pTERT C250T mutation: A potential biomarker of poor prognosis in metastatic melanoma.

Melanoma is the most aggressive form of skin cancer and the leading cause of death from cutaneous tumors. Several studies have associated alterations in the TERT promoter region (pTERT) with gene overexpression, aggressiveness and poor prognosis of the disease. The aim of this study was to clarify the role of pTERT molecular status in paired samples of primary melanoma and metastasis using tissue and plasma to establish a correlation with disease progression and survival. A total of 88 FFPE tissue samples from 53 patients with advanced melanoma were analyzed. Of these, 35 had paired samples. We also examined cfDNA samples from plasma of 25 patients. We detected a good correlation between primary tumors and metastases in pTERT mutation and methylation status. We were also able to identify pTERT mutations in plasma samples that correlated with mutational status in tissue samples. Interestingly, the C250T mutation was associated with worse survival and higher TERT mRNA expression, compared to the other most common mutation: C228T. In addition, hyper-methylation of the promoter region seems to be related to the progression of pTERT wild type (WT) patients. These results suggest that TERT gene alterations plays an important role during tumor progression, with the detection of the C250T mutation in tissue and plasma as a potential biomarker of poor prognosis in patients with advanced melanoma.

Ten simple rules for making training materials FAIR.

Everything we do today is becoming more and more reliant on the use of computers. The field of biology is no exception; but most biologists receive little or no formal preparation for the increasingly computational aspects of their discipline. In consequence, informal training courses are often needed to plug the gaps; and the demand for such training is growing worldwide. To meet this demand, some training programs are being expanded, and new ones are being developed. Key to both scenarios is the creation of new course materials. Rather than starting from scratch, however, it's sometimes possible to repurpose materials that already exist. Yet finding suitable materials online can be difficult: They're often widely scattered across the internet or hidden in their home institutions, with no systematic way to find them. This is a common problem for all digital objects. The scientific community has attempted to address this issue by developing a set of rules (which have been called the Findable, Accessible, Interoperable and Reusable [FAIR] principles) to make such objects more findable and reusable. Here, we show how to apply these rules to help make training materials easier to find, (re)use, and adapt, for the benefit of all.

GlyGen data model and processing workflow.

SUMMARY: Glycoinformatics plays a major role in glycobiology research, and the development of a comprehensive glycoinformatics knowledgebase is critical. This application note describes the GlyGen data model, processing workflow and the data access interfaces featuring programmatic use case example queries based on specific biological questions. The GlyGen project is a data integration, harmonization and dissemination project for carbohydrate and glycoconjugate-related data retrieved from multiple international data sources including UniProtKB, GlyTouCan, UniCarbKB and other key resources. AVAILABILITY AND IMPLEMENTATION: GlyGen web portal is freely available to access at https://glygen.org. The data portal, web services, SPARQL endpoint and GitHub repository are also freely available at https://data.glygen.org, https://api.glygen.org, https://sparql.glygen.org and https://github.com/glygener, respectively. All code is released under license GNU General Public License version 3 (GNU GPLv3) and is available on GitHub https://github.com/glygener. The datasets are made available under Creative Commons Attribution 4.0 International (CC BY 4.0) license. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Fostering global data sharing: highlighting the recommendations of the Research Data Alliance COVID-19 working group.

The systemic challenges of the COVID-19 pandemic require cross-disciplinary collaboration in a global and timely fashion. Such collaboration needs open research practices and the sharing of research outputs, such as data and code, thereby facilitating research and research reproducibility and timely collaboration beyond borders. The Research Data Alliance COVID-19 Working Group recently published a set of recommendations and guidelines on data sharing and related best practices for COVID-19 research. These guidelines include recommendations for clinicians, researchers, policy- and decision-makers, funders, publishers, public health experts, disaster preparedness and response experts, infrastructure providers from the perspective of different domains (Clinical Medicine, Omics, Epidemiology, Social Sciences, Community Participation, Indigenous Peoples, Research Software, Legal and Ethical Considerations), and other potential users. These guidelines include recommendations for researchers, policymakers, funders, publishers and infrastructure providers from the perspective of different domains (Clinical Medicine, Omics, Epidemiology, Social Sciences, Community Participation, Indigenous Peoples, Research Software, Legal and Ethical Considerations). Several overarching themes have emerged from this document such as the need to balance the creation of data adherent to FAIR principles (findable, accessible, interoperable and reusable), with the need for quick data release; the use of trustworthy research data repositories; the use of well-annotated data with meaningful metadata; and practices of documenting methods and software. The resulting document marks an unprecedented cross-disciplinary, cross-sectoral, and cross-jurisdictional effort authored by over 160 experts from around the globe. This letter summarises key points of the Recommendations and Guidelines, highlights the relevant findings, shines a spotlight on the process, and suggests how these developments can be leveraged by the wider scientific community.

The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research.

Copy number variations (CNVs) are major causative contributors both in the genesis of genetic diseases and human neoplasias. While "High-Throughput" sequencing technologies are increasingly becoming the primary choice for genomic screening analysis, their ability to efficiently detect CNVs is still heterogeneous and remains to be developed. The aim of this white paper is to provide a guiding framework for the future contributions of ELIXIR's recently established human CNV Community, with implications beyond human disease diagnostics and population genomics. This white paper is the direct result of a strategy meeting that took place in September 2018 in Hinxton (UK) and involved representatives of 11 ELIXIR Nodes. The meeting led to the definition of priority objectives and tasks, to address a wide range of CNV-related challenges ranging from detection and interpretation to sharing and training. Here, we provide suggestions on how to align these tasks within the ELIXIR Platforms strategy, and on how to frame the activities of this new ELIXIR Community in the international context.

Biotea-2-Bioschemas, facilitating structured markup for semantically annotated scholarly publications.

The total number of scholarly publications grows day by day, making it necessary to explore and use simple yet effective ways to expose their metadata. Schema.org supports adding structured metadata to web pages via markup, making it easier for data providers but also for search engines to provide the right search results. Bioschemas is based on the standards of schema.org, providing new types, properties and guidelines for metadata, i.e., providing metadata profiles tailored to the Life Sciences domain. Here we present our proposed contribution to Bioschemas (from the project "Biotea"), which supports metadata contributions for scholarly publications via profiles and web components. Biotea comprises a semantic model to represent publications together with annotated elements recognized from the scientific text; our Biotea model has been mapped to schema.org following Bioschemas standards.

Biotea: semantics for Pubmed Central.

A significant portion of biomedical literature is represented in a manner that makes it difficult for consumers to find or aggregate content through a computational query. One approach to facilitate reuse of the scientific literature is to structure this information as linked data using standardized web technologies. In this paper we present the second version of Biotea, a semantic, linked data version of the open-access subset of PubMed Central that has been enhanced with specialized annotation pipelines that uses existing infrastructure from the National Center for Biomedical Ontology. We expose our models, services, software and datasets. Our infrastructure enables manual and semi-automatic annotation, resulting data are represented as RDF-based linked data and can be readily queried using the SPARQL query language. We illustrate the utility of our system with several use cases. Our datasets, methods and techniques are available at http://biotea.github.io.

Four simple recommendations to encourage best practices in research software.

Scientific research relies on computer software, yet software is not always developed following practices that ensure its quality and sustainability. This manuscript does not aim to propose new software development best practices, but rather to provide simple recommendations that encourage the adoption of existing best practices. Software development best practices promote better quality software, and better quality software improves the reproducibility and reusability of research. These recommendations are designed around Open Source values, and provide practical suggestions that contribute to making research software and its source code more discoverable, reusable and transparent. This manuscript is aimed at developers, but also at organisations, projects, journals and funders that can increase the quality and sustainability of research software by encouraging the adoption of these recommendations.

ProtVista: visualization of protein sequence annotations.

SUMMARY: ProtVista is a comprehensive visualization tool for the graphical representation of protein sequence features in the UniProt Knowledgebase, experimental proteomics and variation public datasets. The complexity and relationships in this wealth of data pose a challenge in interpretation. Integrative visualization approaches such as provided by ProtVista are thus essential for researchers to understand the data and, for instance, discover patterns affecting function and disease associations. AVAILABILITY AND IMPLEMENTATION: ProtVista is a JavaScript component released as an open source project under the Apache 2 License. Documentation and source code are available at http://ebi-uniprot.github.io/ProtVista/ . CONTACT: martin@ebi.ac.uk. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

[Species distribution and antifungal susceptibility of Candida spp. causing superficial mycosis. Coro, Falcon state, Venezuela]. / Distribución de especies y susceptibilidad antifúngica de Candida spp. causantes de micosis superficiales. Coro, estado Falcón, Venezuela.

Candida species other than C. albicans are often described as causative agents of superficial mycosis and are more resistant to treatment with azoles. In order to determine the distribution of species and in vitro antifungal susceptibility of Candida spp., one ambispective study, which analyzed 18 yeast isolates obtained from samples from patients diagnosed with superficial mycosis, was performed. Taxonomic identification was performed by macroscopic visualization of the growth characteristics in chromogenic agar and by conventional methods. The susceptibility to fluconazole and voriconazole was evaluated by the disc diffusion method. Most of the isolates (88.8%), came from nail samples. C. parapsilosis was the most common species, followed by C. tropicalis, C. albicans and C. krusei, which confirmed the prevalence of non-albicans species as a cause of superficial mycoses. The pattern of susceptibility to fluconazole and voriconazole was similar: all isolates of C. parapsilosis and C. albicans were susceptible, while 83.3% of C. tropicalis showed sensitivity to both antifungals. C. krusei, fluconazole-resistant species showed intermediate susceptibility io voriconazole. The use of chromogenic agar allowed to detect mixed infections in nail samples, involving Candida spp. and C. tropicalis in one case, the latter with resistance to both fluconazole and voriconazole. The results demonstrate the importance of species identification and susceptibility testing to avoid therapeutic failures in superficial mycoses.

Distribución de especies y susceptibilidad antifúngica de Candida spp. causantes de micosis superficiales. Coro, estado Falcón, Venezuela / Species distribution and antifungal susceptibility of Candida spp. causing superficial mycosis. Coro, Falcon state, Venezuela.

Las especies de Candida distintas a C. albicans se describen con frecuencia como agentes causales de micosis superficial y presentan una mayor resistencia al tratamiento con los azoles. Con la finalidad de determinar la distribución de especies y la susceptibilidad antifúngica in vitro de Candida spp., se realizó un estudio ambispectivo donde se analizaron 18 aislados de levaduras obtenidas de muestras de pacientes con diagnóstico de micosis superficial. La identificación taxonómica se realizó mediante la visualización de las características macroscópicas de crecimiento en agar cromogénico y por métodos convencionales. La susceptibilidad a fluconazol y voriconazol se evaluó por el método de difusión en disco. El 88,8% de los aislados provenía de muestras de uñas. C. parapsilosis fue la especie más frecuente, seguida de C. tropicalis, C. albicans y C. krusei, lo cual confirmó el predominio de especies no albicans como causa de micosis superficial. El patrón de susceptibilidad a fluconazol y voriconazol fue similar: todos los aislados de C. parapsilosis y C. albicans resultaron sensibles, mientras que el 83,3% de C. tropicalis mostró sensibilidad a ambos antifúngicos. C. krusei, especie resistente a fluconazol, presentó sensibilidad intermedia al voriconazol. El uso de agar cromogénico permitió detectar infecciones mixtas en muestras de uñas, involucrando en uno de los casos a Candid spp. y C.tropicalis, esta última con resistencia tanto a fluconazol como a voriconazol. Los resultados obtenidos demuestran la importancia de la identificación de especies y la realización de pruebas de susceptibilidad con el fin de evitar fracasos terapéuticos en micosis superficiales. Autor de correspondencia: Leyla Humbría-García. Laboratorio de Micología

Candida species other than C. albicans are often described as causative agents of superficial mycosis and are more resistant to treatment with azoles. In order to determine the distribution of species and in vitro antifungal susceptibility of Candida spp., one ambispective study, which analyzed 18 yeast isolates obtained from samples from patients diagnosed with superficial mycosis, was performed. Taxonomic identification was performed by macroscopic visualization of the growth characteristics in chromogenic agar and by conventional methods. The susceptibility to fluconazole and voriconazole was evaluated by the disc diffusion method. Most of the isolates (88.8%), came from nail samples. C. parapsilosis was the most common species, followed by C. tropicalis, C. albicans and C. krusei, which confirmed the prevalence of non-albicans species as a cause of superficial mycoses. The pattern of susceptibility to fluconazole and voriconazole was similar: all isolates of C. parapsilosis and C. albicans were susceptible, while 83.3% of C. tropicalis showed sensitivity to both antifungals. C. krusei, fluconazole-resistant species showed intermediate susceptibility to voriconazole. The use of chromogenic agar allowed to detect mixed infections in nail samples, involving Candida spp. and C. tropicalis in one case, the latter with resistance to both fluconazole and voriconazole. The results demonstrate the importance of species identification and susceptibility testing to avoid therapeutic failures in superficial mycoses.

Anatomy of BioJS, an open source community for the life sciences.

BioJS is an open source software project that develops visualization tools for different types of biological data. Here we report on the factors that influenced the growth of the BioJS user and developer community, and outline our strategy for building on this growth. The lessons we have learned on BioJS may also be relevant to other open source software projects.

BioJS: an open source standard for biological visualisation - its status in 2014.

BioJS is a community-based standard and repository of functional components to represent biological information on the web. The development of BioJS has been prompted by the growing need for bioinformatics visualisation tools to be easily shared, reused and discovered. Its modular architecture makes it easy for users to find a specific functionality without needing to know how it has been built, while components can be extended or created for implementing new functionality. The BioJS community of developers currently provides a range of functionality that is open access and freely available. A registry has been set up that categorises and provides installation instructions and testing facilities at http://www.ebi.ac.uk/tools/biojs/. The source code for all components is available for ready use at https://github.com/biojs/biojs.

FeatureViewer, a BioJS component for visualization of position-based annotations in protein sequences.

SUMMARY: FeatureViewer is a BioJS component that lays out, maps, orients, and renders position-based annotations for protein sequences. This component is highly flexible and customizable, allowing the presentation of annotations by rows, all centered, or distributed in non-overlapping tracks. It uses either lines or shapes for sites and rectangles for regions. The result is a powerful visualization tool that can be easily integrated into web applications as well as documents as it provides an export-to-image functionality. AVAILABILITY: https://github.com/biojs/biojs/blob/master/src/main/javascript/Biojs.FeatureViewer.js; http://dx.doi.org/10.5281/zenodo.7719.

The EBI RDF platform: linked open data for the life sciences.

MOTIVATION: Resource description framework (RDF) is an emerging technology for describing, publishing and linking life science data. As a major provider of bioinformatics data and services, the European Bioinformatics Institute (EBI) is committed to making data readily accessible to the community in ways that meet existing demand. The EBI RDF platform has been developed to meet an increasing demand to coordinate RDF activities across the institute and provides a new entry point to querying and exploring integrated resources available at the EBI.

BioJS: an open source JavaScript framework for biological data visualization.

SUMMARY: BioJS is an open-source project whose main objective is the visualization of biological data in JavaScript. BioJS provides an easy-to-use consistent framework for bioinformatics application programmers. It follows a community-driven standard specification that includes a collection of components purposely designed to require a very simple configuration and installation. In addition to the programming framework, BioJS provides a centralized repository of components available for reutilization by the bioinformatics community. AVAILABILITY AND IMPLEMENTATION: http://code.google.com/p/biojs/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

MyDas, an extensible Java DAS server.

A large number of diverse, complex, and distributed data resources are currently available in the Bioinformatics domain. The pace of discovery and the diversity of information means that centralised reference databases like UniProt and Ensembl cannot integrate all potentially relevant information sources. From a user perspective however, centralised access to all relevant information concerning a specific query is essential. The Distributed Annotation System (DAS) defines a communication protocol to exchange annotations on genomic and protein sequences; this standardisation enables clients to retrieve data from a myriad of sources, thus offering centralised access to end-users.We introduce MyDas, a web server that facilitates the publishing of biological annotations according to the DAS specification. It deals with the common functionality requirements of making data available, while also providing an extension mechanism in order to implement the specifics of data store interaction. MyDas allows the user to define where the required information is located along with its structure, and is then responsible for the communication protocol details.