Pro-iBiosphere meeting notes 27 & 28 September 2012

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Seventh Framework Programme

Topic: Kick-off minutes pro-iBiosphere project
Work package: All work packages
Task: All tasks
Goal: Coordinating a successful start of the project, laying out the work plan for individual work packages for the coming months
Participants: Consortium and non consortium members
Mailing list: Consortium /
Author: Consortium
Place: Leiden, NL
Time: 14.00–19.00 on 27 September, 9.00–17.00 on 28 September
Date: 27 & 28 September 2012
Next meeting date: February 11-15 2013, Leiden, the Netherlands


Minutes – 27 & 28 September 2012

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 Nathalie Kriek, 2012-09-30


pro-iBiosphere consortium members introduce their institutions and give information on their main role in the project: Jan van Tol - Naturalis. Role: Coordination and management of the project; data provider institution. Steven Dessein - NBGB. Role: Networking European and international organizations and individual expertise; data provider institution. Anton Güntsch - BGBM. Role: Improve cooperation of and interoperability between e-infrastuctures; data provider institution. Lyubomir Penev - Pensoft. Role: Technical and semantic mark up; communication of the project. Camille Torrenti - SIGMA. Role: Promotion and dissemination activities and evaluation of business models currently in use by partners. Alan Paton - RBGK. Role: Stakeholders requirements and sustainability; data provider institution. Donat Agosti - Plazi. Role: IPR, Technical and semantic mark up. Henning Scholz - MfN. Role: Semantic integration of biodiversity literature.

Reporting tools

Hayo van Buuren

EU-Xpert (management) and EU-Fin (financial) will be used by the consortium to elaborate the 3-monthly progress and annual reports (M12 and M24) for the Commission. The deviation monitoring related to the budget and the timescale will be reviewed every 3 months. Progress reports will contain information on the major achievements and difficulties per task, status of deliverables (due date and actual submission date), and an indication of the consumed costs (purpose, date, amount). The financial data provided by partners for the 3-month report is different to the content requested by the EC at the end of each reporting periodic report (M12 & M24). At the end of each reporting period, partners will need to ask their accounting department to provide them with final figures regarding their costs and person month consumption. In case of further questions on how to use these tools, every 1st of the month, FP tools provides a webinar on the e-tools.

Grant & Consortium Agreements

Soraya Sierra

Information & Communication. Any publicity, including at a conference or seminar or any type of information or promotional material, must specify that the project has received research funding from the Union and display the European emblem. When displayed in association with a logo, the European emblem should be given appropriate prominence.

Workshops and meetings. Number of physical meetings will be limited to the minimal adequate number. The agendas of workshops and meetings will include the aims and expected results of each workshop. Once the meeting has taken place, the report will include an overall review and evaluation. The project meetings with stakeholders & the pro-iBiosphere governing bodies will take place at the same location and during the same week.

SIGMA will lead the task on "Consortium and Review meetings" (T1.4). Main responsibilities will be: (i) meetings preparation, (ii) list of participants, (iii) drafting meeting agenda, (iv) help preparing presentations, and (v) work on the meetings proceedings (notes, reports, to-do-list, etc.). For the evaluation of the meetings & workshops (with stakeholders and consortium bodies), an example of event evaluation questionnaire will be prepared by SIGMA in collaboration with the consortium and will be shared among partners at M4. The purpose of the questionnaire is to: (i) assess the quality and satisfaction of the events, (ii) collect participants’ inputs & suggestions, and (iii) improve future events. Action

pro-iBiosphere Consortium bodies

Soraya Sierra

pro-iBiosphere has the following bodies: General Assembly (GA), Management Committee (MC) and Advisory Board (AB). In particular, the AB is responsible for:

1. Developing recommendations for improvement of the data integration and interoperability in three main directions:

  • improving coordination and management of biodiversity data and platforms through active discussion and identification of stakeholders’ needs and development of strategies for reduction of duplicated efforts and associated costs;
  • improving the coordination between working groups that have participated or are currently participating in past and ongoing EU projects;
  • analysing and developing of strategies for integration and interoperability in the field of bioinformatics between EU and USA-based global initiatives.

2. Advising the Management Committee (MC) and General Assembly (GA) on strategic issues, like developing recommendations for improvement of the data integration.

The AB will convene at least once per year. The AB will consist of 4-6 representatives from different projects, biodiversity platforms and stakeholders (representing the end user community). At present, the pro-iBiosphere AB consists of the following members:

1. Laurence Bénichou (European Journal of Taxonomy, MNHN)
2. Thomas Janssen (plant taxonomist, Humboldt University)
3. Suzanne Sharrock (end user of taxonomic information, BGCI)
4. Hong Cui (Fl. of N. America & character parsing, University of Arizona, USA), tbc

Financial payments

Koen Berkenbosch

The EC pre-financing received by Naturalis consists of 60%. The first pro-iBiosphere payment (55% of budget) was transferred to all partner institutions on Thursday the 6th of September 2012. 5% of the pre-financing was transferred by the Comission into the Guarantee Fund. For conversion from a foreign currency to euros please use the rates given by the Central European Bank. EU-Fin will be used for gathering all the financial information of the partners.

Communication tools

Lyubomir Penev

A website will be made available by Pensoft at the end of M2. Depending on the visitor profile, the pro-iBiosphere website will display two kinds of libraries. Project partners will be able to log into the website and have access to the internal library. The general public only has access to the external library. In order to facilitate the communication among partners (ie. Work Packages, Advisory Board, etc.) mailing lists will be available. Important emails sent from the website will be automatically archived. Pensoft, Sigma Orionis and the project coordinator (Naturalis) will have access to the website for posting news and articles. Pensoft will also be responsible for creating the different project social networks accounts (Facebook, Twitter, LinkedIn, etc). News posted on the website will be automatically published on these social networks. In order to broadcast project news to a broader community and to reach different audiences, every partner will contribute to the dissemination activities of the project by supplying information that can be posted on the website, wiki, and social networks.

Camille Torrenti

According to the Grant Agreement, dissemination activities have to be reported to the EC Commission 45 days minimum before being implemented. However, it is clear that if the project wishes to publish news on project updates on the website this rule can not easily be followed. The suggested methodology is as follows: (i) each partner willing to disseminate information on the project should contact WP5 leader (SIGMA) and the coordinator for information approval; (ii) a list of partners’ contributions will be prepared (T5.2) and made available to the European Commission in D5.2.1 (M12) and D5.2.2 (M24). Action

The first press release announcing the start of the project will be prepared by SIGMA. Action

Gregor Hagedorn

The Biowikifarm is a shared technical platform supporting a number of mediawiki installations. It is similar to Wikipedia with the exception that the editing is more limited. Most of the wikis are shared, once project members have an account, they can also log in into all the other wikis. Wikis can be used for many purposes.

The pro-iBiosphere wiki platform will be used to prepare and share information and comments on a dedicated event page (e.g., tentative agenda, potential speakers, concept and objectives, potential participants, etc.). The event page will, hence, be created and available on the wiki. The website will be used for announcements and news regarding events, with links redirecting to the wiki for complementary information and details.

In order to facilitate drafting and sharing of documents that are not ready to be released to the public, the pro-ibiosphere wiki ( will use a user-management separate from biowikifarm. By prefixing a page title with the text "Internal:" the page will be visible only to logged-in users. Two separate accounts will exists, one for public documents and information, the other for and internal project documents and reports that will only be accessible with a log in and be invisible for other users.

Gregor Hagedorn will: (i) send mail to all project participants to ask them to request an account on the wiki. Action, (ii) distribute a document with information about the privacy on the biowikifarm. This document will detail and explain the difference and complementarity of use with the website, it will be integrated into the Dissemination and Communication Implementation Plan by SIGMA as part of T5.1. Action

Work package 2 European and international policy coordination

Steven Dessein

Taxonomists are bright people who are very creative in using systems and tools. They want to remain in control of their own data and benefit from the flow of data brought by digitization. The current toolbox available for taxonomist is not fully equipped with everything that is needed. Given the diversity of approaches, the software needs to be flexible and common standards need to be supported. Data should flow seamlessly between systems and taxonomists do not necessarily need to understand the details of data formats for this to happen. There is a requirement for institutional commitment and training, i.e. professors can encourage their students to use a tool and make sure that their institution informs and supports the use of e-tools for taxonomy. Various obstacles that have been identified on the uptake of e-tools for taxonomy are: a lack of knowledge of its existence and its capabilities, difficulties in reformatting legacy formats, worries about a lack of continued support, incompatibility with other systems, and lack of appropriate output formats, a.o.

Task 2.1 Coordination and routes for cooperation across organizations, projects and e-infrastructures

Donat Agosti & Gregor Hagedorn

Each of the work package organisers should first think about the questions and then invite the people who can answer them. Not the other way around. The focus must be on where we want to go instead of where we are now. It is important to have goals and that the roles and responsibilities are clear. Then build a working system around it. This task is not a stand-alone. It cannot exist without the consortium. For this task we are open to use the resources most efficiently, so please provide suggestions. The first report can be a draft (i.e. a working document), because it might influence what happens in WP6. The final deliverable for WP6 is a strategy. Plazi should come up with a high level view on the gaps rather than a big catalogue.

Task 2.2 Stakeholder requirements

Don Kirkup

As presented in the DoW, the purpose of task 2.2 Stakeholder (or User) Requirements is an analysis of current and potential, providers and consumers, of the Floras and Faunas e-Infrastructure. Overlap with task 2.3 was discussed and for the sake of clarity it was decided by the meeting that task 2.2 would deal with information whereas task 2.3 deals with the e-tools. The job of ask 2.2 is in short therefore to see what information users use, how they get it and what they do with it. This will be done firstly via questionnaire and then follow-up interviews. The results will feed into the linked Task 6.2, and for both of these the first step is to draw up a list of who the users are, and which sectors they represent, and a sampling matrix could be constructed. The workshop participants lists are a starting point but will need to be broadened out much wider, ie. beyond the taxonomist stakeholder group.

Task 2.3 e-tools for taxonomy

Quentin Groom

The way to get a broader user base is to invite scientists, teachers, policymakers and taxonomists. To invite representatives per group and get the information from them. Nevertheless, we don't have enough time and resources for such an analysis. It is strongly recommended to have a workshop on e-tools for taxonomists only. That is the only way to establish communication. The taxonomists who put the data into the system are interrelated to the group that use the data. Should the focus of the workshop be just on the taxonomists or should it be broader? Jeremy Miller recommends ANTweb as an example as to how a system like that could work.

Task 2.4 Legal issues of data acquisition, curation and dissemination

Willi Egloff

To get the practical requirements you need local contacts in every country. And we hope to get those contacts through the partners. Since external to this pro-iBiosphere project, some partners are already working on these data, we are planning to incorporate it into the project. Initial contacts have been and further will be made. This requires two actions: 1. To study ongoing EU-funded projects regarding copyright policies, and 2. Parallel to it, to analyze EU- and national legislation related to an operational biodiversity knowledge management system.

To make a case to legislators, we need to collect cases of research that depend on open access to a large number of data.

Work package 3 Scientific content and workflow coordination

Walter Berendsohn

The aims of WP3 are to review existing methods and approaches towards creating reusable data in publication workflows and from literature and providing the results to communities involved. WP3 focuses on the review and analysis of existing methods for data acquisition, curation and semantic integration, as well as the review of current methods for semantic mark up and their use. Together with data-curators we want to find ways to facilitate crowdsourcing [random individual markup] and auth-sourcing [identified individuals recruited to do markup]. Another aim is to align ongoing and forthcoming efforts for semantic mark up of biodiversity literature and provide technical and social solutions for their use. Last but not least we want to attract potential new users to biodiversity informatics infrastructures and collect user feedback. Partners involved in WP3 alongside FU-BGBM are Naturalis, NBGB, Pensoft, RBGK, Plazi and MfN.

Task 3.1 Data acquisition and curation starts in November 2012 and ends in May 2013. The task includes Milestone 10, a workshop on data curation and acquisition of Floras and Faunas in February 2013, and Deliverable 3.1, a Best Practices Guide on Editorial Policies due in May 2013. The task is linked within pro-iBiosphere with Task 2.1 and 2.3.

Task 3.2 Semantic mark-up generation, data quality, and user-participation infrastructure starts in November 2012 and ends in August 2013. It contains Milestone 11, a workshop on semantic mark-up generation, data quality and user-participation infrastructure, scheduled for February 2013. As well as Deliverable 3.2.1, a concept paper for involvement [in semantic markup] of individual experts, commercial vendors, and citizen scientists due in May 2013, and Deliverable 3.2.2, a report on the state and quality of biosystematics documents and survey reports due in August 2013. Link to Task 2.1.

Task 3.3 Semantic integration of biodiversity literature starts in September 2012 and ends in August 2014. It includes Deliverable 3.3.1, a report on state-of the art and research horizons of semantic integration of biodiversity literature due in December 2013 and Milestone 12, a workshop on mark-up of biodiversity literature to be held in February 2014. Also Deliverable 3.3.2, a report on progress during the coordination process of partners and non consortium partners due in April 2014. Linked with task 2.4, 3.2 and 4.2.

All tasks have links with WP5 (Dissemination) and WP6 (Sustainability). Further links to ongoing projects and initiatives exist to World Flora Online (initiative), EU-BON, e.g., BioVeL, LifeWatch, i4Life and ENVIRONFII (proposal).

Task 3.1 Data acquisition and curation

Soraya Sierra

This task deals with best practices for data acquisition and curation using e-tools for taxonomy. Main objectives are to identify and promote good practices for entering new field data and collaboratively writing of taxonomic treatments.

Task 3.2 Semantic mark-up generation, data quality, and user-participation infrastructure

Donat Agosti

We want to take all the lessons learned to show what we can do to improve in providing access to the content of legacy publications. With having increasing access to the content, the publishers hopefully can be convinced that they should publish in an advanced way, so that the tedious step of converting published matter into a semantically enhanced document can be avoided altogether. At the same time we should come up with a way to convince everybody to help to convert legacy publications. Several ways are explored and described, from the author to the publisher, from a voluntary worker to a commercial service, and involving the crowd. Incentives might play an important role. But what are they? Since the meaning of semantic enhanced publications are not well defined, the underlying concept will be defined and described, and at the same time its consequences will be explored, such as ontologies, linking to external resources, or mark-up.

The goal of task 3.2 and the related workshop will be to write a report that outlines the concepts and goals of providing access to the content of taxonomic publications, the status quo of the technology and resources available today and what will be needed to make this happen. A central point will be to demonstrate the additional value of having access to semantically enhanced content over just unstructured content.

Task 3.3 Semantic integration of biodiversity literature

Henning Scholz

The Biodiversity Heritage Library today contains more than 100,000 books of biodiversity literature. A major problem is that this enormous data source is unstructured and the OCR of all texts is uncorrected. This makes it difficult to extract information and integrate it in the workflow of taxonomists. A number of tools and services are in place or tested to improve the situation. Task 3.3 should review these solutions and existing mark-up processes, identify gaps that prevent the integration of marked-up legacy literature into a knowledge management system, discuss with experts and stakeholders priorities for future developments and eventually develop a roadmap, workplan and project concept to close the existing gaps efficiently.

One report will be delivered to prepare the workshop and a second report after the workshop will then summarise the outcomes of the workshop and describe the way forward.

Review of Work package 4 Technical and infrastructure coordination

Lyubo Penev

In order to facilitate the implementation of an Open Knowledge Biodiversity Management System, a total of four pilots will be conducted. These pilots will deal with:

1 Interoperability model between taxonomic content management platforms, taxon treatment repositories and electronic registers.
2 Interoperability model between taxon treatments from both legacy and prospective literature from three organismic domains (fungi, plants and animals).
3 Common query/response model for automated registration of higher plants (International Plant Names Index, IPNI), fungi (Index Fungorum, MycoBank) and animals (ZooBank).
4 Revision of a tool (CharaParser) that generates identification keys by reusing morphological characters from published species descriptions.

For pilot 3, the automated XML query/response model for registration of new names with IPNI is already available. The XML workflow between the three registers (i.e. ZooBank (Rich Pyle), Index Fungorum (Paul Kirk) and MycoBank (Vincent Roberts)) and the querying side (i.e. Pensoft and any other party in the future) needs to be adjusted.

Walter Berendsohn: It is an important topic to the EU to be market leader of globalisation of that information. This project should focus on supplying content for other projects (i.e. World Flora Online). We can use all the political information and use it to argue why we should take this broader.

Gregor Hagedorn: pro-iBiosphere should be a counterpart for other projects/initiatives (e.g. World Flora Online, EoL, CoL, etc.) and not just to become part of the supply chain to other projects.

Donat Agosti: Agrees with Gregor. The primary goal is to create content, not to be a supplier.

Jan van Tol: The pilots should be a steppingstone for Horizon 2020. If certain topics for pilots (e.g.identification for European spiders) are separately funded, then this brings added value to the project, but if it takes away from this project’s funding it is dangerous. Use pilot programmes to illustrate what we do but don’t fall into the trap of making it about the pilot. We could invest more than we get from this project with this approach.

Soraya Sierra: A meeting to establish the criteria for taxa and to select taxa for pilots will be needed. Partners might have several entry points. We should look at how the topic and subsequently the pilot benefit the project.

Lyubomir Penev: To those who are involved in the pilots, the suggestion is to suggest taxa for the different pilots during the next four weeks.

Task 4.1 Improve technical cooperation and interoperability at the e-infrastructure level

Anton Güntsch

Examples of European e-infrastructure projects include EDIT, BHL-E, BioCASE, ViBRANT, PLAZI, biowikifarm, Pensoft, diversity workbench, BioVeL, and PESI. Over the last year 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 WP4 focuses on optimized information- and workflows associated related to mobilization, storage, and publication of data from biodiversity literature. Task 4.1 will look at interoperability of e-infrastructures. The task includes:

  • Review of existing system, working interfaces, successfully shared standards.
  • Identification of issues hindering full interoperability between literature markup data and biodiversity e-infrastructures.
  • Recommendation for markup standard to achieve maximum compliance with e-infrastructures.
  • Specification of workflows and information flows for importing markup documents into e-platforms.
  • Organizing a workshop addressing the above points.

A pilot implementation will be used as a proof of concept and establish a pipieline between data PLAZI and the EDIT Platfrom for Cybertaxonomy. With this, PLAZI data will be made accessible through the EDIT platform portal software. The pipeline will use several stylesheet transformations and the import layer of the EDIT platform.

  • The MS13 workshop on "how to improve technical cooperation and interoperability at the e-infrastructure level" will adress the following topics:
  • Bring together representatives of e-infrastructures, data providers, and scientific Users
  • Interoperability between platforms: state of the art
  • Identification of issues hindering true interoperability
  • Specification of workflows for importing markup documents into e-platforms.

Task 4.2 Promote and monitor the development and adoption of common mark-up standards and interoperability between schemas

Donat Agosti

An alternative to actually building software as pilots (not necessarily funded by pro-iBiosphere) would be (i) to find one or more user with particular datasets and to engage them and to measure and show the benefits of a new approach/tools, (ii) to have a group of users and to engage them to see if we can look at the process/workflows and make inventory of their issues and make them better. Then to ask their opinion what the changes mean to them. Hence to improve the current software and measure the benefits.

Alan Paton: Create a baseline of current operation and work out what has to change and then change that. What does the vision mean: it is important to have one place where a taxonomist has all his data online and that he can easily polish it and share it with other computers. We should think about globalisation and platforms. What happens with globalisation is that on the web people get together to share and combine their knowledge into coherent information in one place under one common name. Clearly it is possible to have individual brands represented in this one platform, but on the surface it is one name, one brand.

Review of Work package 5 Dissemination, communication and public awareness

Camille Torrenti

Sigma has prepared tables for the dissemination strategy detailing the other EU projects, Biodiversity initiatives and social networks. This list of other initiatives is linked to task 2.1 “Coordination and routes for cooperation across organizations, projects and e-Infrastructures” led by Plazi. These tables will be transmitted to Gregor Hagedorn (Plazi) for update in the framework of D2.1 and will be placed on the wiki for partners inputs and review. Action

Anton Güntsch from BGBM offered to share a report Lifewatch on "Infrastructures for Biodiversity Research" with Plazi and Sigma Orionis. The report provides (on 244 pages) a comprehensive overview of relevant standards, protocols, and networks.Action

Other partners also raise the point that is also important to have some feedback from stakeholders and users incorporated as well, as the dissemination represents outputs generation but does not generates input. How are we going to get input? This is part of Task 2.2 and Task 6.2.

Task 5.1 Development of the project image, documentation and external communication web platform

Lyubomir Penev

Partners were asked to share their comments on the pro-iBiosphere logo, several logos design have been created by Pensoft and Sigma Orionis and proposed to partners before the start of the project. A pool was set up to allow every partner to vote and to decide on the final logo design in a democratic way. The logo has been selected and agreed among partners.

Following the logo design, Sigma Orionis drafted templates for presentations (PowerPoint) and documents. Feedback from partners were provided before the kick-off meeting through email exchanges between partners so the final design of the presentation has been agreed upon. However, as regards to the project documents and reports template, partners expressed their feeling that the template is very crowded with lots of pictures and symbols. After discussing this matter during the meeting, it is decided that the three symbols in the middle should be removed and will only be left in the header. To conclude, partners finally like the templates and approve them.

The templates will be available on the website for everybody to download.

Task 5.2 Dissemination of the project results through outreach activities

Camille Torrenti

To prepare the list of partners’ contribution to events and publications being part of D5.2.1 (M12) and D5.2.2 (M24), Sigma will share the template with the other partners. The partners are requested to review the existing list of prospective events and to add missing events of interest for the project to participate. This list will enable partners to announce contributions to events, to write articles etc. Action

Partners decided this template should be put on the biowikifarm to simplify the contribution process and to limit the sending of emails. Whereas the second template, following partners effective contribution to events and publications is already available on the website and can be revised by Sigma Orionis and Pensoft by comparing it to the template designed by Sigma Orionis and modifying the information entry fields. Action

Task 5.3 Stakeholder engagement and communication

Camille Torrenti

Task 5.3 consists of organizing an open event in Brussels or another major European city. The location and dates of this event have already been decided at the early stages of the project, it is scheduled in month 22 and set for 23-27 June 2014. The event venue will be Leiden, Netherlands.

The issue of engaging stakeholders during the preparation of pro-iBiosphere has been raised as being too early. It has been agreed that we do need to engage them at some level, but it is a concern to prematurely engage them. The solution could be to involve representatives of the stakeholders instead of the stakeholders self.

We must decide which stakeholders we would like to target and to invite during this event, shall the project address all project initiatives or do we have to be more selective. Anyway, stakeholders of the project will depend on the status of the project and are likely to change depending on the period and advancement of the project. The question is how do we prioritize and how do you sample users, producers and stakeholders? This matter will be decided in task 2.1 in particular.

Naturalis informed all partners that there is 4 000 € available per person for conferences, meetings etc. All meetings expenses should be covered by this budget.

Work Package 6 Sustainability planning

Don Kirkup

The evaluation of business models in support of Open Science and financial sustainability (task 6.4) depends entirely on the successful delivery of of tasks 6.1, 6.2 and 6.3, which in turn have dependencies on earlier tasks (such as 2.2, 2.3). Because of the complexity of dependencies, there is considerable risk to the main deliverable of WP6 (D6.4) unless there is a clear understanding of the needs of information (quality, quantity and timing) that is required for T6.4.

We also have to be clear when talking about the project whether we mean within the context of the pro-iBiosphere project deliverables, or are we talking in a much wider sense about a future realisation of an iBiosphere infrastructure.

Task 6.1 Measuring and Constraining the costs of delivering services

Jan van Tol

We will have to further discuss the costs and delivering services part, but we also have to deliver recommendations. To create sustainability we will have to know the costs now and the costs in future. We are open to suggestions on how to tackle this issue. We have to see what we have invested in the past and what is the annual cost of sustaining the systems. We have to find a mechanism to come to this for future. One option could be to have one institution doing the mark-up for all the institutions. It will be much cheaper and more efficient to do it this way. We should use these cases as a baseline e.g. to stop making pdfs and publishing at a different level. We do have to separate costs to build it from the maintenance costs. The benefits will be efficiency saving among others.

Task 6.2 Identifying and measuring the benefits of delivering services

Don Kirkup

The objective is to explore who really stands to benefit from (pro-)iBiosphere, and what the benefits in terms of the cost savings (and other non-monetary measures) are.

Task 6.3 Evaluating business models currently in use by partners

Camille Torrenti

Sigma Orionis shares a methodology from their experiences with past projects. With this methodology and each partners’ support in providing inputs and sharing their expertise Sigma Orionis can define the market and prepare the deliverable D6.3. The draft report will be shared on the biowiki to be updated every 6 months. Action

The main question of this task and the expected outputs are how can pro-iBiosphere results could be exploited. Envisioned business models could either be to generate business and/or to find other sources of funding. It is therefore important to further discuss as it is a political and touchy area and as pro-iBiosphere does not have any products to exploit.

Sustainability also means where would the cost of sustaining the project go, Lyubomir Penev suggest, on his side, to sustain mark-ups. The broader objective would be to frame WP6 into a work plan to achieve sustainability of things into a bigger project (iBiosphere?). Another problem that Sigma Orionis may face is the fact pro-iBiosphere partners represent very different institutions so the methodology presented must be adapted to take into consideration this project particularity. Sigma Orionis will therefore revise this methodology to better adapt it to the raised issues and comments discussed and will share it with partners after the kick-off meeting.Action

Task 6.4 Towards Sustainability for Services

Bob Alkin

Task 6.4 entails pulling all together to be able to recommend a model (or models) to follow. Thus we need to ensure that we are gathering the correct information to feed into our final analysis. This task is important for our commitment and communication with the EU. We need to agree as a group as to what we are trying to achieve with this work package. Everything derives on the services and requirements and we have to have those clear in our heads.

It is a replacement to the static system that we have now into an open knowledge shared platform. The question is how to derive to a common understanding about this. The biowiki might be the vehicle where term will be trashed out and the group chips in to come to a common understanding. It may function as a place of communication. An evaluation of costs is needed.

The business plan is not the same as the exploitation plan. If we share and coordinate the resources going into the knowledge system that they can be part of the business plan. If we do that, then it can maintain the system, creating sustainability. You can see this project as a pilot, something concrete, for future projects.

What would be the cost and benefits and how can this workflow and this system be made sustainable. We have to write strategies for these services and write an add on about how to make this sustainable in future. The important question is; is there a vision for a platform? The vision for coordination for something on a platform level like the Atlas of Living Australia or GBIF or EOL? We will address this question after lunch.

Strategic question: to look at the services that provide information to our community opposed to delivering information to the broader public. And if we focus on the services to our community alone the project fails. If we can work out our costs and identify the benefits to a wider audience this provides us with a baseline now, current situation. We can then look at how to reduce costs and maximize benefits. This might guide the development of a future proposal to implement the recommendations on reducing costs and maximizing benefits.

Side meeting between Sigma and RBGK to discuss the relation between Task 6.3 & Task 6.4

The relation between Task 6.3 & Task 6.4 was discussed. Both partners agreed they would meet at M4 in London (RBGK's premises) on the occasion of an office meeting to discuss in further detail both tasks.

User Engagement and benefits Requirements gathering activities (18 small-scale visits to stakeholders).

Bob Alkin

We should try to share as many documents as possible in the biowiki to create progress as it takes time to think about.

Meeting 2 in Leiden

Workshop on e-platforms & e-tools for taxonomy

Quentin Groom
We intend to invite both developers, users and potential users of e-taxonomy tools to this workshop.
The aims are, to:

  • foster the free flow of ideas between taxonomists and software developers.
  • promote e-taxonomic tools amongst taxonomists.
  • understand the current uses of e-tools.
  • identify the obstacles to the use of e-tools.
  • frankly examine the current pros and cons of these tools.

Some of the tools we intend to present at the workshops are Scratchpads, Edit Taxonomic Editor & Xper2. Before the kick-off meeting we've already contacted a number of potential participants, particularly those from Africa and Asia. We felt that they may need more time to organize their attendance. The response from these initial contacts has be positive and encouraging.


We will discuss who to invite using a biowiki. The clarity of the purpose is critical. Please be clear on what that workshop is for: what the criteria is, the training, etc. Also mention the product of the outcome of that day. Not all invitees will present during the workshops, various participants come to learn and in return we hope to learn from them.

Workshop on Legacy literature – Semantic mark-up generation, data quality and user-participation infrastructure

Donat Agosti

We have to think if we want training or just a demonstration of existing tools and approaches during the workshop. If we want training, then we need to break up in small groups. We have to look to the future. Create user feedback to specify the “ultimate system” for Horizon 2020. Suggestion is also to invite some editors to do some mark-up. It should be referred to as example demonstration instead of training.

Workshop on Prospective Literature – Toward Best Practices for data acquisition and curation using e-tools for taxonomy

Soraya Sierra

This workshop is meant for the editors of Floras and Faunas, and online data curators. Main objective is to identify and promote good practices for entering new field data and collaboratively writing of taxonomic treatments. Expected results of the workshop are:

  • Establish what are the new and standardized editorial policies that are needed for the curation and publication of biodiversity data in an e-environment
  • Establish how to address IPR management
  • Collect data that will facilitate writing the Best Practices e-Guide on Editorial Policies

Envisaged participants have already been contacted.

Meeting nr 3 in Berlin

Workshop on coordination and routes for cooperation across organizations, projects and e-infrastructures

Donat Agosti

What are the incentives to foster cooperation across organizations that are important to leverage support to adopt policies for advanced flora and fauna creation? What are the major relevant organizations, and who are their representatives that could become the jumping board for the successful implementation of pro-iBiosphere's vision? An input from all the participants is needed to decide upon who the invitees should be, and what should be proposed. Since this will involve high level staff, a conclusion should be reached the latest by December 2012.

Workshop on measuring and constraining the costs of delivering services

Jan van Tol

Workshop on stakeholder requirements

Don Kirkup

The matrix presented by Bob Alkin will need to be filled in first.

Meeting 4 in Berlin

Workshop on how to improve technical cooperation and interoperability on the e-infrastructure level

Anton Güntsch

An agenda for this workshop has already been drafted. It is important to define what the intended outcome of the workshop is before deciding on participants.

Workshop on how to promote and foster the development and adoption of common mark-up standards and interoperability between schemas

Terrence Catapano

What are, if there is at all, the golden roads to create a common mark-up standard? Standards are usually created by the need to have a means to formalize a subject, rather then by thinking and proposing of one, and of the desire of a community to have a means to exchange, in the case of digital literature, all or parts thereof. The workshop will be based on the analyses and recommendations of workshops W3 and W4. Planning will begin 8 months before the actual workshop.

Towards sustainability for services: Meeting to evaluate business models currently in use by partners and relevant non-partners.

Camille Torrenti

The target audience cannot be determined yet until we define the desired outcome of the meeting, we must decide later the criteria for the selection of participants depending on outputs and needs from task 6.3. Some partners express their feeling that it might be a bit ambitious to get input from 30 people in that short amount of time during this meeting, therefore we should consider this issue when drafting the event concept and objectives document.

Meeting nr 5 in Berlin

Workshop with institutions involved in the mark-up of biodiversity literature

Henning Scholz

The workshop will be held at MfN north building.

Aims/objectives are:

  • Review of the pilot: "Interoperability between taxon treatments from both legacy and prospective literature from three organismic domains (fungi, plants and animals)"
  • Review of D3.3.1 - Report on state-of the art and research horizons of semantic integration of biodiversity literature.
  • Consensus building on development priorities for tools/service to allow and facilitate the mark-up and integration of marked-up biodiversity literature into a future iBiosphere system.
  • Produce outline and some draft elements for D3.3.2 - Report on progress during the coordination process of partners and non consortium partners.

Participants: Task leader, William Ulate, Heimo Rainer, Wolfgang Koller, Donat Agosti, Terry Catapano, Lyubomir Penev, Vince Smith, Rod Page plus six more depending on future developments.

Workshop on towards sustainability for services alternative business models

Bob Alkin

Model evaluation is presented together with the before mentioned topic as they are related. This will be a small group of people who are selected based on their role, to get answers to some questions we have. Based on that, if we know where we want to go, we will know who to invite. Please comment, it is available to you.

Two days will be better because each of these cases are too conceptual to get some concrete questions, otherwise there won’t be enough time. And if we get two days, there will be enough time left for the other meetings.

Meeting nr 6 in Leiden

Project Final event

Camille Torrenti

The final pro-iBiosphere event duration is one day in the week of 23-27 June 2014. It includes participants from the pro-iBiosphere research community and 60 selected participants (EU and non-EU). On the occasion of this meeting, the final project outputs have to be presented. However, as this meeting will occur at M22 and not at the end of the project (so at the end of WP6), we should just consider the participants inputs as the best available knowledge at that time.

The event preparation information (event concept and objectives, list of potential participants,…) will be available on the biowiki and on the website. So as to facilitate events preparation, Camille Torrenti (Sigma Orionis) will share an example of event concept and objectives, event materials online on the biowiki for partners to use. Action

Questions or comments

Walter Berendsohn asks where we can request to pursue a follow up of this project. Camille Torrenti says that In Sept 2013 the ICT event of Horizon 2020 will take place and that would be a perfect place to present the project outputs and the envisioned iBiosphere follow-up project.


Work Package 1

Soraya Sierra

EU-xpert will be used to produce the quarterly and annual reports. EU-fin will be used for the financial reports (two in total). First progress will be sent to the EU in Nov 2012. The advisory board meeting and management meeting will take place on the 15th of February 2013. SIGMA and Naturalis will coordinate the management and advisory meetings that will take place on the 15th of February 2013.

Work Package 2

Steven Dessein

There is potential overlap between tasks 2.2 (Stakeholder requirements) and 2.3 (Proof of concept reports on the use of e-tools). The overlap comes about from the broad definition of stakeholders and users. We have decided the task 2.2, led by RBGK, will concentrate on the end users of taxonomic information; whereas in 2.3, we will focus on data providers, particularly taxonomists.

The audience was requested to provide suggestions for participants for the February workshops. It is important to invite participants from wide range of interest groups, such as zoologists, botanists and mycologists. For task 2.3 we will put online a list of potential participants on wiki for the February workshop. Task 2.1 will start in 6 months and we will not focus too much on the pre-existent e-infrastructures and software landscape, but focus on what should be done in the future.

Work Package 3

Walter Berendsohn

New FUB-BGBM staff will be working on this project as of 1 October. Patricia Kelbert, IT-support & CDM-import and Sabrina Eckert, coordination & user perspective.

Work Package 4

Lyubomir Penev

We have to write two documents and strategies. As a partner I am committed to the four pilots in cooperation with the WP3 and WP4 task leaders (i.e. FUB-BGBM, Plazi and MfN) and the other partners that will be involved.

Work Package 5

Camille Torrenti

A document has to be prepared by Gregor and Lyubo to detail the usage and functionalities of the website and the wiki tools (to avoid duplication). Action

The wiki should be used to share documents/reports amongst partners. In this way there will be one place where all the materials are available and open for revision. Regarding the official documents (such as deliverables destined to the European Commission), they must be placed on the website.

Lyubomir Penev (Pensoft) will prepare the design of the dissemination materials to be produced at M4, which are the first project factsheet, the poster and the newsletter. The factsheet and poster should be available for the TDWG annual conference (to be held on October 22-26, 2012) that will be attended by several pro-iBiosphere partners. Pensoft will also be responsible for creating the 4-page project brochure at month 22.

Sigma Orionis will transmit the list of other initiatives to Gregor Hagedorn (Plazi) for the wiki. The partners are requested to check if anything is missing and to enhance the list.

Regarding the final event, all partners are kindly requested to provide the names of participants that should be included in the event. On its side, Sigma Orionis will provide examples of event preparation materials and participant survey, etc. to be used by each task leaders to organize their workshops.

What is the project name on Twitter? The Twitter account is not settled yet, but the name will be pro-iBiosphere. It is important for all partners to agree and note from now on that the name of the project is pro-iBiosphere where the only capital in the name is the B.

Work Package 6

Don Kirkup

For work package 6 we will put something up on wiki that everybody can comment to regarding the matrix. Kew and Sigma have agreed to start work immediately on a list of criteria for business modeling and we will get a draft on wiki as soon as we can. We have an office meeting scheduled in December to finalise that. A methodology for task 6.3 “Evaluating business models currently in use by partners” has been proposed by Sigma (task leader) in order to get inputs for reporting on the diversity and strengths of existing business plans and discuss of sustainability (D6.3). However, it remains important that Sigma Orionis first take time to get to know the different partners representing different institutions while presenting a revised methodology in the coming weeks.

Image of participants

201209 pro-iBiosphere Kickoff tableau.jpg