A Semantic Web methodological framework to evaluate the support of integrity in thesaurus tools

12 p.With the Semantic Web, thesauri recover a relevant role supporting semantic searches and other added-value services. Thesaurus standards define what constructs a thesaurus can have and the integrity rules it must comply with. Thesaurus editors can be helped in their work if thesaurus tools offer them support for integrity, warning when integrity rules are violated and/or helping them to correct these mistakes. The most recent thesaurus standard is ISO 25964, which supersedes ISO 2788, evolving towards concept-based thesauri, better aligned with the Semantic Web approach than the term-based thesauri of ISO 2788. However, the W3C recommendation for KOS (Knowledge Organization System) representation in the semantic web context is SKOS, which is in fact prior to ISO 25964. This paper focuses on thesaurus integrity and the evolution from ISO 2788 to ISO 25964. Its effect on integrity issues is analyzed. A methodological proposal for evaluating integrity support in thesaurus tools, arising from the results of this work, is presented. Its target audience is professionals in charge of thesaurus edition. Besides being adapted to the most recent thesaurus standard, ISO 25964, it also includes the comparison of ISO standards with SKOS. The paper is completed with the presentation of the results of applying it to three thesaurus tools

Towards VocBench 3: Pushing collaborative development of thesauri and ontologies further beyond

More than three years have passed since the release of the second edition of VocBench, an open source collaborative web platform for the development of thesauri complying with Semantic Web standards. In these years, a vibrant user community has gathered around the system, consisting of public organizations, companies and independent users looking for open source solutions for maintaining their thesauri, code lists and authority resources. The focus on collaboration, the differentiation of user roles and the workflow management for content validation and publication have been the strengths of the platform, especially for those organizations requiring a centralized and controlled publication environment. Now the time has come to widen the scope of the platform: funded by the ISA2programme of the European Commission, VocBench 3 will offer a general-purpose collaborative environment for development of any kind of RDF dataset, improving the editing capabilities of its predecessor, while still maintaining the peculiar aspects that determined its success. In this paper, we review the requirements and the new objectives set for version 3, and then introduce the new characteristics that were implemented for this next iteration of the platform

In cellulo serial crystallography of alcohol oxidase crystals inside yeast cells

The possibility of using femtosecond pulses from an X-ray free-electron laser to collect diffraction data from protein crystals formed in their native cellular organelle has been explored. X-ray diffraction of submicrometre-sized alcohol oxidase crystals formed in peroxisomes within cells of genetically modified variants of the methylotrophic yeast Hansenula polymorpha is reported and characterized. The observations are supported by synchrotron radiation-based powder diffraction data and electron microscopy. Based on these findings, the concept of in cellulo serial crystallography on protein targets imported into yeast peroxisomes without the need for protein purification as a requirement for subsequent crystallization is outlined

Semantic and Knowledge Engineering Using ENVRI RM

The ENVRI Reference Model provides architects and engineers with the means to describe the architecture and operational behaviour of environmental and Earth science research infrastructures (RIs) in a standardised way using the standard terminology. This terminology and the relationships between specific classes of concept can be used as the basis for the machine-actionable specification of RIs or RI subsystems. Open Information Linking for Environmental RIs (OIL-E) is a framework for capturing architectural and design knowledge about environmental and Earth science RIs intended to help harmonise vocabulary, promote collaboration and identify common standards and technologies across different research infrastructure initiatives. At its heart is an ontology derived from the ENVRI Reference Model. Using this ontology, RI descriptions can be published as linked data, allowing discovery, querying and comparison using established Semantic Web technologies. It can also be used as an upper ontology by which to connect descriptions of RI entities (whether they be datasets, equipment, processes, etc.) that use other, more specific terminologies. The ENVRI Knowledge Base uses OIL-E to capture information about environmental and Earth science RIs in the ENVRI community for query and comparison. The Knowledge Base can be used to identify the technologies and standards used for particular activities and services and as a basis for evaluating research infrastructure subsystems and behaviours against certain criteria, such as compliance with the FAIR data principles

Anti-EGFR Therapy in Metastatic Small Bowel Adenocarcinoma: Myth or Reality?

Background: Due to the relative rarity of small bowel adenocarcinoma (SBA), prospective trials, helping to guide therapeutic decisions, are lacking and the optimal therapy for advanced SBA is unknown. The role of targeted agents, such as anti\u2013epidermal growth factor receptor (EGFR) and anti\u2013vascular endothelial growth factor (VEGF), is unknown. Patients and Methods: This is a retrospective multicenter observational study that included patients with metastatic SBA treated with anti-EGFR antibodies (cetuximab or panitumumab) \ub1 chemotherapy in the first (I) or second (II) line. Results: Thirteen patients with metastatic SBA, recruited from 5 Italian referral institutions, were included in the present retrospective analysis. All patients received anti-EGFR inhibitors as a single agent or in association with chemotherapy. More common G2 treatment\u2013related side effects were skin reaction (8 patients, 53.8%), hypomagnesemia (6 patients, 46.2%), and diarrhea (8 patients, 61.5%). Grade 3 diarrhea was observed in only 1 patient. Conjunctivitis was not reported in any patients. Grade 4 toxicity was not reported. In the overall population, median progression-free survival was 5.526 months (95% confidence interval [CI]: 3.684-12.467). Median overall survival was 15.86 months (95% CI: 14.43-24.30). Complete response was observed in 15% of patients, partial response in 39% of patients, stable disease in 23% of patients, and progression disease in 15% of patients. Conclusions: In this retrospective analysis, anti-EGFR inhibitors showed to be a suitable addendum to chemotherapy in the I and II line, with an excellent tolerance and safety profile both in I and II line