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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.

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Related in: MedlinePlus

Distribution of MIAME and MINSEQE scores for all automatically retrieved Alzheimer’s Disease gene expression experiments in ArrayExpress Database (for human, mouse and rat), as of December 2014. Percentage is calculated as (total number of AD experiments with a certain score)/(total number of AD experiments). ‘NA’ are the experiments which were not present in ArrayExpress. These scores reflect adherence to compliance standards by the data submitters, needed for re-investigation and reproducibility. It is observed that large percentage of experiments fall under score 4, shows that the required minimum information is still incomplete. The list of experiment IDs along with their associated scores, used for generating this statistics are provided in Supplementary File S1.
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bav099-F5: Distribution of MIAME and MINSEQE scores for all automatically retrieved Alzheimer’s Disease gene expression experiments in ArrayExpress Database (for human, mouse and rat), as of December 2014. Percentage is calculated as (total number of AD experiments with a certain score)/(total number of AD experiments). ‘NA’ are the experiments which were not present in ArrayExpress. These scores reflect adherence to compliance standards by the data submitters, needed for re-investigation and reproducibility. It is observed that large percentage of experiments fall under score 4, shows that the required minimum information is still incomplete. The list of experiment IDs along with their associated scores, used for generating this statistics are provided in Supplementary File S1.

Mentions: Authors tend to provide minimum information as required by the guidelines in archives; publishing major part of the experimental metadata annotations in associated publication. To test, whether the authors adhere to the minimum compliant standards, we performed an assessment of the complaint scores provided by ArrayExpress, the highest score being 5, for Alzheimer’s studies. Figure 5 shows the trend in distribution of retrieved AD experiments (see Data Retrieval section) in ArrayExpress, based on the published MIAME and MINSEQE scores (for human, mouse and rat experiments). We observe the trend of submission is concentrated around the score of 4, showing that the submitted data are not fully MIAME or MINSEQE compliant; leading to variable levels of information stored in these archives.Figure 5.


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)

Distribution of MIAME and MINSEQE scores for all automatically retrieved Alzheimer’s Disease gene expression experiments in ArrayExpress Database (for human, mouse and rat), as of December 2014. Percentage is calculated as (total number of AD experiments with a certain score)/(total number of AD experiments). ‘NA’ are the experiments which were not present in ArrayExpress. These scores reflect adherence to compliance standards by the data submitters, needed for re-investigation and reproducibility. It is observed that large percentage of experiments fall under score 4, shows that the required minimum information is still incomplete. The list of experiment IDs along with their associated scores, used for generating this statistics are provided in Supplementary File S1.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

bav099-F5: Distribution of MIAME and MINSEQE scores for all automatically retrieved Alzheimer’s Disease gene expression experiments in ArrayExpress Database (for human, mouse and rat), as of December 2014. Percentage is calculated as (total number of AD experiments with a certain score)/(total number of AD experiments). ‘NA’ are the experiments which were not present in ArrayExpress. These scores reflect adherence to compliance standards by the data submitters, needed for re-investigation and reproducibility. It is observed that large percentage of experiments fall under score 4, shows that the required minimum information is still incomplete. The list of experiment IDs along with their associated scores, used for generating this statistics are provided in Supplementary File S1.
Mentions: Authors tend to provide minimum information as required by the guidelines in archives; publishing major part of the experimental metadata annotations in associated publication. To test, whether the authors adhere to the minimum compliant standards, we performed an assessment of the complaint scores provided by ArrayExpress, the highest score being 5, for Alzheimer’s studies. Figure 5 shows the trend in distribution of retrieved AD experiments (see Data Retrieval section) in ArrayExpress, based on the published MIAME and MINSEQE scores (for human, mouse and rat experiments). We observe the trend of submission is concentrated around the score of 4, showing that the submitted data are not fully MIAME or MINSEQE compliant; leading to variable levels of information stored in these archives.Figure 5.

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