to the 23rd of May 2013. The meeting offered me many brainstorming opportunities to grasp advanced scientific and technical knowledge.

The meeting also allowed me to reflect on how my research is connected with other activities and used by various stakeholders. My research pursues the generic trends of trait and physiology variation in the context of key environmental factors and the translation of that variation into improved process representation in vegetation models. Discussion with other workshop participants, for instance, Jens Kattge (TRY Database Initiative) and Henry Ford (Ecological Flora of the British Isles, Bath University), made me aware of how my research work is connected to their database and being used by other disciplines. In my view, fundamental work on data collection and data quality control with specific standards is very important but easily ignored.

[1] PhD student, Macquarie University, Australia

Exploring a pro-iBiosphere - Korean collaboration

Mon, 17 Jun 2013 13:55:00 +0300

Yong-Shik KIM, FLS, Ph.D.[1]

I attended the pro-iBiosphere meeting that took place during the 21^st and 23^rd of May 2013 in Berlin, and found the topics of the workshops diverse and useful. It was an unusual opportunity for me to brainstorm with an expert group on the user requirements of fundamental biodiversity data and information.

During the workshops, I was very impressed to learn about the progress made by various European countries and the USA in documenting biodiversity information, including Biotas (e.g. Floras, Faunas, Mycotas).

The Global Biodiversity Information Facility (GBIF) Korea is one of the key partners to document information on biodiversity, and approximately 1,680 thousand records have been documented so far. Also, the Korea National Arboretum has documented 280 thousand herbarium specimens and 260 thousand insect specimens in the Korea National Herbarium. After my return to Korea, I discussed the outcomes of the pro-iBiosphere meeting in Berlin with the representative of GBIF Korea. We agreed to work closely together to collaborate with the relevant organizations and institutions in Korea and pro-iBiosphere. We think that there is a need to make a significant step to interweave the collaboration on national, regional, as well as international levels.

I am involved on the Global Strategy for Plant Conservation (GSPC). One of the core strategies of GSPC is the documentation of plant diversity. In my view, linking the European Plant Conservation Strategy (EPCS) under the regional and national levels would be very helpful to the participants from Asian countries.

I think that the topics addressed during the workshops organised by pro-iBiosphere are of interest to biodiversity colleagues in Korea and other East Asian countries. We look forward to being more actively involved in future pro-iBiosphere workshops.

[1] Chair of the Korean Plant Specialist Group, Species Survival Commission, The World Conservation Union. Member of the Advisory Committee of the National Plant Red Listing in Korea, President of the Korean Association of Botanic Gardens and Arboreta (KABGA), and Korean Coordinator of the East Asia Botanic Gardens Network (EABGN).

Producing an e-Flora for South Africa

Fri, 14 Jun 2013 14:14:00 +0300

Marianne le Roux[1]

An online Flora for South Africa will be compiled during the next few years in response to the updated Global Strategy for Plant Conservation (GSPC) 2011-2020. The GSPC includes five objectives and 16 targets. The first target states that an online Flora of all known plants must be created by 2020 (CBD, 2013). South Africa has agreed to participate in the global project and will produce an e-Flora for the country which can be incorporated into the World Flora Online. At present, seven regional Floras are being produced for South Africa. These Floras will form the foundation of the data published online. Information on the e-Flora will include: identification keys to families, genera and species, scientific names with author citations; descriptions; images; references; and environmental and organismal information relevant to conservation.

At the pro-iBiosphere workshops, held during May 2013 in Berlin, discussions were facilitated to determine:

who the users of biodiversity information are?
what services are typically required from institutions that generate the information?
what are the costs involved in these processes? and
how to deliver information in a sustainable manner?

During the breakout sessions and general discussions, emphasis was laid on important aspects that should be taken into consideration in, for example, compiling a Flora and how this information has to be presented to ensure intercommunication with other databases and its re-usability by different disciplines.

The workshop provided an opportunity to interact with people from a wide range of backgrounds (taxonomists to database developers) and to join forces in making progress towards sharing biodiversity information. At the pro-iBioshpere meeting I was introduced to peers who are also in the process of compiling Floras as well as publishers and database developers who were able to share their knowledge, insight and ideas around technical aspects involved in producing an e-Flora and finding solutions to common obstacles.

Reference

Decisions adopted by the Conference of the Parties to the Convention on Biological Diversity (CBD) at its Eleventh Meeting (Hyderabad, India, 8-19 October 2012) UNEP/CBD/COP/11/35 http://www.cbd.int/doc/decisions/cop-11/full/cop-11-dec-en.pdf

[1] E-Flora Coordinator, South African National Biodiversity Institute (SANBI). Contact: m.leroux@sanbi.org.za; Tel. +7212 843 5124

The 6th issue of the Pace-Net (Pacific European Network) project newsletter is now available

Fri, 14 Jun 2013 10:34:00 +0300

The EU FP7 funded project Pace-Net presents the 6^th issue of its newsletter, where stress is placed on Recommendations for a Strategic Plan on Research, Innovation and Development in the Pacific formulated during the final Conference held in Suva (Fiji) in March 2013. The project will extend its life through the Pace-Net Plus, another Inco-net that already positively evaluated by the EC.

The newsletter also contains an evaluation of Pacific-European partnership in scientific research the External Advisory Board (EAB), where positive examples are given for bi-regional scientific cooperation. The issue presents a call for strengthening the science collaboration with developing countries in the Asia-Pacific Region, Latin America and the Caribbean.

European Citizen Science Association (ECSA): A major new EU-wide initiative

Thu, 13 Jun 2013 14:38:00 +0300

European Environment Commissioner Janez Potočnik welcomed the creation of the European Citizen Science Association (ECSA) at an event at EU Green Week on Thursday, 7 June 2013.

The new body will be based in London and headed by Dr Linda Davies of Imperial College London – the director of OPAL.

ECSA aims to involve all European Union member states and engage five million people across the EU over the next four years.

Earlier at the Brussels-based EU Green Week conference, Dr Davies presented OPAL's experiences in engaging citizen scientists to collect air quality data for the OPAL air survey.

Find out more about OPAL and ECSA here.

ERA-NET: European Network for co-ordination of policies and programmes on e-infrastructures

Wed, 05 Jun 2013 11:04:00 +0300

A new ERA-NET is proposed to further the integration of national, EC and global e-infrastructure programmes. An experienced consortium comprising relevant national programme managers is proposed to develop the ERA-NET, called e-InfraNet.

e-InfraNET Project is ambitious to address the need for harmonising and co-ordinating the related national efforts and establishing a common European endeavour in order to serve successful integration of the diverse and parallel local and regional policies in the field of e-Infrastructures. The ERA-NET will be targeted at national programme managers and policy makers which will improve policy collaboration and build further on the outputs of existing groups, making sure the innovative policy ideas will be integrated properly in national and EC policy.

A key long-term impact will be the more efficient use of resources, and the adoption of best-practice in national e-infrastructure programmes. E-InfraNet will lead to a convergence of funding programmes and avoid unnecessary overlap. The variable geometry approach will allow for progress to be made, while giving flexibility to adjust to national requirements and leave the route open to all to build on successful joint actions.

To read more about the project please follow the link: http://e-infranet.eu/overview/

San Francisco Declaration on Research Assessment (DORA) calls for reassessment of the importance of Impact Factor

Fri, 17 May 2013 13:25:00 +0300

The San Francisco Declaration on Research Assessment (DORA) was initiated by the American Society for Cell Biology (ASCB) together with a group of editors and publishers of scholarly journals after a meeting in December 2012 during the ASCB Annual Meeting in San Francisco. The document recognizes the need to improve the ways in which the outputs of scientific research are evaluated.

DORA puts into question the use of Journal Impact Factor as a main tool for assessment, and proposes the consideration of various other factors towards more sophisticated and meaningful approaches. DORA is a worldwide initiative covering all scholarly disciplines.

To read the whole declaration, please follow the link: http://am.ascb.org/dora/

DRYAD announces nonprofit sustainability plans

Thu, 09 May 2013 09:50:00 +0300

The data repository invites community input on the future of data archiving at upcoming membership meeting

Dryad, a repository for data underlying the international scientific and medical literature, works with a variety of journals, societies and publishers to archive research data at the time of publication. The project began in 2009 and has published more than 3,000 data packages. In 2012, Dryad incorporated as a nonprofit organization with the mission to make scientific and medical research data permanently available to all researchers and educators free-of-charge without barriers to reuse.
For the past four years, Dryad has worked with its stakeholders to develop a sustainability plan to realize this vision. Central to the sustainability plan is a one-time submission fee that will offset the actual costs of preserving data indefinitely. A variety of pricing plans are available for journals and other organizations such societies, funders and libraries to purchase discounted submission fees on behalf of their researchers. For data not covered by a pricing plan, the researcher will be asked to pay upon submission, with waivers provided to researchers from World Bank low and lower-middle income economies. Submission fees will apply to all new submissions starting September 2013. Dryad will also be supported in part by its membership, by grants for research and innovation, and by donors. Membership in Dryad is open to any organization that supports research and education. Dryad is pleased to include Pensoft Publishers among its Charter Members.
The Dryad Membership meeting, to be held in Oxford, UK on Friday, May 24 is open to members, prospective members, researchers and other interested parties. Attendees will hear about recent and upcoming developments in the repository and the nonprofit organization. In addition, there will be an Emerging Issues Forum with presentations from the community about future directions for Dryad, its members, and partner journals, including models for the technical and peer review of data, ideas for promoting the adoption of data citations, measuring data reuse, funder perspectives on the use of research grants for data management costs and the relevance of larger data networks.
Dryad’s Membership Meeting is part of a series of free public events in Oxford spotlighting trends in scholarly communication with an emphasis on research data, including a Symposium on the Now and Future of Data Publication on Wednesday, May 22nd and an ORCID Outreach Meeting with a special joint Dryad-ORCID Symposium on Research Attribution on Thursday, May 23rd. Registration for these events closes on May 13th. Remote attendance will be available for those unable to attend in person.

For more information about submitting data, becoming a member or the sustainability plan, please visit http://datadryad.org. The website also offers an Ideas Forum where people can make their voice heard by suggesting and voting for new features and offering comments.

CONTACT:
Laura Wendell, Executive Director
lwendell@datadrayd.org
+1-919-668-4005 or +1-919-423-3889

MTSR 2013 : VII Metadata and Semantics Research Conference

Wed, 08 May 2013 12:11:00 +0300

November 19-22, 2013 Alexander Technological Educational Institute of Thessaloniki, Greece

Continuing the successful mission of previous MTSR Conferences (MTSR'05, MTSR'07, MTSR'09, MTSR'10, MTSR'11 and MTSR’12), the seventh International Conference on Metadata and Semantics Research (MTSR'13) aims to bring together scholars and practitioners that share a common interest in the interdisciplinary field of metadata, linked data and ontologies. Participants will share novel knowledge and best practice in the implementation of these semantic technologies across diverse types of Information Environments and applications. These include Cultural Informatics; Open Access Repositories & Digital Libraries; E-learning applications; Search Engine Optimisation & Information Retrieval; Research Information Systems and Infrastructures; e-Science and e-Social Science applications; Agriculture, Food and Environment; Bio-Health & Medical Information Systems.

pro-iBiosphere series of meetings in Berlin

Wed, 08 May 2013 11:22:00 +0300

The pro-iBiosphere project is organising 3 workshops to be held on May 21-23, 2013 in Berlin:

May 21st: Workshop on Requirements of users of Flora, Fauna or Mycota publications or services - more information here.
May 22nd: Workshop on Measuring and constraining the costs of delivering services - more information here.
May 23rd: Workshop on Coordination and routes for cooperation - more information here.

The workshops will take place at the JKI Biological Research Center located nearby the Berlin Botanical Garden and Museum.

You are invited to follow and/or participate in the discussions on Twitter by using the hashtag #pibber !

For complementary information on these events (concept and objectives, accommodation and transportation), please visit the dedicated project wiki pages here or contact us.

Towards a Roadmap for Biodiversity and Ecosystem research in Europe

Mon, 29 Apr 2013 18:29:00 +0300

The "Towards a Roadmap for Biodiversity and Ecosystem research in Europe" Workshop is took place in Brussels on 19-20 March 2013. The overall objective of this workshop, organised in cooperation with the LifeWatch project, was to develop synergies between ESFRI research infrastructures (RI), existing research infrastructures implemented as Integrating Activities (IA), Integrated Projects (IP) and Joint Programming Initiatives (JPI) which are relevant to biodiversity and ecosystem research.

Among the hot topics discussed was the synergy between the biodiversity components of different initiatives, also in view of the supporting role of the European research infrastructures in this area. A strategy for the development of biodiversity research infrastructures in the next ten years in view of emerging scientific and technical challenges was also reviewed during the workshop.

For more information about the workshop and to view the presentation given please click here.

The new EUBrazilOpenBio e-newsletter is now out announcing an opportunity for e-training

Wed, 24 Apr 2013 11:37:00 +0300

The latest EUBrazilOpenBio newsletter is now out announcing a new e-training Programme aiming at educating and enabling current and potential users of EUBrazilOpenBio to unlock new knowledge and shape effective policy on biodiversity challenges. The EUBrazilOpenBio anytime, anywhere eTraining tools are designed for researchers in the spheres of Biodiversity, Life science, Climate Change, application Developers as well as regulatory authorities and policy decision-makers.

EUBrazilOpenBio is focused on tackling the complexity of biodiversity science such as the diversity of multidisciplinary datasets spanning from climatology to earth sciences by integrating advanced computing resources with data sources across Europe and Brazil.

For more information find the complete version of the newsletter here.

Ecoscope Conference: Network of Research Observatories on Biodiversity

Wed, 24 Apr 2013 11:27:00 +0300

Toward a Network of Research Observatories on Biodiversity - What stakes and advances?

The ECOSCOPE conference has been scheduled to take place on May 23 - 24, 2013, in Institut Océanographique, Paris. The conference has been announced under the slogan "Toward a Network of Research Observatories on Biodiversity - What stakes and advances?"

The event will run over two days with a focus on observation and research infrastructures on biodiversity, during the first day, and data management and value, during the second.

For more Information visit: http://www.fondationbiodiversite.fr/agenda/seminaire-ecoscope

The first SPREE newsletter is now available

Mon, 22 Apr 2013 11:31:00 +0300

SPREE is a three-year EU (FP7) funded research project launched in July 2012. Its overarching goal is to bring the European community closer to achieving a truly sustainable and prosperous economy characterized by efficient use of resources. The project focuses on the concept of Servicizing which represents the shift from traditional purchasing to service acquisition.

The first SPREE newsletter is now a fact providing a project description, key facts, a list of partners and a workflow overview for the project. There is also a useful link to a video explaining the concept of Servicizing for the wider public.

SPREE project aims at designing innovative servicizing systems in the water, mobility and agrifood sectors that will enable a more radical and at the same time practical change in the way resources are being used and consumed. The Agent-Based Modeling (ABM) of these systems together with simulations of their potential effects will be supplemented by the composition of Servicizing Policy for Resource Efficient Economy.

For more information please find the first SPREE newsletter attached below.

A new article provides a decadal view on the importance and future of biodiversity informatics

Fri, 19 Apr 2013 11:19:00 +0300

A new article "A decadal view of biodiversity informatics: challenges and priorities" published by BMC Ecology focuses on the challenges and perspectives for biodiversity informatics after a decade of development. The authors Alex Hardisty and Dave Roberts alongside 77 contributions from the biodiversity informatics community share experience and set future directions of biodiversity informatics as a tool for addressing conservation and ecological issues.

Biodiversity informatics plays a central enabling role in the research community's efforts to address scientific conservation and sustainability issues. This community consultation paper positions the role of biodiversity informatics, for the next decade, presenting the actions needed to link the various biodiversity infrastructures invisibly and to facilitate understanding that can support both business and policy-makers. The community considers the goal in biodiversity informatics to be full integration of the biodiversity research community, including citizens’ science, through a commonly-shared, sustainable e-infrastructure across all sub-disciplines that reliably serves science and society alike

The full text of the article can be accessed here.

The "ICT2013 – Create, Connect, Grow" event held in Vilnius - call for proposals

Thu, 18 Apr 2013 18:44:52 +0300

Europe’s most visible forum for ICT research and innovation, namely ICT2013, will take place from November 6 to 8th, 2013 in Vilnius, Lithuania.

This event will bring together Europe’s best & brightest in ICT research, with businesses old & new, web start-ups and digital strategists to chart a path for Europe’s ICT research policy.

Participants will have the opportunity to share their vision for the future with EU policy-makers, and see the latest advances in EU-funded ICT research.

ICT2013 will be the first opportunity to learn the details of research funding for ICT-related projects under Horizon 2020, the EU’s new research program for 2014-2020.

ICT2013 will also offer participants opportunities to showcase their most advanced research, ICT products and most innovative creations and to meet delegates with common or similar topical interests with whom they could collaborate in the future. This would be possible by organising networking sessions and holding an exhibition stand.

So as to participate, you should submit proposals:

For networking sessions before 26 April 2013 by completing the online form,
For exhibition, until 7th June 2013 16.00, log in here.

To follow the latest news on ICT2013 on Twitter go to @ict2013eu.

The 3rd BioVel newsletter is now available

Thu, 18 Apr 2013 11:30:00 +0300

The newest newsletter of the BioVel project is now available, offering a range of biodiversity related news, including brief coverage of the EU BON Kick-off and International Symposium Workshop in February, 2013. Among the other stories covered are:

Letter from Alex Hardisty, Project Coordinator
Running Workflows Just Got a Whole Lot Simpler
Friends of BioVeL: Friendships and collaborations are also blooming! (featuring news about: LifeWatch-BioVeL cooperation;; i4Life project; Micro B3 and GENSC are now friends of BioVeL.

The newsletter also contains information about the upcoming workflows and research within the project, as well about events planned for the future.

To read the article and find out more about the news stories covered click here.

"Bee" a taxonomist!

Tue, 09 Apr 2013 14:08:00 +0300

I am working as a postdoctoral researcher at the Naturalis Biodiversity Center on bee systematics and bee identification. At present, my morphological studies focus on wing shape analyses using geometric morphometrics. During the pro-iBiosphere workshop and training on "e-platforms and e-tools for taxonomy" (http://wiki.pro-ibiosphere.eu/wiki/Workshops_Leiden_February_2013) that took place in February 2013 (Leiden, the Netherlands) I gained information about state-of-the-art platforms & tools that I could use for my work and learnt how to use them.

In bees, wing shape is a reliable diagnostic trait at different taxonomical levels: from families to species and sometimes even populations. This encouraged me to develop an identification tool for bee species based on wing venation patterns. During the session on "Developing organism identification apps for Android devices", given by Dr. Alexander Krings, I developed a prototype of an android app that includes morphological keys, tips for rapid identification, and general information about most common bees. This app can be a handy tool for taxonomists and naturalists to obtain information while doing field work. Of course, the thousands of published keys, papers, and books are very precious, but they are mainly available in the lab or at home. e-tools bring us highly valuable published information everywhere we go, where we need it, and where we find the bees.

My PhD research on bee systematics included description and taxonomic revision of several bee fossils. For these studies, wing shape allowed for quantitative assessment of taxonomic affinities of bee fossils with extant taxa. One of the best examples of the power of this method was the identification of a fossil bee wing (which was all that was available) as a Bombus randeckensis specimen from the Miocene. Bee fossils are rare, and until recently a comprehensive list was not available. e-platforms such as "scratchpads" (funded by the EU FP7 ViBRANT project) are an easy-to-use tool that allows sharing knowledge among taxonomists. As a result of the pro-iBiosphere training, I managed to upload the complete bee fossil list, including general information on each fossil and on the main deposits into a scratchpad. This platform facilitates open access and provides a significant help for my scientific work: the website makes available a fast search tool for taxonomical names, and allows easy publication of the new updates of our research activities.

e-tools and e-platforms for taxonomy help to diffuse and share scientific knowledge among taxonomists and the general public. Training on these tools and platforms invites taxonomists to change their way of thinking about the design of their projects and on how to effectively disseminate their results to a wider audience. With continuously updated information, collaborative platforms, interactive keys, and android apps, taxonomy can hardly be considered an ‘old-fashioned’ field!. If scientists want to increase their impact on society, they have to follow the evolution of our knowledge-hungry society.

pro-iBiosphere is helping to close the gap between technology and taxonomists!.

* The bee identification app and the bee fossil scratchpad are under construction and will be available very soon

Thibaut DeMeulemeester, Postdoctoral researcher (Naturalis Biodiversity Center, Leiden, the Netherlands). Contact: thibaut.demeulemeester@naturalis.nl; koos.biesmeijer@naturalis.nl

Join the project community!

Fri, 29 Mar 2013 15:40:00 +0200

Looking for even more ways to interact with the pro-iBiosphere project and the main stakeholders in the field, while getting real time access to the latest news, event and project activities information?

Be sure to check out our social media, follow us and join the conversation!

	Facebook - like us here - Access information on the latest biodiversity research developments - Interact with key stakeholders in the field - Discover our project events latest pictures and videos
	Twitter - follow us here - Be instantly updated on the latest project, biodiversity and EU news - Get involved in the discussions during project events - Follow other key biodiversity initiatives and players
	LinkedIn - join us here - Get the latest news on EU fundings - Participate in the fruitful discussions and debates - Promote your project among experts

BiodiversityKnowledge Side Event - IPBES Plenary January 2013

Wed, 20 Mar 2013 17:17:00 +0200

The first meeting of the Platform's plenary (IPBES-1) took place in Bonn Germany from 21 to 26 January 2013. BiodiversityKnowledge together with SPIRAL, EBONE and EUBON - organized a side event on Regional support approaches to IPBES – Europe as showcase. This side event aimed to outline the importance of regional interactions to support and facilitate input into the work programme activities of IPBES. (Full report, pdf)

Research Data Alliance (RDA) is now launched

Wed, 20 Mar 2013 17:16:33 +0200

The Research Data Alliance (RDA) has been recently launched. Its First Plenary took place between 18-20 March, 2013 in Gothenburg, Sweden. The hot topic of the Plenary was the RDA vision towards open access data without barriers. The 3 days of meetings and working sessions brought the research data community together to contribute and set milestones for the future work of the RDA towards open access data-driven innovation.

Over the last decade, significant investments have been made all over the globe
for developing scientific data infrastructures to support the work of research communities and improving shared access to data. There is a common understanding that solutions must be global and that the development of an integrated and interoperable data domain can only be achieved through increased global cooperation.

As "big data" emerges as an international priority, the Research Data Alliance (RDA) is a newly formed organization whose goal is to accelerate data-driven innovation world-wide through research data sharing and exchange.

At its first Plenary, the RDA was launched by sponsors from the European Commission, the U. S. Government and the Australian Government and leaders in the data community. The Plenary was used as a working meeting to accelerate discussion, Working and Interest Group interaction, and data community development.

ICSU-WDS Data Publication Charter: http://www.icsu-wds.org/working-groups/data-publication

BiodiversityKnowledge Second Conference in Berlin, September 24-26

Wed, 20 Mar 2013 17:11:00 +0200

BiodiversityKnowledge is organizing its second international conference on September 24^th to 26^th 2013.
For the venue we choose the green and atypical Jerusalemkirche, right in the middle of Berlin between Checkpoint Charlie and the Jewish museum.
The objective of this second conference is to discuss and finalize the recommended design of a future Network of Knowledge (NoK) on biodiversity and ecosystem services in Europe.
Registration for the conference will be open in beginning of April 2013.
More information on the conference will soon be available on conference website.

ALTER-Net Conference in Ghent, April 15-18

Wed, 20 Mar 2013 16:39:00 +0200

We kindly invite you to attend the BiodiversityKnowledge side event on the first day of the ALTER-Net Conference "Science Underpinning the EU 2020 Biodiversity Strategy". The primary focus of the conference will be the objectives and targets of the EU's 2020 Biodiversity Strategy, which should be realized by the end of this decade. Being a science-policy interface network, ALTER-Net wants to help the EU in realizing these targets by providing scientific knowledge, e.g. by pointing out possible weaknesses, opportunities and necessities, and by helping to find solutions and evidence-based actions.
The BiodiversityKnowledge session on Monday afternoon will first present our project's approach in short, concise talks and then give the opportunity for discussing major issues related to governance of the structure, involvement and acknowledgment, quality control and other main challenges.

New "LinkOut" tool by National Center for Biotechnology Information (NCBI) providing easy link to PubMed and GenBank data

Mon, 18 Mar 2013 11:01:00 +0200

A new "LinkOut" feature introduced by the National Center for Biotechnology Information (NCBI) NCBI’s allows the easy linking to content on PubMed and GenBank. Dryad has already introduced the feature benefitting from easy and fast linking of associated content to the two resources.

PubMed and GenBank, from the National Center for Biotechnology Information (NCBI), are hugely popular resources for searching and retrieving article abstracts and nucleotide sequence data, respectively. PubMed indexes the vast majority of the biomedical literature, and deposition of nucleotide sequences in GenBank or one of the other INSDC databases is a near universal requirement for publication in a scientific journal. LinkOut allows the data from an article to be distributed among repositories without compromising its discoverability.

Dryad, intends to expand on this feature in a couple of ways. First, it is planned to make Dryad content searchable via the PubMed and GenBank identifiers, which because of their wide use will provide a convenient gateway for other biomedical databases to link out to Dryad. Second, open web standards will be used to expose relationships between content in Dryad and other repositories, not just NCBI.

Original source: Dryad news and views

pro-iBiosphere participated in the the European Commission's 10th e-Infrastructure Concertation Meeting

Wed, 13 Mar 2013 10:50:33 +0200

The 10th e-Infrastructure Concertation Meeting (March 6-7, 2013 - Brussels) was organised by the European Commission (e-Infrastructure Unit, DG CONNECT) with the support of the e-ScienceTalk project. The main aim of the meeting was to bring EU funded infrastructure projects together to discuss issues related to the completion of the EC 7th Framework Programme (FP7) and the start of the framework of Horizon 2020 (2014-2020).

The first day was dedicated to discuss the EU e-Infrastructure vision, impact and metrics. The second day focused on the e-infrastructure priorities (parallel tracks) and on future sustainability of e-infrastructures. The meeting provided excellent networking opportunities and helped participants to gain a better understanding of the current and the future Horizon 2020 programme's challenges. Slides of the meeting are available on the event web-page here.

Thank you pro-ibiosphere

Fri, 08 Mar 2013 10:23:00 +0200

By Siti-Munirah, M.Y. (sitimunirah@frim.gov.my) Forest Research Institute Malaysia

I am a Research Officer and a young botanist at the Kepong Herbarium (KEP), Forest Research Institute Malaysia (FRIM), Kuala Lumpur, Malaysia. At present, I'm working for the Flora of Malaysia project, revising families for the Flora of Peninsula Malaysia, such as, Lythraceae, Rafflesiaceae, Droseraceae, Cabombaceae, Ranunculaceae and a few others. I am also interested in Rafflesia (a parasitic group of plants), Drosera (a carnivorous plant group), and Cabomba (an invasive plant group). From my botanical exploration in the green forests of Malaysia I also focus on, Sonerilla, Argostemma and Thismia. I have been conducting fieldwork throughout Peninsular of Malaysia since 2007, and have collected more than 958 herbarium specimens. I am also involved with monitoring Rafflesia distribution and in its conservation in Malaysian Peninsular.

After attending the pro-iBiosphere workshops and hands-on training sessions (http://wiki.pro-ibiosphere.eu/wiki/Workshops_Leiden_February_2013), I gained new knowledge and understanding on how to use various e-platforms and e-tools for taxonomy. It benefited my career path development as a taxonomist and gave me the opportunity to share and spread the information among my colleagues, also within my country.

Recently, I have published my first new species via Phytokeys, my first encounter with an online journal. The whole process only took around 4 months.

The main resources of biodiversity data are from basic research, therefore the foundation support for basic research exploring biodiversity should be available and sustained persistently. In my opinion, e-tools and e-platforms for taxonomy should be taught during degree or school level and applied for masters and PhD students. The extensive promotion should be done widely especially in the countries with high biodiversity. This will help to develop a good biodiversity center base for a region or country key players.

Technology transfer should be an important concern by the institutes involved in biodiversity studies.
I think pro-iBiosphere is in the right direction, pro-iBiosphere is functioning as the meeting point for those who are involved with biodiversity activities, such as scientists, taxonomists, IT people and developers. It also fosters collaboration among projects and key players. Last but not least, I would like to suggest a 'One stop centre: Biodiversity of the world' website, where all the related links of Biodiversity are gathered in one place.

First report on diversity and strengths of existing business models and discussion of sustainability (D6.3.1)

Wed, 06 Mar 2013 16:36:32 +0200

The first pro-iBiosphere report on "Diversity and strengths of existing business models and discussion of sustainability (D6.3.1)" was released on March 4, 2013. This report summarises the exploitation plans foreseen to date by each project partner and the business models they use. The next phase will be to bring this information in the light of a "market context" or "market background".

In order to gather inputs from project partners, a questionnaire was sent to all pro-iBiosphere consortium partners. The questionnaire included three parts, addressing:

:: Exploitation plans at the level of each organization,

:: Business models currently is use by organization, and

:: Market context and sustainability perspectives.

The answers have been consolidated, analysed and complemented with a desktop research by Sigma Orionis (see D6.3.1, http://www.pro-ibiosphere.eu/documents/)

Successive versions of this deliverable with updated inputs from all consortium partners will be produced in the next months. In addition, a plenary meeting: "Meeting to evaluate business models currently in use by partners and relevant non-partners" will be organised in November 2014. The plenary will provide a significant step towards sustainability plans.

Evaluation of pro-iBiosphere workshops

Fri, 01 Mar 2013 17:54:31 +0200

The pro-iBiosphere workshops that took place on the 11^th to 14^th of February 2013 aimed to get taxonomists and IT developers together to discuss digital tools for taxonomy; the digital mobilization of legacy literature and developments towards the next generation of digital taxonomic literature.

In a packed agenda, which included an intense day of training workshops, participants learned about Biovel, Charparser, EDITor, Android Apps, BiowikiFarm, Scratchpads, XPer2 and many more active projects.

After the event attendees were asked to evaluate the event. Forty percent of the 101 participants responded to our questionnaire and 88% of them rated the content either "excellent" or "very good". Other positive indicators of a successful event were that only one person would not recommend our events to others and only one person had no intension to attend another pro-iBiosphere event.

The event was a good opportunity for people to network. Almost three-quarters felt they had made five or more useful contacts. We also received a positive evaluation for the level of interest in the event. Again more than three-quarters of the respondents rated it "very interesting" and only two rated it "not so interesting".

We hope to do even better during our next event in May (21^st-23^rd) 2013, when we examine the requirements of the downstream users of taxonomic information and mechanisms for paying for taxonomic services and coordination and routes for cooperation.

pro-iBiosphere Management Meetings in Leiden

Wed, 27 Feb 2013 19:39:44 +0200

On Friday the 15^th of February 2013, meetings with the pro-iBiosphere Advisory Board (AB) and Consortium members took place.

At present, the AB is composed of four members from major global biodiversity initiatives with interests from the users’ and the developers’ side. AB members will meet at least once per year to provide their recommendations for improvement of the overall project results and activities. Additional members have been contacted and will join the project AB during the next months.

The Consortium Meeting, aimed at providing an overview of the project status, progress of the different work packages and tasks, and to take actions for the next 3 months of the project.

Discussions centered on the outputs and first impressions on the project series of workshops organised in Leiden and the suggestions on how to improve the quality and effectiveness of future workshops to be organised in the coming months. Taking into account the feedback received by participants of the meeting, all partners agreed that the first series of workshops that were organised resulted in being a success.

The first report on partners’ "exploitation plans and sustainability" was released by the end of February 2013. Further dissemination efforts undertaken by all partners in the coming months will ensure a broad project visibility among the biodiversity community and also that first project results reach a wide audience.

At present, various pro-iBiosphere pilots are being conducted and first results will be available by the end of May 2013.

The next and third Consortium Meeting will take place on May 24, 2013 in Berlin on the occasion of pro-iBiosphere Meeting #3 http://wiki.pro-ibiosphere.eu/wiki/Workshops_Berlin,_May_2013.

The Future of Botanical Monography: Report from an international workshop, 12–16 March 2012, Smolenice, Slovak Republic

Thu, 21 Feb 2013 17:46:00 +0200

Monographs are fundamental for progress in systematic botany. They are the vehicles for circumscribing and naming taxa, determining distributions and ecology, assessing relationships for formal classification, and interpreting long-term and short-term dimensions of the evolutionary process. Despite their importance, fewer monographs are now being prepared by the newer generation of systematic botanists, who are understandably involved principally with DNA data and analysis, especially for answering phylogenetic, biogeographic, and population genetic questions. As monographs provide hypotheses regarding species boundaries and plant relationships, new insights in many plant groups are urgently needed. Increasing pressures on biodiversity, especially in tropical and developing regions of the world, emphasize this point. The results from a workshop (with 21 participants) reaffirm the central role that monographs play in systematic botany. But, rather than advocating abbreviated models for monographic products, we recommend a full presentation of relevant information. Electronic publication offers numerous means of illustration of taxa, habitats, characters, and statistical and phylogenetic analyses, which previously would have been prohibitively costly. Open Access and semantically enhanced linked electronic publications provide instant access to content from anywhere in the world, and at the same time link this content to all underlying data and digital resources used in the work. Resources in support of monography, especially databases and widely and easily accessible digital literature and specimens, are now more powerful than ever before, but interfacing and interoperability of databases are much needed. Priorities for new resources to be developed include an index of type collections and an online global chromosome database. Funding for sabbaticals for monographers to work uninterrupted on major projects is strongly encouraged. We recommend that doctoral students be assigned smaller genera, or natural portions of larger ones (subgenera, sections, etc.), to gain the necessary expertise for producing a monograph, including training in a broad array of data collection (e.g., morphology, anatomy, palynology, cytogenetics, DNA techniques, ecology, biogeography), data analysis (e.g., statistics, phylogenetics, models), and nomenclature. Training programs, supported by institutes, associations, and agencies, provide means for passing on procedures and perspectives of challenging botanical monography to the next generation of young systematists.

Source: Crespo, A., Crisci, J.V., Dorr, L.J., Ferencová, Z., Frodin, D., Geltman, D.V., Kilian, N., Linder, H.P., Lohmann, L.G., Oberprieler, C., Penev, L., Smith, G.F., Thomas, W., Tulig, M., Turland, N. & Zhang, X.-C. 2013. The Future of Botanical Monography: Report from an international workshop, 12–16 March 2012, Smolenice, Slovak Republic. Taxon 62: 4–20.

Data paper describes Antarctic biodiversity data gathered by 90 expeditions since 1956

Wed, 20 Feb 2013 12:01:00 +0200

Huge data encompassed into a unique georeferenced macrobenthic assemblages database

A new peer-reviewed data paper offers a comprehensive, open-access collection of georeferenced biological information about the Antarctic macrobenthic communities. The term macrobenthic refers to the visible-for-the-eye organisms that live near or on the sea bottom such as echinoderms, sponges, ascidians, crustaceans. The paper will help in coordinating biodiversity research and conservation activities on species living near the ocean bottom of the Antarctic.
The data paper "Antarctic macrobenthic communities: A compilation of circumpolar information", published in the open access journal Nature Conservation, describes data from approximately 90 different expeditions in the region since 1956 that have now been made openly available under a CC-By license. The paper provides unique georeferenced biological basic information for the planning of future coordinated research activities, for example those under the umbrella of the biology program Antarctic Thresholds – Ecosystem Resilience and Adaptation (AnT-ERA) of the Scientific Committee on Antarctic Research (SCAR). The information collected could be also beneficial for current conservation priorities such as the planning of Marine Protected Areas (MPAs) by the Commission for the Conservation of Antarctic Marine Living Resources (CCAMLR).
The expeditions were organised by several famous explorers of the Antarctic. The area covered by the paper consists of almost the entire Southern Ocean, including sites covered by a single ice-shelf. The vast majority of information is from shelf areas around the continent at water depth shallower than 800m. The information from the different sources is then attributed to the classified macrobenthic assemblages. The results are made publicly available via the "Antarctic Biodiversity Facility" (data.biodiversity.aq).
A specific feature of this paper is that the manuscript was automatically generated from the Integrated Publishing Toolkit of the Antarctic Node of the Global Biodiversity Information Facility (AntaBIF IPT) and then submitted to the journal Nature Conservation through a novel workflow developed by GBIF and Pensoft Publishers. (see previous press release). Data are made freely available through the AntaBIF IPT, and sea-bed images of 214 localities through the data repository for geoscience and environmental data, PANGAEA- Data Publisher for Earth and Environmental Science (sample: http://doi.pangaea.de/10.1594/PANGAEA.198682).

Speaking from on board the research vessel 'Polarstern', the paper's lead author Prof. Julian Gutt of the Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Germany commented:

"The most important achievement of this paper is that data collected over many years and by various institutions are now not only freely available for anyone to download and use, but also properly described to facilitate future work in re-using the data. The Data Paper concept is certainly a great approach that multiplies the effect of funds and efforts spent by generations of scientists."

The data will also be used for a comprehensive Biogeography Atlas of the Southern Ocean project to be released during the XI SCAR Biology Symposium in Barcelona July 2013.

SOURCE: EurekAlert!

EU BON: Working towards integrated and comprehensive global biodiversity data

Tue, 12 Feb 2013 18:06:35 +0200

The European Union funded EU BON "Building the European Biodiversity Observation Network" project now holds its official Kick-off Meeting, taking place from 13 to 15 February 2013 in Berlin. An International Symposium "Nature and Governance – Biodiversity Data, Science, and the Policy Interface" precedes the kick-off (11-12 February 2013), to discuss the current landscape of monitoring and integration of biodiversity data, and stress on the relevance of EU BON on both European and global scales.

The EU BON project will be working towards advancement and development of the technological platform for GEO BON (Group on Earth Observations Biodiversity Observation Network), which operates and systemizes biodiversity data on a global scale.

Launched in 2005, the Group on Earth Observations, GEO, is a response to the need to address issues of biodiversity preservation as well as eight other societal benefit areas: agriculture, climate, disasters, ecosystems, energy, health, water and weather. The GEO BON venture was established to coordinate the provision of sustained, cross-cutting, integrated and accessible earth observation data and information.

The aim of GEO BON is to build a monitoring network that presents a full picture of what is happening to biological diversity worldwide. The system will use masses of biological information with data and forecasts on climate change, pollution, land use, biological invasions and other threats to biodiversity. Currently, the lack of comprehensive information about the world's biological resources continues to undermine the efforts of policymakers and managers to set priorities, elaborate strategies and assess the effectiveness of their actions.

EU BON project offers an innovative approach in terms of integration of biodiversity information system from on-ground to remote sensing data, for addressing policy and information needs in a timely and customized way. The project will reassure integration between social networks of science and policy and technological networks of interoperating IT infrastructures. EU BON's aims to facilitate GEO BON's work towards the creation of global biodiversity data network through contributing to the overall European capacities and infrastructures for environmental information management.

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All interested parties are most welcome to attend the symposium or to follow it on Twitter, Facebook, or Google+.

Additional information

EU BON (2012) stands for "Building the European Biodiversity Observation Network" and is an European research project, financed by the 7th EU framework programme for research and development (FP7). EU BON seeks ways to better integrate biodiversity information and implement into policy and decision-making of biodiversity monitoring and management in the EU.

GEO BON stands for "Group on Earth Observations Biodiversity Observation Network". It coordinates activities relating to the Societal Benefit Area (SBA) on Biodiversity of the Global Earth Observation System of Systems (GEOSS). Some 100 governmental, inter-governmental and non-governmental organisations are collaborating through GEO BON to organise and improve terrestrial, freshwater and marine biodiversity observations globally and make their biodiversity data, information and forecasts more readily accessible to policymakers, managers, experts and other users. Moreover, GEO BON has been recognized by the Parties to the Convention on Biological Diversity. More information at: http://www.earthobservations.org/geobon.shtml.

International biodiversity data symposium to mark the kickoff of the EU BON project

Tue, 12 Feb 2013 17:54:27 +0200

EU BON (2012) stands for "Building the European Biodiversity Observation Network". This European research project, financed by the 7th EU framework programme for research and development (FP7), started activities on the 1^st of December 2012 and will continue for 4.5 years. EU BON seeks ways to better integrate biodiversity information and implement into policy and decision-making of biodiversity monitoring and management in the EU. The aim of EU BON is to build a substantial part and contribute to the Group on Earth Observation's Biodiversity Observation Network (GEO BON)*, through an innovative approach of integration of biodiversity information systems. The project, built as an answer to the need of a new integrated biodiversity data, will facilitate access to this knowledge and will effectively improve the work in the field of biodiversity observation in general.

The EU BON International Symposium "Nature and Governance – Biodiversity Data, Science, and the Policy Interface", took place in Berlin from 11 to 12 February 2013. The symposium, hosted by the Museum für Naturkunde Berlin, brought together high-ranking speakers and guests from across the world to talk and discuss the different aspects of the EU BON Project. The symposium aimed at clarifying and popularizing EU BON's objectives prior to the official EU BON Kick-off Meeting. Main issues covered were the future of biodiversity information, challenges in front of new data policies, new approaches in collecting information, and ways to engage the public in biodiversity monitoring and assessments, a.o.

For more information on the EU BON project please visit Twitter, Facebook, or Google+.

* Launched in 2005, the Group on Earth Observations, GEO, is a response to the need to address issues of biodiversity preservation as well as eight other societal benefit areas: agriculture, climate, disasters, ecosystems, energy, health, water and weather. The GEO BON venture was established to coordinate the provision of sustained, cross-cutting, integrated and accessible earth observation data and information.

Biodiversity exploration in the 3D era

Wed, 06 Feb 2013 12:42:00 +0200

Taxonomy – the discipline that defines and names groups of organisms – is a field of science that still employs many of the methods used during the beginnings of the discipline in the 18th century. Despite the increasing use of molecular information to delineate new species, the study of the morphology of specimens remains one of the major tasks of taxonomists. These studies often require first-hand examination of the reference specimens (so-called type material) deposited at museum collections around the globe - a time-consuming and laborious task.

To facilitate this procedure, a group of researchers from the Hellenic Centre for Marine Research (HCMR) are exploring the possibilities offered by 3D digital imaging. In a recent article published in the open-access journal ZooKeys, the researchers use X-ray computed tomography to create digital, three-dimensional representations of tiny animals, displaying both internal and external characteristics of the specimens at a detail level similar to that of the microscope.

To demonstrate their method, the researchers imaged a number of polychaete species (marine bristle-worms)—the choice of this group being obvious to Sarah Faulwetter, the leading author, because "despite being ecologically very important, these animals exhibit a fascinating diversity of forms and tissue types, allowing to test the methodology across a range of samples with different characteristics".

The resulting interactive 3D models allow any researcher to virtually rotate, magnify or even dissect the specimen and thus extracting new scientific information, whereas the structure and genetic material of the analysed specimen are kept intact for future studies.

The team stress the importance of 3D imaging methods for taxonomy on its way into the twenty-first century: "Our vision for the future is to provide a digital representation of each museum specimen, simultaneously accessible via the internet by researchers and nature enthusiasts worldwide," says the team leader, Dr Christos Arvanitidis from HCMR.

The instant accessibility of specimens will speed up the creation and dissemination of knowledge. As the authors point out, "human efforts, combined with novel technologies, will help taxonomy to turn into a cyberscience whose discoveries might rival those made during the great naturalist era of the nineteenth century."

See also the playlist in the Pensoft video channel at http://www.youtube.com/playlist?list=PLrYfgSbGP4qRsKnc-47wkxgz6ww1HMHox

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The study was supported by the European Union projects MARBIGEN (FP7-REGPOT-2010-1) and ViBRANT (RI-261532)

Original Source:

Faulwetter S, Vasileiadou A, Kouratoras M, Dailianis T, Arvanitidis C (2013) Micro-computed tomography: Introducing new dimensions to taxonomy. ZooKeys 263: 1-45. doi: 10.3897/zookeys.263.4261

An appraisal of megascience platforms for biodiversity information

Wed, 30 Jan 2013 12:55:00 +0200

A second article acknowledging results accomplished within the EC FP7 project pro-iBiosphere has now been published. The paper titled: An appraisal of megascience platforms for biodiversity information, reflects the aspects of processing and provision of biological research data on various online platforms, in an environment where data driven approaches, are increasingly important.
Pro-iBiosphere is recognized as a coordination project that provides global generic organismic knowledge and a platform that brings the traditional Flora and Fauna editorial efforts into the digital world.
The full contents of the article are available online at: http://dx.doi.org/10.3897/mycokeys.5.4302>
PDF version is also available here.

Symposium: Nature and Governance – Biodiversity Data, Science, and the Policy Interface

Tue, 29 Jan 2013 18:48:00 +0200

The EU BON project which is coordinated by the Museum für Naturkunde in Berlin/Germany has started on 1 December and will continue for 4.5 years. The EU BON Kickoff Meeting will be held in Berlin from 13 to 15 February 2013.

With respect to EU BON’s objectives the International Symposium "Nature and Governance – Biodiversity Data, Science, and the Policy Interface" will be held prior to the EU BON Kickoff Meeting from 11 to 12 February in Berlin with high-ranking speakers. You are most welcome to attend the Symposium.

Improving technical cooperation and interoperability at the e-infrastructure level

Fri, 21 Dec 2012 19:13:04 +0200

There is an increasing demand for biodiversity data, information and knowledge by the public and stakeholders. For this information to be widely available the existing technical barriers for interaction of e-infrastructures have to be opened. The pro-iBiosphere project has been launched for a period of two years (September 1st, 2012 to August 31st, 2014), with the goal of addressing technical and semantic interoperability challenges and preparing the ground for the creation of a system for intelligent management of biodiversity knowledge which will improve the present system of taxonomic literature.

One of the objectives of pro-iBiosphere is to promote and increase cooperation between the major biodiversity projects, initiatives and platforms at EU and global level (for additional objectives please seehttp://wiki.pro-ibiosphere.eu/wiki/Explaining_pro-iBiosphere).The persisting traditional workflow for producing taxonomic information, such as Floras and Faunas, is a very time-consuming process for most institutes (i.e. Natural History Museums, Herbaria, Botanic Gardens, etc.). These institutions have the responsibility to make sure that data are generated, curated and disseminated, and that technical operations are working adequately. An Open Biodiversity Knowledge Management System would not only facilitate the open access of taxonomic data, but it would create synergies with other initiatives / projects and through this allow to link taxonomic data in a wider context. These linkages will also offer many means of enhancement for the authors of this taxonomic information.

Examples of European e-infrastructure initiatives include EDIT, BHL-E, BioCASE, ViBRANT, PLAZI, biowikifarm, Pensoft, diversity workbench, BioVeL, and PESI. Over the last years a great number of software platforms have been developed with different functional scopes, content scopes, strengths and weaknesses. Biodiversity informatics infrastructures were often developed as database-driven web-applications which were later equipped with services for machine to machine communication. True interoperability is still hindered by a lack of data standards, standard protocols and solid service implementations.

Pro-iBiosphere will conduct four pilot studies (http://wiki.pro-ibiosphere.eu/wiki/Pilots) and organize six meetings with stakeholders (http://wiki.pro-ibiosphere.eu/wiki/Meetings). ; The FUB-BGBM and Plazi will be responsible for the pilot on "Interoperability model between PLAZI and the EDIT Platform for Cybertaxonomy based on transformations between XML-repositories and CDM-stores". Main focus will be optimized information- and workflows associated to mobilization, storage and publication of data from biodiversity literature. This includes the review of the existing system, working interfaces, successfully shared standards. The pilot implementation will be used as a proof of concept and establish a transformation pipeline between data from PLAZI (XML-based repositories) and the CDM-stores of the EDIT Platform for Cybertaxonomy (highly granular object-oriented data stores). The pilot will provide both human readable and web-service access to the Plazi data.

With the aim of identifying issues hindering true interoperability (e.g. lack of standards and different conceptual models etc.), a workshops on "How to improve technical cooperation and interoperability at the e-infrastructure level" will take place on October 8-11, 2013, in Berlin (http://wiki.pro-ibiosphere.eu/wiki/Pro-iBiosphere_stakeholders_meetings_and_workshops). The workshop will bring together IT- experts and representatives of e-infrastructures, data providers, and scientific users to identify the technical constraints and problems in the interoperability between platforms. Main outputs of the workshop are: (i) to specify workflows for importing mark-up documents into e-platforms, and (ii) a proposal of optimal solutions that will account the "different start" approach implied by the various stakeholder groups.

Eckert, S., Kelbert, P., Güntsch, A., Berendsohn, W. G. Botanischer Garten und Botanisches Museum Berlin-Dahlem Freie Universität Berlin (FUB-BGBM) & Sierra, S. Naturalis Biodiversity Center Leiden

Semantic enhancement of biodiversity literature: the Biodiversity Heritage Library contribution to pro-iBiosphere

Fri, 21 Dec 2012 17:16:08 +0200

In the field of biodiversity, the traditional workflow for producing core taxonomic information, such as Floras and Faunas, has not changed much over the years. The process is time-consuming process usually performed by individual specialists. Legacy (i.e. existing) literature is still the foundation and starting point for taxonomic studies. This literature contains all relevant data for a certain taxon, such as morphological characters, geographic distribution, taxonomic status, but also information that is needed to locate the physical specimens that were used to describe the taxon in the past. However, accessibility to legacy literature is uneven and a major drag on the pace of biodiversity research.

Since 2007, ten major biodiversity libraries have collaborated in digitising a large body of biodiversity literature (with a focus on English language literature) in an open access milieu via the Biodiversity Heritage Library (BHL) project. Since 2009, the eContentplus project Biodiversity Heritage Library for Europe (BHL-Europe) has achieved substantial progress in coordinating the digitisation of biodiversity literature in the EU. In the recent years, BHL has become a real global initiative: The Global Biodiversity Heritage Library (gBHL) is now a cooperative network of autonomous decentralised members operating programs and projects to make biodiversity literature more widely available. The current gBHL partner projects are: BHL, BHL-Europe, BHL-China, BHL-Australia, the BHL-SciELO Network (Brazil) and the BHL Arabic node organised by the Bibliotheca Alexandrina (Egypt). At the time of this writing (December 2012), more than 39 million pages from more than 109,000 books and journals are accessible online in an open access Creative Commons framework to a wide spectrum of end-users. This significantly facilitates the process of discovering and accessing literature that is relevant for taxonomic studies.

Currently, BHL content is available through various online portals (e.g. www.biodiversitylibrary.org, http://citebank.org/, www.bhl-europe.eu). Currently, most literature relevant to taxonomic studies are still manually extracted from this corpus of digitised literature. Semantic enhancements of the digitized literature could make the information in the literature even more accessible to researchers as well as amenable to searches and sophisticated queries. Taxonomic literature is ideal for (semi-)automatic enhancements as the description of the world’s biodiversity is a highly standardized process with a distinct language and format. Taxonomic treatments, for example, are a key structural element in taxonomic publications, where the various taxa (families, genera, species, etc.) are described.

Binomial species names are another key element that is highly standardized in taxonomic literature. Improving the power of users to search electronically for species names that appear in the literature has been a major focus for data enhancement in the various gBHL projects in recent years. The application of a name finding algorithm based on the OCRed (OCR = Optical Character Recognition) page images of the digitised literature facilitate the search for binomial species names. A search term expansion for common names and synonyms of scientific names further facilitates the search for animals and plants described in the literature. However, these are just first steps. Large-scale data mining of taxonomic literature is still very difficult, but further improvements in the structure of digitised taxonomic literature to facilitate increasingly sophisticated searches and queries are on the horizon. The pro-iBiosphere project will help identify current gaps in the process and recommend priorities for further development of tools and services to optimize the semantic mark-up of taxonomic literature. The project also helps to identify the necessary steps to improve the integration of biodiversity literature into a biodiversity knowledge management system (i-Biosphere). Ultimately, more effective data mining from taxonomic literature will significantly enhance taxonomic research and streamline the discovery and description of new species.

Calling all users past and present of Floras and Faunas information!

Fri, 21 Dec 2012 17:14:16 +0200

If you have used Floras or Faunas (hard copy or online) at any point in your work, research or leisure we'd love to hear from you. Perhaps you have used them in the past to try and identify species, to piece together the geographical distribution of particular taxa, to compile geographical or habitat based checklists of species, or to extract morphological or ecological traits from the descriptions. Even if your experience with them wasn't as successful as you'd hoped, we'd very much like to hear your views!

Producers of Floristic and Faunistic information face choices in the information that is prioritised, for example for digitisation and in the ways it is eventually presented to consumers. Often these important choices are based on an incomplete understanding of user needs, particularly of those users working outside of the taxonomic disciplines, but is also true to a lesser extent within the taxonomic community itself. The producers of information may be unaware exactly how their core biodiversity sources such as Floras and Faunas are being used, and which information is particularly valued. On the other hand, consumer groups who could benefit from primary information and associated services may be unaware of the existence of these resources, or else face other practical or technical barriers to their use.

Task 2.2 (within Workpackage 2) aims to identify the existing and the potential new consumers of Flora and Fauna information and services and to better understand their needs. A workshop is planned in May 2013 in Berlin. If you are interested in either filling out a short questionnaire or in attending the workshop please contact Soraya.Sierra [at] naturalis.nl

Science from Recycled Data

Fri, 21 Dec 2012 17:09:46 +0200

My PhD research programme is all about cladistic data congruence, compatibility, convergent evolution and phylogenetic tree-to-tree distance measures, while in parallel I work on a Panton Fellowship on data mining. The latter is about the mining of data direct from the literature and encouraging a culture of openness and data sharing. I shall be presenting this work at the pro-iBiosphere workshop in February 2013. My mentor for this project is Peter Murray-Rust, a Cambridge-based computational chemist and co-author of the Panton Principles for Open Data in Science. I'm fairly new to data mining techniques and machine learning methods, but am learning fast, and am certainly looking forward to meeting researchers at this event using similar techniques and methods for taxonomic data.

Specifically I'm looking to extract phylogenetic tree data direct from the figures of phylogenetic papers; including the exact relationships between taxa, branch lengths and support values. Unlike with some other data mining efforts that are entirely text-based, this requires some data extraction from non-textual sources. Some attempts have already been made to do this with programs like TreeThief, TreeRipper and TreeSnatcher but none of these are realistically and systematically applicable to tens of thousands of phylogenetic papers in their current state.

There is a huge wealth of phylogenetic data in the literature – I was co-author on a paper recently that shows that there are more than 66,000 separate papers containing novel empirically-generated phylogenetic trees in just the 21^st century, and that less than 4% of these data are publicly available in a re-usable form. I, and many others, think this hugely valuable and repurposable data should be kept and made openly available for re-use, hence I'm trying to systematically salvage it from the literature.

Another novel aspect of our approach is that we're mining PDF's rather than publisher-provided XML or HTML. The latter do not contain the figures, just links to them, and thus they can only help us recover metadata on each phylogenetic tree. The PDF is often the only format in which it's all there and sometimes in clearly machine-interpretable format. Peter has been particularly vocal on his blog about the quality, or lack, of PDF files produced by some publishers on behalf of authors. Personally I feel that all supporting data for a paper should be made openly available, as the 'default' with exceptions to this rule only allowed with clear and explicit justification. I'm still surprised, and slightly disappointed, that this isn't yet the norm in scientific publishing – we certainly have the technology to do this. In 2013 I shall be submitting my PhD thesis; looking for further academic funding/employment and will assume the new role of Science Community Coordinator at the Open Knowledge Foundation – working to join together all the various open science labs around the world. I heartily look forward to meeting everyone at February’s pro-iBiosphere workshop.

Ross Mounce

PhD Student & Panton Fellow, University of Bath, United Kingdom

European Journal of Taxonomy

Fri, 21 Dec 2012 17:02:47 +0200

Journals not only disseminate information, they also provide a mechanism of quality control and certification for the results published. Species names and descriptions are the primary metrics in quantifying biodiversity, including communicating information about food and agriculture, ecologically important species, pests, and pathogens, and species of popular and conservation interest. For taxonomy, the close link between publication and research is even more crucial, as publications are the legal document validating the names of organisms.

Moving online increases accessibility to taxonomic information and ensures the long-term preservation through electronic archiving. However, this is a mission that requires public sector commitment and funding. Initiated under the umbrella of the European Distributed Institute for Taxonomy (EDIT), the European Journal of Taxonomy (EJT) is an example of institutions adapting to modern technologies so as to better fulfil their public mission.

Launched in September 2011, EJT is jointly published by a consortium of European natural History Institutes (NHI), namely those of Paris, London, Brussels, Meise, Tervuren, and Copenhagen, who have pooled their resources to publish an international, fully electronic, fast-track, peer-reviewed, non-for-profit and fully open access journal in descriptive taxonomy, covering subjects in zoology, entomology, botany (including mycology and algology), and palaeontology. There are no size limits to articles. EJT’s scope is global; authorship and geographical region of study are not exclusively European.

EJT supports the need to deposit type specimens in public collections (e.g. museums, herbaria). This policy anchors the title in a collection-based research environment.

The journal builds on the three main principles: high scientific quality, electronic and permanent Open Access archives; no financial costs to authors or readers.

The creation of this journal sends a strong political message to national and international funders of natural history research, showing the interest and capacity of NHIs in different countries to join forces and collectively claim a significant role in the organization of access to and dissemination of scientific information in their domain of research. By publishing their own joint journal, the institutions will be able to set conditions of access to the publicly funded research they perform.

Run by an editorial and a production team scattered throughout the NHIs that own and fund the title, EJT builds a European cross-institutional cooperation through light governance, enhancing coordination, establishing a cross-institutional strategy at the European level. EJT is designed to encourage and promote networking between publishing staff in NHIs and the biodiversity production and user community.

By addressing the current barriers for e-publishing, EJT aims at helping institutional journals within NHIs to movetheir publications to the Web efficiently and thus spread their scientific results more broadly and increase their citability and accessibility.

EJT’s team particularly welcomes pro-iBiosphere project and shares its main objectives: to enhance interoperability through coordination and promote the adoption of technological standards which are the only way to facilitate the access, dissemination, and use of scholarly publications in the fields of environmental and natural history.

We warmly invite you to explore the possibilities of publishing in EJT today, just click to www.europeanjournaloftaxonomy.eu

Laurence Bénichou
Responsable d'éditions/Publications manager Publications scientifiques du Muséum & European Journal of Taxonomy

Global Names Project

Fri, 21 Dec 2012 16:56:57 +0200

Wouldn't it be lovely, when writing a paper, or compiling data, for the computer to tell you if you have spelled the name correctly, or that that the name has been superseded because of some taxonomic activity. Wouldn't it be nice to read documents and databases, have older names replaced with current names of organisms brought up to date automatically. This is the kind of functionality that is being pursued through the Global Names project.

The project capitalizes on the almost universal use of the Linnaean system of Latin binomials to annotate most of our meaningful observations of life made over the past 250 years. Those names offer us a way of indexing and linking information about species; whether in the 500 million or so estimated pages of literature; the billions of specimens located in museums and herbaria or in the tens of thousands of web sites and databases. Unfortunately, we don't have a unique name for each species because species may be split or moved from one genus to another. Nor is every name unique because the codes of nomenclature allow for the same name to be used for a plant and an animal. Because of this, we have to build an infrastructure that is taxonomically intelligent.

The potential of delivering names as part of the mechanism of integrating data distributed across the internet led GBIF and the Encyclopedia of Life to set up a series of Nomina workshops to conceive of what a future names-based cyberinfrastructure might be like. Last year, the USA’s National Science Foundation funded a two year 'Global Names' project (globalnames.org). Our goal is to provide openly available infrastructural tools that will assist in management of information about biodiversity. We have been building databases of names, developing various names discovery and names matching tools - such as the Chrome Names Spotter plug-in or the name discovery tool at http://gnrd.globalnames.org/). New names parsing algorithms help to convert name strings into canonical forms, or to offer the mechanisms for searches and browsing based on dates, authors, or genera. Our code is openly available at GitHub. Numerically, the most significant challenge lies with incorrectly spelled names that create variant 'name-strings' that prevent information on the same species in different data bases do be joined together. The solution is 'reconciliation', a process that maps all alternative names for the same species to each other so that a search initiated with one name can lead to an action that calls on all names. We hold over 22 million name strings, and there are many more to come, especially as older texts are digitized and OCR'd. We have extended the Rees / Giddens fuzzy matching tools to map variant spellings against each other.

Working with the Biodiversity Heritage Library, we have built a new indexing tool that includes names recognition, names discovery, names parsing, and a validation service. In the future, as necessary internal databases get increasingly populated, we can offer more validation services that will, for example, help biologists who are compiling research data or are writing papers to ensure that their names are spelled correctly, that they have the correct authority information, or that the name is the most current one for that taxon.

Our vision is of an open and very flexible cyberinfrastructure that all projects can contribute to and draw from so that we do not have to build multiple copies of databases. The result will be a more flexible and relevant suite of databases and services that will make it increasingly easier to discover and interconnect data. There remain many challenges, such as the capture of 250 years worth of synonymy information, full integration of vernacular names, and integration of the 'surrogates' for names that are increasingly flooding out of environmental surveys that rely solely on molecular techniques.

Reading: Patterson, D. J., Cooper, J., Kirk, P. M., Pyle, R.L. and Remsen D. P. 2010. Names are key to the big new biology. TREE 25: 686-691, doi:10.1016/j.tree.2010.09.004

David Patterson
dpatterson@mbl.edu

Disseminating High Quality Information on Alien Plants

Fri, 21 Dec 2012 16:34:59 +0200

There are several important requirements for providing information on alien species. The information needs to be up-to-date, reliable and comprehensive, while its publication needs to be available to a wide range of stakeholders, clearly written and well illustrated. Traditional print media cannot fulfill all of these roles, but internet publication can.

The Manual of the Alien Plants of Belgium is a comprehensive guide to the plants that have been introduced to, and grow wild in Belgium. This includes a wild variety of plants, ranging from vigorous invasive species to rare casuals. Some are important agricultural weeds, some are escaped garden plants. In an era of environmental change, alien species occupy newly created niches. Halophytes spread along salted roads, new weeds grow amongst new crops; mountain plants find homes in the walls of cities and aquarium plants escape into ponds and rivers. Many of these plants cause real environmental and economic damage.

The Manual has been created using the Scratchpad system. The ability to add, correct, move and delete content at a moment’s notice means that the Manual can be reactive to new discoveries, to changes in taxonomy and to improve upon illustrations as they become available. It also allows the publication of a wide variety of other material including related publications, diagnostic keys and images of herbarium specimens.

The pro-iBiosphere project aims to promote IT publishing tools such as Scratchpads to a wider range of taxonomists. Tools such as these will make authoritative taxonomic, conservation and distributional information available to a much larger audience. These tools will allow much more efficient data reuse and the remobilization of legacy literature. Belgium might be a small country and alien plants might seem like an obscure subject. However, Belgium has a dense population; is an important transport hub; is intensive in agriculture and has hosts many industries, so despite its size it is highly susceptible to colonization by non-native species and dissemination of information on Belgium’s colonists has relevance far beyond its borders.

Quentin Groom & Filip Verloove
National Botanic Garden of Belgium

Bringing big data to biodiversity

Fri, 21 Dec 2012 16:08:16 +0200

On 1^st December 2012, 30 research institutions from 15 European countries, Brazil, Israel and the Philippines, and more than 30 associated partners started EU BON - "Building the European Biodiversity Observation Network". This €9 million, EU-funded research project aims to advance biodiversity knowledge by building a European gateway for biodiversity information, which will integrate a wide range of biodiversity data – both from on ground observations to remote sensing datasets – and make it accessible for scientists, policy makers, and the public.

The project plans to advance the technological platform for GEO BON (Group on Earth Observations Biodiversity Observation Network) to improve the assessment, analysis, visualisation and publishing of biodiversity information, and to enable better linkages between biodiversity and environmental data. EU BON will ensure a timely provision of integrated biodiversity information needed to meet the global change challenges and to contribute for next generation environmental data management at national and regional levels.

EU BON will deliver several important products, including a European integrated biodiversity portal, a roadmap for EU citizen sciences gateway for biodiversity data, an open data publishing and dissemination framework and toolkit, a policy paper on strategies for data mobilisation and use in conservation, a prototype of integrated, scalable, global biodiversity monitoring schemes, strategies for EU-integrated national and regional future biodiversity information infrastructures, and a sustainability plan for regional and global biodiversity information network.

The cooperation for data integration between biodiversity monitoring, ecological research, remote sensing and information users will result in proposing a set of best-practice recommendations and novel approaches with applicability under various environmental and societal conditions. A key task of EU BON is to harmonise future biodiversity monitoring and assessments and to engage wider society groups, such as citizen scientists and other communities of practise. Although focussing primarily on European biodiversity and collaborating with major EU initiatives (e.g. LifeWatch and others), EU BON will also collaborate closely with worldwide efforts such as GEO BON, GBIF, the Convention on Biological Diversity (CBD), the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) and others. EU BON will be a valuable European contribution to the Global Earth Observation System of Systems (GEOSS), and be built on the GEO principles of open data sharing.

The kick-off meeting of EU BON will take place on 13-15 February 2013 at the Museum für Naturkunde – MfN in Berlin, Germany and will be preceded by a symposium "Nature and governance: biodiversity data, science and policy interface" on 11-12 February 2013.

Additional information

EU BON (2012–2017) stands for "Building the European Biodiversity Observation Network" and is an European research project, financed by the 7^th EU framework programme for research and development (FP7). EU BON seeks ways to better integrate biodiversity information and implement into policy and decision-making of biodiversity monitoring and management in the EU.

GEOSS stands for Global Earth Observation System of Systems, built by the Group on Earth Observations (GEO). GEO is constructing GEOSS on the basis of a 10-Year Implementation Plan for the period 2005 to 2015. The Plan defines a vision statement for GEOSS, its purpose and scope, expected benefits, and the nine "Societal Benefit Areas" of disasters, health, energy, climate, water, weather, ecosystems, agriculture and biodiversity.

Link to the original press release.

9th International Flora Malesiana Symposium

Fri, 21 Dec 2012 10:48:47 +0200

Herbarium Bogoriense, Research Center for Biology-LIPI, is honored to be hosting the 9th International Flora Malesiana Symposium that will be held in Bogor on August 27-31, 2013. We would like to inform you that the website for the Symposium has been uploaded. Please visit http://www.fm9.biologi.lipi.go.id / for more details about the symposium and program.

A Framework of Scientific-Cloud for iFlora

Sun, 16 Dec 2012 17:25:30 +0200

PDR 2012, 34(6) 623-630 DOI: 10.3724/SP.J.1143.2012.12139
PENG Hui-Fu, WANG Yu-Hua

In order to meet the broad requirements of the public and state departments to recognize and distinguish plant species, a plan for the next-generation Flora was proposed, which is internet, DNA-sequence- and information-technology- based, i.e., iFlora. In this paper, we suggest and present a research framework of "Scientific-Cloud for iFlora", which is a combination of Resource-Cloud (Resource and Service layer), Intelligent Re-organization System, Mobile-Clients (Application layer) and Key-Users. (1) Resource-Cloud: a collaborative working platform in the cloud site. This platform is used to integrate all relevant information resources, including DNA barcoding reference library, plant biodiversity information, and analysis models. (2) Intelligent Re-organization System of Virtualization: a system to retrieve, re-organize and present iFlora-records of a given plant species automatically and intelligently. (3) Mobile-Clients: software applications of mainstream mobile platforms, such as iOS, android and Windows phone. Constructed by these three parts, the framework will not only service for the key users with co-operating platform but also providing web service for the general public. The construction of this project will gradually combine botany and informatics. We are aiming to construct a sharing, easily accessible, and seamless connected Scientific-Cloud, with which numerous scientists co-operate together for iFlora. In addition, the Scientific-Cloud will integrate cognitive abilities of the machine, network, and taxonomists. It will provide an intelligent public service to perceive the plant world in a new dimension.

Source: A Framework of Scientific-Cloud for iFlora.

Identifying Audiences of E-Infrastructures - Tools for Measuring Impact

Sun, 16 Dec 2012 17:14:08 +0200

PLoS ONE (2012) 7(12): e50943. doi:10.1371/journal.pone.0050943
Duin D, King D, van den Besselaar P

Research evaluation should take into account the intended scholarly and non-scholarly audiences of the research output. This holds too for research infrastructures, which often aim at serving a large variety of audiences. With research and research infrastructures moving to the web, new possibilities are emerging for evaluation metrics. This paper proposes a feasible indicator for measuring the scope of audiences who use web-based e-infrastructures, as well as the frequency of use. In order to apply this indicator, a method is needed for classifying visitors to e-infrastructures into relevant user categories. The paper proposes such a method, based on an inductive logic program and a Bayesian classifier. The method is tested, showing that the visitors are efficiently classified with 90% accuracy into the selected categories. Consequently, the method can be used to evaluate the use of the e-infrastructure within and outside academia.

Source: Identifying Audiences of E-Infrastructures - Tools for Measuring Impact (PloS)

New Species in the Old World: Europe as a Frontier in Biodiversity Exploration, a Test Bed for 21st Century Taxonomy

Tue, 27 Nov 2012 18:08:00 +0200

PLoS ONE 7(5): e36881. doi:10.1371/journal.pone.0036881
Fontaine B, van Achterberg K, Alonso-Zarazaga MA, Araujo R, Asche M, et al.

The number of described species on the planet is about 1.9 million, with ca. 17,000 new species described annually, mostly from the tropics. However, taxonomy is usually described as a science in crisis, lacking manpower and funding, a politically acknowledged problem known as the Taxonomic Impediment. Using data from the Fauna Europaea database and the Zoological Record, we show that contrary to general belief, developed and heavily-studied parts of the world are important reservoirs of unknown species. In Europe, new species of multicellular terrestrial and freshwater animals are being discovered and named at an unprecedented rate: since the 1950s, more than 770 new species are on average described each year from Europe, which add to the 125,000 terrestrial and freshwater multicellular species already known in this region. There is no sign of having reached a plateau that would allow for the assessment of the magnitude of European biodiversity. More remarkably, 1over 60% of these new species are described by non-professional taxonomists. Amateurs are recognized as an essential part of the workforce in ecology and astronomy, but the magnitude of non-professional taxonomist contributions to alpha-taxonomy has not been fully realized until now. Our results stress the importance of developing a system that better supports and guides this formidable workforce, as we seek to overcome the Taxonomic Impediment and speed up the process of describing the planetary biodiversity before it is too late. (full article text)

From taxonomic literature to cybertaxonomic content

Tue, 27 Nov 2012 17:22:00 +0200

BMC Biology 2012, 10:87 doi: 10.1186/1741-7007-10-87

Miller J, Dikow T, Agosti D, Sautter G, Catapano T, Penev L, Zhang ZQ, Pentcheff D, Pyle R, Blum S, Parr C, Freeland C, Garnett T, Ford LS, Muller B, Smith L, Strader G, Georgiev T, Bénichou L.

Taxonomy is a fundamental science that provides the scaffolding for biology. But the true value of taxonomic data remains unrealized because basic biodiversity information remains fragmented and unevenly accessible. Taxonomy helps us recognize species and map their distributions by generating text descriptions, images, and records of when and where they have been observed. Current rates of species extinction, habitat loss, and climate change mean that taxonomy has never been more relevant. Biodiversity is one of the most information-rich fields of human knowledge , but advances in basic cybertaxonomic infrastructure have only recently provided the tools to organize biodiversity information in ways that respond to a wide range of user groups, including ecologists, land managers, and interested citizens, not to mention the benefits of readily accessible information to the global taxonomic community. The call to revitalize taxonomy by embracing the internet has been sounded for more than a decade. The time is ripe to significantly increase the volume of taxonomic information freely available online. But simply posting information online will not automatically reinvigorate taxonomy. There are myriad online sites dedicated to particular taxa or projects. These are useful to users interested in questions within the site's domains. But the greater potential lies in mechanisms for aggregating primary source data in ways that allow users to filter and recombine data easily and flexibly for whatever purposes they imagine. full article

pro-iBiosphere launched

Mon, 22 Oct 2012 16:48:33 +0300

The FP7 eInfrastructure project proiBiosphere targeting the preparation of the European Open Biodiversity Knowledge Management System was launched in Leiden in September 2012

The first article acknowledging pro-iBiosphere published

Wed, 03 Oct 2012 00:00:00 +0300

The first article acknowledging pro-iBiosphere published: Penev L, Catapano T, Agosti D, et al. Implementation of TaxPub, an NLM DTD extension for domain-specific markup in taxonomy, from the experience of a biodiversity publisher. In: Journal Article Tag Suite Conference (JATS-Con) Proceedings 2012 [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2012. Available from: http://www.ncbi.nlm.nih.gov/books/NBK100351/. It is a result of WP 3 (survey and analysis of the status quo) in combination with an earlier review of XML-schemas in taxonomy.