Table 3 Biological catagories for the interpretation of functional annotations. The interpretation of extracted annotations is based on the automatic assignment of semantic labels to the arguments of a PAS. Because a comprehensive ontology is not available two categorisation schema are tested in this study. The first is the design of a scheme (MAN) based on an analysis of relevant MEDLINE sentences for residue annotation (bottom-up approach). Alternatively, the categories in the feature table of UniProtKb (FEAT) can be reused (top-down approach). Both categorisation schemes reflect concepts of biological interest. However the bottom-up approach has the advantage that proposed categories are data-driven, while in a top-down approach examples of listed categories may not be present in natural language text, or other categories are missing in the scheme.

Defintion

Defintion

Structure component. Class denoting concepts that represent pieces and parts of the protein structure.

Extent of a domain, which is defined as a specific combination of secondary structures organised into a characteristic three-dimensional structure of fold.

Short (up to 20 amino acids) sequence motif of biological interest.

Topological domain.

Extent of a polypeptide chain in the mature protein.

Extent of a transmembrane region.

Extent of a coiled-coil region.

Chemical modification. Class denoting changes to the protein sequence and the chemical composition.

Authors report that sequence variants exist.

Posttranslational modification of a residue.

Extent of a released active peptide.

Description of sequence variants produced by alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting.

Covalent binding of a lipid moiety.

Glycosylation site.

Structural modification. Class denoting the changes to the protein structure without changes to the chemical composition.

Extent of a region of interest in the sequence.

Any interesting single amino-acid site on the sequence, that is not defined by another feature key.

Binding type. Class denoting different physico-chemical forces leading to a bond formation between a protein structure component and a chemical entity.

Binding site for any chemical group (co-enzyme, prosthetic group, etc.).

Binding site for a metal ion.

Disulfide bond.

Posttranslationally formed amino acid bonds.

Extent of a DNA-binding region.

Extent of a nucleotide phosphate-binding region.

Extent of a zinc finger region.

Extent of a calcium-binding region.

Enzymatic activity. Types of enzymatic reactions as a subpart to protein functions.

Amino acid(s) involved in the activity of an enzyme.

Cellular phenotype. Class denoting different cellular phenotypes that can be affected by structural or compositional changes of a protein.