BioDWH2: an automated graph-based data warehouse and mapping tool.
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ABSTRACT:
SUBMITTER: Friedrichs M
PROVIDER: S-EPMC8238471 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundThe American Society for Clinical Oncology recently launched the minimal common oncology data elements project to facilitate cancer data interoperability. However, clinical data are often unrecorded in an organized way, and converting them into a structured format can be time-consuming. Clinical Data Warehouse (CDW) is a database that consolidates data from different clinical sources. However, the clinical data extracted from this database include not only structured data but also natural language generated during clinical practice. Therefore, applying these data to a clinical study is challenging because they are unstructured, and unformatted to allow essential content to be found. This study determined how best to organize a huge amount of clinical data to evaluate the upper aerodigestive tract cancers' clinical features and outcomes, including cancer of the head and neck, esophagus, lung, thymus, and mesothelioma.MethodsThe Real-time autOmatically updated data warehOuse in healThcare (ROOT) uses six main regions to describe the journey of cancer patients. This study, developed an algorithm optimized for each disease category using natural language processing of unstructured data and data capture of structured data. Data from patients diagnosed at the Samsung Medical Center from 2008-2020 were used.ResultsComprehensive clinical data for 67,617 patients across six tumor types: 28,954 with non-small-cell lung cancer, 2,540 with small-cell lung cancer, 30,035 with head and neck cancer, 4,950 with esophageal cancer, 966 with thymic cancer, and 172 with mesothelioma were collected. Additionally, the results of a longitudinal molecular study, including epidermal growth factor receptor (EGFR) mutations, anaplastic lymphoma kinase (ALK) tests, and next-generation sequencing (NGS), were included. Scattered information was integrated and automatically built up to match the cohort, allowing users to capture the most updated test results and treatment outcomes.ConclusionsThis landmark study documented the successful construction of a real-time updating system for medical big data, based on the CDW program.
| S-EPMC8577969 | biostudies-literature
Project description:MotivationWith the development in single-cell multi-omics sequencing technology and data integration algorithms, we have entered the single-cell multi-omics era. Current multi-omics analysis algorithms failed to systematically dissect the heterogeneity within the datasets when inferring cis-regulatory events. Thus, there is a need for cis-regulatory element inferring algorithms that considers the cellular heterogeneity.ResultsHere, we propose scGREAT, a single-cell multi-omics regulatory state analysis Python package with a rapid graph-based correlation measurement L. The graph-based correlation method assigns each cell a local L index, pinpointing specific cell groups of certain regulatory states. Such single-cell resolved regulatory state information enables the heterogeneity analysis equipped in the package. Applying scGREAT to the 10X Multiome PBMC dataset, we demonstrated how it could help subcluster cell types, infer regulation-based pseudo-time trajectory, discover feature modules, and find cluster-specific regulatory gene-peak pairs. Besides, we showed that global L index, which is the average of all local L values, is a better replacement for Pearson's r in ruling out confounding regulatory relationships that are not of research interests.Availabilityhttps://github.com/ChaozhongLiu/scGREAT.
| S-EPMC9900895 | biostudies-literature
Project description:BACKGROUND:Flow cytometry (FCM) is a powerful single-cell based measurement method to ascertain multidimensional optical properties of millions of cells. FCM is widely used in medical diagnostics and health research. There is also a broad range of applications in the analysis of complex microbial communities. The main concern in microbial community analyses is to track the dynamics of microbial subcommunities. So far, this can be achieved with the help of time-consuming manual clustering procedures that require extensive user-dependent input. In addition, several tools have recently been developed by using different approaches which, however, focus mainly on the clustering of medical FCM data or of microbial samples with a well-known background, while much less work has been done on high-throughput, online algorithms for two-channel FCM. RESULTS:We bridge this gap with flowEMMi, a model-based clustering tool based on multivariate Gaussian mixture models with subsampling and foreground/background separation. These extensions provide a fast and accurate identification of cell clusters in FCM data, in particular for microbial community FCM data that are often affected by irrelevant information like technical noise, beads or cell debris. flowEMMi outperforms other available tools with regard to running time and information content of the clustering results and provides near-online results and optional heuristics to reduce the running-time further. CONCLUSIONS:flowEMMi is a useful tool for the automated cluster analysis of microbial FCM data. It overcomes the user-dependent and time-consuming manual clustering procedure and provides consistent results with ancillary information and statistical proof.
| S-EPMC6902487 | biostudies-literature
Project description:The objective of this case report is to evaluate the use of a clinical data warehouse coupled with a clinical information system to test and refine alerts for medication orders control before they were fully implemented. A clinical decision rule refinement process was used to assess alerts. The criteria assessed were the frequencies of alerts for initial prescriptions of 10 medications whose dosage levels depend on renal function thresholds. In the first iteration of the process, the frequency of the 'exceeds maximum daily dose' alerts was 7.10% (617/8692), while that of the 'under dose' alerts was 3.14% (273/8692). Indicators were presented to the experts. During the different iterations of the process, 45 (16.07%) decision rules were removed, 105 (37.5%) were changed and 136 new rules were introduced. Extensive retrospective analysis of physicians' medication orders stored in a clinical data warehouse facilitates alert optimization toward the goal of maximizing the safety of the patient and minimizing overridden alerts.
| S-EPMC3422842 | biostudies-other
Project description:Long reads that cover more variants per read raise opportunities for accurate haplotype construction, whereas the genotype errors of single nucleotide polymorphisms pose great computational challenges for haplotyping tools. Here we introduce KSNP, an efficient haplotype construction tool based on the de Bruijn graph (DBG). KSNP leverages the ability of DBG in handling high-throughput erroneous reads to tackle the challenges. Compared to other notable tools in this field, KSNP achieves at least 5-fold speedup while producing comparable haplotype results. The time required for assembling human haplotypes is reduced to nearly the data-in time.
| S-EPMC11009271 | biostudies-literature
Project description:MitoMiner (http://mitominer.mrc-mbu.cam.ac.uk/) is a data warehouse for the storage and analysis of mitochondrial proteomics data gathered from publications of mass spectrometry and green fluorescent protein tagging studies. In MitoMiner, these data are integrated with data from UniProt, Gene Ontology, Online Mendelian Inheritance in Man, HomoloGene, Kyoto Encyclopaedia of Genes and Genomes and PubMed. The latest release of MitoMiner stores proteomics data sets from 46 studies covering 11 different species from eumetazoa, viridiplantae, fungi and protista. MitoMiner is implemented by using the open source InterMine data warehouse system, which provides a user interface allowing users to upload data for analysis, personal accounts to store queries and results and enables queries of any data in the data model. MitoMiner also provides lists of proteins for use in analyses, including the new MitoMiner mitochondrial proteome reference sets that specify proteins with substantial experimental evidence for mitochondrial localization. As further mitochondrial proteomics data sets from normal and diseased tissue are published, MitoMiner can be used to characterize the variability of the mitochondrial proteome between tissues and investigate how changes in the proteome may contribute to mitochondrial dysfunction and mitochondrial-associated diseases such as cancer, neurodegenerative diseases, obesity, diabetes, heart failure and the ageing process.
| S-EPMC3245170 | biostudies-literature
Project description:The selection of coarse-grained (CG) mapping operators is a critical step for CG molecular dynamics (MD) simulation. It is still an open question about what is optimal for this choice and there is a need for theory. The current state-of-the art method is mapping operators manually selected by experts. In this work, we demonstrate an automated approach by viewing this problem as supervised learning where we seek to reproduce the mapping operators produced by experts. We present a graph neural network based CG mapping predictor called Deep Supervised Graph Partitioning Model (DSGPM) that treats mapping operators as a graph segmentation problem. DSGPM is trained on a novel dataset, Human-annotated Mappings (HAM), consisting of 1180 molecules with expert annotated mapping operators. HAM can be used to facilitate further research in this area. Our model uses a novel metric learning objective to produce high-quality atomic features that are used in spectral clustering. The results show that the DSGPM outperforms state-of-the-art methods in the field of graph segmentation. Finally, we find that predicted CG mapping operators indeed result in good CG MD models when used in simulation.
| S-EPMC8161155 | biostudies-literature
Project description:Several challenges remain in data-independent acquisition (DIA) data analysis, such as to confidently identify peptides, define integration boundaries, remove interferences, and control false discovery rates. In practice, a visual inspection of the signals is still required, which is impractical with large datasets. We present Avant-garde as a tool to refine DIA (and parallel reaction monitoring) data. Avant-garde uses a novel data-driven scoring strategy: signals are refined by learning from the dataset itself, using all measurements in all samples to achieve the best optimization. We evaluate the performance of Avant-garde using benchmark DIA datasets and show that it can determine the quantitative suitability of a peptide peak, and reach the same levels of selectivity, accuracy, and reproducibility as manual validation. Avant-garde is complementary to existing DIA analysis engines and aims to establish a strong foundation for subsequent analysis of quantitative mass spectrometry data.
| S-EPMC7723322 | biostudies-literature
Project description:Exploration of the chemical reaction space of chemical transformations in multicomponent mixtures is one of the main challenges in contemporary computational chemistry. To remove expert bias from mechanistic studies and to discover new chemistries, an automated graph-theoretical methodology is proposed, which puts forward a network formalism of homogeneous catalysis reactions and utilizes a network analysis tool for mechanistic studies. The method can be used for analyzing trajectories with single and multiple catalytic species and can provide unique conformers of catalysts including multinuclear catalyst clusters along with other catalytic mixture components. The presented three-step approach has the integrated ability to handle multicomponent catalytic systems of arbitrary complexity (mixtures of reactants, catalyst precursors, ligands, additives, and solvents). It is not limited to predefined chemical rules, does not require prealignment of reaction mixture components consistent with a reaction coordinate, and is not agnostic to the chemical nature of transformations. Conformer exploration, reactive event identification, and reaction network analysis are the main steps taken for identifying the pathways in catalytic systems given the starting precatalytic reaction mixture as the input. Such a methodology allows us to efficiently explore catalytic systems in realistic conditions for either previously observed or completely unknown reactive events in the context of a network representing different intermediates. Our workflow for the catalytic reaction space exploration exclusively focuses on the identification of thermodynamically feasible conversion channels, representative of the (secondary) catalyst deactivation or inhibition paths, which are usually most difficult to anticipate based solely on expert chemical knowledge. Thus, the expert bias is sought to be removed at all steps, and the chemical intuition is limited to the choice of the thermodynamic constraint imposed by the applicable experimental conditions in terms of threshold energy values for allowed transformations. The capabilities of the proposed methodology have been tested by exploring the reactivity of Mn complexes relevant for catalytic hydrogenation chemistry to verify previously postulated activation mechanisms and unravel unexpected reaction channels relevant to rare deactivation events.
| S-EPMC9753598 | biostudies-literature
Project description:BackgroundWe present a biological data warehouse called Atlas that locally stores and integrates biological sequences, molecular interactions, homology information, functional annotations of genes, and biological ontologies. The goal of the system is to provide data, as well as a software infrastructure for bioinformatics research and development.DescriptionThe Atlas system is based on relational data models that we developed for each of the source data types. Data stored within these relational models are managed through Structured Query Language (SQL) calls that are implemented in a set of Application Programming Interfaces (APIs). The APIs include three languages: C++, Java, and Perl. The methods in these API libraries are used to construct a set of loader applications, which parse and load the source datasets into the Atlas database, and a set of toolbox applications which facilitate data retrieval. Atlas stores and integrates local instances of GenBank, RefSeq, UniProt, Human Protein Reference Database (HPRD), Biomolecular Interaction Network Database (BIND), Database of Interacting Proteins (DIP), Molecular Interactions Database (MINT), IntAct, NCBI Taxonomy, Gene Ontology (GO), Online Mendelian Inheritance in Man (OMIM), LocusLink, Entrez Gene and HomoloGene. The retrieval APIs and toolbox applications are critical components that offer end-users flexible, easy, integrated access to this data. We present use cases that use Atlas to integrate these sources for genome annotation, inference of molecular interactions across species, and gene-disease associations.ConclusionThe Atlas biological data warehouse serves as data infrastructure for bioinformatics research and development. It forms the backbone of the research activities in our laboratory and facilitates the integration of disparate, heterogeneous biological sources of data enabling new scientific inferences. Atlas achieves integration of diverse data sets at two levels. First, Atlas stores data of similar types using common data models, enforcing the relationships between data types. Second, integration is achieved through a combination of APIs, ontology, and tools. The Atlas software is freely available under the GNU General Public License at: http://bioinformatics.ubc.ca/atlas/
| S-EPMC554782 | biostudies-literature