Gene Ontology (GO)
GO depicts three complementary biological concepts including Biological Process (BP), Molecular Function (MF) and Cellular Component (CC). The hierarchical structure of GO is organized as a directed acyclic graph (DAG) by viewing an individual term as a node and its relations to parental terms (allowing for multiple parents) as directed edges. To navigate this hierarchy, we display all parental GO terms to the current GO term of interest ordered by their shortest distances to the current term. Also, only direct children GO terms of the current GO term are listed.
Structural Classification of Proteins (SCOP)
SCOP classifies evolutionary-related domains into
Superfamily level and
Family level. Accordingly, we have generated the domain-centric GO annotations for each of the three concepts at each of the two domain levels.
Structural Domain Functional Ontology (SDFO)
As domain-centric ontology, SDFO only refers to those GO terms which are the most informative to annotate SCOP domains.
GO annotations for SCOP domains
For details, please visit
Documentation: GO annotations for SCOP domains. Therein, we provide several relevant files (
Data Availability) for the download. It includes two mapping results: Domain2GO supported by both, and Domain2GO supported only by all. For each mapping result, the ontology and annotation files are available. The annotation (i.e.,
Domain2GO_supported_by_both.txt) and the corresponding ontology (i.e.,
SDFO.both.txt) are suitable for small-scale studies (high-quality, and
BROWSABLE BELOW), while the annotation (i.e.,
Domain2GO_supported_only_by_all.txt) and the corresponding ontology (i.e.,
SDFO.all.txt) for large-scale studies (high-coverage, like functional enrichment analysis).
Supra-domain Functional Ontology (SPFO)
As an extension, SPFO includes those GO terms which are the most informative to annotate supra-domains and individual SCOP domains at the
Superfamily level.
GO annotations for Supra-domains
For details, please visit
Documentation: GO annotations for Supra-domains. Therein, we provide several relevant files (
Data Availability) for the download, including a annotation file (i.e.,
SP2GO.txt) and an ontology (i.e.,
SPFO.txt). For the sake of being browsable, listed below are those supra-domains (single, dual, triple, quad).
Trees by TreeVector
A presence/absence matrix is generated using protein domains and supradomains
for all genomes in SUPERFAMILY. The RAxML
software is used to produce a single, large tree topology using
heuristic parsimony methods. Genome combinations, or specific clades, can be displayed as
if individual trees had been produced. However, this data is extracted from the single
large tree. This produces a higher quality topology than if the trees had been produced
on their own, and allows the trees to be displayed instantly.
Trees by TreeVector
A presence/absence matrix is generated using protein domains and supradomains
for all genomes in SUPERFAMILY. The RAxML
software is used to produce a single, large tree topology using
heuristic parsimony methods. Genome combinations, or specific clades, can be displayed as
if individual trees had been produced. However, this data is extracted from the single
large tree. This produces a higher quality topology than if the trees had been produced
on their own, and allows the trees to be displayed instantly.
