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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

Automated data retrieval of Alzheimer’s Disease specific gene expression studies from ArrayExpress and GEO. Here, the dotted line represents the sequence of query performed. Alzheimer’s disease specific experiment IDs were automatically retrieved from GEO and ArrayExpress, using keywords, through eSearch and REST service respectively. Metadata information was extracted by automatically parsing sample information files (SDRF and SOFT) of these experiment IDs.
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bav099-F2: Automated data retrieval of Alzheimer’s Disease specific gene expression studies from ArrayExpress and GEO. Here, the dotted line represents the sequence of query performed. Alzheimer’s disease specific experiment IDs were automatically retrieved from GEO and ArrayExpress, using keywords, through eSearch and REST service respectively. Metadata information was extracted by automatically parsing sample information files (SDRF and SOFT) of these experiment IDs.

Mentions: Putative AD studies were programmatically retrieved from GEO and ArrayExpress by applying a recall-optimized keyword search approach, cf.Figure 2. The keywords include a set of AD synonyms such as ‘Alzheimer’, ‘Alzheimer’s’ or ‘AD’ in combination with a species filter. Since ArrayExpress imports and curates the majority of GEO experiments, we firstly queried the former through its REST service (http://www.ebi.ac.uk/arrayexpress/help/programmatic_access.html). Conjointly, we further queried GEO using the eSearch Entrez Programming Utilities (E-utils) service to fetch additional identifiers (IDs), which were not picked up by the previous query (http://www.ncbi.nlm.nih.gov/geo/info/geo_paccess.html). The final list of unified experiment IDs was downloaded (along with their metadata) and stored in NeuroTransDB. Metadata information was captured from Sample and Data Relationship Format (SDRF) file of ArrayExpress and SOFT file of GEO (https://www.ebi.ac.uk/fgpt/magetab/help/creating_a_sdrf.html and http://www.ncbi.nlm.nih.gov/geo/info/soft.html). The above-described steps are fully automated; enabling an automatic update procedure we run every 6 months to obtain new published studies.Figure 2.


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)

Automated data retrieval of Alzheimer’s Disease specific gene expression studies from ArrayExpress and GEO. Here, the dotted line represents the sequence of query performed. Alzheimer’s disease specific experiment IDs were automatically retrieved from GEO and ArrayExpress, using keywords, through eSearch and REST service respectively. Metadata information was extracted by automatically parsing sample information files (SDRF and SOFT) of these experiment IDs.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

bav099-F2: Automated data retrieval of Alzheimer’s Disease specific gene expression studies from ArrayExpress and GEO. Here, the dotted line represents the sequence of query performed. Alzheimer’s disease specific experiment IDs were automatically retrieved from GEO and ArrayExpress, using keywords, through eSearch and REST service respectively. Metadata information was extracted by automatically parsing sample information files (SDRF and SOFT) of these experiment IDs.
Mentions: Putative AD studies were programmatically retrieved from GEO and ArrayExpress by applying a recall-optimized keyword search approach, cf.Figure 2. The keywords include a set of AD synonyms such as ‘Alzheimer’, ‘Alzheimer’s’ or ‘AD’ in combination with a species filter. Since ArrayExpress imports and curates the majority of GEO experiments, we firstly queried the former through its REST service (http://www.ebi.ac.uk/arrayexpress/help/programmatic_access.html). Conjointly, we further queried GEO using the eSearch Entrez Programming Utilities (E-utils) service to fetch additional identifiers (IDs), which were not picked up by the previous query (http://www.ncbi.nlm.nih.gov/geo/info/geo_paccess.html). The final list of unified experiment IDs was downloaded (along with their metadata) and stored in NeuroTransDB. Metadata information was captured from Sample and Data Relationship Format (SDRF) file of ArrayExpress and SOFT file of GEO (https://www.ebi.ac.uk/fgpt/magetab/help/creating_a_sdrf.html and http://www.ncbi.nlm.nih.gov/geo/info/soft.html). The above-described steps are fully automated; enabling an automatic update procedure we run every 6 months to obtain new published studies.Figure 2.

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