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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

Priority classification statistics for Alzheimer’s disease gene expression experiments retrieved from ArrayExpress and GEO (for human, mouse and rat). Alzheimer’s disease experiments were retrieved using keywords. Applying the Experiment Prioritization guidelines, they were manually classified to one of the priority classes. Among them, 20% of the experiments were not related to Alzheimer’s disease. The digits on the bars represent number of experiments.
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bav099-F6: Priority classification statistics for Alzheimer’s disease gene expression experiments retrieved from ArrayExpress and GEO (for human, mouse and rat). Alzheimer’s disease experiments were retrieved using keywords. Applying the Experiment Prioritization guidelines, they were manually classified to one of the priority classes. Among them, 20% of the experiments were not related to Alzheimer’s disease. The digits on the bars represent number of experiments.

Mentions: Further on, just by applying these two filter criteria does not assure that all retained experiments were specific to AD. For example, there could be some experiments that aim at a certain pathway that are also relevant in the area of neurodegeneration, but the experiment submitted to the repository does not deal with AD pathology. As a consequence, additional disease relevancy conditions were included before prioritization (cf. Experiment Prioritization section). An overview of all the retrieved AD experiments, categorized to one of the priority classes is shown in Figure 6. In addition, a list of priority 1 experiments (for human, mouse and rat) is provided in Supplementary file S5. This figure indicates that nearly 20% of the retrieved studies are in any case not related to AD. On the other hand, to identify the remaining 80% of the experiments (prioritized as 1 and 2) we need massive manual filtering by trained personnel. Only if the archives take an initiative to apply such a structured classification for all uploaded experiments, individual time-cost can be reduced to a greater extent.Figure 6.


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)

Priority classification statistics for Alzheimer’s disease gene expression experiments retrieved from ArrayExpress and GEO (for human, mouse and rat). Alzheimer’s disease experiments were retrieved using keywords. Applying the Experiment Prioritization guidelines, they were manually classified to one of the priority classes. Among them, 20% of the experiments were not related to Alzheimer’s disease. The digits on the bars represent number of experiments.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

bav099-F6: Priority classification statistics for Alzheimer’s disease gene expression experiments retrieved from ArrayExpress and GEO (for human, mouse and rat). Alzheimer’s disease experiments were retrieved using keywords. Applying the Experiment Prioritization guidelines, they were manually classified to one of the priority classes. Among them, 20% of the experiments were not related to Alzheimer’s disease. The digits on the bars represent number of experiments.
Mentions: Further on, just by applying these two filter criteria does not assure that all retained experiments were specific to AD. For example, there could be some experiments that aim at a certain pathway that are also relevant in the area of neurodegeneration, but the experiment submitted to the repository does not deal with AD pathology. As a consequence, additional disease relevancy conditions were included before prioritization (cf. Experiment Prioritization section). An overview of all the retrieved AD experiments, categorized to one of the priority classes is shown in Figure 6. In addition, a list of priority 1 experiments (for human, mouse and rat) is provided in Supplementary file S5. This figure indicates that nearly 20% of the retrieved studies are in any case not related to AD. On the other hand, to identify the remaining 80% of the experiments (prioritized as 1 and 2) we need massive manual filtering by trained personnel. Only if the archives take an initiative to apply such a structured classification for all uploaded experiments, individual time-cost can be reduced to a greater extent.Figure 6.

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