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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

Frequency distribution and Trend Analysis of human priority 1 Alzheimer’s disease gene-expression experiments for availability of five basic annotation fields in GEO/ArrayExpress sample page versus manual curation. The five basic annotations considered here are age, gender, stage, phenotype and raw filename. (A) Red and blue line represents the linear trend analysis of the availability of meta-annotations for experiments (represented as dots) over years, which has declined. (B) The black line represents mean value of the number of annotation fields filled. It is evident from the shift in mean of the distribution analysis that manual curation plays a very important role in capturing the missing metadata information.
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bav099-F8: Frequency distribution and Trend Analysis of human priority 1 Alzheimer’s disease gene-expression experiments for availability of five basic annotation fields in GEO/ArrayExpress sample page versus manual curation. The five basic annotations considered here are age, gender, stage, phenotype and raw filename. (A) Red and blue line represents the linear trend analysis of the availability of meta-annotations for experiments (represented as dots) over years, which has declined. (B) The black line represents mean value of the number of annotation fields filled. It is evident from the shift in mean of the distribution analysis that manual curation plays a very important role in capturing the missing metadata information.

Mentions: We selected five of the most common metadata fields (common to any disease domain such as age, gender, phenotype, stage and raw filename) and carried out a trend analysis of information availability versus time. Figure 8 (A) shows the trend over time for the metadata information provided in the archives versus the number of annotation fields that can be harvested after manual curation for human AD priority 1 experiments. Although a bit obscure, we can observe that the level of information submitted to the databases remains almost stable in the last decade (between 2 and 4 metadata fields). Moreover, with manual curation support, we were able to capture the majority of the remaining metadata from associated publications, Figure 8 (B) shows the shift in the mean value of the metadata availability. However, the trend is recently declining since the authors submit relatively lesser level of detailed information than in former times in the associated publications.Figure 8.


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)

Frequency distribution and Trend Analysis of human priority 1 Alzheimer’s disease gene-expression experiments for availability of five basic annotation fields in GEO/ArrayExpress sample page versus manual curation. The five basic annotations considered here are age, gender, stage, phenotype and raw filename. (A) Red and blue line represents the linear trend analysis of the availability of meta-annotations for experiments (represented as dots) over years, which has declined. (B) The black line represents mean value of the number of annotation fields filled. It is evident from the shift in mean of the distribution analysis that manual curation plays a very important role in capturing the missing metadata information.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

bav099-F8: Frequency distribution and Trend Analysis of human priority 1 Alzheimer’s disease gene-expression experiments for availability of five basic annotation fields in GEO/ArrayExpress sample page versus manual curation. The five basic annotations considered here are age, gender, stage, phenotype and raw filename. (A) Red and blue line represents the linear trend analysis of the availability of meta-annotations for experiments (represented as dots) over years, which has declined. (B) The black line represents mean value of the number of annotation fields filled. It is evident from the shift in mean of the distribution analysis that manual curation plays a very important role in capturing the missing metadata information.
Mentions: We selected five of the most common metadata fields (common to any disease domain such as age, gender, phenotype, stage and raw filename) and carried out a trend analysis of information availability versus time. Figure 8 (A) shows the trend over time for the metadata information provided in the archives versus the number of annotation fields that can be harvested after manual curation for human AD priority 1 experiments. Although a bit obscure, we can observe that the level of information submitted to the databases remains almost stable in the last decade (between 2 and 4 metadata fields). Moreover, with manual curation support, we were able to capture the majority of the remaining metadata from associated publications, Figure 8 (B) shows the shift in the mean value of the metadata availability. However, the trend is recently declining since the authors submit relatively lesser level of detailed information than in former times in the associated publications.Figure 8.

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