Lost in translation: data integration tools meet the Semantic Web (experiences from the Ondex project)

More information is now being published in machine processable form on the web and, as de-facto distributed knowledge bases are materializing, partly encouraged by the vision of the Semantic Web, the focus is shifting from the publication of this information to its consumption. Platforms for data integration, visualization and analysis that are based on a graph representation of information appear first candidates to be consumers of web-based information that is readily expressible as graphs. The question is whether the adoption of these platforms to information available on the Semantic Web requires some adaptation of their data structures and semantics. Ondex is a network-based data integration, analysis and visualization platform which has been developed in a Life Sciences context. A number of features, including semantic annotation via ontologies and an attention to provenance and evidence, make this an ideal candidate to consume Semantic Web information, as well as a prototype for the application of network analysis tools in this context. By analyzing the Ondex data structure and its usage, we have found a set of discrepancies and errors arising from the semantic mismatch between a procedural approach to network analysis and the implications of a web-based representation of information. We report in the paper on the simple methodology that we have adopted to conduct such analysis, and on issues that we have found which may be relevant for a range of similar platformsComment: Presented at DEIT, Data Engineering and Internet Technology, 2011 IEEE: CFP1113L-CD

The stuffed crocodile of "Castel Nuovo" in Naples (Italy): new insights from ancient DNA and radiocarbon

In the present study, a stuffed crocodile displayed for centuries at the "Castel Nuovo" (New Castle) in Naples was radiocarbon dated and examined using ancient DNA analysis. The specimen was classified as Crocodylus niloticus based on its large body size and the mitochondrial DNA haplotype obtained, already described for a living population in Lake Nasser (Egypt). Radiocarbon analysis indicated an age of 585 ± 40 14C year BP, which coincides with the end of the Middle Ages. These results are commented in the light of Medieval religious symbolism and ancient legends which link the crocodile to the history of Naples during the mid-fifteenth century. The data obtained seem to confirm the explanation found in an old guidebook to Naples, according to which the stuffed crocodile was offered by a soldier returning from Egypt as an ex-voto to the image of the "Madonna del Parto" in the chapel of the castle. In addition, the radiocarbon dating shows that the individual analysed could be the oldest taxidermied vertebrate in Europe

Results of the ontology alignment evaluation initiative 2019

The Ontology Alignment Evaluation Initiative (OAEI) aims at comparing ontology matching systems on precisely defined test cases. These test cases can be based on ontologies of different levels of complexity (from simple thesauri to expressive OWL ontologies) and use different evaluation modalities (e.g., blind evaluation, open evaluation, or consensus). The OAEI 2019 campaign offered 11 tracks with 29 test cases, and was attended by 20 participants. This paper is an overall presentation of that campaign

Matching disease and phenotype ontologies in the ontology alignment evaluation initiative

Background: The disease and phenotype track was designed to evaluate the relative performance of ontology matching systems that generate mappings between source ontologies. Disease and phenotype ontologies are important for applications such as data mining, data integration and knowledge management to support translational science in drug discovery and understanding the genetics of disease. Results: Eleven systems (out of 21 OAEI participating systems) were able to cope with at least one of the tasks in the Disease and Phenotype track. AML, FCA-Map, LogMap(Bio) and PhenoMF systems produced the top results for ontology matching in comparison to consensus alignments. The results against manually curated mappings proved to be more difficult most likely because these mapping sets comprised mostly subsumption relationships rather than equivalence. Manual assessment of unique equivalence mappings showed that AML, LogMap(Bio) and PhenoMF systems have the highest precision results. Conclusions: Four systems gave the highest performance for matching disease and phenotype ontologies. These systems coped well with the detection of equivalence matches, but struggled to detect semantic similarity. This deserves more attention in the future development of ontology matching systems. The findings of this evaluation show that such systems could help to automate equivalence matching in the workflow of curators, who maintain ontology mapping services in numerous domains such as disease and phenotype

Ontology mapping for semantically enabled applications

In this review, we provide a summary of recent progress in ontology mapping (OM) at a crucial time when biomedical research is under a deluge of an increasing amount and variety of data. This is particularly important for realising the full potential of semantically enabled or enriched applications and for meaningful insights, such as drug discovery, using machine-learning technologies. We discuss challenges and solutions for better ontology mappings, as well as how to select ontologies before their application. In addition, we describe tools and algorithms for ontology mapping, including evaluation of tool capability and quality of mappings. Finally, we outline the requirements for an ontology mapping service (OMS) and the progress being made towards implementation of such sustainable services

Biparametric (bp) and multiparametric (mp) magnetic resonance imaging (MRI) approach to prostate cancer disease: a narrative review of current debate on dynamic contrast enhancement

Prostate cancer is the most common malignancy in male population. Over the last few years, magnetic resonance imaging (MRI) has proved to be a robust clinical tool for identification and staging of clinically significant prostate cancer. Though suggestions by the European Society of Urogenital Radiology to use complete multiparametric (mp) T2-weighted/diffusion weighted imaging (DWI)/dynamic contrast enhancement (DCE) acquisition for all prostate MRI examinations, the real advantage of functional DCE remains a matter of debate. Recent studies demonstrate that biparametric (bp) and mp approaches have similar accuracy, but controversial evidences remain, and the specific potential benefits of contrast medium administration are still poorly discussed in literature. The bp approach is in fact sufficient in most cases to adequately identify a negative test, or to accurately define the degree of aggressiveness of a lesion, especially if larger or with major characteristics of malignancy. This feature would give the DCE a secondary role, probably limited to a second evaluation of the lesion location, for detecting small cancer or in case of controversy. However, DCE has proved to increase the sensitivity of prostate MRI, though a less specificity. Therefore, an appropriate decision algorithm is needed to standardize the MRI approach. Aim of this review study was to provide a schematic description of bpMRI and mpMRI approaches in the study of prostatic anatomy, focusing on comparative validity and current DCE application. Additional theoretical considerations on prostate MRI are provided

Interventional radiology of the thyroid gland : critical review and state of the art

Thyroid nodules are a common incidental finding during a routinely ultrasound (US) exam unrelated to the thyroid gland in the healthy adult population with a prevalence of 20-76%. As treated before with surgery, in the last years new minimally invasive techniques have been developed as an alternative to surgery. The aim of this review, based on newly revised guidelines, is to provide some information regarding the basic principles, indications, materials, techniques, and results of mini-invasive procedures or treatments for thyroid nodules. We performed a narrative review including both newest and representative papers and guidelines based on the different procedures of ablation techniques developed in the last years for the diagnosis and the treatment of thyroid nodules. All examined papers referred very good results in term of volume nodule reduction, improvement in related symptoms and cosmetic problems, with a very low rate of complications and side effects for all the minimally invasive technique analyzed. Obviously, some differents between technique based on different kind of thyroid nodules and different indication were found. In conclusion, many thyroid nodules nowadays could be treated thanks to the advent of new mini-invasive technique that are less expensive and present a lower risk of major complications and side effects compared to surgery

Advanced diagnostic imaging and intervention in tendon diseases

Degenerative tendon pathology represents one of the most frequent and disabling musculoskeletal disorders. Diagnostic radiology plays a fundamental role in the clinical evaluation of tendon pathologies. Moreover, several minimally invasive treatments can be performed under imaging guidance to treat tendon disorders, maximizing the efficacy and reducing procedural complications. In this review article we describe the most relevant diagnostic features of conventional and advanced US and MRI imaging in tendon disorders, along with the main options for image-guided intervention. (www.actabiomedica.it)

Semiconducting Monolayer Materials as a Tunable Platform for Excitonic Solar Cells

The recent advent of two-dimensional monolayer materials with tunable optoelectronic properties and high carrier mobility offers renewed opportunities for efficient, ultra-thin excitonic solar cells alternative to those based on conjugated polymer and small molecule donors. Using first-principles density functional theory and many-body calculations, we demonstrate that monolayers of hexagonal BN and graphene (CBN) combined with commonly used acceptors such as PCBM fullerene or semiconducting carbon nanotubes can provide excitonic solar cells with tunable absorber gap, donor-acceptor interface band alignment, and power conversion efficiency, as well as novel device architectures. For the case of CBN-PCBM devices, we predict the limit of power conversion efficiencies to be in the 10 - 20% range depending on the CBN monolayer structure. Our results demonstrate the possibility of using monolayer materials in tunable, efficient, polymer-free thin-film solar cells in which unexplored exciton and carrier transport regimes are at play.Comment: 7 pages, 5 figure

Results of the ontology alignment evaluation initiative 2017

Ontology matching consists of finding correspondences between semantically related entities of different ontologies. The Ontology Alignment Evaluation Initiative (OAEI) aims at comparing ontology matching systems on precisely defined test cases. These test cases can be based on ontologies of different levels of complexity (from simple thesauri to expressive OWL ontologies) and use different evaluation modalities (e.g., blind evaluation, open evaluation, or consensus). The OAEI 2017 campaign offered 9 tracks with 23 test cases, and was attended by 21 participants. This paper is an overall presentation of that campaign