Dataset Information

GROMeR: A Pipeline for Geodesic Refinement of Mesh Registration.

ABSTRACT: The electrical signals produced by the heart can be used to assess cardiac health and diagnose adverse pathologies. Experiments on large mammals provide essential sources of these signals through measurements of up to 1000 simultaneous, distributed locations throughout the heart and torso. To perform accurate spatial analysis of the resulting electrical recordings, researchers must register the locations of each electrode, typically by defining correspondence points from post-experiment, three-dimensional imaging, and directly measured surface electrodes. Often, due to the practical limitations of the experimental situation, only a subset of the electrode locations can be measured, from which the rest must be estimated. We have developed a pipeline, GRÖMeR, that can perform registration of cardiac surface electrode arrays given a limited correspondence point set. This pipeline accounts for global deformations and uses a modified iterative closest points algorithm followed by a geodesically constrained radial basis deformation to calculate a smooth, correspondence-driven registration. To assess the performance of this pipeline, we generated a series of target geometries and limited correspondence patterns based on experimental scenarios. We found that the best performing correspondence pattern required only 20, approximately uniformly distributed points over the epicardial surface of the heart. This study demonstrated the GRÖMeR pipeline to be an accurate and effective way to register cardiac sock electrode arrays from limited correspondence points.

SUBMITTER: Bergquist JA

PROVIDER: S-EPMC6889814 | biostudies-literature | 2019 Jun

REPOSITORIES: biostudies-literature

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Publications

GRÖMeR: A Pipeline for Geodesic Refinement of Mesh Registration.

Bergquist Jake A JA Good Wilson W WW Zenger Brian B Tate Jess D JD MacLeod Rob S RS

Functional imaging and modeling of the heart : ... International Workshop, FIMH ..., proceedings. FIMH 20190530

The electrical signals produced by the heart can be used to assess cardiac health and diagnose adverse pathologies. Experiments on large mammals provide essential sources of these signals through measurements of up to 1000 simultaneous, distributed locations throughout the heart and torso. To perform accurate spatial analysis of the resulting electrical recordings, researchers must register the locations of each electrode, typically by defining correspondence points from post-experiment, three-d ...[more]

PMID: 31799512

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Project description:BackgroundIntegration of medicinal chemistry data from numerous public resources is an increasingly important part of academic drug discovery and translational research because it can bring a wealth of important knowledge related to compounds in one place. However, different data sources can report the same or related compounds in various forms (e.g., tautomers, racemates, etc.), thus highlighting the need of organising related compounds in hierarchies that alert the user on important bioactivity data that may be relevant. To generate these compound hierarchies, we have developed and implemented canSARchem, a new compound registration and standardization pipeline as part of the canSAR public knowledgebase. canSARchem builds on previously developed ChEMBL and PubChem pipelines and is developed using KNIME. We describe the pipeline which we make publicly available, and we provide examples on the strengths and limitations of the use of hierarchies for bioactivity data exploration. Finally, we identify canonicalization enrichment in FDA-approved drugs, illustrating the benefits of our approach.ResultsWe created a chemical registration and standardization pipeline in KNIME and made it freely available to the research community. The pipeline consists of five steps to register the compounds and create the compounds' hierarchy: 1. Structure checker, 2. Standardization, 3. Generation of canonical tautomers and representative structures, 4. Salt strip, and 5. Generation of abstract structure to generate the compound hierarchy. Unlike ChEMBL's RDKit pipeline, we carry out compound canonicalization ahead of getting the parent structure, similar to PubChem's OpenEye pipeline. canSARchem has a lower rejection rate compared to both PubChem and ChEMBL. We use our pipeline to assess the impact of grouping the compounds in hierarchies for bioactivity data exploration. We find that FDA-approved drugs show statistically significant sensitivity to canonicalization compared to the majority of bioactive compounds which demonstrates the importance of this step.ConclusionsWe use canSARchem to standardize all the compounds uploaded in canSAR (> 3 million) enabling efficient data integration and the rapid identification of alternative compound forms with useful bioactivity data. Comparison with PubChem and ChEMBL pipelines evidenced comparable performances in compound standardization, but only PubChem and canSAR canonicalize tautomers and canSAR has a slightly lower rejection rate. Our results highlight the importance of compound hierarchies for bioactivity data exploration. We make canSARchem available under a Creative Commons Attribution-ShareAlike 4.0 International License (CC BY-SA 4.0) at https://gitlab.icr.ac.uk/cansar-public/compound-registration-pipeline .

Dataset Information

GROMeR: A Pipeline for Geodesic Refinement of Mesh Registration.

Publications

GRÖMeR: A Pipeline for Geodesic Refinement of Mesh Registration.

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