AgINFRA Software Components

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agINFRA Powered Software Components

During the agINFRA project, innovative versions of either existing already used software components or novel software components to support agricultural data management, processing, visualization and navigation. have been specified , adapted, improved and deployed.
More specific the following tools have been deployed over the agINFRA e-infrastructure

Data Management Components

The Agricultural Learning Repository tool (AgLR tool) is a repository tool that has been developed based on the open-source Omeka ( Web Content Management, Collections Management, and Archival Digital Collections System.

This component provides agricultural institutions with a web-based content management system pre-customized for some typical usage scenarios of small institutions: have a web presence, manage news, events, a document repository and directories of experts and organizations, everything indexed using agricultural terms coming from an authoritative thesaurus (AGROVOC).

AgriOcean DSpace allows to manage a document repository with standard-compliant cataloguing, retrieving and preservating functionalities out of the box, therefore the primarily users are librarians that manage institutional or thematic repositories.

A framework to build and manage data repositories on local, grid and cloud storage resources distributed geographically

The VocBench 2.0 is ready to be used for the publication of new Knowledge Organization Systems (KOSs) in agINFRA. It has been already deployed on different servers and can be deployed on additional servers depending on the requirements of the agINFRA partners. Moreover, code and installation instructions are provided to create other instances. VocBench will be used to import/create KOSs related to the agINFRA project. No further development is foreseen.

Provides a java application that will allow for the importing, enriching and exporting of bibliographic data in VIVO ( format, based on a mapping to the VIVO ontology. More specifically, it will set up an agINFRA VIVO RDF store that application developers will be able to enrich, ingest and expose to the users of the VIVO network.

Data Processing Components

This is a document processing component that will post-process documents (literature/documents that have already been scanned) in order to refine/improve OCR accuracy, as well as extract additional metadata that have not been provided by the original contributor/annotator (such as the structure of the document, or additional annotation such as identifying the research method, variables and results described in a scientific study). It will allow application developers to add a scientific literature post-analysis/processing component/service that will extract additional semantic information/annotations for targeted thematic communities.

This component will allow the data mining and extraction of bibliographic citations from specific systems (namely, Mendeley, BHL and Bibliography of Life) filtering and annotating them according to various agricultural taxonomies/classifications within the AGRIS linked data framework and will allow application developers to add a scientific literature visualization component/interface.

AgroTagger is a highly experimental service that takes a set of URLs, retrieves the resources found at those URLs and extracts keywords using the MAUI framework and the AGROVOC concept scheme. There is also a Nutch-based crawler that given a set of URLs can crawl for related resources that can then be consumed by AgroTagger.

The recommendation component is a tool that runs in the Grid and allows users to process user annotations such as ratings, tags and reviews in order to execute content-based and collaborative filtering algorithms and create various lists of recommended/suggested content resources/items, individualized per user.

Data Visualisation & Navigation Components

The Linked Media Framework (LMF), formerly KiWi, is a Semantic Web software component that can be used by developers for applications in areas such as knowledge organization, content annotation with various KOSs, search & retrieval base on the concepts, visualization, and use of the results for further purposes. In the context of agINFRA, this can be information management (e.g. analysis of the content that is managed) or further research in fields for which available publications and data/datasets can be discovered and accessed with the concepts.

This component allows to visualize the relationships of entities in a network graph.

This component integrates the local database previously described and the Social Network Visualization component.

The improved version of the Semantic navigation component uses several ontologies to retrieve documents. To manage several KOS, an ontology aggregator is deployed. In this layer, several computational expensive tasks are performed, such as KOS ingestion and harvesting, and cross-terminology link calculation.

The Social Navigation Component provides the user with a navigation interface for
browsing through the content of interconnected repositories using a visualization of a thematic

This component provides customizable mobile clients both for iOS and Android devices able to access digital collections (aka, repositories) built with gLibrary services, consuming the gLibrary REST APIs

The Scratchpads Component is a virtual research environment that enables communities of researchers to manage, share and publish natural history data online ( Scientific data/content are automatically classified and grouped around a taxonomy chosen or supplied by the user.

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