scholarly journals The FAANG Data Portal: Global, Open-Access, “FAIR”, and Richly Validated Genotype to Phenotype Data for High-Quality Functional Annotation of Animal Genomes

2021 ◽  
Vol 12 ◽  
Author(s):  
Peter W. Harrison ◽  
Alexey Sokolov ◽  
Akshatha Nayak ◽  
Jun Fan ◽  
Daniel Zerbino ◽  
...  
Keyword(s):  
Open Access ◽  
Functional Annotation ◽  
Prediction Models ◽  
Open Data ◽  
Analysis Data ◽  
Aquatic Animal ◽  
High Quality ◽  
Data Archives ◽  
Data Portal ◽  
Animal Genomes

The Functional Annotation of ANimal Genomes (FAANG) project is a worldwide coordinated action creating high-quality functional annotation of farmed and companion animal genomes. The generation of a rich genome-to-phenome resource and supporting informatic infrastructure advances the scope of comparative genomics and furthers the understanding of functional elements. The project also provides terrestrial and aquatic animal agriculture community powerful resources for supporting improvements to farmed animal production, disease resistance, and genetic diversity. The FAANG Data Portal (https://data.faang.org) ensures Findable, Accessible, Interoperable and Reusable (FAIR) open access to the wealth of sample, sequencing, and analysis data produced by an ever-growing number of FAANG consortia. It is developed and maintained by the FAANG Data Coordination Centre (DCC) at the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI). FAANG projects produce a standardised set of multi-omic assays with resulting data placed into a range of specialised open data archives. To ensure this data is easily findable and accessible by the community, the portal automatically identifies and collates all submitted FAANG data into a single easily searchable resource. The Data Portal supports direct download from the multiple underlying archives to enable seamless access to all FAANG data from within the portal itself. The portal provides a range of predefined filters, powerful predictive search, and a catalogue of sampling and analysis protocols and automatically identifies publications associated with any dataset. To ensure all FAANG data submissions are high-quality, the portal includes powerful contextual metadata validation and data submissions brokering to the underlying EMBL-EBI archives. The portal will incorporate extensive new technical infrastructure to effectively deliver and standardise FAANG's shift to single-cellomics, cell atlases, pangenomes, and novel phenotypic prediction models. The Data Portal plays a key role for FAANG by supporting high-quality functional annotation of animal genomes, through open FAIR sharing of data, complete with standardised rich metadata. Future Data Portal features developed by the DCC will support new technological developments for continued improvement for FAANG projects.

Promote Good Governance in Public Financial: The Practice of Local Budget (APBD) Transparency Through Open Data Jakarta in Jakarta Provincial Government

2019 ◽  
Vol 15 (1) ◽  
Author(s):  
Dodi Faedlulloh ◽  
Fetty Wiyani
Keyword(s):  
Public Finance ◽  
Good Governance ◽  
Open Data ◽  
Public Trust ◽  
Provincial Government ◽  
Financial Governance ◽  
One Stop ◽  
Data Portal ◽  
Data Transparency ◽  
Local Budget

This paper aimed to explain public financial governance based on good governance implementation in Jakarta Provincial Government. This paper specifically discussed towards transparancy implementation of local budget (APBD) through open data portal that publishes budget data to public. In general, financial transparency through open data has met Transparency 2.0 standards, namely the existence of encompassing, one-stop, one-click budget accountability and accessibility. But there are indeed some shortcomings that are still a concern in order to continue to maintain commitment to the principle of transparency, namely by updating data through consistent data visualization.Transparency of public finance needs to continue to be developed and improved through various innovations to maintain public trust in the government.Keywords: Public Finance, Open Data, Transparency

scholarly journals Fengyun Meteorological Satellite Products for Earth System Science Applications

2021 ◽  
Author(s):  
Di Xian ◽  
Peng Zhang ◽  
Ling Gao ◽  
Ruijing Sun ◽  
Haizhen Zhang ◽  
...  
Keyword(s):  
Data Sharing ◽  
Satellite Data ◽  
Prediction Models ◽  
Weather Forecasting ◽  
Numerical Models ◽  
Weather Prediction ◽  
Vegetation Indices ◽  
Open Data ◽  
Earth System ◽  
Inversion Algorithm

AbstractFollowing the progress of satellite data assimilation in the 1990s, the combination of meteorological satellites and numerical models has changed the way scientists understand the earth. With the evolution of numerical weather prediction models and earth system models, meteorological satellites will play a more important role in earth sciences in the future. As part of the space-based infrastructure, the Fengyun (FY) meteorological satellites have contributed to earth science sustainability studies through an open data policy and stable data quality since the first launch of the FY-1A satellite in 1988. The capability of earth system monitoring was greatly enhanced after the second-generation polar orbiting FY-3 satellites and geostationary orbiting FY-4 satellites were developed. Meanwhile, the quality of the products generated from the FY-3 and FY-4 satellites is comparable to the well-known MODIS products. FY satellite data has been utilized broadly in weather forecasting, climate and climate change investigations, environmental disaster monitoring, etc. This article reviews the instruments mounted on the FY satellites. Sensor-dependent level 1 products (radiance data) and inversion algorithm-dependent level 2 products (geophysical parameters) are introduced. As an example, some typical geophysical parameters, such as wildfires, lightning, vegetation indices, aerosol products, soil moisture, and precipitation estimation have been demonstrated and validated by in-situ observations and other well-known satellite products. To help users access the FY products, a set of data sharing systems has been developed and operated. The newly developed data sharing system based on cloud technology has been illustrated to improve the efficiency of data delivery.

57 Precision neoantigen discovery using novel algorithms and expanded HLA-ligandome datasets

2020 ◽  
Vol 8 (Suppl 3) ◽  
pp. A62-A62
Author(s):  
Dattatreya Mellacheruvu ◽  
Rachel Pyke ◽  
Charles Abbott ◽  
Nick Phillips ◽  
Sejal Desai ◽  
...  
Keyword(s):  
Machine Learning ◽  
Cell Lines ◽  
Antigen Processing ◽  
Large Scale ◽  
Prediction Models ◽  
K562 Cells ◽  
Machine Learning Algorithms ◽  
Training Data ◽  
High Quality ◽  
Tissue Samples

BackgroundAccurately identified neoantigens can be effective therapeutic agents in both adjuvant and neoadjuvant settings. A key challenge for neoantigen discovery has been the availability of accurate prediction models for MHC peptide presentation. We have shown previously that our proprietary model based on (i) large-scale, in-house mono-allelic data, (ii) custom features that model antigen processing, and (iii) advanced machine learning algorithms has strong performance. We have extended upon our work by systematically integrating large quantities of high-quality, publicly available data, implementing new modelling algorithms, and rigorously testing our models. These extensions lead to substantial improvements in performance and generalizability. Our algorithm, named Systematic HLA Epitope Ranking Pan Algorithm (SHERPA™), is integrated into the ImmunoID NeXT Platform®, our immuno-genomics and transcriptomics platform specifically designed to enable the development of immunotherapies.MethodsIn-house immunopeptidomic data was generated using stably transfected HLA-null K562 cells lines that express a single HLA allele of interest, followed by immunoprecipitation using W6/32 antibody and LC-MS/MS. Public immunopeptidomics data was downloaded from repositories such as MassIVE and processed uniformly using in-house pipelines to generate peptide lists filtered at 1% false discovery rate. Other metrics (features) were either extracted from source data or generated internally by re-processing samples utilizing the ImmunoID NeXT Platform.ResultsWe have generated large-scale and high-quality immunopeptidomics data by using approximately 60 mono-allelic cell lines that unambiguously assign peptides to their presenting alleles to create our primary models. Briefly, our primary ‘binding’ algorithm models MHC-peptide binding using peptide and binding pockets while our primary ‘presentation’ model uses additional features to model antigen processing and presentation. Both primary models have significantly higher precision across all recall values in multiple test data sets, including mono-allelic cell lines and multi-allelic tissue samples. To further improve the performance of our model, we expanded the diversity of our training set using high-quality, publicly available mono-allelic immunopeptidomics data. Furthermore, multi-allelic data was integrated by resolving peptide-to-allele mappings using our primary models. We then trained a new model using the expanded training data and a new composite machine learning architecture. The resulting secondary model further improves performance and generalizability across several tissue samples.ConclusionsImproving technologies for neoantigen discovery is critical for many therapeutic applications, including personalized neoantigen vaccines, and neoantigen-based biomarkers for immunotherapies. Our new and improved algorithm (SHERPA) has significantly higher performance compared to a state-of-the-art public algorithm and furthers this objective.

Chip formation and the interaction of mesoscopic geometric features of cutter

2021 ◽  
pp. 095440542110284
Author(s):  
Xin Tong ◽  
Yanxiang Ren ◽  
Jianing Shen ◽  
Song Yu
Keyword(s):  
Synergistic Effect ◽  
Prediction Models ◽  
Cutting Tools ◽  
Chip Morphology ◽  
Orthogonal Test ◽  
Cutting Performance ◽  
Geometric Features ◽  
High Quality ◽  
Milling Tool ◽  
Interaction Test

Most of the researches on the properties of micro-textured tools are based on an orthogonal test, while the interaction between micro-textured parameters is ignored. Therefore, this thesis is based on an interaction test to study the cutting performance of cutting tools. According to the chip morphology obtained from the interactive test, the micro texture diameter of 60 μm is obtained when the cutting is stable. It was also found that the synergistic effect of multiple mesoscopic geometric features had a significant influence on cutting performance. By analysis, we found the optimized parameters for the milling tool were D = 60 μm, l = 100 μm, l1 = 150 μm, r = 60 μm. Furthermore, prediction models of the cutting performance were established by univariate linear regression and the validity of these models was verified. Thus, this thesis provides a reference for improving the performance of cutting tools and for achieving efficient and high-quality machining of titanium alloys.

scholarly journals Presenter: Werner Paulus, University Hospital Muenster, Muenster. Publishing A High-quality, Non-commercial Neuropathology Journal Without a Publisher: The First Nine Months

2021 ◽  
Vol 48 (s2) ◽  
pp. S11-S11
Author(s):  
Marta Margeta ◽  
Peter Gould ◽  
Lili-Naz Hazrati ◽  
Veronica Hirsch-Reinshagen ◽  
Werner Paulus
Keyword(s):  
Open Access ◽  
Driving Forces ◽  
Scholarly Communication ◽  
University Hospital ◽  
Website Design ◽  
Final Decision ◽  
List Type ◽  
Ethical Challenges ◽  
High Quality ◽  
Commercial Publishing

Scholarly communication faces increasing economical and ethical challenges, including pricing policies and overbearing behavior of commercial publishing houses. Based on the hypothesis that a diamond open access neuropathology journal of a high scientific and technical quality can be run entirely by neuropathologists, we launched Free Neuropathology (FNP; freeneuropathology.org) in January 2020. Classical publisher activities, such as copyediting, layout, website maintenance, and journal promotion, are undertaken by neuropathologists and neuroscientists using free open access software. The journal is free for both readers and authors, and papers are published under a Creative Commons BY SA licence, where copyright remains with the authors. Based on 26 articles published by August 2020, it takes FNP 11.1 days from submission to first, and 19.9 days to final, decision. High-quality copyediting, layout, and online publishing in the final format is accomplished in only 8 days. Absence of a commercial publisher enables prioritization of democratic and scientifically-driven decisions on editorial structure, website design, journal promotion, paper formatting, special article series, and number of accepted papers. This new model of journal publishing, which returns the control of scholarly communication to scientists, will be of interest to neuropathologists and wider scientific community alike.Learning ObjectivesSummarize the current state and driving forces behind commercial and non-commercial scientific publishing in neuropathology.Describe the advantages and challenges of a non-commercial publishing platform for neuropathology.

scholarly journals Is Access Enough? Interrogating the Influence of Money and Power in Shaping Information

2020 ◽  
Vol 4 (1) ◽  
pp. 29-38
Author(s):  
Heather Brodie Perry
Keyword(s):  
Open Access ◽  
Critical Evaluation ◽  
Access To Information ◽  
Power Structures ◽  
High Quality ◽  
Information Power ◽  
Complex Information ◽  
Community Information ◽  
Truth Claims ◽  
Information Consumers

AbstractAccess to information encourages innovation and leads to participation in society of individuals. The emergence of Open Access supports the inclusion of all, including the voices of the traditionally marginalized, yet access alone is insufficient to enable consumers to effectively use information. Power structures can influence the information available and silence opposing viewpoints. Industry disinformation can influence viewpoints and shape policy in ways that can be detrimental to individuals and the community. Information consumers may not possess the competence required to navigate the complex information ecosystem to find the accurate, high-quality, resources required to meet their need. Libraries have a role in assisting consumers develop the critical evaluation capabilities essential to the exercise of informed skepticism when evaluating truth claims. Access is essential; however, without the knowledge to determine the quality and validity of information, a consumer can be misled in ways that can cause harm to themselves and society.

scholarly journals GO-FAANG meeting: a Gathering On Functional Annotation of Animal Genomes

2016 ◽  
Vol 47 (5) ◽  
pp. 528-533 ◽  
Author(s):  
Christopher K. Tuggle ◽  
Elisabetta Giuffra ◽  
Stephen N. White ◽  
Laura Clarke ◽  
Huaijun Zhou ◽  
...  
Keyword(s):  
Functional Annotation ◽  
Animal Genomes

scholarly journals Critérios para avaliação de ferramentas para repositório conforme a Ciência Aberta

2017 ◽  
Vol 6 (2) ◽  
Author(s):  
Angélica Conceição Dias Miranda ◽  
Milton Shintaku ◽  
Simone Machado Firme
Keyword(s):  
Open Access ◽  
Evaluation Criteria ◽  
Open Data ◽  
Open Science ◽  
Scientific Production ◽  
Open File ◽  
Research Institutes ◽  
Criteria For Evaluation ◽  
Science Movement ◽  
Bibliographic Study

Resumo: Os repositórios têm se tornado comum nas universidades e institutos de pesquisa, como forma de ofertar acesso à produção científica e, com isso, dar visibilidade à instituição. Entretanto, em muitos casos ainda estão restritos aos conceitos do movimento do arquivo aberto e acesso aberto, sendo que já se discute o Movimento da Ciência Aberta, revelando certo descompasso, requerendo estudos que apoiem a atualização dessa importante ferramenta. Nesse sentido, o presente estudo verifica os requisitos envolvidos nos movimentos abertos, de forma a apoiar a discussão técnica e tecnológica. Um estudo bibliográfico, que transforma as informações sobre os movimentos em critérios para avaliação de ferramentas para criação de repositórios, apresentando a implementação da interação como um novo desafio. Nas considerações procura-se contribuir com a discussão sobre a Ciência Aberta, de forma mais aplicada bem como o ajuste dos repositórios a esse movimento.Palavras-chave: Repositórios.  Critérios de avaliação. Arquivo aberto. Acesso aberto. Dados abertos. Ciência aberta.SURVEY OF CRITERIA FOR EVALUATION OF REPOSITORY TOOLS ACCORDING TO OPEN SCIENCE Abstract: Repositories have become common in universities and research institutes, as a way of offering access to scientific production, thereby giving visibility to the institution. Meanwhile, in many cases, repositories are restricted to the concepts of open movement and open access considering that the Open Science Movement is already being discussed. Regarding this matter, this study verifies the requirements involved in the open movements, in order to support a technical and technological discussion.  A bibliographic study that transforms information about movements into criteria to evaluate tools used to create repositories, presenting an implementation of interaction as a new challenge. In the considerations, we contribute with a discussion about an Open Science, in a more applied way, as well as the adjustment of the repositories to this movement.Keywords: Repositories. Evaluation Criteria. Open File. Open Access. Open Data. Open Science.

scholarly journals Estimating the reproducibility & transparency of smoking cessation behaviour change interventions

2020 ◽  
Author(s):  
Emma Norris ◽  
Yiwei He ◽  
Rachel Loh ◽  
Robert West ◽  
Susan Michie
Keyword(s):  
Open Access ◽  
Behaviour Change ◽  
Conflict Of Interest ◽  
Open Data ◽  
Smoking Behaviour ◽  
Funding Source ◽  
Behaviour Change Intervention ◽  
Behaviour Change Interventions ◽  
Replication Studies ◽  
Randomised Controlled

Introduction: Activities promoting research reproducibility and transparency are crucial for generating trustworthy evidence. Evaluation of smoking interventions is one area where vested interests may motivate reduced reproducibility and transparency. Aims: Assess markers of transparency and reproducibility in smoking behaviour change intervention evaluation reports.Methods: One hundred evaluation reports of smoking behaviour change intervention randomised controlled trials published in 2018-2019 were identified. Reproducibility markers of pre-registration, protocol sharing, data-, materials- and analysis script-sharing, replication of a previous study and open access publication were coded in identified reports. Transparency markers of funding and conflict of interest declarations were also coded. Coding was performed by two researchers, with inter-rater reliability calculated using Krippendorff’s alpha.Results: Seventy-one percent of reports were open access and 73% pre-registered. However, only 13% provided accessible materials, 7% accessible data and 1% accessible analysis scripts. No reports were replication studies. Ninety-four percent of reports provided a funding source statement and eighty-eight percent of reports provided a conflict of interest statement.Conclusions: Open data, materials, analysis and replications are rare in smoking behaviour change interventions, whereas funding source and conflict of interest declarations are common. Future smoking research should be more reproducible to enable knowledge accumulation.

Sign in / Sign up

Export Citation Format

Share Document