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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

Overall workflow for curation of gene expression studies related to neurodegeneration from public archives. The first step involves automated retrieval of gene expression studies (along with metadata) from public archives such as GEO, and ArrayExpress. The related studies were further assigned to one of the two prioritization classes (priority 1 or priority 2), based on the specific experimental variables. Next, manual curation was applied to capture missing metadata information on priority 1 studies. All the harvested metadata was normalized using standard vocabularies. Both raw and normalized data are stored in NeuroTransDB.
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bav099-F1: Overall workflow for curation of gene expression studies related to neurodegeneration from public archives. The first step involves automated retrieval of gene expression studies (along with metadata) from public archives such as GEO, and ArrayExpress. The related studies were further assigned to one of the two prioritization classes (priority 1 or priority 2), based on the specific experimental variables. Next, manual curation was applied to capture missing metadata information on priority 1 studies. All the harvested metadata was normalized using standard vocabularies. Both raw and normalized data are stored in NeuroTransDB.

Mentions: This section discusses the workflow we followed to retrieve relevant gene-expression datasets and to generate detailed metadata annotations for each study (Figure 1). First, we retrieved all functional genomics studies from GEO and ArrayExpress that reference Alzheimer’s disease (AD) or a set of AD synonyms, along with the provided metadata (cf. Data Retrieval section). Each study was then prioritised (cf. Experiment Prioritization section) based on the disease relevancy, experimental type and sample source. Only studies in the top prioritization category were subjected to rigorous, semiautomated metadata curation (cf. Metadata Curation section). Annotations are standardized by reference to controlled vocabularies for each extracted metadata dimension (cf. Normalization of Metadata Annotations section). The curated Alzheimer’s data is stored in NeuroTransDB, but in principle the proposed workflow can be applied with little adaptation to any disease indication, especially NDD.Figure 1.


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)

Overall workflow for curation of gene expression studies related to neurodegeneration from public archives. The first step involves automated retrieval of gene expression studies (along with metadata) from public archives such as GEO, and ArrayExpress. The related studies were further assigned to one of the two prioritization classes (priority 1 or priority 2), based on the specific experimental variables. Next, manual curation was applied to capture missing metadata information on priority 1 studies. All the harvested metadata was normalized using standard vocabularies. Both raw and normalized data are stored in NeuroTransDB.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

bav099-F1: Overall workflow for curation of gene expression studies related to neurodegeneration from public archives. The first step involves automated retrieval of gene expression studies (along with metadata) from public archives such as GEO, and ArrayExpress. The related studies were further assigned to one of the two prioritization classes (priority 1 or priority 2), based on the specific experimental variables. Next, manual curation was applied to capture missing metadata information on priority 1 studies. All the harvested metadata was normalized using standard vocabularies. Both raw and normalized data are stored in NeuroTransDB.
Mentions: This section discusses the workflow we followed to retrieve relevant gene-expression datasets and to generate detailed metadata annotations for each study (Figure 1). First, we retrieved all functional genomics studies from GEO and ArrayExpress that reference Alzheimer’s disease (AD) or a set of AD synonyms, along with the provided metadata (cf. Data Retrieval section). Each study was then prioritised (cf. Experiment Prioritization section) based on the disease relevancy, experimental type and sample source. Only studies in the top prioritization category were subjected to rigorous, semiautomated metadata curation (cf. Metadata Curation section). Annotations are standardized by reference to controlled vocabularies for each extracted metadata dimension (cf. Normalization of Metadata Annotations section). The curated Alzheimer’s data is stored in NeuroTransDB, but in principle the proposed workflow can be applied with little adaptation to any disease indication, especially NDD.Figure 1.

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