Annotation

Annotations in Cytoscape are stored as a set of ontologies (e.g. the Gene Ontology - GO). An ontology consists of a set of controlled vocabulary terms that annotate the genes for a given organism and a synonym table for gene names. For example, using the Gene Ontology, the Saccharomyces Cerevisiae GAL4 gene's biological process is described as "regulation of transcription", to which GO has assigned the number 45449 (a GO ID). You can see below that "regulation of transcription" is a subcategory of "transcription", which is a subcategory of "nucleobase, nucleoside, nucleotide and nucleic acid metabolism", etc.

GO 8150  biological_process
  GO 7582  physiological processes
    GO 8152  metabolism
      GO 6139  nucleobase, nucleoside, nucleotide and nucleic acid metabolism
        GO 6350  transcription
         GO 45449  regulation of transcription
Cytoscape can use this "hierarchical" ontology to annotate recognized genes if the user chooses a level of the hierarchy to use for a given set of annotations. The ontology provided to Cytoscape does not have to be hierarchical, but if it is not, there is no real advantage to storing annotations this way compared to just storing the annotation terms in a node attribute file.

The Gene Ontology Server (originally called the biodata server) is a Cytoscape feature which allows you to load, navigate, and assign annotation terms to nodes in a network.

In version 2.2, Cytoscape has a new feature called the Gene Ontology Server Wizard, which enables users to select a local ontology and annotation files from the user interface. Although 2.2 is backwards compatible with the old file formats (the manifest file, which includes a list of anno (annotation) and onto (ontology) files), we strongly suggest using the new file formats. See Appendix B for a description of how the old file formats can be created and used.

New Ontology and Annotation Files

The standard file formats used in this release are OBO and gene association. The GO website details these file formats:

Cytoscape provides a copy of the Gene_ontology.obo text file in the annotation directory for use with the software. An up-to-date Gene_ontology.obo file is maintained by the GO project (updated every 30 minutes). Please download the latest version of this file (from http://www.geneontology.org) if you intend to use it during analysis. In addition to the gene ontology file, we also provide gene association files for Yeast and Human (gene_association.sgd and gene_association.goa_human, both in the annotations directory). Other gene association files can be found at the gene ontology web site.

Sample Files

gene_ontology.obo:

format-version: 1.0
date: 11:08:2005 16:57
saved-by: midori
auto-generated-by: DAG-Edit 1.419 rev 3
default-namespace: gene_ontology
remark: cvs version: $Revision: 1.3 $
subsetdef: goslim_yeast "Yeast GO slim"
subsetdef: goslim_goa "GOA and proteome slim"
subsetdef: goslim_plant "Plant GO slim"
subsetdef: goslim_generic "Generic GO slim"
subsetdef: gosubset_prok "Prokaryotic GO subset"

[Term]
id: GO:0000001
name: mitochondrion inheritance
namespace: biological_process
def: "The distribution of mitochondria\, including the mitochondrial genome\, into daughter cells after mitosis or meiosis\, mediated by interactions between mitochondria and the cytoskeleton." [PMID:10873824, PMID:11389764, SGD:mcc]
is_a: GO:0048308 ! organelle inheritance
is_a: GO:0048311 ! mitochondrion distribution

[Term]
id: GO:0000002
name: mitochondrial genome maintenance
namespace: biological_process
def: "The maintenance of the structure and integrity of the mitochondrial genome." [GO:ai]
is_a: GO:0007005 ! mitochondrion organization and biogenesis

gene_association.sgd (annotation file for yeast):

SGD     S000003916      AAD10           GO:0006081      SGD_REF:S000042151|PMID:10572264        ISS             P       aryl-alcohol dehydrogenase (putative)        YJR155W gene    taxon:4932      20020902        SGD
SGD     S000005275      AAD14           GO:0008372      SGD_REF:S000069584      ND              C       aryl-alcohol dehydrogenase (putative)        YNL331C gene    taxon:4932      20010119        SGD

Gene Ontology Server Wizard

The Gene Ontology Server Wizard is a new graphical user interface used to select ontology and annotation files. By following the wizard, you do not have to write manifest files, which were used in older versions of Cytoscape to specify the file location of the ontology and gene annotation files.

Step 1. Select Data Format

Ontology Wizard

In this panel you can select two types of data formats: Cytoscape BioDataServer or Gene Ontology. Select Gene Ontology to use the new formats (obo and gene_association files). If you want to use the old file formats, select Cytoscape Bio DataServer. A description of how the old formats can be created and used can be found in Appendix A.

Step 2. Select OBO and Gene Association Files

Ontology Select Gene Ontology

If you choose Gene Ontology in the first step, this panel appears to help you select OBO (ontology) and gene_association files. This panel has the following functions: