Considering that human phenotype ontology is now available and it well annotates to disease phenotypes, disease similarity can be semantically calculated based on such the controlled vocabulary using semantic-based similarity measures.
The genomes of several invasive species have now been sequenced and assembled as well as annotated to differing extents.
Following this approach, network based learning algorithms might benefit of the availability of a priori functional knowledge coming from well annotated species to effectively perform a functional transfer to the proteins of poorly annotated organisms.
Clearly, when long reads (such as Sanger-based methods) are being used, or long contigs, one can rely on BLAST comparisons of the extracted putative proteins with well annotated databases, to carry out the taxonomical classification of the data, and attempt to resolve the taxa-counting problem.
In this study Snf1 and Pka1 was found to share 55 substrates in vitro of which 53 proteins with well annotated interactions to both Snf1 and Pka1 are also included in the network reconstruction presented here.
Its compact genome is well annotated, owing to many years of genetic experimentation [33], and has been mined extensively for coding as well as non-coding gene loci [28], [34], [35].
It was chosen since it is almost fully sequenced and well annotated compared to the other species involved.
Since the bovine genome is not well annotated compared to the human genome, we used the human orthologs for gene ontology analyses.
Introns in S. cerevisiae have been well annotated due to the extensive efforts of the yeast scientific community (Saccharomyces Genome Database [SGD]).
The transcript with the strongest homology to phenylalanine ammonia lyase (PAL), the third most abundant DE plant transcript in the contaminated trees across all tissues, was the only well annotated transcript to prominently stand out using weighted fold change.
