dcGO - A comprehensive domain-centric ontology resource for post-genomic research on functions, phenotypes, diseases and more   
  
  

dcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more

Basic ...

What is dcGO (Background)
  • As a biomedical ontology resource, dcGO integrates knowledge from a variety of contexts, ranging from functional information like Gene Ontology (GO) to others on enzymes and pathways, from phenotype information across major model organisms to information about human diseases and drugs. In dcGO, all Biomedical Ontologies that are not GO are collectively referred to as BO.

  • As a protein domain resource, dcGO includes annotations to both the individual domains and supra-domains (i.e., combinations of two or more successive domains). By default, the domain classifications are taken from the Structural Classification Of Proteins (SCOP) at both the superfamily and family levels.

  • How dcGO is built (Algorithm)
  • As a general method, dcGO has an automated procedure for statistically inferring associations between ontological terms and domains or combinations of domains. An automatic pipeline regularly updates dcGO on a fortnightly basis.

  • Similar to the concept of GO slim, dcGO has a partition procedure for deriving a reduced, more manageable version of the ontology. In dcGO, each ontology slim contains terms at four levels of increasing granularity (i.e., highly general, general, specific, and highly specific).

  • How to access dcGO (Download)
  • Both flat files and MySQL tables are available for download along with detailed documentation.

  • Domain classifications and ontologies are organized in hierarchies, and dcGO includes the facility to browse the hierarchies: SCOP Hierarchy for browsing domains, GO Hierarchy for browsing GO terms, and BO Hierarchy for browsing other terms (mostly phenotypes).

  • In addition to SCOP domains, GO annotations to Pfam families are also provided (see PFAM Hierarchy and PFAM2GO Download).

  • Advanced ...

    Phenotype similarity network (PSnet)
  • As a domain-oriented tool for understanding genotype-phenotype relationships, given one phenotype, PSnet can be used to search for similar phenotype (and other) ontological terms; these are matched on the basis of their shared domain annotations (both at the superfamily and family levels).

  • OBO-formated phenotype and anatomy ontologies:
  • Other ontologies with fixed-length or a much simpler hierarchy (or adapted from vocabulary):
  • Species Tree Of Life (sTOL)
  • As an evolutionary-oriented tool, dcGO can be combined with sTOL to provide a phylogenentic context to function and phenotype.

  • The distribution, across the tree of life for all completely seqeunced genomes, can be explored of both: SCOP domains or by GO/BO term.

  • When browsing the sTOL tree hierarchy, enriched GO/BO terms for extant and ancestral genomes (by domainome-based enrichment analysis) will be displayed.

  • dcGO Predictor
  • As a knowledge predictor, dcGO uses domain-centric annotations to predict functions and other higher-order knowledge (phenotypes, diseases and more) for sequences in your query.

  • The dcGO Predictor relies on the assignment to a sequence in your query of a domain with associated ontology. It will only report predictions for seqeunces with significant domain assignments using the SUPERFAMILY hidden Markov model library.

  • dcGO Enrichment
  • For a list of input domains (e.g., a list of unusual domains found in a genome as compared to another genome) and the target ontologies (e.g., GO), the dcGO Enrichment identifies the ontology terms enriched within the input domains.

  • The dcGO Enrichment takes all annotatable domains (with respects to ontology) as the test background. It is able to process a list of domains containing single group or multiple groups.

  • dcGOnet
  • The dcGOnet is a domain network from a functional perspective, with nodes consisting of protein domains (at the superfamily/evolutionary level) and edges weighted by the semantic similarity according to dcGO annotation profile.

  • It also features a general methodology (and the software freely available). The predicted drug-disease-phenotype matrix provides rich targets for investigation.

  • dcGO Pevo
  • Plasticity potential (PP) is defined as the tendency for a list of related domains (sharing certain common characteristics; annotated by a dcGO term) to occur in different architectures (or architecture diversity), as measured by the median number of architectures per domain.

  • The dcGO Pevo calculates PP-scores for a list of input dcGO terms, and displays their dynamic changes during the eukaryotic genome evolution.

  • Mining hub ...


    Quick start to mining the dcGO resource

    • SCOP domains (LINKTO SCOP Hierarchy and sTOL)
      • SCOP unique identifier (sunid) of a SCOP, e.g. 46458
      • SCOP name or part thereof, e.g. hemoglobin
      • Enrichment analysis for a list of input protein domains via dcGO Enrichment.
    • Genomes (LINKTO SUPERFAMILY database and sTOL)
      • A common organism name, e.g. human
      • A genome name or part thereof, e.g. Homo sapiens

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