Diff for "Cytoscape_User_Manual/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 44238 primary metabolism
    GO 19538 protein metabolism
     GO 6412 protein biosynthesis

attachment:ontology_dag1.png

Cytoscape can use this ontology DAG (Directed Acyclic Graph) to annotate recognized genes. 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 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 2.4, Cytoscape has enhanced GUI for loading Ontology and Annotation, which enables users to select a local/remote ontology and annotation files from lists.

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:

• Ontologies and Definitions: http://www.geneontology.org/GO.downloads.shtml#ont

• Current Annotations: http://www.geneontology.org/GO.current.annotations.shtml

From version 2.4, Cytoscape can load all ontology files written in OBO format. The full listing of ontology files are available from Open Biomedical Ontologies (OBO) website:

• OBO Ontology Browser: http://obo.sourceforge.net/browse.html

Although Cytoscape can import all kinds of ontologies in OBO format, users need to provide annotation file to annotate node/edge/network in Cytoscape.

Cytoscape provides a list of ontologies and their data file URLs available in OBO format. If network connection is available, Cytoscape load ontology and annotation file directly from the remote source.

Sample Files gene_ontology.obo: http://www.geneontology.org/ontology/gene_ontology_edit.obo

format-version: 1.2
date: 27:11:2006 17:12
saved-by: midori
auto-generated-by: OBO-Edit 1.002
subsetdef: goslim_generic "Generic GO slim"
subsetdef: goslim_goa "GOA and proteome slim"
subsetdef: goslim_plant "Plant GO slim"
subsetdef: goslim_yeast "Yeast GO slim"
subsetdef: gosubset_prok "Prokaryotic GO subset"
default-namespace: gene_ontology
remark: cvs version: $Revision: 5.49 $

[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." [GOC:mcc, PMID:10873824, PMID:11389764]
synonym: "mitochondrial inheritance" EXACT []
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." [GOC: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

Import Ontology and Annotation

• attachment:ontology_and_annotation_Import_main.png

Cytoscape 2.4 provides a graphical user interface used to import both ontology and annotation files.

Step 1. Select Data Format

• attachment:ontology_wizard_begin.png

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 BioDataServer. A description of how the old formats can be created and used can be found in Appendix B.

Step 2. Select OBO File

attachment:ontology_wizard_obo.png If you choose Gene Ontology in the first step, this panel appears to help you first select an OBO (ontology) file. The wizard displays the header information of the OBO file loaded. Once an OBO file is loaded, the Next button becomes enabled. Click the Next button to proceed.

Step 3. Select Gene Association File

attachment:ontology_wizard_goa.png

You can add a gene_association file to the list by pressing Add button. Once you select a file, the file name will be shown in the list in the left. If you click on the file name, the header information will be displayed in the center window. You can select multiple gene_association files.

The "Transfer GO Species Name to Nodes" can be used to apply the species name (taxon) found in the selected Gene Association file to the nodes of the currently selected network. This may be an important feature if the nodes of your network do not have a species attribute set. You can can see the current network's nodes and species attribute for the nodes in the left hand window. You can see the GO symbols, terms, aspects, synonyms, and taxons (species), in the bottom window. For nodes in your network to map to GO terms, either a symbol or synonym of a term must match the node ID.

Step 4.

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. This will then open up the Ontology Mapper dialog.

attachment:ontology_mapper.png

The Ontology Mapper is used to reduce the number of node attributes created from the gene ontology. Selecting a term in the left hand column and clicking the >> button will select that term to create an attribute for. You can unselect a term using the << button. The Apply All button will select all terms for attribute creation. In most cases, Apply All should be used to import all GO Terms for the network. Otherwise, only subset of GO Terms in the tree is imported. Once the desired terms have been selected, click the OK button. This will create node attributes for all selected GO terms. If you select some GO Terms in the right-side window, nodes with the GO Terms will be shown in the Node AttributeBrowser. By right-clicking on a GO Term in the GO Data as Attributes window, you can search the GO Term in AmiGO (this function requires internet connection and a web browser). The GO terms will now be visibile in the Node Attribute Browser by clicking on the Select button ( attachment:attributes_select_icon.png ).

If you would like to choose deifferent GO terms from the same gene association file, you do not need to re-import the files. Instead, you can click the GO button ( attachment:attributes_go_icon.png ) in the Attribute Browser panel or on the File → Import → Ontology → Ontology Mapper menu and the Ontology Mapper dialog will open.

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 (Symbol or Synonym column). Otherwise, the annotations will not appear in the Annotation Panel.