Furthermore, the server only provides classifiers for 111 Molecular function and 86 Biological Process categories that represent more general annotations, which limits its usage in deciphering specific annotations.
We did not include genes with more general annotations (as for instance "axon" or "neuromuscular junction") to render our analysis more neutral to potential differences related to variation among organisms in the morphology of their dendrites and axon terminals.
In this module, the analysis is expanded from single genes to more general biological annotations, allowing the inferred clusters of trans-factors to be compared by the gene ontology (GO) enrichment analysis of their target mRNAs.
These are based on more general GO annotations derived from the GO-slims database at EBI, and allow us an insight into the different classes of genes present on the array without having to look at detailed functional annotation for each individual gene.
Of the 5,978 candidate BP annotations, 697 (12%) were direct matches to gene-function annotations in the GOA reference, 123 (2%) matched narrower terms than existing annotations, 1,667 (28%) matched more general terms than existing annotations, and the remaining 3,491 (58%) did not match any annotations in the GOA database.
More recently, service frameworks that relied on more general ontologies for service annotation and input/output specification have also become available [19, 20].
More specific annotations are preferred over more general ones where there are overlapping annotations.
In all, 693 (23%) of the 2,983 candidate annotations exactly matched an annotation from the DO reference annotations, 157 (5%) matched a more general term in the same lineage as a reference annotation, 63 (2%) matched a more specific term, and 2070 (70%) had no match.
daTAA provides considerably wider and more accurate coverage than a general annotation server and compares favorably with manual annotation.
However, the design of this annotation is more general than may be needed for a translation of the data in the ChEMBL relational database into RDF.
