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The present study compared gene coverage by using sequence annotations equivalent to public accession numbers available for 29,195 probes.
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Entities and event trigger words are transcribed to BioC annotations, whereas equivalent entities and events are transcribed to BioC relations.
Here, the specific annotations from equivalent terms for ANNOVAR and VEP have been aggregated to enable the comparison (see Additional file 1: Table S4).
If the annotation of such semantically equivalent entities is highly reproducible, we may be able to aggregate across datasets, and obtain valid results, emergent from separate, partially overlapping models.
Provided that the tokeniser is fine enough to avoid tokens with overlapping annotations, this redefined problem is equivalent to the original one.
If no gene function annotations are available, DWCN is equivalent to the tight clustering method.
Figure 3B shows that for the mismatch class of 157 genes whose manual GO annotations could be improved, roughly equivalent numbers of genes required each of the three types of improvement, with the 'Add' category being the smallest (65 genes).
But if semantic annotation is not reproducible, then semantically equivalent data may be annotated with different concepts or non-equivalent data may be annotated with identical concepts.
Ensembl genes contain both automated genome annotation and manual curation, while the gene set of GENCODE corresponds to Ensembl annotation since GENCODE version 3c (equivalent to Ensembl 56).
Although pre- and post-composed terms may be semantically equivalent, the parallel annotation process required with post-composition is not well suited to community curation.
Therefore, TrEMBL and Swiss-Prot are ideal resources to compare equivalent human and automated annotations.
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CEO of Professional Science Editing for Scientists @ prosciediting.com