ComPath: An ecosystem for exploring, analyzing, and curating mappings across pathway databases

AbstractAlthough pathways are widely used for the analysis and representation of biological systems, their lack of clear boundaries, their dispersion across numerous databases, and the lack of interoperability impedes the evaluation of the coverage, agreements, and discrepancies between them. Here, we present ComPath, an ecosystem that supports curation of pathway mappings between databases and fosters the exploration of pathway knowledge through several novel visualizations. We have curated mappings between three of the major pathway databases and present a case study focusing on Parkinson’s disease that illustrates how ComPath can generate new biological insights by identifying pathway modules, clusters, and cross-talks with these mappings. The ComPath source code and resources are available at https://github.com/ComPath and the web application can be accessed at http://compath.scai.fraunhofer.de/.

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A decoupled, modular and scriptable architecture for tools to curate data platforms

10.1101/2020.09.28.282699 ◽

2020 ◽

Author(s):

Moritz Langenstein ◽

Henning Hermjakob ◽

Manuel Bernal Llinares

Keyword(s):

Web Application ◽

Production Systems ◽

Source Code ◽

Black Box ◽

Command Line ◽

Web Interface ◽

Link Type ◽

Data Platform ◽

The Web

AbstractMotivationCuration is essential for any data platform to maintain the quality of the data it provides. Existing databases, which require maintenance, and the amount of newly published information that needs to be surveyed, are growing rapidly. More efficient curation is often vital to keep up with this growth, requiring modern curation tools. However, curation interfaces are often complex and difficult to further develop. Furthermore, opportunities for experimentation with curation workflows may be lost due to a lack of development resources, or a reluctance to change sensitive production systems.ResultsWe propose a decoupled, modular and scriptable architecture to build curation tools on top of existing platforms. Instead of modifying the existing infrastructure, our architecture treats the existing platform as a black box and relies only on its public APIs and web application. As a decoupled program, the tool’s architecture gives more freedom to developers and curators. This added flexibility allows for quickly prototyping new curation workflows as well as adding all kinds of analysis around the data platform. The tool can also streamline and enhance the curator’s interaction with the web interface of the platform. We have implemented this design in cmd-iaso, a command-line curation tool for the identifiers.org registry.AvailabilityThe cmd-iaso curation tool is implemented in Python 3.7+ and supports Linux, macOS and Windows. Its source code and documentation are freely available from https://github.com/identifiers-org/cmd-iaso. It is also published as a Docker container at https://hub.docker.com/r/identifiersorg/[email protected]

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Evaluating the Feasibility and the Potential Efficacy of e-Learning-Based Speech Therapy (EST) as a Web Application for Speech Training in Dysarthric Patients with Parkinson's Disease: A Case Study

Telemedicine Journal and e-Health ◽

10.1089/tmj.2009.0183 ◽

2010 ◽

Vol 16 (6) ◽

pp. 732-738 ◽

Cited By ~ 10

Author(s):

Lilian J. Beijer ◽

Toni C.M. Rietveld ◽

Vera Hoskam ◽

Alexander C.H. Geurts ◽

Bert J.M. de Swart

Keyword(s):

Parkinson’S Disease ◽

Parkinson's Disease ◽

Web Application ◽

Speech Therapy ◽

Potential Efficacy ◽

E Learning ◽

Speech Training

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ROLE OF ENVIRONMENTAL RISK FACTORS IN PARKINSON'S DISEASE: BUCOVINA REGION CASE STUDY

Environmental Engineering and Management Journal ◽

10.30638/eemj.2015.260 ◽

2015 ◽

Vol 14 (10) ◽

pp. 2435-2444

Author(s):

Oana Geman ◽

Hariton Costin

Keyword(s):

Risk Factors ◽

Parkinson’S Disease ◽

Parkinson's Disease ◽

Environmental Risk ◽

Environmental Risk Factors

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Exenatide once weekly over 2 years as a potential disease-modifying treatment for Parkinson’s disease: protocol for a multicentre, randomised, double blind, parallel group, placebo controlled, phase 3 trial: The ‘Exenatide-PD3’ study

BMJ Open ◽

10.1136/bmjopen-2020-047993 ◽

2021 ◽

Vol 11 (5) ◽

pp. e047993

Author(s):

Nirosen Vijiaratnam ◽

Christine Girges ◽

Grace Auld ◽

Marisa Chau ◽

Kate Maclagan ◽

...

Keyword(s):

Parkinson’S Disease ◽

Parkinson's Disease ◽

Primary Outcome ◽

Phase 3 ◽

Double Blind ◽

Treatment Groups ◽

Link Type ◽

South Central ◽

Disease Modifying ◽

Secondary Outcomes

IntroductionParkinson’s disease (PD) is a common neurodegenerative disorder with substantial morbidity. No disease-modifying treatments currently exist. The glucagon like peptide-1 receptor agonist exenatide has been associated in single-centre studies with reduced motor deterioration over 1 year. The aim of this multicentre UK trial is to confirm whether these previous positive results are maintained in a larger number of participants over 2 years and if effects accumulate with prolonged drug exposure.Methods and analysisThis is a phase 3, multicentre, double-blind, randomised, placebo-controlled trial of exenatide at a dose of 2 mg weekly in 200 participants with mild to moderate PD. Treatment duration is 96 weeks. Randomisation is 1:1, drug to placebo. Assessments are performed at baseline, week 12, 24, 36, 48, 60, 72, 84 and 96 weeks.The primary outcome is the comparison of Movement Disorders Society Unified Parkinson’s Disease Rating Scale part 3 motor subscore in the practically defined OFF medication state at 96 weeks between participants according to treatment allocation. Secondary outcomes will compare the change between groups among other motor, non-motor and cognitive scores. The primary outcome will be reported using descriptive statistics and comparisons between treatment groups using a mixed model, adjusting for baseline scores. Secondary outcomes will be summarised between treatment groups using summary statistics and appropriate statistical tests to assess for significant differences.Ethics and disseminationThis trial has been approved by the South Central-Berkshire Research Ethics Committee and the Health Research Authority. Results will be disseminated in peer-reviewed journals, presented at scientific meetings and to patients in lay-summary format.Trial registration numbersNCT04232969, ISRCTN14552789.

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Vitamin D supplementation helps to struggle musculoskeletal pain in Parkinson's disease - Clinical case study

Parkinsonism & Related Disorders ◽

10.1016/j.parkreldis.2020.06.245 ◽

2020 ◽

Vol 79 ◽

pp. e66-e67

Author(s):

G. Sahakyan ◽

H. Manvelyan

Keyword(s):

Parkinson’S Disease ◽

Vitamin D ◽

Parkinson's Disease ◽

Musculoskeletal Pain ◽

Clinical Case ◽

Vitamin D Supplementation ◽

Clinical Case Study

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A Case Study of Balance Rehabilitation in Parkinson's Disease

Global Journal of Health Science ◽

10.5539/gjhs.v3n1p90 ◽

2011 ◽

Vol 3 (1) ◽

Author(s):

Stanley John Winser ◽

Priya Kannan

Keyword(s):

Parkinson’S Disease ◽

Parkinson's Disease ◽

Balance Rehabilitation

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Allelic variant in SLC6A3 rs393795 affects cerebral regional homogeneity and gait dysfunction in patients with Parkinson’s disease

PeerJ ◽

10.7717/peerj.7957 ◽

2019 ◽

Vol 7 ◽

pp. e7957

Author(s):

Lina Wang ◽

Yongsheng Yuan ◽

Jianwei Wang ◽

Yuting Shen ◽

Yan Zhi ◽

...

Keyword(s):

Parkinson’S Disease ◽

Parkinson's Disease ◽

Allelic Variation ◽

Inferior Frontal Gyrus ◽

Freezing Of Gait ◽

Clinical Manifestations ◽

Regional Homogeneity ◽

Allelic Variant ◽

Analysis Of Covariance ◽

Link Type

Aims We sought to explore the role of the SLC6A3 rs393795 allelic variant in cerebral spontaneous activity and clinical features in Parkinson’s disease (PD) via imaging genetic approach. Methods Our study recruited 50 PD and 45 healthy control (HC) participants to provide clinical, genetic, and resting state functional magnetic resonance imaging (rs-fMRI) data. All subjects were separated into 16 PD-AA, 34 PD-CA/CC, 14 HC-AA, and 31 HC-CA/CC four subgroups according to SLC6A3 rs393795 genotyping. Afterwards, main effects and interactions of groups (PD versus HC) and genotypes (AA versus CA/CC) on cerebral function reflected by regional homogeneity (ReHo) were explored using two-way analysis of covariance (ANCOVA) after controlling age and gender. Finally, Spearman’ s correlations were employed to investigate the relationships between significantly interactive brain regions and clinical manifestations in PD subgroups. Results Compared with HC subjects, PD patients exhibited increased ReHo signals in left middle temporal gyrus and decreased ReHo signals in left pallidum. Compared with CA/CC carriers, AA genotype individuals showed abnormal increased ReHo signals in right inferior frontal gyrus (IFG) and supplementary motor area (SMA). Moreover, significant interactions (affected by both disease factor and allelic variation) were detected in right inferior temporal gyrus (ITG). Furthermore, aberrant increased ReHo signals in right ITG were observed in PD-AA in comparison with PD-CA/CC. Notably, ReHo values in right ITG were negatively associated with Tinetti Mobility Test (TMT) gait subscale scores and positively related to Freezing of Gait Questionnaire (FOG-Q) scores in PD-AA subgroup. Conclusions Our findings suggested that SLC6A3 rs393795 allelic variation might have a trend to aggravate the severity of gait disorders in PD patients by altering right SMA and IFG function, and ultimately result in compensatory activation of right ITG. It could provide us with a new perspective for exploring deeply genetic mechanisms of gait disturbances in PD.

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