DW contributed to the design of the semantic connector report format so that the entities could be properly annotated and ordered for processing by the UML Loader.
Also, we needed to make sure that all the AUs that we are analyzing are coded in the CK+ database which we use for AUs' classification training and testing, hence why we settled with only these 27 AUs which are properly annotated in CK+ database.
This number is supposed to be even higher because not all disulfide bridges are properly annotated in the structure entries.
For example, I did not detect pclob because this gene has not been properly annotated, likely due to the duplications I describe herein.
During orthology assignment, we find that a number of genes have not been properly annotated in some strains.
Manual adjustments were performed, in particular for genes on the last two segments (M2, M1, NS2 and NS1) and the second segment, for which some sequences are not properly annotated; misaligned sequences were removed.
Therefore, repeats produce a large number of short contigs that cannot be properly positioned or annotated within the assembly.
Eribulin with the eighth highest rate (36%), for example, is known to directly bind tubulin, thus disrupting microtubule structures, which was not properly annotated in neither DrugBank nor TTD.
For example, 5'UTRs of many macaque genes are not properly annotated (contain 'NNNNN'), making it difficult to identify the upstream 5'UTR boundary.
This tool reports on missing documentation and on documentation which is not properly annotated in the Java source files.
