SWISS-PROT manual curation of GO terms was also utilized to assign terms.
Although community efforts exist for the expert curation of neuroanatomical terms pertaining to brain regions [5] and grass root scholarly collation of neuroscience terminology [6], the continuously increasing pace of data acquisition is paradoxically yielding an ever more fractured lexicon, creating serious impediment to progress.
UniProt is a major contributor to the GO (22), a major bioinformatics initiative that aims to standardize the representation of gene and gene product attributes across species and databases, and manual curation of GO terms based on experimental data from the literature is part of the UniProt curation process.
The resulting compartmentalized mouse metabolic reconstruction (Additional file 5), created by curation of modelA, termed iMM1415, contains a total of 3,724 reactions and 1,415 metabolic genes (Additional file 6 contains detailed description of all reactions in iMM1415, including the biomass reaction).
The first is curation effort or number of terms manually curated, which corresponds to number of terms in the TP and FP in our experiment, as they are the terms that the curator examines.
For example, the curation effort up to iteration #3 is the sum of the number of terms curated from iteration 1 to 3. Finally, the curation effort is plotted against curation hit as a measurement of curation efficiency.
The second is curation hit, or the number of lipid-related GO terms discovered, which includes not only TP found by curation but also the number of terms in desc+ derived from the inheritance constraint.
In particular, we have addressed the problem of varying levels of resolution in the GO hierarchy by selecting the gold standard set of terms through curation by six expert biologists.
Curation of the novel GO terms implied contrasting against scientific papers and established functional databases, such as UniProt, Tair, Saccharomyces Genome Database, Entrez, etc. From these 20 sequences one (AT5G35370.1) resulted to have doubtful sequence identity and was not considered in further computations.
In the beginning, the number of GO+ terms found can be even greater than the number of terms predicted for curation, thanks to the inheritance constraint.
As a result, archival repositories face an even greater need for well-organized and standardized metadata strategy in order to allow integrated access to and long-term curation of diverse digital holdings.
