AgroPortal : a proposition for ontology-based services in the agronomic domain

Our project is to develop and support a reference ontology repository for the agronomic domain. By reusing the NCBO BioPortal technology, we have already designed and implemented a prototype ontology repository for plants and a few crops. We plan to turn that prototype into a real service to the community. The AgroPortal project aims at reusing the scientific outcomes and experience of the biomedical domain in the context of plant, agronomic and environment sciences. We will offer an ontology portal which features ontology hosting, search, versioning, visualization, comment, but we will also offer services for semantically annotating data with the ontologies, as well as storing and exploiting ontology alignments and data annotations. All of these within a fully semantic web compliant infrastructure. The main objective of this project is to enable straightforward use of agronomic related ontologies, avoiding data managers and researchers the burden to deal with complex knowledge engineering issues to annotate the research data. The AgroPortal project will specifically pay attention to respect the requirements of the agronomic community and the specificities of the crop domain. We will first focus on the outputs of a few existing driving agronomic use cases related to rice and wheat, with the goal of generalizing to other Crop Ontology related use cases. AgroPortal will offer a robust and stable platform that we anticipate will be highly valued by the community

A UIMA wrapper for the NCBO annotator

Summary: The Unstructured Information Management Architecture (UIMA) framework and web services are emerging as useful tools for integrating biomedical text mining tools. This note describes our work, which wraps the National Center for Biomedical Ontology (NCBO) Annotator—an ontology-based annotation service—to make it available as a component in UIMA workflows

39 hints to facilitate the use of semantics for data on agriculture and nutrition

In this paper, we report on the outputs and adoption of the Agrisemantics Working Group of the Research Data Alliance (RDA), consisting of a set of recommendations to facilitate the adoption of semantic technologies and methods for the purpose of data interoperability in the field of agriculture and nutrition. From 2016 to 2019, the group gathered researchers and practitioners at the crossing point between information technology and agricultural science, to study all aspects in the life cycle of semantic resources: Conceptualization, edition, sharing, standardization, services, alignment, long term support. First, the working group realized a landscape study, a study of the uses of semantics in agrifood, then collected use cases for the exploitation of semantics resources – a generic term to encompass vocabularies, terminologies, thesauri, ontologies. The resulting requirements were synthesized into 39 “hints” for users and developers of semantic resources, and providers of semantic resource services. We believe adopting these recommendations will engage agrifood sciences in a necessary transition to leverage data production, sharing and reuse and the adoption of the FAIR data principles. The paper includes examples of adoption of those requirements, and a discussion of their contribution to the field of data science

Reusing the NCBO BioPortal technology for agronomy to build AgroPortal

Many vocabularies and ontologies are produced to represent and annotate agronomic data. By reusing the NCBO BioPortal technology, we have already designed and implemented an advanced prototype ontology repository for the agronomy domain. We plan to turn that prototype into a real service to the community. The AgroPortal project aims at reusing the scientific outcomes and experience of the biomedical domain in the context of plant, agronomic, food, environment (perhaps animal) sciences. We offer an ontology portal which features ontology hosting, search, versioning, visualization, comment, recommendation, enables semantic annotation, as well as storing and exploiting ontology alignments. All of these within a fully semantic web compliant infrastructure. The AgroPortal specifically pays attention to respect the requirements of the agronomic community in terms of ontology formats (e.g., SKOS, trait dictionaries) or supported features. In this paper, we present our prototype as well as preliminary outputs of four driving agronomic use cases. With the experience acquired in the biomedical domain and building atop of an already existing technology, we think that AgroPortal offers a robust and stable reference repository that will become highly valuable for the agronomic domain

Negotiating the Web Science Curriculum through Shared Educational Artefacts

EXTENDED ABSTRACT The far-reaching impact of Web on society is widely recognised and acknowledged. The interdisciplinary study of this impact has crystallised in the field of study known as Web Science. However, defining an agreed, shared understanding of what constitutes Web Science requires complex negotiation and translations of understandings across component disciplines, national cultures and educational traditions. Some individual institutions have already established particular curricula, and discussions in the Web Science Curriculum Workshop series have marked the territory to some extent. This paper reports on a process being adopted across a consortium of partners to systematically create a shared understanding of what constitutes Web Science. It records and critiques the processes instantiated to agree a common curriculum, and presents a framework for future discussion and development. The need to study the Web in its complexity, development and impact led to the creation of Web Science. Web Science is inherently interdisciplinary. Its goal is to: a) understand the Web growth mechanisms; b) create approaches that allow new powerful and more beneficial mechanisms to occur. Teaching Web Science is a unique experience since the emerging discipline is a combination of two essential features. On one hand, the analysis of microscopic laws extrapolated to the macroscopic realm generates observed behaviour. On the other hand languages and algorithms on the Web are built in order to produce novel desired computer behaviour that should be put in context. Finding a suitable curriculum that is different from the study of language, algorithms, interaction patterns and business processes is thus an important and challenging task for the simple reason that we believe that the future of sociotechnical systems will be in their innovative power (inventing new ways to solve problems), rather than their capacity to optimize current practices. The Web Science Curriculum Development (WSCD) Project focuses European expertise in this interdisciplinary endeavour with the ultimate aim of designing a joint masters program for Web Science between the partner universities. The process of curriculum definition is being addressed using a negotiation process which mirrors the web science and engineering approach described by Berners-Lee (figure 1 below). The process starts on the engineering side (right). From the technical design point of view the consortium is creating an open repository of shared educational artefacts using EdShare [1] (based on EPrints) to collect or reference the whole range of educational resources being used in our various programmes. Socially, these resources will be annotated against a curriculum categorization [2] which in itself is subject to negotiation and change, currently via a wiki. This last process is represented by complexity and collaboration at the bottom of the diagram. The resources necessarily extend beyond artefacts used in the lecture and seminar room encompassing artefacts associated with the administrative and organisational processes which are necessary to assure the comparability of the educational resources and underwrite the quality standards of the associated awards. Figure 1: Web Science and Engineering Approach (e.g. See http://www.w3.org/2007/Talks/0314-soton-tbl/#%2811%29) From the social point of view the contributions will be discussed and peer reviewed by members of the consortium. Our intention is that by sharing the individual components of the teaching and educational process and quality assuring them by peer review we will provide concrete examples of our understanding of the discipline. However, as Berners-Lee observes, it is in the move from the micro to the macro that the magic (complexity) is involved. The challenge for our consortium, once our community repository is adequately populated, is to involve the wider community in the contribution, discussion and annotation that will lead to the evolution of a negotiated and agreed but evolving curriculum for Web Science. Others have worked on using community approaches to developing curriculum. For example, in the Computer Science community there is a repository of existing syllabi [3] that enables designers of new courses to understand how others have approached the problem, and the Information Science community is using a wiki [4] to enable the whole community to contribute to the dynamic development of the curriculum. What makes this project unique is that rather than taking a top down structured approach to curriculum definition it takes a bottom up approach, using the actual teaching materials as the basis on which to iteratively negotiate and refine the definition of the curriculum

Negotiating the Web Science Curriculum through Shared Educational Artefacts

EXTENDED ABSTRACT The far-reaching impact of Web on society is widely recognised and acknowledged. The interdisciplinary study of this impact has crystallised in the field of study known as Web Science. However, defining an agreed, shared understanding of what constitutes Web Science requires complex negotiation and translations of understandings across component disciplines, national cultures and educational traditions. Some individual institutions have already established particular curricula, and discussions in the Web Science Curriculum Workshop series have marked the territory to some extent. This paper reports on a process being adopted across a consortium of partners to systematically create a shared understanding of what constitutes Web Science. It records and critiques the processes instantiated to agree a common curriculum, and presents a framework for future discussion and development. The need to study the Web in its complexity, development and impact led to the creation of Web Science. Web Science is inherently interdisciplinary. Its goal is to: a) understand the Web growth mechanisms; b) create approaches that allow new powerful and more beneficial mechanisms to occur. Teaching Web Science is a unique experience since the emerging discipline is a combination of two essential features. On one hand, the analysis of microscopic laws extrapolated to the macroscopic realm generates observed behaviour. On the other hand languages and algorithms on the Web are built in order to produce novel desired computer behaviour that should be put in context. Finding a suitable curriculum that is different from the study of language, algorithms, interaction patterns and business processes is thus an important and challenging task for the simple reason that we believe that the future of sociotechnical systems will be in their innovative power (inventing new ways to solve problems), rather than their capacity to optimize current practices. The Web Science Curriculum Development (WSCD) Project focuses European expertise in this interdisciplinary endeavour with the ultimate aim of designing a joint masters program for Web Science between the partner universities. The process of curriculum definition is being addressed using a negotiation process which mirrors the web science and engineering approach described by Berners-Lee (figure 1 below). The process starts on the engineering side (right). From the technical design point of view the consortium is creating an open repository of shared educational artefacts using EdShare [1] (based on EPrints) to collect or reference the whole range of educational resources being used in our various programmes. Socially, these resources will be annotated against a curriculum categorization [2] which in itself is subject to negotiation and change, currently via a wiki. This last process is represented by complexity and collaboration at the bottom of the diagram. The resources necessarily extend beyond artefacts used in the lecture and seminar room encompassing artefacts associated with the administrative and organisational processes which are necessary to assure the comparability of the educational resources and underwrite the quality standards of the associated awards. Figure 1: Web Science and Engineering Approach (e.g. See http://www.w3.org/2007/Talks/0314-soton-tbl/#%2811%29) From the social point of view the contributions will be discussed and peer reviewed by members of the consortium. Our intention is that by sharing the individual components of the teaching and educational process and quality assuring them by peer review we will provide concrete examples of our understanding of the discipline. However, as Berners-Lee observes, it is in the move from the micro to the macro that the magic (complexity) is involved. The challenge for our consortium, once our community repository is adequately populated, is to involve the wider community in the contribution, discussion and annotation that will lead to the evolution of a negotiated and agreed but evolving curriculum for Web Science. Others have worked on using community approaches to developing curriculum. For example, in the Computer Science community there is a repository of existing syllabi [3] that enables designers of new courses to understand how others have approached the problem, and the Information Science community is using a wiki [4] to enable the whole community to contribute to the dynamic development of the curriculum. What makes this project unique is that rather than taking a top down structured approach to curriculum definition it takes a bottom up approach, using the actual teaching materials as the basis on which to iteratively negotiate and refine the definition of the curriculum

Brainwaves and Sound Synchronization in a Dance Performance

In a previous work (Lucchiari and Folgieri, 2015) we considered communication among young people. New digital-natives do not communicate in a traditional way, but they choose different means and ways. It is not a surprising conclusion that a large part of digital-natives considers obsolete both Web sites\u2019 structure and Internet navigation modes, learning instruments and paradigms and communication tools, choosing, instead, fast and immediate media like mobile phone communication, social networking and so on (Croitoru et al. 2011). Notwithstanding we could think they lack of communication skills, actually, they communicate with each other much more than ever done, using not only the verbal language, but also images, videos, sounds, and especially emotions. We named this phenomenon telepatheia or, better, sympateia, meaning that they seem to keep in contact independently by the mean. Of course, on our intention, this does not mean that we are observing a new organic evolution, but surely a kind of evolution can be traced: an era in which human and machines are evolving, influencing one each other, determining a specific kind of communication strongly influenced and related to technology. In this paper, starting from our previous studies and from our concept of \u201csympateia\u201d, we performed a new experiment related to brain rhythms synchronization. Through our experiment, described in the following chapter, We want to explore the communication mechanisms of telepathy (in the ancient Greek assumption of \u201ctelepatia\u201d\uf020that is [tele]=\u201ddistance\u201d and [pateia]=\u201demotion, feeling\u201d). This does not mean that we are trying to make humans telepathic, but we aim to deeply understand communication mechanisms among humans through human-computer interaction BCI devices. This means to change the point of view of brain and Information Technology researches, stressing the point of view of self-understanding of the own brain

BioPortal: ontologies and integrated data resources at the click of a mouse

Biomedical ontologies provide essential domain knowledge to drive data integration, information retrieval, data annotation, natural-language processing and decision support. BioPortal (http://bioportal.bioontology.org) is an open repository of biomedical ontologies that provides access via Web services and Web browsers to ontologies developed in OWL, RDF, OBO format and Protégé frames. BioPortal functionality includes the ability to browse, search and visualize ontologies. The Web interface also facilitates community-based participation in the evaluation and evolution of ontology content by providing features to add notes to ontology terms, mappings between terms and ontology reviews based on criteria such as usability, domain coverage, quality of content, and documentation and support. BioPortal also enables integrated search of biomedical data resources such as the Gene Expression Omnibus (GEO), ClinicalTrials.gov, and ArrayExpress, through the annotation and indexing of these resources with ontologies in BioPortal. Thus, BioPortal not only provides investigators, clinicians, and developers ‘one-stop shopping’ to programmatically access biomedical ontologies, but also provides support to integrate data from a variety of biomedical resources

AgroPortal: a vocabulary and ontology repository for agronomy

Many vocabularies and ontologies are produced to represent and annotate agronomic data. However, those ontologies are spread out, in different formats, of different size, with different structures and from overlapping domains. Therefore, there is need for a common platform to receive and host them, align them, and enabling their use in agro-informatics applications. By reusing the National Center for Biomedical Ontologies (NCBO) BioPortal technology, we have designed AgroPortal, an ontology repository for the agronomy domain. The AgroPortal project re-uses the biomedical domain’s semantic tools and insights to serve agronomy, but also food, plant, and biodiversity sciences. We offer a portal that features ontology hosting, search, versioning, visualization, comment, and recommendation; enables semantic annotation; stores and exploits ontology alignments; and enables interoperation with the semantic web. The AgroPortal specifically satisfies requirements of the agronomy community in terms of ontology formats (e.g., SKOS vocabularies and trait dictionaries) and supported features (offering detailed metadata and advanced annotation capabilities). In this paper, we present our platform’s content and features, including the additions to the original technology, as well as preliminary outputs of five driving agronomic use cases that participated in the design and orientation of the project to anchor it in the community. By building on the experience and existing technology acquired from the biomedical domain, we can present in AgroPortal a robust and feature-rich repository of great value for the agronomic domain. Keyword

BIRI: a new approach for automatically discovering and indexing available public bioinformatics resources from the literature

<p>Abstract</p> <p>Background</p> <p>The rapid evolution of Internet technologies and the collaborative approaches that dominate the field have stimulated the development of numerous bioinformatics resources. To address this new framework, several initiatives have tried to organize these services and resources. In this paper, we present the BioInformatics Resource Inventory (BIRI), a new approach for automatically discovering and indexing available public bioinformatics resources using information extracted from the scientific literature. The index generated can be automatically updated by adding additional manuscripts describing new resources. We have developed web services and applications to test and validate our approach. It has not been designed to replace current indexes but to extend their capabilities with richer functionalities.</p> <p>Results</p> <p>We developed a web service to provide a set of high-level query primitives to access the index. The web service can be used by third-party web services or web-based applications. To test the web service, we created a pilot web application to access a preliminary knowledge base of resources. We tested our tool using an initial set of 400 abstracts. Almost 90% of the resources described in the abstracts were correctly classified. More than 500 descriptions of functionalities were extracted.</p> <p>Conclusion</p> <p>These experiments suggest the feasibility of our approach for automatically discovering and indexing current and future bioinformatics resources. Given the domain-independent characteristics of this tool, it is currently being applied by the authors in other areas, such as medical nanoinformatics. BIRI is available at <url>http://edelman.dia.fi.upm.es/biri/</url>.</p