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NeuroTransDB: highly curated and structured transcriptomic metadata for neurodegenerative diseases.

Bagewadi S, Adhikari S, Dhrangadhariya A, Irin AK, Ebeling C, Namasivayam AA, Page M, Hofmann-Apitius M, Senger P - Database (Oxford) (2015)

Bottom Line: Much of the information to complete, or refine meta-annotations are distributed in the associated publications.Curated metadata for Alzheimer's disease gene expression studies are available for download.Database URL: www.scai.fraunhofer.de/NeuroTransDB.html.

View Article: PubMed Central - PubMed

Affiliation: Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, 53754 Sankt Augustin, Germany, Rheinische Friedrich-Wilhelms-Universitaet Bonn, Bonn-Aachen International Center for Information Technology, 53113, Bonn, Germany, shweta.bagewadi@scai.fraunhofer.de.

No MeSH data available.


Related in: MedlinePlus

Experiment prioritization for metadata curation in NeuroTransDB. All the downloaded Alzheimer’s Disease experiments were first checked for their disease relevancy. Those experiments which were falsely retrieved, are marked as unrelated. The remaining experiments were classified into one of two priority classes based on the experiment type: In vivo or In vitro studies. For priority 1, we considered direct/primary samples from human or animal models such as brain tissue, blood, etc. Experiments that were conducted on derived sample sources such as cell lines, were put into priority 2 class.
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bav099-F3: Experiment prioritization for metadata curation in NeuroTransDB. All the downloaded Alzheimer’s Disease experiments were first checked for their disease relevancy. Those experiments which were falsely retrieved, are marked as unrelated. The remaining experiments were classified into one of two priority classes based on the experiment type: In vivo or In vitro studies. For priority 1, we considered direct/primary samples from human or animal models such as brain tissue, blood, etc. Experiments that were conducted on derived sample sources such as cell lines, were put into priority 2 class.

Mentions: For integrative meta-analysis, combining studies that address the same objectives could minimize biases from cohort selection (inclusion and exclusion criteria) and other design effects. Anatomical and functional heterogeneity arising from experimental sample source, imposes yet another challenge for integrative analysis. Moreover, keyword-based, recall optimized retrieval of experiments does not guarantee its clinical relevancy to the queried indication or organism. Thus, we propose a straightforward binning approach to select potentially eligible studies for AD as illustrated in Figure 3.Figure 3.


NeuroTransDB: highly curated and structured transcriptomic metadata for neurodegenerative diseases.

Bagewadi S, Adhikari S, Dhrangadhariya A, Irin AK, Ebeling C, Namasivayam AA, Page M, Hofmann-Apitius M, Senger P - Database (Oxford) (2015)

Experiment prioritization for metadata curation in NeuroTransDB. All the downloaded Alzheimer’s Disease experiments were first checked for their disease relevancy. Those experiments which were falsely retrieved, are marked as unrelated. The remaining experiments were classified into one of two priority classes based on the experiment type: In vivo or In vitro studies. For priority 1, we considered direct/primary samples from human or animal models such as brain tissue, blood, etc. Experiments that were conducted on derived sample sources such as cell lines, were put into priority 2 class.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4608514&req=5

bav099-F3: Experiment prioritization for metadata curation in NeuroTransDB. All the downloaded Alzheimer’s Disease experiments were first checked for their disease relevancy. Those experiments which were falsely retrieved, are marked as unrelated. The remaining experiments were classified into one of two priority classes based on the experiment type: In vivo or In vitro studies. For priority 1, we considered direct/primary samples from human or animal models such as brain tissue, blood, etc. Experiments that were conducted on derived sample sources such as cell lines, were put into priority 2 class.
Mentions: For integrative meta-analysis, combining studies that address the same objectives could minimize biases from cohort selection (inclusion and exclusion criteria) and other design effects. Anatomical and functional heterogeneity arising from experimental sample source, imposes yet another challenge for integrative analysis. Moreover, keyword-based, recall optimized retrieval of experiments does not guarantee its clinical relevancy to the queried indication or organism. Thus, we propose a straightforward binning approach to select potentially eligible studies for AD as illustrated in Figure 3.Figure 3.

Bottom Line: Much of the information to complete, or refine meta-annotations are distributed in the associated publications.Curated metadata for Alzheimer's disease gene expression studies are available for download.Database URL: www.scai.fraunhofer.de/NeuroTransDB.html.

View Article: PubMed Central - PubMed

Affiliation: Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, 53754 Sankt Augustin, Germany, Rheinische Friedrich-Wilhelms-Universitaet Bonn, Bonn-Aachen International Center for Information Technology, 53113, Bonn, Germany, shweta.bagewadi@scai.fraunhofer.de.

No MeSH data available.


Related in: MedlinePlus