Difference between revisions of "IMarine Liaisons"

Revision as of 09:46, 23 August 2013

This page realizes D2.5 Report on inter-projects coordination and collaboration. It reports on interactions with FP7 projects and other R&D national/international programmes on inter-project coordination and collaboration. The page will be enriched with information when individual collaborations and coordinations are added and/or edited.

The collaboration initiatives are first summarized in an overview table.

For each collaboration the following details are then reported:

A description of the Project/Initiative and its Objectives;
The description of the Community of PracticeA term coined to capture an "activity system" that includes individuals who are united in action and in the meaning that "action" has for them and for the larger collective. The communities of practice are "virtual", ''i.e.'', they are not formal structures, such as departments or project teams. Instead, these communities exist in the minds of their members, are glued together by the connections they have with each other, as well as by their specific shared problems or areas of interest. The generation of knowledge in communities of practice occurs when people participate in problem solving and share the knowledge necessary to solve the problems. served/involved;
A description of the established collaboration agreement;
The detailed plan and dates, if this is available.

Inter project collaboration

Collaboration plan

The plan at the start of the project for collaboration is described in the third iMarine objective:

"(iii) the extension, adaptation and deployment of a rich set of software components that implement these services. Instrumental in the activities of iMarine will be the establishment of an active set of collaborations with other international initiatives. The aim will be to reuse and render interoperable existing policies, technologies, and e-infrastructures. By leveraging on these collaborations and by taking advantage of additional funding that these organizations invest in the project, the number of available resources brought into play will be maximized."

Collaboration opportunities that were already identified at project inception were with EMI, ERINA+, EUBrazilOpenBio, VLIZ, and NEAFC. Most of these collaboration are now either established or planned, with the understanding that the preparation of such a collaboration requires a preparation of the technical and human infrastructure, and the collaboration may not have been actuated as of the time of preparation of this document.

New opportunities for collaboration

Many collaboration opportunities emerged during P1 of the project, and this dynamic list is expected to grow substantially towards project completion. Not all opportunities are listed here, but only those where a collaboration or coordination action was discussed at WP level or above. In addition, some collaborations were discussed but not pursued due to non-disclosure agreements, software incompatibilities, or other blocking issues. Only real "prospects" are included.

The collaboration opportunities and the co-ordination thereof collected here summarize the effort. Where the collaboration has resulted in concrete activities, these are described elsewhere. This deliverable documents the collaboration at high-level only.

Each Collaboration is first described by the names, the entities involved, the goal and objectives, and some activities. A brief overview of the activity table is given, and also the intended type of collaboration is mentioned. These types go from a loose, consumption like collaboration, to a full sharing of project resource development. In a short overview as presented in this page, a detailed classification of collaboration types is not feasible, and they have to be summarized as follows:

Data sharing; exchange data programmatically between infrastructures;
VREVirtual Research Environment. Exploitation; deliver a VREVirtual Research Environment. to a new community;
Software development; share the development of services between frameworks;
Software integration; convert existing code to execute on to e-InfrastructureAn operational combination of digital technologies (hardware and software), resources (data and services), communications (protocols, access rights and networks), and the people and organizational structures needed to support research efforts and collaboration in the large., e.g. in gCube;
Co-development; write software and share code to execute on the e-InfrastructureAn operational combination of digital technologies (hardware and software), resources (data and services), communications (protocols, access rights and networks), and the people and organizational structures needed to support research efforts and collaboration in the large..

Ultimately, also the status of the collaboration is activity is reported, which can be only one of :

Prospect; The iMarine collaboration opportunity has been presented;
Aborted; The collaboration was not achieved;
On-hold; The activities are on hold, pending a decision on continuation;
Planning; The collaboration plan is being drafted;
Development; the collaboration resources are being developed for implementation;
Validation; the delivered components (or resource, or the exploitation of existing resources) is being validated by collaboration partners;
Completed; the collaboration is active.

Progress table

*iMarine co-ordination and collaboration*
Collaboration	Planned / New	Last activity	Type	Status
VLIZ	Planned	03.2013	Data sharing	Development
NEAFC	Planned	07.2013	Software development	Planning
EMI	Planned	02.2012	Software integration	Completed
ERINA+	Planned	02.2012	Software integration	Completed
EUOpenBio	Planned	07.2013	Software integration	Development
EMODNet Biodiv	New	03.2013	Data sharing	Development
ENVRI	New	10.2012	Data sharing	Planning
FishFinder	New	06.2013	VREVirtual Research Environment. Exploitation	Completed
SmartFish	New	08.2013	VREVirtual Research Environment. Exploitation	Development
VocBench	New	05.2013	Software	On-hold
Tuna Atlas	Planned	06.2013	Data sharing	Validation
Data.fao.org	New	07.2013	Data sharing	Development
FAO/Chronicles	New	06.2013	Software development	Planning
Eurostat	Planned	10.2012	Data sharing	Completed
DCF-DGM	New	07.2013	Data sharing	Prospect
MCS-DGM	New	07.2013	Data sharing	Prospect
VME-DB	New	08.2013	VREVirtual Research Environment.	Planning
ABNJ	New	07.2013	Data sharing	Planning
GBIF	New	10.2012	Data sharing	Completed
Lifewatch	Planned	10.2012	Data sharing	Development
GOLD	New	08.2013	Data sharing	Planning
BestTuna	New	01.2013	VREVirtual Research Environment.	Prospect
RDA	New	01.2013	Data sharing	Development
SciencePad	New	01.2013	Software development	Prospect
IGI	New	10.2012	Software development	Prospect
Helix Nebula	New	05.2013	Software development	Prospect
GEO WOW	New	05.2013	Software development	Planning
ACRI-ST	New	05.2013	Software development	Prospect
Agrocampus	New	09.2012	Software development	Prospect
GEO BON	New	09.2012	Data sharing	Prospect
TBTI	New	07.2013	VREVirtual Research Environment.	Prospect
AustralFish	New	06.2013	Data sharing	Prospect
FIPS SpeciesNameFinder	New	06.2013	VREVirtual Research Environment.	Proposal

Inter-projects Coordination

The inter-project coordination is undertaken with several clear objectives in mind. iMarine is an ambitious initiative the first phase of which aims specifically to establish an e-infrastructure supporting 3 business cases. For iMarine, coordination activities are pursued that can bring benefits in the areas of i) technology development, ii) services and product re-utilization, interoperability and marketing, and iii) sustainable governance of the e-InfrastructureAn operational combination of digital technologies (hardware and software), resources (data and services), communications (protocols, access rights and networks), and the people and organizational structures needed to support research efforts and collaboration in the large..

The inter-projects activities may not only result in collaboration (i.e. partaking in a shared activity), but can also result in a co-ordination effort. This can manifest itself in bundling resources to approach external communities, reduce overlap in development effort by aligning activities, and avoid duplication of effort by building on components from other projects. This is mainly an activity of negotiating and information exchange.

Another aspect of inter-project coordination is the planning and scheduling of collaboration activities. This is not detailed for each individual case, rather an approach was adopted where roles were distributed between the iMarine Board, the Steering Board, and the wider EA-CoPCommunity of Practice.. Where appropriate, a note is made in the collaboration activity list below. Important cases where iMarine participates in co-ordination efforts, but where collaboration is not the objective are:

FLUX

As an outcome of the activities in BC-1, iMarine managed to raise awareness on the importance of adopting a standard exchange protocol for the fisheries operations data domain (Flux – Fisheries Language for Universal eXchange), and of streamlining the data-flows from the fisheries Monitoring-Control-Surveillance (MCS) to the scientific domains in Europe. Through the iMarine Board, the project is now consulted to contribute to several elements of the data-infrastructure related to the support of EU’s common fisheries policy. Through global fisheries standard setting bodies where iMarine Board members are active (CWP), the FLUX initiative was introduced in order to sense the interest of the global community towards joining this initiative.

SDMX

One example that exemplifies the coordination activity results in this area is the invite to take a seat in the SDMX-Steering Committee. Through the activities of FAO Fisheries and CIO departments, the shared FAO / ESTAT datasets development, the iMarine OpenSDMX initiative and informal activities, representatives of iMarine become well known in the SDMX community.

ABNJ-Tuna

FAO manages important sections of this GEF-project. Effort is made to ensure that software developments are not initiated in parallel by comparing work-plans and activities. These contacts are important to position the iMarine infrastructure and to be able to quickly respond if concrete requirements are brought forward to support this large initiative with data or other resources. Such efforts are developed in the logic of a public partnership business model, whereby each involved organization highlights the benefits expected from joining the iMarine platform with the expected result that new projects will contribute to new developments for the overall benefit of the entire community.

Collaboration priorities

From the above initiatives, several priority collaborations emerge that are pursued with more vigor than the others. They promise to deliver clear advantages to the the project consortium and will be important to achieve a sustainable solution for iMarine functionality, the underlying D4ScienceAn e-Infrastructure operated by the D4Science.org initiative. infrastructure, and the gCube technologies.

iMarine technology collaboration priorities

EMI

http://www.eu-emi.eu/

The collaboration with the EMI project, developed during the D4ScienceAn e-Infrastructure operated by the D4Science.org initiative.-II project, has continued in the context of iMarine with a signed Memorandum of Understanding between the two projects. The MoU defines three main goals of the collaboration:

Access to EMI build services: iMarine depends on the EMI to build its core software, gCube. EMI should provide iMarine access to its build services (ETICS) where the project can register its gCube projects, create configurations for their components, build and test these projects and access the service repository and associated reports.. iMarine, through its partner Engineering SPA, is responsible for maintaining and providing support for ETICS web configuration UI, a component of the the EMI build services components developed by Engineering SPA.

EMI release preview and exploitation: iMarine has access to pre-production release of EMI products via the EMI Integration Testbed and subject to its acceptance criteria, iMarine should upgrade its infrastructure’s gLite nodes to the latest versions of the components released by EMI.

iMarine feedback and requirements: iMarine will evaluate the suitability of EMI products to meet its requirements and reliability of the services it provides. Feedback, recommendations and lessons learned should be provided to validate and improve EMI services. Feature requests for EMI products may be submitted for new or improved capabilities of EMI products

ERINA+

http://www.erinaplus.eu/

ERINA+ is an EU funded project to assess the socio-economic impact of e-Infrastructures and develop an assessment methodology for e-Infrastructures projects to self-evaluate their own impact.

EUBrazilOpenBio

http://www.eubrazilopenbio.eu/

This project is co-funded by the European Commission and the Brazilian Minister of Science Technology and Innovation (MCTI). The project aims at offering to the biodiversity scientific community an e-infrastructure giving access to domain relevant open-access resources (data, tools, services and computing) and supporting their exploitation. The e-InfrastructureAn operational combination of digital technologies (hardware and software), resources (data and services), communications (protocols, access rights and networks), and the people and organizational structures needed to support research efforts and collaboration in the large. is epected to be built by federating and integrating existing European and Brazilian technologies and resources.

The liaison between iMarine and EUBrazilOpenBio is oriented to share the infrastructure and software artifacts and to promote a cross fertilization among the two Community of Practices the projects deal with. The infrastructure needs of the EUBrazilOpenBio community have been covered by creating a specific Virtual OrganizationA dynamic set of individuals or institutions defined around a set of resource-sharing rules and conditions. All these virtual organizations share some commonality among them, including common concerns and requirements, but may vary in size, scope, duration, sociology, and structure. in the D4ScienceAn e-Infrastructure operated by the D4Science.org initiative. e-InfrastructureAn operational combination of digital technologies (hardware and software), resources (data and services), communications (protocols, access rights and networks), and the people and organizational structures needed to support research efforts and collaboration in the large.. The use of the same infrastructure facilitates the sharing of the resources that are deployed in the infrastructures, for example, gCube Hosting nodes can be shared, as well as specific service instances, can be used by both the projects thus realising an economy of scale scenario.

Among the shared software artifacts, a primary role is played by the gCube Species Data Discovery service, i.e. a service conceived to provide its users with seamless access to Species Data (Taxonomy Items and Occurrence Points) from the major providers and Information Systems, like GBIF and Catalogue of Life. The core of the service has been designed and developed in the iMarine project while a number of plugins (specifically conceived to interface with a target Information System) have been developed in the context of EUBrazilOpenBio, namely plugins interfacing with speciesLink and The List of Species of the Brazilian Flora. EUBrazilOpenBio in turn has contributed to the design and development of facilities supporting the production of checklists, i.e. lists of taxonomy items that can be used to compare the Species characterizations own by each Information System as to discover potential misplacements and incomplete characterizations. Other software artifacts characterising this collaboration are the Cross Mapping and the Niche Modeling Services. These have been developed by EUBrazilOpenBio project and they are expected to be reused by iMarine. The former is a Service for comparing two checklists, the latter is a Service for using the openModeller technology to model, test and project species distribution probabilistic models.

As a side effect of this strict collaboration at technological level, there was also an involvement of the Communities of Practice addressed. For example, iMarine has been invited to present its achievements at relevant events organized by the EUBrazilOpenBio community members (e.g. Advancing Biodiversity e-science innovation through Global Cooperation Workshop), both in Europe and in Brazil.

ENVRI (Common Operations of Environmental Research infrastructures)

http://www.envri.eu

ENVRI is a project that aims at establishing a collaboration between the cluster of ESFRI projects operating in the Environment area, with support from ICT experts, to develop common e-science components and services for their facilities. The expected result is a speed up the construction of these infrastructures and a common layer for scientists to use the data and software from each facility to enable multi-disciplinary science.

The liaison between iMarine and ENVRI is oriented to share technological artifacts and to promote a cross fertilisation among the two Community of Practices the projects deal with.

As a result of the analysis of the requirements specified from the different ESFRI infrastructures, it has emerged that a primary role is played by services specifically conceived to deal with Geospatial data. In order to satisfy this need it was decided that the suite of services initially designed and developed in the context of iMarine will be consolidated and enhanced when used in the ENVRI settings. This suite is a comprehensive yet open set of services implementing and benefitting from the OGC standards (namely WCSWeb Coverage Service, WMSSee Workload Management System or Web Mapping Service., WFSWeb Feature Service, WPS, CSW) enabling the Discovery of such data, their processing as well as their publications. ENVRI will contribute to this framework by developing specific data processing methods that can also be reused by iMarine.

ENVRI does not plan to set up an own infrastructure. The services developed will be hosted for experimentation purposes in the D4ScienceAn e-Infrastructure operated by the D4Science.org initiative. infrastructure. This will facilitate their exploitation also in the iMarine application environments.

On the other side, the availability of a specific VREVirtual Research Environment. dedicated to ENVRI in the D4ScienceAn e-Infrastructure operated by the D4Science.org initiative. infrastructure, ENVRI VRE, offers iMarine an opportunity for demonstrating some of its facilities to this CoPCommunity of Practice.. One potential target is the LifeWatch part of the ENVRI consortium.

LifeWatch

http://www.lifewatch.eu

LifeWatch is a European Research Infrastructure for Biodiversity currently under development. The first services to users are planned for 2013. Through this infrastructure users may benefit from integrated access to a variety of data, analytical and modeling tools as served by a variety of collaborating initiatives. The LifeWatch infrastructure is also expected to give access to selected workflows for specific scientific communities able to exploit offered data and tools and to offer facilities for constructing personalized "virtual labs" allowing to enter new data and analytical tools. New data will be shared with the data providers cooperating with LifeWatch.

A number of meetings have been held between iMarine and LifeWatch Service Center representatives to explore possible common interests and synergies. During these meetings the two parties have recognized that iMarine services might be usefully exploited also in the LifeWatch application context. It has then decided to start-up an explorative collaboration that has initially included the following actions:

iMarine representatives have been following the requirements of the LifeWatch "Alien Species Showcase" to evaluate the feasibility of hosting on the iMarine infrastructure also a VREVirtual Research Environment. dedicated to scientists studying alien species in the marine environment. This study case is developed through an interoperability exercise on a set of databases covering collections of species along a ideal transect ranging from the deep regions of the Southern Adriatic-Ionian Sea to the high altitude woodlands in Central and Northern Italy.  Ecosystem fragility will be evaluated from the proportion of native and alien species; similarly the vulnerability of taxonomic or functional groups will be evaluated from the proportion of native and alien species within every group. The accessibility of data stored in distributed databases will allow mapping ecosystem vulnerability on the layer of ecosystem types in Italy.  Bio-molecular data on selected species and species groups will provide services with the observation of individuals and populations.  By using the simple traits selected for the analysis, estimates of the scenario of change for ecosystem services in the different types of ecosystems will be performed. The study case is easily expansible to ecosystems in other EU countries, covering a wider range of ecosystem types and taxonomic groups. 
The joint "Data Sharing and Enrichment: iMarine and LIFEWATCH Solutions & Experiences" Workshop will be held at the EUDAT Conference on 28 October 2013 [1]:
Training material produced by iMarine is being incorporated in the LifeWatch training modules disseminated by the Lifewatch Service Center.

SciencePAD

http://sciencepad.web.cern.ch/

SciencePAD is an initiative coordinated by EMI in collaboration with ILL, EMBL-EBI, Ex Machina with the participation of other projects and companies developing or using software for scientific applications.

It aims at assisting scientific communities in finding the software they need, to promote the development and use of open source software for scientific research and provide a one-stop-shop to match user needs and software products and services.

The initiative was started informally in September 2011 with a first round of discussions among representatives of various projects and other interested parties. In December 2011 a Steering Commitee (SC) was formed to formally discuss the mandate, scope, functions, funding models, governance structure and membership rules. The SC presented the outcome of the initial discussion to a larger community of software developers and users in February 2012 at a workshop organized at CERN on open source software for scientific research and currently a project proposal has been submitted to EC in the context of FP7 framework.

iMarine - which is supporting and developing the gCube Software Framework (together with EUBrazilOpenBio and ENVRI) - is part of the SciencePAD software catalogue and it took part to the brainstorming phase of the initiative. Depending on the approval of the EC project proposal, iMarine will also evaluate to sign an MoU with the project in order to further exploit the catalogue and other initiatives that may follow.

OpenAIREPlus

http://www.openaire.eu/

OpenAIREplus (2nd Generation of Open Access Infrastructure for Research in Europe) was launched in December 2011. The 30 month project, funded by the EC 7th Framework Programme, works in tandem with OpenAIRE, extending the mission further to facilitate access to the entire Open Access scientific production of the European Research Area, providing cross-links from publications to data and funding schemes. This large-scale project brings together 41 pan-European partners, including three cross-disciplinary research communities.

Communities served/involved are all EC Projects and their members and scientists.

The collaboration agreement is established around:

Alignment of technologies (mid and long term vision)
Exchange of technologies (tentative)
Exchange of expertise
Joint development of new technologies (we envisage a common mobile client for information retrieval)

Up to now the collaboration activities include a number of meetings / teleconferences such as a joint teleconference CNR / NKUA on technical aspects of the infrastructure (January 2013) and a series of NKUA meetings including members of the two teams.

In the future, the objective of the collaboration is to evaluate further options for technological convergence.

EarthServer

http://www.earthserver.eu

EarthServer is establishing open access and ad-hoc analytics on extreme-size Earth Science data, based on and extending leading-edge Array Database technology. The community of practice served/involved is the earth Observation Scientists and Geologists

The established collaboration agreement includes

Evaluation of the applicability of Array DBs for iMarine data
Evaluation of standards for adoptability
Exchange of best practices

Performed actions include

Joint meeting in July 2012 on the feasibility of technology exchange
Joint participation to the EarthCube Brehmen Workshop
Aligned technologies: Java, Liferay portals.

For the future, the planned actions include revisiting of the case of technology exchange in appropriate time and the exchange of best practices

RDA

The objective of the Research Data Alliance isto accelerate and facilitate research data sharing and exchange. The work of the Research Data Alliance is primarily undertaken through its working and interest groups. Participation these working groups, starting new working groups, and attendance at the twice-yearly plenary meetings is open to all. The initiative is currently supported by he European Commission, NSF and Australian Government through the Australian National Data Service (ANDS),

iMarine is represented in RDA through Donatella Castelli who is both a member of the the RDA Europe Forum & the Marine Data Harmonisation Interest Group, and by others that have registered as members in a number of other working groups.

The iMarine Steering Board, recognizing the importance of the RDA initiative, has decided to put in place actions to increase the active participation of its partners in it.

FP7 RDA-Europe for Ocean Data Interoperability

[RDA-Europe focuses on coordinating a series of cross-infrastructure experiments on global interoperability with a selected group of projects and communities. Each prototype addresses a specific community driven use case indentifying best-of-breed solutions and the remaining challenges. The RDA Europe Prototype Programme is developed in synergy with the RDA Europe Analysis Programme devoted to analyzing data organizations and solutions as they emerge from the various scientific communities and the RDA Europe Workshop Programme covering the investigation data infrastructure convergence and reaching out to new research communities.

In this context iMarine collaborates within a focus group (user community) for Ocean Data Interoperability.

ROpenSci

rOpenSci develops R-based tools to facilitate acess to open data and open science. iMarine plans to align activity with representatives of the Advisory board members of ROpenSci.

rOpenSci develops R-based tools for acess to Open Data and Open Science. The 2013 RopenSci data challenge is now just launched

Several R packages are already curated, including on the Fisheries.

GEOWOW

Synergies exist between between iMarine & GEOWOW that have been identified, and have been now discussed (joint telecons) and tested (services accessed) for exploitation. A two way collaboration between iMarine and GEOWOW FP7 projects is foreseen as follows:

iMarine supports the GEOWOW effort to outreach scientific community (WPS-Hadoop processing Service),
GEOWOW develops cloud-based services to access and process ocean acidification projections (ESGF CMIP5 Gateway).

Additional services can be considered in this perspective (e.g. Species Kernel Density algorithm)

The shared objective is to have a MoU highlighting how to strengthen the linkages between: scientific communities accross marine ecosystem experts, biologists (studies on pteropods...) and the Climate specialists, as well as the outreach towards GEOSS communities that GEOWOW is addressing (Global Earth Observing System of Systems).

As user community brokers, both projects also share a common role in bringing users and data towards European Research e-Infrastructures (EGI, Helix Nebula, D4ScienceAn e-Infrastructure operated by the D4Science.org initiative.), where business models need to be established and validated against user communities needs and operations.

The GEOWOW project has already a connection with ESFRI (ENVRI cluster for instance) via inclusion of results from the GENESI-DEC FP7 project (brought by ESA and Terradue project partners).

There is also an interest to further develop that connection especially expressed by the UNESCO IOC partner. iMarine is in discussion with them to clarify objectives in this regard; these relate to ENVRI contribution to GEOSS, and possibly the BluePlanet activity stream.

Helix Nebula

Helix Nebula (HN) has recently achieved important milestones, and concrete steps, more opened to the outside world, are now starting. Especially, the recently created Services Architecture and the soon to be launched Business Architecture activity streams in HN are of interest for iMarine. On the Services Architecture side:

Work is starting on the Data Management topic;
Terradue delivered several inputs to this group, that can provide good anchors to the way the iMarine e-InfrastructureAn operational combination of digital technologies (hardware and software), resources (data and services), communications (protocols, access rights and networks), and the people and organizational structures needed to support research efforts and collaboration in the large. operates / plans to operate;
A synergy at this level would address the processing between Helix Nebula (compute infrastructure) and iMarine (science data curation), with a linkage between them for externalizing to the HN Cloud some highly demanding compute operations.

iMarine has many tools available or planned to enact such data staging and application provisioning operations for on-demand, time constrained operations. Terradue intends to play an active role as part of iMarine in supporting these operations.

IGI

IGI is the Italian branch of the EGI initiative, and has been contacted to align the iMarine plans for the exploitation of EGI facilities with the IGI planning.

"Current situation"

iMarine provides access to a Spatial Data Infrastructure (SDI) that covers all steps of a spatial data lifecycle: from registration of spatial products, generation and publication of ISO 10139 metadata, product discovery, storage of the data product, access via Web Map Service, Web Coverage ServiceSupports the networked interchange of geospatial data as "coverages" containing values or properties of geographic locations. Unlike the Web Map Service, which returns static maps (server-rendered as pictures), the Web Coverage Service provides access to intact (unrendered) geospatial information., and Web Feature ServiceOpenGIS Specification that supports INSERT, UPDATE, DELETE, QUERY and DISCOVERY of geographic features. WFS delivers GML representations of simple geospatial features in response to queries from HTTP clients. Clients access geographic feature data through WFS by submitting a request for just those features that are needed for an application., processing of data via Web Processing Service, and visualization. iMarine maintains and operates a computational infrastructure to offer those features by integrating and enhancing several heterogeneous technologies, including but not limited to cluster of balanced GeoServer instances, replicated GeoNetwork servers, and cluster of Thredds servers.

"Vision"

Enhancing the current IGI infrastructure by offering support for spatial data products could greatly enlarge the consumers of the IGI infrastructure. iMarine could provide a complete and operational SDI to the IGI users. A collaboration will be proposed later in 2013.

EA-CoPCommunity of Practice. collaboration priorities

Collaborations triggered under BC1 framework

FishFrame RDB (DG MARE/DCF/IRD-MEDDE)

Current situation

Fisheries data in Europe are managed with different data formats (different labels for same entities, codelists..) which are covering different needs (DG-MARE: ERS, VMS, DCF / Fishframe) but are mainly dealing with the same objects (vessels, fishing gears, species, locations...) and events (fishing operations, landings..). Member states (MS) have to handle elogbooks (ERS XML schema, version 3) to feed their databases. Fishframe is not mandatory but is, so far, the most relevant format to answer DCF data calls and to enable scientists, managers to make decisions about related fisheries (elogbooks are “just” declarative data). DG-MARE plans to merge these different schemas within a single standard: FLUX. In practice, dozens of databases will need to comply with these data formats. However, even if stakeholders agree with the approach, they usually have limited IT resources to help them in doing this. In this context, complying with TDWG, OGC, SDMX data formats and protocols are additional steps that are crucial to cover the needs of different communities of user but can't be achieved in the short term.

Vision

In few years, MS will only have to deal with FLUX as single data format for fisheries data. They will deliver their data through XML files that are FLUX compliant to the related infrastructure. The infrastructure could be made of either a network of regional databases (nodes) or a single node. On top of these regional nodes, different kinds of data exports will be enabled according to the needs of communities of users: Fishframe XML (and CSV), statistical analysis (SDMX), spatial analysis (OGC), biodiversity (TDWG).. By furnishing FLUX compliant data, MS will then get additional services without any additional developments.

Contribution of IRD

ADDED BY MARC, PLEASE CHECK AND CONFIRM The following collaboration takes place under DCF/french ministry of fisheries funded project. In 2012, IRD has set up a SQL database based on Fishframe XML schema. In 2013, IRD reused an application of french ministry of fisheries transforming ERS version 3 XML schema in a SQL database. IRD will help in mapping ERS and Fishframe XML schema as well as suggesting new elements to extend the FLUX XML schema. This will be achieved in creating UML class diagrams. If needed IRD can set up an SDMX export on top of its Fishframe database.

ADDED BY MARC, PLEASE CHECK AND CONFIRM Following-up from Board2, Board3 meeting will discuss on the practical use cases which will contribute to show the value of the infrastructure. This would include the provision of code list services, of transformation services back and forth between FishFrame format and other formats (CSV, OGC, SDMX, TDWG), the connection of IRD-DB with the iMarine infrastructure. A scope could be to do this in the Tuna context, in relation with the Tuna Atlas.

FishFrame North Sea - North Atlantic - Baltic RDB (ICES)

iMarine has maintained liaison with these northern europe FishFrame regional frameworks through ICES while pursuing the FLUX discussions. While awaiting a DG-MARE budget for supporting a study proposal, ICES (FishFrame RDB host) is concentrating on moderate changes to the data format to cope with a wider range of data/data sampling scenarios. iMarine will be welcomed to participate to a workshop on RDB-Fishframe at ICES in the first half of June, which will focus on data uploading.

Med&BS-RDB (GFCM)

iMarine attended the SC for Mediterranean and Black Sea Regional Database (SC Med&BS-RDB) in Nov. 2012. It is envisaged that the GFCM Secretariat will host this Med&BS-RDB. Scope of the RDB is to host the data collected from EU Member States under DCF. The Regional Coordination Meeting for the Mediterranean and Black Sea (RCMMed&BS) will be responsible for the content governance of the Med&BS-RDB and it will indicate priority areas for development, reports and data requirement.

The SC Med&BS-RDBagreed that Med&BS-RDB should constitute, as a first step, a depository for biological and transversal data (ie catch and effort), allowing for regional analysis of available data as well as sampling coverage on a temporal and spatial scale. Fisheries scientific surveys data bases (e.g. MEDITS series) are also considered in this scope.

The SC Med&BS-RDB was informed about the iMarine initiative which collaborates on similar RDBs developments, with reference to FishFrame RDBs hosted by ICES and IRD, and on the potential benefits of pooling efforts on similar goals in respect of development of such data infrastructures. The proposal made by the GFCM Secretariat to build this Med&BS-RDB on the MS Sharepoint proprietary framework might however prevent such collaboration (at least on the software tools).

GFCM SCSI

iMarine attended the GFCM SCSI (Feb.2012) which was informed about the iMarine initiative and its goal to set up web-based data infrastructure capacities to format and process VMS related data for scientific exploitation (VTI). GFCM welcomed this information and the potential support which such infrastructure might provide in the future, however indicated that the issue of scientific exploitation of VMS data in the GFCM context seems to be quite premature to be tackled at this stage. The current policy states: " In line with the established practices for the ongoing data submissions obligations by members, VMS data shall be directly and expressly transmitted by contracting parties in accordance with data structures, formats and codifications formulated within the Secretariat. This implies that no post processing and/or transformation activities on data should be carried out by external parties prior to the reception by the Secretariat. Moreover, data sensitivity issues will be matter of discussion by members at a later stage and in accordance with the GFCM resolution on data confidentiality policy and procedures; therefore VMS data from GFCM members submitted through the addressed recommendation is not supposed to be subject to disclosure to any third party until further decision of the Commission."

VocBench (FAO)

The collaboration with the VocBench aims to enrich the e-InfrastructureAn operational combination of digital technologies (hardware and software), resources (data and services), communications (protocols, access rights and networks), and the people and organizational structures needed to support research efforts and collaboration in the large. with vocabulary management tools. The need is in the management of code lists of relevance to the iMarine EA-CoPCommunity of Practice.; Local Species names, Gears, Ports, etc. To this end, the VocBench is enriched by the project with specific facilities, this collaboration, known as [Cotrix] started in Jan 2013, and FAO oversees the activities. A first result is expected in early April 2013, after which the mapping between code lists and data will be added. The priority is high.

Geospatial services to FLUX (DG MARE/MCS)

Assessment of Geospatial services which the iMarine infrastructure can deliver to FLUX Anton to describe

VTI2 project (NEAFC)

The sub-contract with NEAFC has been drafted, and will be discussed shortly. It will support the implementation of the VTI2 project, aiming at realizing a secure data workflow from VMS data stored in the NEAFC servers to aggregated Fishing effort statistics available in standard format (SDMX or Flux) in iMarine registry, for use by e.g. ICES scientists under the conditions planned by the NEAFC-ICES MoU.

ABNJ-Tuna (GEF/FAO)

Marc/Anton to describe

BESTTuna / Wageningen University

BESTTuna is a programme at Wageningen University on tuna fisheries in the Western and Central Pacific (www.besttuna.wur.nl). A newly funded component of this programme has just been started in which is intended to set up an Open Source data system for tuna in this region. The idea is to cover both quantitative stock and trade data as well as qualitative data around the various treaties in the region. The overall goal is to have an information system that is available online and contributed to by industry and consumers in the region.

This component is very ambitious and at scoping study phase level to see what experiences already exist around interactive information systems on fisheries and seafood. FAO is one of the key organisations of interest in this scoping phase, and a meeting took place in January 2013 where iMarine offering was presented raising strong interest from BESTTuna project side.

Tuna Atlas (FAO/ICIS)

The collaboration with the Tuna Atlas data managers in FAO primarily aims at fully proofing the Integrated Catch Information System VREVirtual Research Environment. (ICIS): when the harmonization workflow will be fully validated according to the Tuna Atlas requirements, the ICIS VREVirtual Research Environment. prospect will be considered by FAO/FI as a product which has realized the initial objective of ICIS, and as such can enter in a production stage and can be strongly promoted at the level of RFBs and beyond.

Tuna Atlas (IRD)

SEIF2 project (Eurostat)

FAO has a long-term collaboration with Eurostat through the SEIF project. This has resulted in the alignment of codes, and the sharing of data using SDMX. The integration of SDMX in the e-InfrastructureAn operational combination of digital technologies (hardware and software), resources (data and services), communications (protocols, access rights and networks), and the people and organizational structures needed to support research efforts and collaboration in the large. will enable a collaboration also at the level of software development and work-flow support. Priority is medium, as most of the components have already been delivered.

SDMX at Data.fao.org (FAO)

The collaboration with data.fao.org is a key if iMarine manages to position itself a a data suite for resource poor initiatives. This would enable a cost-effective means to geographically dispersed institutions to share their data with FAO and the world at large. In FAO, the core IT department collaborates with iMarine to develop data sharing facilities. iMarine has contributed the OpenSDMX codebase and is now co-developing with CIO. The resources can already be consumed by iMarine through the SDMX Registry and Repository: http://data.fao.org/sdmx/index.html

The registry base URL is: http://data.fao.org/sdmx/registry

For instance, the indicator codelist can be obtained with: http://data.fao.org/sdmx/registry/codelist/FAO/CL_INDICATOR/1.0

Collaboration at this stage is implemented at the level of aligning iMarine and FAO standards and protocols, and data exchange.

Fisheries Chronicles (FAO)

Statistical data processing in support to the FAO chronicles and production of indicators, including those for robust future projections on catch trends. For these catch trends, access to large corpora of data is a must and collaborative action is imperative to hear as many opinions as necessary to come to a balanced projection. The prospect emerged late in 2012, and will be further pursued in 2013.

Fleets socio-economic performance (DG MARE / SocioEconomicUnit / FIRMS)

At FIRMS FSC8 meeting (Feb.2013), DG MARE's unit in charge of provision of fisheries socio-economic advice presented its data base on EU Fleets key socio-economic performance indicators (socio-economic indicators, graphs, charts, tables of fish prices, fuel consumption and cost, fleet structure etc.), drawn from a very extensive Economic Report on EU Fleets (STECF). This data base supports the yearly Annual Economic Report (AER). It was pointed out that the data collected under the Data Collection Framework (DCF) provided a solid basis for scientific analysis of fisheries and scientific support to policy advice in the framework of the Common Fisheries Policy.

This database is an important attribute to facilitate matching up fishery or resource data reported in FIRMS with socio-economic aspects. The comprehensive set of indicators can be utilized at supra-region level (North Atlantic, Mediterranean, other areas), while at higher geographic resolution (e.g. ecoregion) only transversal data (catches and effort) data can be utilized combined with proper methods for allocating economic data at disaggregated level. It was agreed that the iMarine infrastructure could be assessed and tested so to provide such services to FIRMS reports.

Sustainability indicators for EU fisheries (Rennes University AgroCampus)

The University of Rennes / AgroCampus is involved in the production of indicators required in framework of EU common fishery policy.

les calculs d’indicateurs de durabilité des pêcheries européennes auquel je participe (via le CSTEP - STECF). Je pense aussi au modèle écosystémique développé par Didier Gascuel (EcoTroph) qui offre une vision synthétique des écosystèmes mondiaux au travers des spectres trophiques L ínteret que nous avons pour les édudiants travaillant sous la supervision d’un professeur est le suivant: pour un objectif donné sur lequel iMarine se mettrait d’accord avec le professeur, brancher les étudiants sur l’usage de la platte forme afin d’évaluer la faisabilité du sujet, d’identifier les forces et les limites des outils disponibles et de l’interface utilisateur, de suggérer des directions. Le fait est que les étudiants ont plus de temps à dédier que les professionnels.

At the level of collaboration on data exchange and analysis, a software development and component sharing initiative is being fostered among FAO and this French research institute. The prospect is moving towards a planning stage, and will receive further attention later in 2013 pending the availability in the iMarine e-InfrastructureAn operational combination of digital technologies (hardware and software), resources (data and services), communications (protocols, access rights and networks), and the people and organizational structures needed to support research efforts and collaboration in the large. of several services and software to align with this institute’s expectations.

Collaborations triggered under BC2 framework

VME-DB (FAO)

FAO has a leadership role in the Vulnerable Marine Ecosystem Data Base project, where it also proposed the exploitation of iMarine services for e.g. geospatial data management, access to species taxonomy and occurrence data and related quality control data management capacities, biodiversity modeling capacities, access to environmental data, and maps. The development of requirements for collation of necessary data sources is on-going iMarine might also provide its reporting environment in order to enable distributed data input. The project has yet to decide on the software infrastructure, but the exploitation of one or more VREVirtual Research Environment.'s is foreseen. The priority is high

ABNJ deep seas programme (GEF/FAO)

it is intended to earmark the iMarine data infrastructure as supporting platform in the ABNJ deep seas programme project document (under development as of March 2013). iMarine would provide i) a repository of scientific data with virtual collaborative scientific environment capacities for VMEs identification, ii) a toolbox for ecological niche modeling in support to VMEs (and possibly EBSAs) processes, iii) VREs for collaborative science in support to joint VMEs-EBSA processes, iv) a collaborative reporting facility in support of deep sea species identification.

Data quality assurance services (VLIZ)

The sub-contract with VLIZ aims to reduce the data-management burden for VLIZ, while increasing access to quality indicators for VLIZ data Quality Assurance services. VLIZ is interested to consume services provided through the iMarine infrastructure that will enable it to improve the quality of its geospatial and biodiversity data. VLIZ closely collaborates with the iMarine partner IOC / Unesco – OBIS. VLIZ has proceeded to install a gCube Node.

The collaboration with VLIZ, which includes access to the WORMS taxonomic repository, facilitates the straight access to the deep seas species sub-set elaborated in the framework of InDEEP-WoRMS collaboration on "World Register of Deep-Sea Species (WoRDDS)”.

EMODNet project - Biodiversity (DG MARE - VLIZ)

The collaboration with EMODNet/Biodiversity is given shape through a collaboration with VLIZ. The consumption of Species data by the infrastructure allows biodiversity data managers to harmonize and upgrade the quality of their data products. The collaboration is currently at the level of aligning standards, but when effective products are made available in the e-InfrastructureAn operational combination of digital technologies (hardware and software), resources (data and services), communications (protocols, access rights and networks), and the people and organizational structures needed to support research efforts and collaboration in the large., this may result in collaboration at service and VREVirtual Research Environment. level

GEO BON project

This initiative brings together some 100 governmental, inter-governmental and non-governmental organizations to organize and improve terrestrial, freshwater and marine biodiversity observations. At October 2012 GeoBon meeting, the iMarine environmental layers service (first building a detailed inventory, and secondly building access and integration) were earmarked on the deliverable wish-list/to-do-list and iMarine was added as a partner to work with (also other groups are building on this). It was felt that only iMarine is doing that second step in providing access in a research environment.

With iMarine a potential collaboration will be discussed to allow users of the imarine to align with the formats and standrads of this intiative to make their biodiversity data, information and forecasts more readily accessible to policymakers, managers, experts and other users. The prospect will be further described in 2013.

EUBon project (EU/FP7)

For Nicolas Bailly and Ward Appeltans to describe

EcoKnows project (EU/FP7)

See the project website: www.ecoknows.eu

The general aim of the ECOKNOWS project is to improve the use of biological knowledge in fisheries and management through the use of the most recent statistical methodologies such as the statistical Bayesian approach that will form the methodological backbone of the project and will enable realistic estimations of uncertainty: it helps for estimating parameters that have been usually studied on less than 15% of species. The models suggested will include important knowledge about biological processes and the applied statistical inference methods allow to integrate and update this knowledge in stock assessment.

The project is developing a computational learning approach that builds on the extensie information present in FishBase (www.fishbase.org). The developed methodology will be of fundamental importance, especially for the implementation of the Ecosystem Approach to Fisheries Management. It has been a difficult challenge, even for target species with long data series, and now the same challenge is given for new and poorly studied species. We will improve ways to find generic and understandable biological reference points, such as the required number of spawning times per fish, which also supports the management needs in the developing countries.

ECOKNOWS applies decision analysis and bioeconomic methods to evaluate the validity and utility of improved information, helping to plan efficient EU data collection..

The collaboration with iMarine focusses on the use of its computational and statistical capacities. Actual work has started with Rainer Froese (GEOMAR, Kiel, Germany) to compute estimation of Length-Weight Relationships. The technical team of the iMarine infrastructure has implemented an access to R via JAGS, and is able to parallelise several session of Markov chains that are used in the computations (Gianpaolo Coro).

GOLD (Conservation International)

Global seafloor geomorphic features map: applications for ocean conservation and management

Carribean Large Marine Ecosystem (CLME) project (IOC)

iMarine has acknowledged the typical needs of a Large Marine Ecosystem (LME) project which supports the production of a comprehensive set of indicators on the State of the marine environment and ecosystems. Thanks to the above described capacities, iMarine could add value by setting-up VREs with access to all data sources and maps of interest to CLME users, and interactive analytical potential.

Medina project (EU/FP7/ESA)

a preliminary meeting with ESA (an institutional partner of the Medina project) has indicated potential interest in the access to environmental databases and environmental enrichment.

Spatial data infrastructure (FAO)

A review of FAO's business case for a Spatial data infrastructure has been made by iMarine staff.

Collaborations triggered under BC3 framework

SmartFish project (FAO)

The collaboration with the EU/SmartFish project occurs on a co-funding basis and aims at implementing a Fisheries Regional Information System for the South West Indian Ocean providing harmonized and seamless access to information detained by three existing and complementary systems, while minimizing interference with those systems. A prototype building on the FLOD knowledge base has been developed.

AgInfra project (EU/FP7)

Through the iMarine Board, the dialogue with AgInfra has remained open but it is only by the mid-term of the project that a real collaboration opportunity has emerged with AgInfra; it was deemed important to ensure that the Top Level Ontology (TLO) promoted by FORTH be presented to AgInfra to assess its acceptance in a broader framework. Another stream of collaboration opened in March 2013 concerns the publishing of Fisheries glossaries in Linked Open Data format.

Geodiva project (EU/FP7)

The Geodiva project, a new FP7 project proposal which formulation stage two was closed in Feb.2013, can be seen from the iMarine perspective as a super semantic cluster. Four iMarine institutions are part of Geodiva (IRD, FAO, TerraDue, Trust-IT), and iMarine is foreseen to deliver the data infrastructure platform serving the Geodiva semantic web goals.

FishFinder (FAO)

The collaboration with the FAO FishFinder programme (ex FAO Species Identification and Data Programme) has been initiated in June 2012 under the working title [FishFinder]. The collaboration allows the e-InfrastructureAn operational combination of digital technologies (hardware and software), resources (data and services), communications (protocols, access rights and networks), and the people and organizational structures needed to support research efforts and collaboration in the large. access to a rich resource of species information, while FishFinder will be equipped with a Species fact sheets reporting environment (Content Management System) to allow its network of Species information specialists to add Species Identification Sheets. The Toolset evidences the value of the iMarine reporting tools, including the work-flow and templating functions. The collaboration also aims at making available the iMarine reporting tool in developing countries thanks to a standalone plugin which can work off-line.

Others

The iMarine capabilities have been demonstrated to a large number of other initiatives, and /or interested individuals, also with a view on future sustainability. Several of these have expressed an interest to become involved.

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 ==== FP7 RDA-Europe for Ocean Data Interoperability ====
-[https://www.icordi.eu/Content/IcordiEcosystem.aspx?id=17 iCordi] is a forum supporting the convergence between emerging global data infrastructures.
+[[https://europe.rd-alliance.org RDA-Europe]  focuses on coordinating a series of cross-infrastructure experiments on global interoperability with a selected group of projects and communities. Each prototype addresses a specific community driven use case indentifying best-of-breed solutions and the remaining challenges.
+The RDA Europe Prototype Programme is developed in synergy with the RDA Europe Analysis Programme devoted to analyzing data organizations and solutions as they emerge from the various scientific communities and the RDA Europe Workshop Programme covering the investigation data infrastructure convergence and reaching out to new research communities.
-It has a focus group (user community) for Ocean Data Interoperability
+In this context iMarine collaborates within a focus group (user community) for Ocean Data Interoperability.
 ==== ROpenSci ====