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The database was designed as an extension to the GO term [56] database schema for ease of interrogation on the complete GO hierarchy rather than leaf term only (Figure S3).
Furthermore, 41% of proteins are annotated with its child 'protein binding' as a leaf term, and 26% are annotated with it as their sole leaf term.
The distribution of leaf term (MFO) annotations of the assessment proteins is shown in Supplementary Figure S5.
For example, all-pair averaging leads to anomalies where the exact prediction of an annotation containing a single leaf term u would be scored higher than the exact prediction of an annotation containing two distinct leaf terms u and v of equal information content, when it is more natural to think that the latter prediction should be scored higher.
An interesting anomaly with this approach is that the marginal probability, and subsequently the information content, of a single term (i.e. consistent graph with a single leaf term) calculated from a Bayesian network does not necessarily match the relative term frequency in the database (instead, the conditional probability tables are estimated as relative frequencies).
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Fujino et al. (2008) isolated a spontaneous mutant with narrow leaf, termed narrow leaf 7 (nal7).
A set of leaf terms completely describes the annotation graph.
Finally, certain semantic similarity metrics that incorporate pairwise matching between leaf terms tacitly assume that the objects to be compared are annotated by similar numbers of leaf terms.
Second, the leaf terms typically have a low number of annotated examples making it difficult to learn an effective classifier.
For example, when the leaf category is selected, an illustration with illustrated definitions of leaf terms is displayed on the right (Fig. 16A).
Previously, we showed that the distribution of leaf terms in protein annotation graphs exhibits scale-free tendencies (Clark and Radivojac, 2011).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com