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However, once this mapping step is completed, subsequent analyses (such as merging gene families into pathways) proceed quickly, and can rapidly produce clinically relevant results.
The 85.9% success of the mapping step is still insufficient but could be naturally improved since the UMLS Metathesaurus is reviewed and updated regularly.
Nevertheless, sequencing will not help to distinguish between the 10 or so remaining candidate genes with base pair changes, and a mapping step is still very advisable.
The data mapping step is followed by a validation step for checking the flux balance of each reaction (see dialog in Figure 3, field 1).
The mapping step is divided into four stages that are similar to the map integration procedure described by Barrett et al. [ 19].
Each major ontology redesign (including mapping) step is checked by a description logics reasoner, the results of which are then analysed and corrected under two perspectives: first, the classes tagged as 'inconsistent' are identified and the causes are investigated and repaired; second, every time the ontology has reached a consistent state, the logical entailments are analysed for adequacy.
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A BlastX search was performed with Blast2GO using the default parameters (but e-value < e−10) against the nonredundant protein sequence database; the gene ontology (GO) mapping step was run with the plant GO-Slim terms (Conesa et al. 2005).
The main purpose of the MAPMAKER analysis was to allow comparison of mapping distance in B. anynana with other Lepidoptera linkage maps, since this is the first species in this taxon for which the final mapping step was performed in JOINMAP.
The contig mapping step was carried out with ReviSeq algorithm (under development, unpublished).
Variations with an occurrence below 99%% in the mapping step were discarded from the study.
The role of a gene model in the mapping step was then quantified and characterized by comparing the mapping results in Stage #2.
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