NET-GE: a novel NETwork-based Gene Enrichment for detecting biological processes associated to Mendelian diseases

Enrichment analysis is a widely applied procedure for shedding light on the molecular mechanisms and functions at the basis of phenotypes, for enlarging the dataset of possibly related genes/proteins and for helping interpretation and prioritization of newly determined variations. Several standard and Network-based enrichment methods are available. Both approaches rely on the annotations that characterize the genes/proteins included in the input set; network based ones also include in different ways physical and functional relationships among different genes or proteins that can be extracted from the available biological networks of interactions

BIM semantic-enrichment for built heritage representation

In the built heritage context, BIM has shown difficulties in representing and managing the large and complex knowledge related to non-geometrical aspects of the heritage. Within this scope, this paper focuses on a domain-specific semantic-enrichment of BIM methodology, aimed at fulfilling semantic representation requirements of built heritage through Semantic Web technologies. To develop this semantic-enriched BIM approach, this research relies on the integration of a BIM environment with a knowledge base created through information ontologies. The result is knowledge base system - and a prototypal platform - that enhances semantic representation capabilities of BIM application to architectural heritage processes. It solves the issue of knowledge formalization in cultural heritage informative models, favouring a deeper comprehension and interpretation of all the building aspects. Its open structure allows future research to customize, scale and adapt the knowledge base different typologies of artefacts and heritage activities

Knowledge Organization Systems (KOS) in the Semantic Web: A Multi-Dimensional Review

Since the Simple Knowledge Organization System (SKOS) specification and its SKOS eXtension for Labels (SKOS-XL) became formal W3C recommendations in 2009 a significant number of conventional knowledge organization systems (KOS) (including thesauri, classification schemes, name authorities, and lists of codes and terms, produced before the arrival of the ontology-wave) have made their journeys to join the Semantic Web mainstream. This paper uses "LOD KOS" as an umbrella term to refer to all of the value vocabularies and lightweight ontologies within the Semantic Web framework. The paper provides an overview of what the LOD KOS movement has brought to various communities and users. These are not limited to the colonies of the value vocabulary constructors and providers, nor the catalogers and indexers who have a long history of applying the vocabularies to their products. The LOD dataset producers and LOD service providers, the information architects and interface designers, and researchers in sciences and humanities, are also direct beneficiaries of LOD KOS. The paper examines a set of the collected cases (experimental or in real applications) and aims to find the usages of LOD KOS in order to share the practices and ideas among communities and users. Through the viewpoints of a number of different user groups, the functions of LOD KOS are examined from multiple dimensions. This paper focuses on the LOD dataset producers, vocabulary producers, and researchers (as end-users of KOS).Comment: 31 pages, 12 figures, accepted paper in International Journal on Digital Librarie

Metadata enrichment for digital heritage: users as co-creators

This paper espouses the concept of metadata enrichment through an expert and user-focused approach to metadata creation and management. To this end, it is argued the Web 2.0 paradigm enables users to be proactive metadata creators. As Shirky (2008, p.47) argues Web 2.0’s social tools enable “action by loosely structured groups, operating without managerial direction and outside the profit motive”. Lagoze (2010, p. 37) advises, “the participatory nature of Web 2.0 should not be dismissed as just a popular phenomenon [or fad]”. Carletti (2016) proposes a participatory digital cultural heritage approach where Web 2.0 approaches such as crowdsourcing can be sued to enrich digital cultural objects. It is argued that “heritage crowdsourcing, community-centred projects or other forms of public participation”. On the other hand, the new collaborative approaches of Web 2.0 neither negate nor replace contemporary standards-based metadata approaches. Hence, this paper proposes a mixed metadata approach where user created metadata augments expert-created metadata and vice versa. The metadata creation process no longer remains to be the sole prerogative of the metadata expert. The Web 2.0 collaborative environment would now allow users to participate in both adding and re-using metadata. The case of expert-created (standards-based, top-down) and user-generated metadata (socially-constructed, bottom-up) approach to metadata are complementary rather than mutually-exclusive. The two approaches are often mistakenly considered as dichotomies, albeit incorrectly (Gruber, 2007; Wright, 2007) . This paper espouses the importance of enriching digital information objects with descriptions pertaining the about-ness of information objects. Such richness and diversity of description, it is argued, could chiefly be achieved by involving users in the metadata creation process. This paper presents the importance of the paradigm of metadata enriching and metadata filtering for the cultural heritage domain. Metadata enriching states that a priori metadata that is instantiated and granularly structured by metadata experts is continually enriched through socially-constructed (post-hoc) metadata, whereby users are pro-actively engaged in co-creating metadata. The principle also states that metadata that is enriched is also contextually and semantically linked and openly accessible. In addition, metadata filtering states that metadata resulting from implementing the principle of enriching should be displayed for users in line with their needs and convenience. In both enriching and filtering, users should be considered as prosumers, resulting in what is called collective metadata intelligence

The Semantic Grid: A future e-Science infrastructure

e-Science offers a promising vision of how computer and communication technology can support and enhance the scientific process. It does this by enabling scientists to generate, analyse, share and discuss their insights, experiments and results in an effective manner. The underlying computer infrastructure that provides these facilities is commonly referred to as the Grid. At this time, there are a number of grid applications being developed and there is a whole raft of computer technologies that provide fragments of the necessary functionality. However there is currently a major gap between these endeavours and the vision of e-Science in which there is a high degree of easy-to-use and seamless automation and in which there are flexible collaborations and computations on a global scale. To bridge this practice–aspiration divide, this paper presents a research agenda whose aim is to move from the current state of the art in e-Science infrastructure, to the future infrastructure that is needed to support the full richness of the e-Science vision. Here the future e-Science research infrastructure is termed the Semantic Grid (Semantic Grid to Grid is meant to connote a similar relationship to the one that exists between the Semantic Web and the Web). In particular, we present a conceptual architecture for the Semantic Grid. This architecture adopts a service-oriented perspective in which distinct stakeholders in the scientific process, represented as software agents, provide services to one another, under various service level agreements, in various forms of marketplace. We then focus predominantly on the issues concerned with the way that knowledge is acquired and used in such environments since we believe this is the key differentiator between current grid endeavours and those envisioned for the Semantic Grid