2013.11 Activity Report

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Contents

This Activity Report captures the activities performed in November 2013

This report is organized in two parts:

Progress and Achievements at WP level

WP1: Administrative and Financial Management

WP Leader: ERCIM - Participants: CNR

  • Exchanges made with NKUA and the EC in order to find a solution for the missing CFS
  • A thorough financial analysis was performed to identify the resources required for the project's demands from here to project end (e.g., NeafC reallocation, creation of Task 3.4 for Sustainability, iMarine Final Event)


  • The EC will continue processing the Period 2 cost claim for the consortium, rejecting the NKUA costs for the period on the basis of "non-submission of the CFS". The NKUA will provide a final cost statement with an adjustment including the Period 2 costs at project end.
  • A new Description of Work (including new activities) must be produced before year end.


  • The Project Officer agreed to a 4 month project extension, on condition that new activities are included in the DoW.
  • A sound financial plan has been identified that could carry iMarine successfully to project end (including the 4 month extension), subject to the approval of all consortium members.

WP2: Project Management

WP Leader: CNR - Participants: NKUA, FAO

  • Preparation of an integrated version of D2.3 Management Report
  • Preparation of a first draft of the new version of the DoW and collection of feedback by project partners;
  • Organization, chairing and minutes preparation of the PEB meeting (12.11);
  • Supervision of scientific and technical activities (including the participation of the TD in teleconferences dedicated to coordinate specific community-driven activities);
  • Establishment of new exploratory liaisons (e.g. Marine Observatories, Cefas (UK), SEON (South Africa));
  • Participation in the EMSO Workshop as iMarine representative.


No major issues to report


  • Draft version of D2.3
  • First draft of the new version of the DoW a
  • PEB monthly meeting
  • New potential liaisons

WP3: Governance and Policy Development

WP Leader: FAO - Participants: ERCIM, CNR, NKUA, FORTH, TERRADUE, FIN, UNESCO, CRIA, IRD

In Tasks 3.1; Outreach

  • Activities with CoP continued; WCMC, Indeso (FAO Terradue)
  • External Board report dispatch, and preparation for iMarine march event
  • Board message on product achievements
  • Training in France of AgroCampus Rennes; some 40 persons attended. (Y.Laurent)

In taks 3.2; Governance

  • iMarine terms of use and data access and sharing policy discused with FAO Legal
  • Update of several use-case templates and content to capture the community exploitation of infrastructure resources.
  • Proposal for StatBase migration (Ticket 2425)

In task 3.3; Harmonization and metadata standards

FAO activities included:

  • Interaction with NEAFC on DataExchange; the components to connect to the NEAFC database, and make the semestral reports available to ICES for further analysis;
  • Liaise with the VME-DB team to facilitate the exchange of data between the iMarine and VME-DB (Oracle) database;
  • Discuss with ESTAT on SDMX;
  • Continue development of Cotrix.

FORTH

  • continued the design of a new release (Version 4.0.0) of the MarineTLO:
  • Ontological analysis of the iMarine sources (FISHBASE, ECOSCOPE, WoRMS, FLOD and DBpedia) w.r.t. the new requirements
  • Extended the of Mapping and Transformation rules between MarineTLO and iMarine sources


none to report


  • Extended Board report dispatch
  • Extended Board New members
  • Terms of use feed back received
  • Milestones
    • MS 17 M25 Meetings of the iMarine Board
    • MS 12 M24 Guidelines and Best Practices

A related paper that acknowledges the support of iMarine that has been presented during this period is the following:

  • Y. Tzitzikas, C. Allocca, C. Bekiari, Y. Marketakis, P. Fafalios, M. Doerr, N. Minadakis, T. Patkos, L. Candela. Integrating Heterogeneous and Distributed Information about Marine Species through a Top Level Ontology. In Proceedings of the 7th Metadata and Semantics Research Conference (MTSR'2013), Thessaloniki, Greece, November 2013.

WP4: Communication, Dissemination and Training

WP Leader: TRUST-IT - Participants: CNR, NKUA, FAO

The WP leader should report here a summary of the activities performed in the reporting period

  • Website fine-tuning: Liasion Page, e-Infrastructure page
  • Events:
  • ICT2013 e-Infrastructure for Open Research Data in Agriculture, Fisheries & Biodiversity (iMarine & agINFRA) - 90' NETWORKING BOOTH ON THURS 7TH NOV @ 14:00, 6-8 November, 2013 - Vilnius, Lithuania
  • EMSO Ocean Observatories: Challenges and Progress EMSO - European Multidisciplinary Seafloor and water column Observatory

Wednesday, 13 November 2013 at 10:00 - Friday, 15 November 2013 at 13:00 Rome, Italy. iMarine attended the event.

  • 7th Metadata and Semantic Research Conference MTSR-2013; Special track on Metadata & Semantics for Open Repositories, Research Information Systems and Data Infrastructures, 19-22 November, 2013 - Thessaloniki, Greece Presenting the paper: Integrating Heterogeneous and Distributed Information about Marine Species through a Top Level Ontology. The presentation of MarineTLO (and iMarine in general) went very well, both in MUMIA mgmt meeting (where Yannis has stressed the value of the MarineTLO-based repository in the seach process), and in MTSR (where he stressed the value of the ontology per se). Feedback have been asked.
  • Organisation of the March iMarine event: agenda preparation and liasion with Martin Pastoors, FDI - Fishery Dependent Information organiser
  • Deliverable D2.3: WP4 contribution


The major issues faced in the reporting period and the identified corrective actions should be reported here


The WP leader should report here a bullet list highlighting the main achievements of the reporting period

WP5: iMarine Data e-Infrastructure Deployment and Operation

WP Leader: CERN - Participants: CNR, NKUA, FAO, FIN

In the context of T5.1:

CERN was involved in the deployment and validation in QA environment of the artifacts coming from the 2.17 release (2338). The release was successfully validated and a plan for the production upgrade was prepared (2337). ( the actual upgrade was performed on Dec the 2nd)

A plan for the upgrade of the EUBrazilOpenBio VOVirtual Organization; was prepared and together with CNR the upgrade was performed with the indexing of some OAI-PMH collections.

In addition 4 new GHN with the Statistical Manager service were configured in the production infrastructure.

Finally a wiki page describing some details on some service installation has started to be edited at: https://gcube.wiki.gcube-system.org/gcube/index.php/ServiceManager_Guide

In the context of T5.2:

NKUA performed maintenance of the provided nodes hosting GHNs, UMD and the gcube wiki.

In the context of T5.3:

No activity to report


none


none

WP6: Virtual Research Environments Deployment and Operation

WP Leader: CNR - Participants: ERCIM, NKUA, FAO, FIN, UNESCO, CRIA, IRD

For Virtual Research Environments Operation:

  • the previously deployed Virtual Research Environments have been maintained in operation;

For resources and tools provision:

  • Species Name Reconciliation (Bionym) development continued, e.g. YASMEEN matching process improved, memory consumption reduced;
  • VME-DB-related activity continued, e.g. Reports Store Gateway implemented;
  • The RFigisGeo package have been enriched with intersection facilities;
  • OAI-PMH support (OAI-TM plugin + Harvester) has been reinforced, e.g. UTF-8 encoding for resumption token;

For common interfaces and tools:

  • A lot of Tabular Data Widgets have been developed, including CVS import/export, SDMX import/export;
  • Report Management portlet has been reinforced to better support VME-DB, e.g. support for Referenced objects, add a dedicated import facility from Reports Store Gateway;
  • SPD has been reinforced with proper data encoding (UTF-8);
  • Workspace data visualisation policy has been revised, e.g. display last-update time;
  • GeoExplorer initialisation policy has been revised to reduce load time;
  • Android Search Application has been revised;
  • Information Space Editor has been revised to support OpenSearch collections (bug fixing);


None


  • Existing VREs have been maintained;
  • A number of portlets have been reinforced;

WP7: Enabling-technology Integration and Distribution

WP Leader: E-IIS - Participants: CNR, NKUA

  • E-IIS cooordinated the integration of gCube 2.17.0 that was completed and closed on 29 Nov.
  • A total of 35 integration builds have been executed and 30 integration issues have been identified and managed through Trac system.
  • Enhancement of checks to highlights issues in the release process.
  • NKUA updated the distribution site with artefacts and news for gCube 2.17.0

None


  • gCube 2.17.0

WP8: iMarine Data e-Infrastructure Enabling Technology Development

WP Leader: CNR - Participants: NKUA, E-IIS, FAO

Completed in October 2013.

WP9: Data Management Facilities Development

WP Leader: CNR - Participants: NKUA, CERN, TERRADUE, FAO

In T9.1:

CNR enhanced "lock" and "unlock" operations on the Storage Manager, for locking and unlocking a remote objects. The scope of this functionality is to allow multiple users to work simultaneously on the same remote object.

In T9.2:

CERN worked on the Storage Management portlet, where they added upload, copy, directory creation and deletion facilities which interact also with the Workspace. NKUA reviewed and validated the gRS2 Developer's Guide wiki pages. Terradue tested a 52 North SOS server installation on their infra, and studied how to apply the related data model to the use cases of i-Marine.

In T9.3: CNR created a GWT module allowing the GWT javascript translation of tabular data model classes. On the service side, they added capabilities for a process to support fallback. Furthermore, they developed transformation operations to declare a table or a column to be of a certain codelist type. In order to support this, they built a data casting module. Operations on tables were added, in particular duplicate rows deletion and the creation of a codelist endowed with the time dimension, to be used by Mondrian. Finally, operations were added which allow to link values in a column to tuples of a codelist table. Wiki pages were written to document these topics. About the legacy time series application, issues were solved on the portlets when integrating gCube 2.17.


No deviations to report.


  • The Storage Management portlet has been enhanced with file-system like functionalities
  • The SOS sever was installed on Terradue side and investigated

WP10: Data Consumption Facilities Development

WP Leader: NKUA - Participants: CNR, FORTH, TERRADUE, FAO

During November, in T10.1, index rebuilding procedure for periodic updates with zero downtime has been investigated and designed. Also, a Resource Registry bug was fixed that caused duplicate field resources. The developer’s guides “OpenSearch Framework”, “Index Management Framework” and “Search Operators” have been reviewed and validated. At last, the analysis of data sources supporting the Environmental enrichment continued.

In T10.2, the developer's guide of Data Transformation has been validated.

In T10.3, the interface of Statistical Manager is being transformed to be used as a Widget. Ecological Engine library can now invoke Runtime resources. The files import facility has been designed while implementation has started. Moreover, every Algorithm has been transformed into a Generic Resources that can be associated to different VREs. Also, BiOnym algorithms have been revisited. A preliminary set of experiments have been made in the field of Common Species classification. Finally, a facility to geo-spatialize tables and produce GIS maps has been developed, in compliance to the INSPIRE directives.

In T10.4, the 3rd version of MarineTLO warehouse has been constructed. The contents of the new warehouse are exploited by the latest version of xsearch-service.


none


  • Algorithms are now Generic Resources
  • Construction of the MarineTLO warehouse V3

WP11: Data e-Infrastructures Integration and Interoperability Facilities Development

WP Leader: NKUA - Participants: CNR, CERN, E-IIS, FORTH, TERRADUE, FAO

During November, in T11.2 effort spent was on implementing of a set of integration API to provide the possibility to store SAML Assertion ID in ASL session, in the context of the integration between Federated portal and client libraries. Moreover, the documentation produced by ENG has been revised. Also, TLS integration on the portal has been tested and the implementation of WFS Utils for the OWC4J has been continued.

In T11.3 effort was spent on designing of the RESTFul API of XSearch. Also, a wiki page that describes the the objectives, the requirements and the designed APIs has been created. Furthermore, gCube-search-library and ASL OAI-ORE have been updated in order to provide compact result presentation of the search results and a generic OAI-PMH interface respectively.


None


None

Progress and Achievements by WP and Beneficiary

WP1: Administrative and Financial Management Monthly Activity By Task and Beneficiary

WP2: Project Management Monthly Activity By Task and Beneficiary

WP3: Governance and Policy Development Monthly Activity By Task and Beneficiary

WP4: Communication, Dissemination and Training Monthly Activity By Task and Beneficiary

WP5: iMarine Data e-Infrastructure Deployment and Operation Monthly Activity By Task and Beneficiary

WP6: Virtual Research Environments Deployment and Operation Monthly Activity By Task and Beneficiary

WP7: Enabling-technology Integration and Distribution Monthly Activity By Task and Beneficiary

WP8: iMarine Data e-Infrastructure Enabling Technology Development Monthly Activity By Task and Beneficiary - Completed in October 2013

WP9: Data Management Facilities Development Monthly Activity By Task and Beneficiary

WP10: Data Consumption Facilities Development Monthly Activity By Task and Beneficiary

WP11: Data e-Infrastructures Integration and Interoperability Facilities Development Monthly Activity By Task and Beneficiary

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