Meeting Notes Advisory Board Meeting Leiden February 15, 2013

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Seventh Framework Programme

Topic: 1st Advisory Board Meeting
Work package: WP2 - Coordination and routes for cooperation among organizations, projects and e-infrastructures
Task: Task 2.1
Goal: To introduce of the Advisory Board members and their contribution in pro-iBiosphere ; to discuss the project activities with the AB and obtain feedback
Participants: Consortium and Advisory Board members
Mailing list: Consortium /
Author: Consortium
Place: Leiden, NL
Time: 08.30–12.30
Date: February 15, 2013
Next meeting date: February 14 2013, Berlin, Germany (TBC)

Minutes – 15 February 2013

Deliverable Status: Final
Dissemination Level: Public

© Copyright 2012 The pro-iBiosphere Consortium, consisting of:

Naturalis Naturalis Biodiversity Center, Netherlands
NBGB Nationale Plantentuin van België, Belgium
FUB-BGBM Freie Universität Berlin, Germany
Pensoft Pensoft Publishers Ltd, Bulgaria
Sigma Sigma Orionis, France
RBGK The Royal Botanic Gardens Kew, United Kingdom
Plazi, Switzerland
Museum für Naturkunde Berlin, Germany


All intellectual property rights are owned by the pro-iBiosphere consortium members and are protected by the applicable laws. Except where otherwise specified, all document contents are: “© pro-iBiosphere project - All rights reserved”. Reproduction is not authorised without prior written agreement.

All pro-iBiosphere consortium members have agreed to full publication of this document. The commercial use of any information contained in this document may require a license from the owner of that information.

All pro-iBiosphere consortium members are also committed to publish accurate and up to date information and take the greatest care to do so. However, the pro-iBiosphere consortium members cannot accept liability for any inaccuracies or omissions nor do they accept liability for any direct, indirect, special, consequential or other losses or damages of any kind arising out of the use of this information.

Revision Control

  • Version 1.0 by Camille Torrenti, 2013-02-22


Among the activities planned in task 2.1 on Coordination and routes for cooperation across organisations, projects and e-infrastructures led by Plazi, an Advisory Board (AB) of representatives from major global biodiversity projects has been established (DoW). This AB will meet on an annual basis to provide their recommendations for improvement of the overall project results and activities. As of today, the AB is constituted of four members. The first pro-iBiosphere Advisory Board meeting took place on February 15, 2013 morning in Leiden, Netherlands.


Soraya Sierra

The meeting first started with a warm welcome and thanks from Naturalis, the project coordinator, followed by the presentation of each participant.

Soraya Sierra (Naturalis) presented the project to the audience (in particular to the Advisory Board members) while providing information on the project goals, vision and the work packages. She presented the overall vision which is to succeed interconnecting, through eInfrastructures, institutions from Europe (and beyond) collecting and processing core biodiversity data, thus leading to the possible implementation of an integrated system allowing each institution and/or all institutions collectively to offer improved or new services to a wide range of users (customers).

Then she pointed out the reasons for setting up an Advisory Board, in particular, the opportunity to share knowledge so as to ensure the project is not going to replicate efforts from other international projects. The Advisory Board will also enable the project to foster liaisons and synergies with other related (EU and non EU-funded) projects within the taxonomic and biodiversity informatics landscape. The Advisory Board will meet once a year so as to take part in the project as an advising body on strategic issues while providing recommendations for the overall success of the project.

There are four Advisory Board members to-date. This number is not definite as new members may join the Advisory Board later in the project depending on opportunities and needs that might arise.

Introduction of Advisory Board members

Laurence Benichou Bénichou (MNHN)

Mrs. Bénichou is the publication manager at the National Museum of Natural History (MNHN, France) and is also responsible for the management of the newly created (17 months old) European Journal of Taxonomy. The Museum is a scientific editor, publishing journals and monographs since 1802. All the series from 1802 to to-date have been digitized thanks to the BHL-Europe project assistance. And the taxonomy journals are now available through BioOne (?).

The interest of Mrs. Bénichou in pro-iBiosphere results from the need to reduce the gap between people thinking and implementing biodiversity data, which makes it difficult for an editor to make necessary adjustments: LSIDs are now being used in EJT, but the scientists seem to declare them dead. There is a big gap between implementing people and the people who need to use the system and it is important to take this issue into account so as to reduce that gap. More emphasis has to be given on understanding the needs of the scientists. There is also a need for common standards from one journal to one database. The policy of the scientific direction of the scientific press of the Museum is in favour of open access of all its publications.

Thomas Janssen (Humboldt Universität)

Thomas Janssen is a systematic botanist working at the Institut für Biologie at Humboldt-Universität in Berlin, Germany. He previously worked at the National Botanic Garden of Belgium (NBGB). Mr Janssen has an interest in systematics and in taxon treatments through collaborative environments such as the Common Data Model system editor (CDM). He pointed out the importance of having a flexible system when entering data to facilitate the contribution of authors. Specimens must be integrated somehow in a manner it works which is not accomplished by most projects/platforms.

Regarding the pro-iBiosphere project, his interest is in connecting digitized content for readers and for the users in to a more efficient system, which represents a very ambitious and substantial project. His advice is to all work together in the same direction, as we need to develop a flexible system for users, which should not necessitate a deep learning curve and should be easy without a need for training users. It is important to involve contributors as this involvement is very low at the moment and we cannot expect authors to adapt to the system.

Hong Cui (University of Arizona)

Dr. Cui's research focuses on informatics with a focus on taxonomic treatments. She is currently involved in 3 projects funded by the National Science Foundation (NSF) and, in particular, the Flora of North America project in which she assists in the transformation of the way the wealth of the knowledge in FNA may be accessed and used. The methodology developed by Dr. Cui has been adopted by several other research groups in the US and abroad. Her objective is to make the taxon descriptions available into a database through usable software. A crucial aspect in her work is to develop this software in a collaborative way with the feedbacks of users.

A problem pool/repository could be created to gather all the users' issues so as to enable developers like her to have a target to address all the problems. It is then important to prioritize the tasks once the problem is known. However, there is neither feedback nor information on users' problems as of today.

Further issues she got aware during the meetings here are the language issues (Floras printed in other languages than English), the potential of crowd sourcing that might help to create a larger corpus of marked up literature and thus character input for their work, quality control at various stages in the conversion process; the process of creating ontologies better to create many small ontologies than create one that includes all but never takes place, and often will not be able to cover all the special cases.

The pro-iBiosphere project would enable projects to work together to deal with these issues and determine what kind of useful and usable system we need for biodiversity. To produce simple systems to address these real cases thanks to users’ inputs. A set of interfaces between the different systems could be envisaged that could talk to each other and combine them to make them more flexible. The system development timeline will directly depend on use-cases. That would mean to establish a drop-box for cases people do have an interest in but cannot go ahead because of conversion (GoldenGATE) and parsing problems (Charapars). The first step would be to make something useful for a wide audience.

Suzanne Sharrock (BGCI)

Suzanne Sharrock is Director of Global Programmes at Botanic Gardens Conservation International (BGCI) in United Kingdom. The Botanic Gardens Conservation International is a networking organisation of Botanic Gardens around the World; they are therefore neither taxonomists nor editors. Bringing the user perspective and ensuring international collaboration motivate Mrs Sharrock involvement in pro-iBiosphere. For instance, BGCI has been involved in the Catalogue of Life project while participating to a survey of users and defining users requirements. They are in contact with many different organizations that are contributors and users. These botanic gardens can contribute with data they have to manage and are interested in the way to make linkages on information about these plants and to have a platform where users can find information of these plants.

She is therefore interested in how to make the connection with constituency and provide feedbacks from users but also on how to bring together all these different initiatives to increase their awareness. BGCI can ensure more involvement of users thanks to their support. She would like to make sure that their constituency is well informed and linked to provide feedback on what is going on in the biodiversity domain and highlight the importance of spreading the news on what’s going on and on project results for dissemination.

She is also interested in creating a link between this work and the Convention of Biological Diversity community.

Introduction of WPs

WP leaders


Soraya Sierra (Naturalis, Netherlands)


Steven Dessein (NBGB, Belgium)

Presentation of WP2 that concerns the European and international policy coordination


Walter Berendsohn (FUB-BGBM, Germany)

The main idea of WP3 is to review processes and to decide how we can use quality improvement measures.

Preliminary results from workshop (MS10): strong accent on linking (“no linking no value”), the main discussion was about actually maintaining links and manage them. If we want to increase inputs we need to be attractive, we may need to be aware that other languages may be required that only English. There exist several methods to address this problem such as custom mark-up schemas for instance.

MS11 workshop outputs: the obstacles in providing open content are to convince editors/authors all those involved that journals and articles should not only be available in paper nor PDF. It is important to share data stores to ensure consistency, to build a network of trust and to educate and promote use of tools for these specialized systems. We also need to safeguard institutional and governmental commitment to ensure a sustainable software development. Our project strength is that the consortium consists of persistent institutions and not universities in which academics are likely to change.

Another main issue of this work package is on Intellectual Property Rights (IPR) in particular in relation to incorporating citizen science. Credits of publications, generating outputs on the credit of the contributor represent essential pipelines. Regarding the database contributions, it is a bit more complicated with the attribution requirements. It is not a big problem to publish lists of attributions but there must be some recognition, need to consider this as the current system is not very good at it.

The task leaders are just starting to digest the results of the workshop. The project will then provide recommendations on semantic interoperability under the pilots and may be incorporated in the future project.


Teodor Georgiev (PENSOFT, Bulgaria)

Presentation of the status of the pilots, which are for the moment in a test phase: - Zoobank is in a test phase but PENSOFT is building-up a schema that would not only be developed for pro-iBiosphere but also for other cases. - Fungi pilot: 3 different repositories are standardized - Golden Gate tool work with Plazi: there is a problem with the scans of the documents, which appeared to be of bad quality; they therefore may need to do it manually, and have to define the input quality.

PENSOFT is developing information exchange with GNUB and Zoobank so as ensure the schemas will be available to all. They also may release a publication about it that would be widely disseminated.

A collaborative publishing platform represents a big potential for synergies with CDM. An Application Programming Interface (API) would be used to import manuscript from different platforms (Scratchpads, GBIF); PENSOFT is also working on new tools to encourage authors to publish treatments. Then partners discussed on the Optical Character Recognition (OCR) and the cost per page scanned.

The system should also provide the possibility for different outputs and all changes made should go back into the system. This results in several concerns that should be taken into consideration when developing the system: - How these feedback mechanisms can be achieved through editing and publishing - Parallel developments with parallel publishing, formatted and unformatted outputs that will go into the project - What can be done with the quality of these outputs?

The pilots that will be investigated among the activities of the pro-iBiosphere project will enable partners to take these issues into consideration and to test them.


Camille Torrenti (Sigma Orionis, France)

The consortium needs to disseminate the activities and results of the pro-iBiosphere project. The main objective of WP5 is to increase public awareness, for this purpose and among WP5 activities, different tools have been created and are available online and on the project website. All the main project tools for dissemination (website, wiki, dissemination materials, social networks…) along with the DCIP, which is the project dissemination strategy and guidelines, have been successfully developed.

Regarding the involvement of the Advisory Board, members are invited to participate to project events and their contribution is kindly requested to facilitate linking with other initiatives and to foster cross-promotional activities with other initiatives and organisations.

The project will also participate to other events as part of task 5.2, for this purpose, a list of potential events has been shared between partners on the project wiki to easily update their prospective contribution and actual contribution to identified events. The Advisory Board members are also invited to contribute to this list by adding any event of interest for the project to participate. An email will be sent to the Advisory Board members with links to the shared dissemination documents on the project wiki.

Suzanne Sharrock from Botanic Gardens Conservation International (BGCI) invited participants to attend the 5th Global Botanic Gardens Congress held at Dunedin Botanic Garden, New Zealand that will take place from October 20- 25 2013.


Don Kirkup (RBGK, United Kingdom)

All activities have a cost but also a value, there should be a balance between cost and value. The consortium needs to identify a revenues stream in order to finance the development of the platform and related activities. An example of revenue stream would be that the financing departments of the participating organisations would allow grants for building the platform.

Regarding the latest developments for task 6.3, all partners provided their first outputs following the sending of a dedicated questionnaire, all information will be further consolidated and will be part of the report D6.3.1 that will be submitted to the European Commission in the end of this month (M6). This report containing the findings of the questionnaires will be shared with the Advisory Board, as their inputs would be quite interesting at this point.


All participants

The discussion was centred on the outputs and first impressions on the project series of workshops organised in Leiden during the week and the suggestions and learning for the future project workshops that will be held in Berlin in May. An online questionnaire has been created to gather feedbacks on the use and interest of the tools of the participants. It should be possible to liaise with Scratchpads to get complementary results and feedbacks in a few months on the use of these tools and the need and outputs on trainings…

There will be a platform workshop this year taking place after the summer and financed by another project. Are there any partners that will join this workshop? Please add the related information on the table on partners’ contributions to events on the project wiki.

Preliminary impressions on the workshops: Firstly, it can be pointed out that these workshops have been a success as these workshops were initially targeting 30 attendees and finally overall 100 people attended these workshops. There was also a good representation and coverage from different countries with the participation of fruitful initiatives, as a result, people could connect with persons from different areas in the World and from different domains and backgrounds.

Secondly, the main aim of these workshops was to promote the different tools and this goal was met.

It resulted in being very easy to engage the IT people and a bit more difficult to engage taxonomists. An institutional policy should promote and decide to use these tools, training and get individuals involved is not enough as they are not decision makers in the end. The problem is that it is difficult for an institution to take such a decision, as they may doubt the durability of this tool/system as, most of the time, such programmes are project based and end-up when the project is over. Stability is indeed a very important issue; this underlines the role of WP6 on sustainability.

Technical persons are familiar with taxonomy, there is a need for more communication between users and developers so that users can provide feedback, and for example to inform developers which features are missing. Another important point that has been experienced by FUB-BGBM in the EDIT project is that, during the project, there appeared to be a gap between the first documentation and the current work so there is a need to update the documentation all along the project period. We should form user groups that will handle it, get this organised and extend from development to management.

Developers and users should develop a long-term relation while meeting and sharing information not only on the occasion of workshops. User groups should be indeed engaged in a more frequent manner in the process of the development of algorithms to gather feedback on what is wrong and to make more helpful products for users.

Overall, the workshops were overall very informative and were integrated with each other and provided a lot of information and new things to learn. In particular, Dr. Cui stressed out there are no such projects comparable in US, projects rather address specific domains and not such a scope of general infrastructure grouping several domains at once.

Regarding the end-users of taxonomy and the editors, it seems that some of them felt a bit intimidated and wished to contribute a bit more than they had the opportunity to. This is therefore important to send questionnaires to participants/users to have feedback as these tools need to adapt to the users and it might result being easier for them to write their opinion and their remarks in words.

Should we therefore create sub-groups sessions for taxonomists and others for IT people as these smaller sessions might facilitate participation and sharing ideas? The drawback of separate sessions would result in being less informative for IT people as the most productive thing them is to hear taxonomists explain the issues they encounter and their needs. Then IT people can take this information home and study it, try to implement it. Maybe another solution would be to try to reach the desk editors as they are between informatics and taxonomists and could break the intimidation while providing a link between IT people and taxonomists. Moderator could also try to identify the groups that do neither contribute nor talk and invite them to participate and share their opinion. This issues might be given attention in the preparation of the workshops.

We should explain the use of these tools, their benefits to improve their impact and increase their interest. This would ensure the user sees both sides of the picture the new functionality versus the benefits and impacts. This is important to make the system optimised for taxonomists.

Golden Gate training: ople with different kinds of background attended this workshop; one of the participants pointed out this system can also be applied to other domains (suicides for instance). The discussion in one group made the point that the software might be used incremental, that is a services so people would only do what they need, and if crowdsourcing would be used then in increments that can easily be done, and possibly repetitively so to avoid too steep a learning curve. The pro and cons have been discussed to create custom software instead of using off the shelve software. It also became obvious how complex pdfs are and although they look very smooth on the surface, they are very difficult to convert into text or xml documents and retaining all the original fonts and styles. Again a plea for avoiding producing work during the process of prospective publishing, ie publish XML )based) as one outcome.The Expert2 training: was very interesting for developers to understand how do biologists work and to see the differences from a biological point of view so as to think about how to integrate these biological outputs into the process.

Users requirements workshop: Thinking ahead, taxonomists are not so keen on using tools. The pilots should investigate on how can they use them and to provide them with concrete outputs, meaning to connect to their every-day work and make them achieve something so that they can see the interest and be willing to use these tools.

A positive output is that participants wished to write about their experience of these workshops and share it on the newsletter on topics such as how will they use it, what do they think of the workshop… People are now aware these tools are there and what are the possibilities they offer.

These workshops represented the opportunity for the different biodiversity stakeholders to meet and talk about the issues they encounter in their work and, more generally, the things they wanted to discuss with other stakeholders to try to find solutions. The gap is indeed very big between people implementing things and people thinking about them, bringing together all stakeholders allowed them speak together and to see what came out of this interaction. People could connect and share views inside the meeting rooms but also outside the rooms. This represented a valuable opportunity for stakeholders but also for the project to cooperate with other initiatives worldwide and to share knowledge and experience.

It is important for pro-iBiosphere to try to reach out to specialists such as publishers, IT people and not only taxonomists this enables to make things easier and in a more professional way. Getting professionals on board, instead of learning all inhouse by taxonomists, provides much more professional tools and deliverables that actually meet the standard of the content, for which the taxonomists are the leading experts.

The workshops also enabled partners to talk about issues to take them into account and to implement them. Partners are not only talking about these issues but also implementing them.

Another general issues on biodiversity platforms have also been discussed such as: - The fact that everyone wants open access but no one is willing to pay for it - The crowd sourcing tendency and its related subjects such as how to use it to add details into platforms, how to curate data and correct mistakes, the system of annotations which is mostly used, how to automatically capture all the annotation…

A report will be produced detailing the outputs of these three workshops and the results of the questionnaires.

Regarding the upcoming workshops, the EU-BON project is likely to organise a two-days meeting in May in the same time of pro-iBiosphere. MfN and/or PENSOFT should liaise with them to identify alternative dates.


The pro-iBiosphere Advisory Board meetings will take place on an annual basis, the next AB meeting should be held on the occasion of pro-iBiosphere Meeting #5 in Berlin in February 2014.

Other additional members have been identified and may join the project Advisory Board in the meantime.