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In our initial coding of the dataset, submissions were divided into fourteen broadly defined disciplines.
We used the binary bioactivity outcome annotations, e.g. active versus inactive, provided in the dataset submissions as the corresponding activities.
Sponsors' dataset submissions were received by the FDA between September 2005 and September 2006 as electronic files (in SAS transport file format).
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The adjusted means of the standard varieties are excluded from the dataset before submission to the second stage.
JAS formatted the datasets for submission.
It is however no longer adequate to share data through traditional modes of publication, and, particularly with high throughput ('-omics') technologies, sharing of datasets requires submission to public databases as has long been the case with nucleic acid and protein sequence data.
At its current incarnation, MIABi will not mandate all dataset or database submissions to be fully compliant with standard nomenclature, controlled vocabularies and standard ontologies, for the practical reason that many scientific communities may not be ready to agree to the standardization process or competing standards or that there are no standard terminologies in many rapidly growing fields.
This table also displays the mean and standard deviation of the SEG, TRA and TIM measures obtained for each dataset, combining all the submissions received.
Taking such a broad range of data types makes data interoperability an issue, and we have been working with the ISA-Commons community to see if GigaDB can capture study and assay metadata along with relationships between dataset components and take submissions using their ISA-Tab format [ 10].
In addition to filtering the transcriptome, Transvestigator also prepared the dataset for NCBI Transcriptome Shotgun Assembly (TSA) submission by ensuring the predicted ORF is in the positive strand, confirming presence of only a single ORF per transcript, and generating a properly formatted NCBI.tbl file for submission.
We mention here that one cannot adjust the parameters for test datasets because the submission can be done only once.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com