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For Amphimedon queries, the matching traces were collected, manually evaluated and assembled into genomic contigs using an in house assembly pipeline (sequential use of MegaBlast [30] for selection of additional traces and PHRAP or PCAP assemblers [31], [32] for construction of the contigs).
Data were manually evaluated and deconvoluted using the Software MassLynx V4.00.00 (Waters).
The flagged values were then manually evaluated and data entry errors were removed as indicated.
The results from the ABI3100 Prism Genetic Analyzer were manually evaluated and each sample was read in duplicate.
After the software has completed tracking these structures they can be manually evaluated, and corrections can be made if necessary.
All of the potential episodes were manually evaluated and validated in order to exclude any false positive cases from the free text searches.
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This list was too long to manually evaluate and we therefore restricted the human curation analysis to the 99.8% specificity level (top 42 proteins, Table S5).
First, we manually evaluated the precision and recall of the automated annotation, revising 50 abstracts randomly chosen from the snippets extracted by our method.
The raw data were manually evaluated to remove duplicates and false-positives and assign gene names.
We only considered peptides with double and multiple charges, and manually evaluated the expression values by inspecting the areas of integration that the software had chosen and by adjusting them as needed.
The automatic word alignment also produced English-Swedish candidate term pairs and we manually evaluated the candidate term pairs and collected the correct term pairs to an English-Swedish medical dictionary.
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