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18 Publications visible to you, out of a total of 18
Methods Included: Standardizing Computational Reuse and Portability with the Common Workflow Language

Abstract (Expand)

A widely used standard for portable multilingual data analysis pipelines would enable considerable benefits to scholarly publication reuse, research/industry collaboration, regulatory cost control, and … to the environment. Published research that used multiple computer languages for their analysis pipelines would include a complete and reusable description of that analysis that is runnable on a diverse set of computing environments. Researchers would be able to easier collaborate and reuse these pipelines, adding or exchanging components regardless of programming language used; collaborations with and within the industry would be easier; approval of new medical interventions that rely on such pipelines would be faster. Time will be saved and environmental impact would also be reduced, as these descriptions contain enough information for advanced optimization without user intervention. Workflows are widely used in data analysis pipelines, enabling innovation and decision-making for the modern society. In many domains the analysis components are numerous and written in multiple different computer languages by third parties. However, lacking a standard for reusable and portable multilingual workflows, then reusing published multilingual workflows, collaborating on open problems, and optimizing their execution would be severely hampered. Moreover, only a standard for multilingual data analysis pipelines that was widely used would enable considerable benefits to research-industry collaboration, regulatory cost control, and to preserving the environment. Prior to the start of the CWL project, there was no standard for describing multilingual analysis pipelines in a portable and reusable manner. Even today / currently, although there exist hundreds of single-vendor and other single-source systems that run workflows, none is a general, community-driven, and consensus-built standard. Preprint, submitted to Communications of the ACM (CACM).

Authors: Michael R. Crusoe, Sanne Abeln, Alexandru Iosup, Peter Amstutz, John Chilton, Nebojša Tijanić, Hervé Ménager, Stian Soiland-Reyes, Carole Goble

Date Published: 14th May 2021

Publication Type: Unpublished

MOLGENIS VIP: an open-source and modular pipeline for high-throughput and integrated DNA variant analysis

Abstract (Expand)

Abstract In silico variant interpretation pipelines have become an integral part of genetics research and genome diagnostics. However, challenges remain for automated variant interpretation and candidate …omated variant interpretation and candidate shortlisting. Their reliability is affected by variability in input data caused due the use of differing sequencing platforms, erroneous nomenclature and changing experimental conditions. Similarly, differences in predictive algorithms can result in discordant results. Finally, scalability is essential to accommodate large amounts of input data, such as in whole genome sequencing (WGS). To accelerate causal variant detection and innovation in genome diagnostics and research, we developed the MOLGENIS Variant Interpretation Pipeline (VIP). VIP is a flexible open-source computational pipeline that generates interactive reports of variants in whole exome sequencing (WES) and WGS data for expert interpretation. VIP can process short- and long-read data from different platforms and offers tools for increased sensitivity: a configurable decision-tree, filters based on human phenotype ontology (HPO) and gene inheritance that can be used to pinpoint disease-causing variants or finetune a query for specific variants. Here, alongside presenting VIP, we provide a step-by-step protocol for how to use VIP to annotate, classify and filter genetic variants of patients with a rare disease that has a suspected genetic cause. Finally, we demonstrate how VIP performs using 25,664 previously classified variants from the data sharing initiative of the Vereniging van Klinisch Genetische Laboratoriumdiagnostiek (VKGL), a cohort of 18 diagnosed patients from routine diagnostics and a cohort of 41 patients with a rare disease (RD) who were not diagnosed in routine diagnostics but were diagnosed using novel omics approaches within the EU-wide project to solve rare diseases (EU-Solve-RD). VIP requires bioinformatic knowledge to configure, but once configured, any diagnostic professional can perform an analysis within 5 hours.

Authors: W.T.K. Maassen, L.F. Johansson, B. Charbon, D. Hendriksen, S. van den Hoek, M.K. Slofstra, R. Mulder, M.T. Meems-Veldhuis, R. Sietsma, H.H. Lemmink, C.C. van Diemen, M.E. van Gijn, M.A. Swertz, K.J. van der Velde

Date Published: 15th Apr 2024

Publication Type: Unpublished

Multi-task analysis of gene expression data on cancer public datasets

Abstract (Expand)

Background There is an availability of omics and often multi-omics cancer datasets on public databases such as Gene Expression Omnibus (GEO), International Cancer Genome Consortium and The Cancer Genome … Atlas Program. Most of these databases provide at least the gene expression data for the samples contained in the project. Multi-omics has been an advantageous strategy to leverage personalized medicine, but few works explore strategies to extract knowledge relying only on gene expression level for decisions on tasks such as disease outcome prediction and drug response simulation. The models and information acquired on projects based only on expression data could provide decision making background for future projects that have other level of omics data such as DNA methylation or miRNAs. Results We extended previous methodologies to predict disease outcome from the combination of protein interaction networks and gene expression profiling by proposing an automated pipeline to perform the graph feature encoding and further patient networks outcome classification derived from RNA-Seq. We integrated biological networks from protein interactions and gene expression profiling to assess patient specificity combining the treatment/control ratio with the patient normalized counts of the deferentially expressed genes. We also tackled the disease outcome prediction from the gene set enrichment perspective, combining gene expression with pathway gene sets information as features source for this task. We also explored the drug response outcome perspective of the cancer disease still evaluating the relationship among gene expression profiling with single sample gene set enrichment analysis (ssGSEA), proposing a workflow to perform drug response screening according to the patient enriched pathways. Conclusion We showed the importance of the patient network modeling for the clinical task of disease outcome prediction using graph kernel matrices strategy and showed how ssGSEA improved the prediction only using transcriptomic data combined with pathway scores. We also demonstrated a detailed screening analysis showing the impact of pathway-based gene sets and normalization types for the drug response simulation. We deployed two fully automatized Screening workflows following the FAIR principles for the disease outcome prediction and drug response simulation tasks.

Author: Yasmmin Martins

Date Published: 28th Sep 2023

Publication Type: Journal

OntoPPI: Towards Data Formalization on the Prediction of Protein Interactions

Abstract (Expand)

The Linking Open Data (LOD) cloud is a global data space for publishing and linking structured data on the Web. The idea is to facilitate the integration, exchange, and processing of data. The LOD cloud … already includes a lot of datasets that are related to the biological area. Nevertheless, most of the datasets about protein interactions do not use metadata standards. This means that they do not follow the LOD requirements and, consequently, hamper data integration. This problem has impacts on the information retrieval, specially with respect to datasets provenance and reuse in further prediction experiments. This paper proposes an ontology to describe and unite the four main kinds of data in a single prediction experiment environment: (i) information about the experiment itself; (ii) description and reference to the datasets used in an experiment; (iii) information about each protein involved in the candidate pairs. They correspond to the biological information that describes them and normally involves integration with other datasets; and, finally, (iv) information about the prediction scores organized by evidence and the final prediction. Additionally, we also present some case studies that illustrate the relevance of our proposal, by showing how queries can retrieve useful information.

Authors: Yasmmin Cortes Martins, Maria Cláudia Cavalcanti, Luis Willian Pacheco Arge, Artur Ziviani, Ana Tereza Ribeiro de Vasconcelos

Date Published: 2019

Publication Type: Journal

Perspectives on automated composition of workflows in the life sciences

Abstract

Not specified

Authors: Anna-Lena Lamprecht, Magnus Palmblad, Jon Ison, Veit Schwämmle, Mohammad Sadnan Al Manir, Ilkay Altintas, Christopher J. O. Baker, Ammar Ben Hadj Amor, Salvador Capella-Gutierrez, Paulos Charonyktakis, Michael R. Crusoe, Yolanda Gil, Carole Goble, Timothy J. Griffin, Paul Groth, Hans Ienasescu, Pratik Jagtap, Matúš Kalaš, Vedran Kasalica, Alireza Khanteymoori, Tobias Kuhn, Hailiang Mei, Hervé Ménager, Steffen Möller, Robin A. Richardson, Vincent Robert, Stian Soiland-Reyes, Robert Stevens, Szoke Szaniszlo, Suzan Verberne, Aswin Verhoeven, Katherine Wolstencroft

Date Published: 2021

Publication Type: Journal

PPIntegrator: semantic integrative system for protein–protein interaction and application for host–pathogen datasets

Abstract (Expand)

Semantic web standards have shown importance in the last 20 years in promoting data formalization and interlinking between the existing knowledge graphs. In this context, several ontologies and data … integration initiatives have emerged in recent years for the biological area, such as the broadly used Gene Ontology that contains metadata to annotate gene function and subcellular location. Another important subject in the biological area is protein–protein interactions (PPIs) which have applications like protein function inference. Current PPI databases have heterogeneous exportation methods that challenge their integration and analysis. Presently, several initiatives of ontologies covering some concepts of the PPI domain are available to promote interoperability across datasets. However, the efforts to stimulate guidelines for automatic semantic data integration and analysis for PPIs in these datasets are limited. Here, we present PPIntegrator, a system that semantically describes data related to protein interactions. We also introduce an enrichment pipeline to generate, predict and validate new potential host–pathogen datasets by transitivity analysis. PPIntegrator contains a data preparation module to organize data from three reference databases and a triplification and data fusion module to describe the provenance information and results. This work provides an overview of the PPIntegrator system applied to integrate and compare host–pathogen PPI datasets from four bacterial species using our proposed transitivity analysis pipeline. We also demonstrated some critical queries to analyze this kind of data and highlight the importance and usage of the semantic data generated by our system.

Authors: Yasmmin Côrtes Martins, Artur Ziviani, Maiana de Oliveira Cerqueira e Costa, Maria Cláudia Reis Cavalcanti, Marisa Fabiana Nicolás, Ana Tereza Ribeiro de Vasconcelos

Date Published: 2023

Publication Type: Journal

survInTime - Exploring surveillance methods and data analysis on Brazilian respiratory syndrome dataset and community mobility changes

Abstract (Expand)

Background The covid-19 pandemic brought negative impacts in almost every country in the world. These impacts were observed mainly in the public health sphere, with a rapid raise and spread of the … disease and failed attempts to restrain it while there was no treatment. However, in developing countries, the impacts were severe in other aspects such as the intensification of social inequality, poverty and food insecurity. Specifically in Brazil, the miscommunication among the government layers conducted the control measures to a complete chaos in a country of continental dimensions. Brazil made an effort to register granular informative data about the case reports and their outcomes, while this data is available and can be consumed freely, there are issues concerning the integrity and inconsistencies between the real number of cases and the number of notifications in this dataset. Results We projected and implemented four types of analysis to explore the Brazilian public dataset of Severe Acute Respiratory Syndrome (srag dataset) notifications and the google dataset of community mobility change (mobility dataset). These analysis provides some diagnosis of data integration issues and strategies to integrate data and experimentation of surveillance analysis. The first type of analysis aims at describing and exploring the data contained in both datasets, starting by assessing the data quality concerning missing data, then summarizing the patterns found in this datasets. The Second type concerns an statistical experiment to estimate the cases from mobility patterns organized in periods of time. We also developed, as the third analysis type, an algorithm to help the understanding of the disease waves by detecting them and compare the time periods across the cities. Lastly, we build time series datasets considering deaths, overall cases and residential mobility change in regular time periods and used as features to group cities with similar behavior. Conclusion The exploratory data analysis showed the under representation of covid-19 cases in many small cities in Brazil that were absent in the srag dataset or with a number of cases very low than real projections. We also assessed the availability of data for the Brazilian cities in the mobility dataset in each state, finding out that not all the states were represented and the best coverage occurred in Rio de Janeiro state. We compared the capacity of place categories mobility change combination on estimating the number of cases measuring the errors and identifying the best components in mobility that could affect the cases. In order to target specific strategies for groups of cities, we compared strategies to cluster cities that obtained similar outcomes behavior along the time, highlighting the divergence on handling the disease.

Authors: Yasmmin Côrtes Martins, Ronaldo Francisco da Silva

Date Published: 27th Sep 2023

Publication Type: Journal

The impact of non-lineage defining mutations in the structural stability for variants of concern of SARS-CoV-2

Abstract (Expand)

Motivation The identification of the most important mutations, that lead to a structural and functional change in a highly transmissible virus variants, is essential to understand the impacts and the … possible chances of vaccine and antibody escape. Strategies to rapidly associate mutations to functional and conformational properties are needed to rapidly analyze mutations in proteins and their impacts in antibodies and human binding proteins. Results Comparative analysis showed the main structural characteristics of the essential mutations found for each variant of concern in relation to the reference proteins. The paper presented a series of methodologies to track and associate conformational changes and the impacts promoted by the mutations.

Authors: Yasmmin Martins, Ronaldo Francisco da Silva

Date Published: 22nd Jun 2023

Publication Type: Journal

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