Context of general requirements in EMBRC

Complete EMBRC report available at:

https://envriplus.manageprojects.com/projects/requirements/notebooks/470/pages/40

EMBRC (the European Marine Biological Resource Centre [1]) is a distributed European RI which is set up to become the major RI for marine biological research, covering everything from basic biology, marine model organisms, biomedical applications, biotechnological applications, environmental data, ecology, etc. Having successfully completed a 3-year Preparatory phase (2011-2014), it is now in its Implementation phase (2014-2016), and operation is planned to start in 2016-2017. It has 9 European countries and associated countries as full members, the stations and laboratories of which contribute their facilities, equipment and human capital to the infrastructure. Apart from ENVRIplus, EMBRC is involved in the biomedical cluster CORBEL ([2]), and in the marine cluster, EMBRIC ([3]).

The main purpose of EMBRC is to promote marine biological science and the application of marine experimental models in mainstream research by providing the facilities (lab space), equipment (e.g. electron microscopes, real time PCR machines, crystallography, lab equipment, equipment for accessing the environments such as research vessels, scientific divers, ROVs etc.), expertise and biological resources that are necessary for carrying out biological research. Users (scientists, the private sector, SMEs) who are interested in working on a particular marine organism can browse through the EMBRC catalogue of labs and facilities and submit an application for visiting one or more sites (from one of the EMBRC member countries). If their application is accepted, during their visit they can either collect organisms using the EMBRC equipment, or EMBRC can collect them for them, and train them on working on them. They can also set up cultures for which EMBRC provides the access, or EMBRC can set them for them. The users can then perform the experiments that they like, depending on the purposes of their research. They can take away the preserved organisms, or they can work in the EMBRC labs to produce the data that they need for their research.

In what concerns data, the role of EMBRC is to generate and make it available. It does not usually do any analysis on the data, unless it is contracted to do so. Data is usually generated through sensors in site in the sea or samples that are collected and then measured in the lab. Environmental data, which is largely produced by the marine biology community through contracts paid by national research councils or environmental agencies, is mostly provided free of charge in public databases (e.g. PANGAEA [4] or the NERC [5] database named BODC [6] in the UK, EMODNET [7]). EMBRC acquires the data and submits it in raw form, depending on the project, to these national or international open access databases. In what concerns the molecular data (anything having to do with omics) that is generated by the EMBRC or by its users, the scientists from member institutes or the users of EMBRC usually do some work on the data to curate it and, if part of a bigger project, they may perform some annotation and assembly. As part of the data policy, users who are scientists and generate molecular data will be required by the EMBRC to deposit it in an open access database. They may impose some timing restrictions depending on the purposes of their research (e.g. until they publish), but they are usually given a deadline to submit the data to the database, after which the EMBRC will submit it. Private sector users retain the IPR of the data that they generate, and the EMBRC cannot impose that they deposit their data, or where to deposit it.

References:

1. http://www.embrc.eu/

2. https://www.elixir-europe.org/about/eu-projects/corbel

3. http://cordis.europa.eu/project/rcn/198465_en.html

4. http://www.pangaea.de/

5. http://www.nerc.ac.uk/

6. http://www.bodc.ac.uk/

7. http://www.emodnet.eu/

Summary of EMBRC general requirements

EMBRC would like to achieve several objectives through participation to ENVRIplus:

• Establishing collaborations with the environmental community, which would benefit from their environmental and ecological data: EMBRC has been heavily involved with the biological and biomedical communities so far, but not with the environmental community.
•  Developing and learning about new standards and best practices in terms of standards: the EMBRC community are very interested in considering new standards in terms of methodologies, workflows and data. They would like to work towards increasing the compatibility of the data generated from their various member institutes such that its analysis can become comparable, but at the same time not lose the compatibility of this data with data which was already generated, sometimes as far back as 100 years ago.
• Developing new standards within INSPIRE [8], which can be used for other datasets: While INSPIRE is particularly focused on spatial data, its disadvantage is that it does not apply for other types of data. Through participation to one of the ENVRIplus work packages, the the RI REP advised that his organisation- the MBA (Marine Biological Association [9]), a member of the EMBRC, will attempt to develop standards within INSPIRE which can be used for other datasets by EMBRC.
• Exploring new data workflows which make use of marine biological and ecological data.
• Networking with other RIs.

The following are some important priorities for EMBRC:

1. Setting up an e-infrastructure within the next year, which would need to provide appropriate connectivity in order to facilitate the movement of data between the labs, in cases where users want to sample data from different locations, and send it to various repositories.
2. Developing several web resources (information about various species, availability of genomes, trasnscriptomes, mutants etc) and platforms: In particular, they are working towards building their access portal, which will include a catalogue of all of their lab locations, equipment, organisms, e-infrastructure services which users (researchers within or outside the marine sector, private sector, SMEs) can search and apply for. The EMBRC community is working on connecting external resources to their access portal, such that information on all of their available molecular resources is available from the same place. They expect their access portal to be ready within at most one year.
3. Negotiating with other RIs within ENVRIplus, the biomedical cluster Corbel and the marine cluster EMBRIC how they could work together to provide their services.
   

The biggest challenge for EMBRC will be looking at the different standards and workflows of the 3 clusters that it is involved in, and deciding on common ones, both for its member institutes, but also with other RIs across domains to facilitate collaboration.

References:

8. http://inspire.ec.europa.eu/index.cfm/pageid/48

9. http://www.mba.ac.uk/

Detailed requirements

EMBRC has plans to develop an e-infrastructure which would need to provide appropriate connectivity in order to facilitate the movement of data between the labs, in cases where users want to sample data from different locations, and send it to various repositories. The EMBRC community have also discussed about having a dedicated data group, which could advise users with their experimental designs (how and where to analyse their data, where to deposit it) and provide support for sequence assembly and annotation. 

EMBRC are discussing with the CORBEL and EMBRIC clusters the possibility of users going to multiple RIs to generate and analyse data, and investigating how difficult this would be to implement. They are considering using ELIXIR [10] for data curation, in particular working with the marine node from Tromso, Norway.

The EMBRC community do not use common software or standards. Some member labs use specialised in-house, non open-access, software, while others open-access one. In terms of standards, the RI REP advised that his organisation, the MBA, is using GBIF based on Darwin Core [11], and the MEDIN [12] metadata standard in the UK which is compliant with the European INSPIRE directive.

EMBRC does not have any non-functional constraints for data handling and exploitation. In what concerns security and access, the RI REP could only tell me about the situation of the MBA, who are using the ISO 27001 Information Security Management standard [13].

EMBRC can share with ENVRIplus or with other RIs instrumentation in terms of a number of buoys that are connected to various labs. It can also provide detectors and lab equipment, which users will be able to apply for through an access portal. Expertise in areas such as taxonomy and specific model organisms is spread across its different member labs, and EMBRC is currently making an inventory of it and of the willingness of the different labs to provide it as a service. It is also investigating the option of having a dedicated data group, which could provide help and support on experimental design, and analytical help on sequence assembly and annotation. As several stations from member countries have small libraries with large amounts of grey literature, some going back hundreds of years, EMBRC intends to run a workshop in the spring of 2016 to investigate how it could connect these libraries in order to make more of this grey literature available.

The biggest challenge for EMBRC will be looking at the different standards and workflows of the 3 clusters that it is involved in, and deciding on common ones, both for its member institutes, but also with other RIs across domains to facilitate collaboration. The community would like to organize a meeting between ENVRIplus, EMBRIC and CORBEL to discuss these issues. One option could be to the rolling out of the ENVRI Reference Model within other RIs.

References:

10. http://www.elixir-europe.org/

11. http://tools.gbif.org/dwca-assistant/

12. http://www.oceannet.org/marine_data_standards/medin_disc_stnd.html

13. http://www.iso.org/iso/home/standards/management-standards/iso27001.htm

Formalities (who & when)