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Database Commons - NeuroTransDB

NeuroTransDB

Citations: 1

z-index 0.06

Short name NeuroTransDB
Full name Highly Curated and Structured Transcriptomic Metadata for Neurodegenerative Diseases
Description NeuroTransDB is a manually curated database containing metadata annotations for neurodegenerative studies.
URL https://www.scai.fraunhofer.de/index.php?id=5704
Year founded 2015
Last update & version 2015-10-16    
Availability Free to academic users only
University/Institution hosted Fraunhofer Institute for Algorithms and Scientific Computing
Address Schloss Birlinghoven, 53754 Sankt Augustin, Germany
City Sankt Augustin
Province/State
Country/Region Germany
Contact name Shweta Bagewadi
Contact email shweta.bagewadi@scai.fraunhofer.de
Data type(s)
Major organism(s)
Keyword(s)
  • neurodegenerative disease
  • transcriptome
Publication(s)
  • NeuroTransDB: highly curated and structured transcriptomic metadata for neurodegenerative diseases. [PMID: 26475471]

    Shweta Bagewadi, Subash Adhikari, Anjani Dhrangadhariya, Afroza Khanam Irin, Christian Ebeling, Aishwarya Alex Namasivayam, Matthew Page, Martin Hofmann-Apitius, Philipp Senger
    Database : the journal of biological databases and curation 2015:2015
    1 Citations (Google Scholar as of 2016-03-28)

    Abstract: Neurodegenerative diseases are chronic debilitating conditions, characterized by progressive loss of neurons that represent a significant health care burden as the global elderly population continues to grow. Over the past decade, high-throughput technologies such as the Affymetrix GeneChip microarrays have provided new perspectives into the pathomechanisms underlying neurodegeneration. Public transcriptomic data repositories, namely Gene Expression Omnibus and curated ArrayExpress, enable researchers to conduct integrative meta-analysis; increasing the power to detect differentially regulated genes in disease and explore patterns of gene dysregulation across biologically related studies. The reliability of retrospective, large-scale integrative analyses depends on an appropriate combination of related datasets, in turn requiring detailed meta-annotations capturing the experimental setup. In most cases, we observe huge variation in compliance to defined standards for submitted metadata in public databases. Much of the information to complete, or refine meta-annotations are distributed in the associated publications. For example, tissue preparation or comorbidity information is frequently described in an article's supplementary tables. Several value-added databases have employed additional manual efforts to overcome this limitation. However, none of these databases explicate annotations that distinguish human and animal models in neurodegeneration context. Therefore, adopting a more specific disease focus, in combination with dedicated disease ontologies, will better empower the selection of comparable studies with refined annotations to address the research question at hand. In this article, we describe the detailed development of NeuroTransDB, a manually curated database containing metadata annotations for neurodegenerative studies. The database contains more than 20 dimensions of metadata annotations within 31 mouse, 5 rat and 45 human studies, defined in collaboration with domain disease experts. We elucidate the step-by-step guidelines used to critically prioritize studies from public archives and their metadata curation and discuss the key challenges encountered. Curated metadata for Alzheimer's disease gene expression studies are available for download. Database URL: www.scai.fraunhofer.de/NeuroTransDB.html. © The Author(s) 2015. Published by Oxford University Press.

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Tags

Metadata
Homo sapiens Mus musculus Rattus norvegicus
neurodegenerative disease transcriptome

Record metadata

  • Created on: 2016-01-15
  • Curated by:
    • Lin Liu [2016-03-28]
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