Sentence examples for based on available annotations from inspiring English sources
We implemented a general and customizable software framework to automatically detect missing biomolecular annotations and "transfer" them from available ones by transitive relationships based on available annotations, as defined in the Methods section and Additional file 1.
In the next scheduled release of the GPKB, besides the detected gene annotations and PPI-genetic disorder potential candidate associations, we plan to include also transcript annotations identified based on available annotations of the proteins that the transcripts encode.
Using more automated approaches, ProtoNet (Rappoport et al., 2014) provides an automatic classification of similar proteins which are further sub-classified into clusters using an information-theoretic protocol based on available annotations.
Alternatively the list of genes within a QTL hotspot (or individual QTL CI) can be examined and a 'short list' determined based on available annotation information.
If such annotation of gene G1 to the biological function B1 is not available, but the annotations of P1 to B1 and G1 to P1 are available, then the annotation of G1 to B1 can be straightforwardly detected as missing and transferred by transitive relationship, with path of length two, based on available annotation data.
Note that based on available sequence annotations divergent N-terminal and C-terminal regions were clipped from the alignments.
We evaluated all cell lines from the ENCODE HAIB track at the UCSC Genome Browser that had a cancer or non-cancer origin (n = 23 and n = 28, respectively), based on available ENCODE annotations (Additional file 5: Table S3).
DAVID looks for over-representation of candidate genes in signaling or metabolic pathways, Gene Ontology processes, etc., based on available gene annotation.
This system provided unbiased genome-wide coverage with sufficient depth to reliably capture the most well characterized mechanism of resistance in all cell lines processed and generate many believable additional hits based on available functional annotation.
Functional analysis based on available gene annotation indicates that most conserved genes (levels 1 and 2) are responsible for basic cellular processes (e.g., DNA replication, transcription, translation, etc), while most genus- and species-specific genes (levels 5 and 6) are hypothetical proteins of unknown function (see Additional files 2 and 3).
Previously, we developed the Genomic and Proteomic Knowledge Base (GPKB) [ 13], an updated public, high-quality and consistent integration of reconciled heterogeneous and distributed annotation and interaction data; it can be profitably leveraged to help unveiling new biomedical knowledge by reliably identifying and supplementing missing annotations based on available ones.
