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 transcriptionCytoscape 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.
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.
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
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
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
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:
SGD S000004660 AAC1 GO:0006839 SGD_REF:S000050955|PMID:2167309 IGI SGD:S000000126 P ADP/ATP translocator YMR056C gene taxon:4932 20040226 SGDThe third element (AAC1, called DB_Object_Symbol in the gene_association format) will be used as a node identifier and canonical name for the gene. However, some network files (gal or sif) instead use the 11th element (YMR056C, the first entry in Synonym) as a node identifier. Since Cytoscape applies annotations based on these identifiers, the identifiers in the network file and in DB_Object_Symbols must match. This check box is used when you load network files that use the Synonym as the node identifier.
Once you have finished specifying the options, click on finish. The OBO file and gene_association files specified in this panel will be automatically loaded.
Note 1: The OBO file and gene_association files MUST be in the same directory, and you must have write permission for the directory.
Note 2: Please make sure that your network file uses exact same ID’s used in the gene association file. Otherwise, the annotations will not appear in the Annotation Panel.