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Usually, confidence in search results must be manually assessed by the user, based on the used search algorithm and the quality of spectrum and library [77].
This means that, on the one hand side, a large amount of expert knowledge is required and many parameters must be manually assessed by experts.
General physical health measures (9%) include all physical health measurements manually assessed by the clinician.
The interobserver reliability of the ADIM manually assessed by two of the assessors (M1 and M2), revealed substantial agreement of 87.5%, (κ=0.71, CI (95%) 0.41 to 1.00) while the SE was 0.15.
A false discovery rate (FDR) used in proteomics is not feasible here for the MS/MS spectral matching as no appropriate decoy metabolite databases can be constructed, therefore the results need to be further manually assessed by the user.
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Ultrasound imaging (USI) was used as the concurrent reference (gold standard) for the manually assessed ADIM by calculating a ratio of the change in muscle thickness between the resting and the contracted states: the correlation between manual test and USI was calculated.
For a more specific assessment of the tool's value as an aid to curators in the case of GEO and PDB links to the literature, we manually assessed the evidence statements automatically retrieved by the tool by classifying them into four main categories: Deposition: If the evidence statement shows the data were deposited.
We did this by comparing the manually assessed test (ADIM) results to the USI findings for the same action.
Each chip image was manually assessed for quality of spot detection and quantitation by at least two independent observers.
Tubes marked as having growth by the automated system were manually assessed for AFB using Ziehl-Neelsen microscopy; all tubes positive for AFB were sub-cultured on L-J media and species identification was performed as above.
To further assess the value added by the predicted secondary phenotypes, we manually assessed diseases that show rank improvements for known causative genes.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com