PIRSF: family classification system at the Protein Information Resource

Abstract

The Protein Information Resource (PIR) is an integrated public resource of protein informatics. To facilitate the sensible propagation and standardization of protein annotation and the systematic detection of annotation errors, PIR has extended its superfamily concept and developed the SuperFamily (PIRSF) classification system. Based on the evolutionary relationships of whole proteins, this classification system allows annotation of both specific biological and generic biochemical functions. The system adopts a network structure for protein classification from superfamily to subfamily levels. Protein family members are homologous (sharing common ancestry) and homeomorphic (sharing full-length sequence similarity with common domain architecture). The PIRSF database consists of two data sets, preliminary clusters and curated families. The curated families include family name, protein membership, parent-child relationship, domain architecture, and optional description and bibliography. PIRSF is accessible from the website at http://pir.georgetown.edu/pirsf/ for report retrieval and sequence classification. The report presents family annotation, membership statistics, cross-references to other databases, graphical display of domain architecture, and links to multiple sequence alignments and phylogenetic trees for curated families. PIRSF can be utilized to analyze phylogenetic profiles, to reveal functional convergence and divergence, and to identify interesting relationships between homeomorphic families, domains and structural classes.

Uncertain Groupings: Probabilistic Combination of Grouping Data

“…For the evaluation, we constructed a test set of homology data from the Homologene (release 67, [10]), PIRSF (release 2012 03, [15]), and eggNOG (release 3.0, [12]) biological databases. The groupings from each of these databases were loaded into a single database for the construction of trust views and querying.…”

“…Such databases are often made accessible to the scientific community. In our research, we aim to combine the insight into orthologous groupings contained in Homologene [10], PIRSF [15], and eggNOG [12]. An automatic combination of these sources may provide a continuously evolving representation of the current combined scientific insight into orthologous groupings of higher quality than any single heuristic could provide for other bioinformaticians to utilize.…”

Plant Protein Annotation in the UniProt Knowledgebase

“…Automatic annotation relies also on the PIRSF family classification concept (Wu et al, 2004a); proteins classified in the same family are both homologous (sharing common ancestry) and homeomorphic (sharing full-length sequence similarity with common domain architecture). Based on this system, rules are developed and manually curated for annotating and propagating position-specific features, such as active or binding sites, and for protein names and gene ontology (GO) terms.…”

Large‐scale, classification‐driven, rule‐based functional annotation of proteins

“…(For the sake of this discussion, it is assumed that the query protein has been accurately assigned to a protein family of interest. This, typically, is done via specialized BLAST search, (e.g., the COG database, Tatusov et al, 2003), HMMer search (e.g., Pfam, Bateman et al, 2004), or combination of both (e.g., PIRSF, Wu et al, 2004a)). Streptococcus agalactiae protein gbs1797 (UniProt accession Q8E3G2) provides a good example of the usefulness of protein families for annotation.…”