Check ISA (Investigation, Study, Assay) formatted metadata records

[tompollard]

I have now completed the metadata records for your article. These records follow the ISA (Investigation, Study, Assay) format (www.isa-tools.org), and in accordance with the Scientific Data specification of these guidelines I have generated Investigation, Study, and Assay files to accompany your manuscript (please see the attached ZIP archive for the complete file package).

The investigation file provides an overview of the work. The study file describes the samples and subjects assayed in each work, and the assay file the manipulations performed on a set of samples to generate one or more related datasets. Please note that many of the fields in the investigation file are currently empty, as these will be automatically filled in during the publication process.

I have been able to obtain most of the necessary information from your manuscript and the data records PhysioNet. However, the datasource table you sent had two additional classes that are not defined in Table 3. Therefore please could you add 'Interventions' and 'Dictionary' classes to Table 3 and send an updated table 3 back to us.

Please could you also perform a sanity check of the metadata files, in case I have mistaken any details of the experimental workflow or if any fields contain erroneous information.

In addition, you may be aware that Scientific Data articles are published with a structured summary table which appears after the article abstract. This table is generated from the machine readable metadata files, and therefore uses standardized structured vocabulary terms. The table for your article is below, please confirm whether the terms used here are factually correct.

Design Type(s) data integration objective Measurement Type(s) Demographics • clinical measurement • intervention • Billing • Medical History Dictionary • Pharmacotherapy • clinical laboratory test • medical data Technology Type(s) Electronic Medical Record • Medical Record • Electronic Billing System • Medical Coding Process Document • Free Text Format Factor Type(s)
Sample Characteristic(s) Homo sapiens

ISA-Tab_Pollard_20160503_1462277300_1.zip

[tompollard]

However, the datasource table you sent had two additional classes that are not defined in Table 3. Therefore please could you add 'Interventions' and 'Dictionary' classes to Table 3 and send an updated table 3 back to us.

The additional classes were added to table 3 (PDF here - mimic-table-3.pdf).

Please could you also perform a sanity check of the metadata files, in case I have mistaken any details of the experimental workflow or if any fields contain erroneous information.

I’m not familiar with the ISA format, but everything looks fine as far as I can see. I deleted “a_procedures.txt” and merged the content with “a_intervention.txt". I also updated “s_study.txt” based on the modified classes. A zipped version of the package is at ISA-tab.zip.

In addition, you may be aware that Scientific Data articles are published with a structured summary table which appears after the article abstract. This table is generated from the machine readable metadata files, and therefore uses standardized structured vocabulary terms. The table for your article is below, please confirm whether the terms used here are factually correct.

Yes, it looks good.

I have replied to the editors with the updated files.

[tompollard]

Many thanks for making the changes to the metadata files and for updating table 3. I have uploaded your final article file to our submission system, and have completed the metadata records (enclosed here for your records). We will now send your article through to the production team.

ISA-Tab_Pollard_20160504.zip