Cytoscape_User_Manual/Annotation

Annotations in Cytoscape are stored as a set of ontologies (e.g. the Gene Ontology, or GO). An ontology consists of a set of controlled vocabulary terms that annotate the objects. For example, using the Gene Ontology, the Saccharomyces Cerevisiae CDC55 gene has a biological process described as “protein biosynthesis”, to which GO has assigned the number 6412 (a GO ID).

GO 8150 biological_process
 GO 7582 physiological processes
   GO 8152 metabolism
    GO 44238 primary metabolism
      GO 19538 protein metabolism
        GO 6412 protein biosynthesis

Graphical View of GO Term 6412: protein biosynthesis

Cytoscape can use this ontology DAG (Directed Acyclic Graph) to annotate objects in networks. The Ontology Server (originally called "BioDataServer") is a Cytoscape feature which allows you to load, navigate, and assign annotation terms to nodes and edges in a network. Cytoscape 2.4 now has an enhanced GUI for loading ontology and associated annotation, enabling you to load both local and remote files.

Ontology and Annotation File Format

The standard file formats used in Cytoscape Ontology Server 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

OBO File

An OBO file is the ontology DAG itself. This file defines the relationships between ontology terms. Cytoscape 2.4 and onwards can load all ontology files written in OBO format. The full listing of ontology files are available from the Open Biomedical Ontologies (OBO) website:

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

Sample OBO File - 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

Default List of Ontologies

Cytoscape provides a list of ontologies available in OBO format. If an Internet connection is available, Cytoscape will import ontology and annotation files directly from the remote source. The table below lists the included ontologies.

Although Cytoscape can import all kinds of ontologies in OBO format, annotation files are associated with specific ontologies. Therefore, you need to provide the correct ontology-specific annotation file to annotate nodes/edges/networks in Cytoscape. For example, while you can annotate human network data using the GO Full ontology with human Gene Association files, you cannot use a combination of the human Disease Ontology file and human Gene Association files, because the Gene Association file is only compatible with GO.

Visualize and Browse Ontology DAG (for Advanced Users)

Relationships between ontology terms are usually represented as Directed Acyclic Graphs (DAGs). This is a special case of a network (or graph), where nodes are ontology terms and edges are relationships between terms. Originally, Cytoscape used a special data structure called BioDataServer to store ontology DAGs. Starting in version 2.4, ontology data will now be stored in the same data structure as normal networks. This enables users and plugin writers to visualize, browse and manipulate ontology DAGs just like other networks. The following is an example of visualization of an ontology DAG (Generic GO Slim):

Every ontology term and relationship can have attributes. In the OBO files, ontology terms have optional fields such as definition, synonyms, comments, or cross-references. These fields will be imported as node attributes. To browse those attributes, please use the attribute browser (see the example below):

• Note 1: Some ontologies have a lot of terms. For example, the full Gene Ontology contains more than 20,000 terms. If you need to save memory, you can remove this ontology DAG from Network Panel (right-click on the ontology name at the left-hand side of the screen and select Destroy Network).
• Note 2: All ontology DAGs will be saved in the session file. To minimize the session file size, you can delete the Ontology DAG before saving session.

Gene Association File

The Gene Association (GA) file provides annotation only for the Gene Ontology. It is a species-specific annotation file for GO terms. Gene Association files will only work with Gene Ontologies and NOT others!

Sample Gene Association File (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

Node Name Mapping

If you have a network file and an attribute file, they should have a common key to map attributes onto network data. If those two do not have a common key, you need to do an extra step to add a shared key. The following is a quick tutorial to learn how to use Gene Name Mapping files.

Import New ID Sets from BioMart

From Cytoscape 2.6.0, you can import various kinds of ID sets from BioMart (http://www.biomart.org/index.html). BioMart web service client is available as a set of plugins. You can install BioMartClient and BioMartUserInterface plugins from Plugin Manager window.

1. Select: File → Import → Import attributes from Biomart...

2. Select a data source. For ID mapping, select one of the Ensemble Genes data set. You need to choose correct species for your network.

3. Select Attribute. If you want to import new ID sets matching current node IDs, select ID.

4. Select Data Type. This should be the type of ID set selected in Attribute list. For example, if you select ID for Attribute and your network uses Entrez Gene ID for its node ID, you need to select EntrezGene ID(s) for Data Type.

5. Select new ID sets from the list. Because BioMart server does not accept query to import lots of annotations at once, you can select only 3-5 attributes for each import.

6. Press Import.

Import Network and Name Mapping Files

1. Download name mapping files. Mapping files are available at: http://chianti.ucsd.edu/kono/genenamemapping.html. In this tutorial, we are going to use dictionary_no_prefix.zip, which is a file set without prefixes for each gene names. Unzip the archive.

2. Load sample network file. Open network import dialog from File-->Import-->Network (multiple file types)... Then click URL radio button and import Human Protein-Protein: Rual et al. (Subnetwork for tutorial).

3. Open attribute table import dialog from File-->Import-->Attribute from Table.

4. Select human.dic_cyto.txt as the input file.

5. Check "Show Text File Import Options and click Transfer first line as attribute names checkbox.

6. Uncheck "Show Text File Import Options and check Mapping Options.

7. Select EntrezGene as Primary Key.

8. Right-click on EntrezGene column name and set the type to String.

9. Do the same for HGNC.

10. Right-click on Other Aliases and select List as the data type.

11. Check Other Aliases as Alias (under "Alias?" checkboxes).

12. Now the Table Import dialog looks like the following screenshot:

    • 

13. Press Import. The network has new names in the text file as attributes.

    • 

At this point, nodes have multiple names including HGNC, UniProt, and EntrezGene ID. You can import other attribute files using these keys. These imported names (IDs) are useful when you import GO Annotation.

Import Ontology and Annotation

Cytoscape 2.4 provides a graphical user interface to import both ontology and annotation files at the same time.

Import Gene Ontology and Gene Association Files

For convenience, Cytoscape has a list of URLs for commonly used ontology data and a complete set of Gene Association files. To import Gene Ontology and Gene Association files for the loaded networks, please follow these steps:

Important: All data sources in the preset list are remote URLs, meaning a network connection is required!

Step 1. Select an Annotation File

• 

  Select File → Import → Ontology and Annotation... to open the "Import Ontology and Annotation" window. From the Annotation dropdown list, select a gene association file for your network. For example, if you want to annotate the yeast network, select "Gene Association file for Saccharomyces cerevisiae".

Step 2. Select an Ontology File

• Select an Ontology data (OBO file) from the Ontology dropdown list. If the file is not loaded yet, it will be shown in red. The first three files are Gene Ontology files. You can load other ontologies, but you need your own annotation file to annotate networks.

Step 3. Import the files

• Once you click the Import button, Cytoscape will start loading OBO and Gene Association files from the remote sources. If you choose GO Full it may take a while since it is a large data file.

Step 4.

• When Cytoscape finishes importing files, the import window will be automatically closed. All attributes mapped by this function have the prefix "annotation" and look like this: annotation.[attribute_name]. All ontologies will be added to the end of the Ontology DAGs branch in the Network Manager.

  • 

Ontology DAGs have some attributes associated with the terms. All attributes associated with ontology terms will have the prefix ontology. They have at least one attribute: ontology.name. For more detailed information about attributes for ontology DAGs, please read the official OBO specification document.

• Note: Cytoscape supports both OBO formats: version 1.0 and 1.2.

Note: Switching Primary Key for Go Annotation Import

If node IDs in a network file are NOT DB_Object_Symbol (3rd column in Gene Association file), you need to select a primary key column. Click Show Mapping Options to change the key. Usually, DB_Object_ID can be an alternative primary key.

Custom Annotation Files for Ontologies Other than GO (for Advanced Users)

• The "Import Ontology and Annotation" function is designed to import general ontology and annotation files. Internally, mapping ontology terms onto existing networks is the same as joining three data tables in Cytoscape. An Ontology DAG, an annotation file, and network data are used in this process (see the example below).

Network Data

Ontology Data

Annotation Data

Mapping Result

If you want to map ontology terms onto network objects, you need to create a custom annotation file. The annotation file should contain at least 2 columns: a primary key and an ontology term ID. The primary key is the value used for mapping between the annotation file and network. Usually, the node/edge ID is used as the primary key, but you may choose any of the available attributes. The Ontology term ID is the key used for mapping between the annotation file and the ontology DAG. Using these data sources, you can annotate network objects in Cytoscape.

Suppose you have a small network:

node_1 pp node_2
node_3 pp node_1
node_2 pp node_3

and you want to annotate this network with Ontology A, which is an ontology DAG available in OBO format. In this case, you need an annotation table file that looks like this:

node_1  OA_0000232
node_2  OA_0000441
node_3  OA_0000702

where OA_*** represents an ontology term ID. This example is a file with the minimum necessary number of columns; however, you can include additional columns that will appear as additional node attributes.

Some ontologies will be used to annotate edges or networks. For example, the Protein-protein interaction ontology is a controlled set of terms for annotating interactions between proteins, so ontology terms should be mapped onto edges (see example below).

node_1 (pp) node_2  MI:0445
node_3 (pp) node_1  MI:0046
node_2 (pp) node_3  MI:0346

The basic operation of the Ontology and Annotation Import function is the same as that of the Attribute Table Import. The main difference is that you need to specify an additional key for mapping:

By selecting a column from the "Key Column in Annotation File" dropdown list, you can specify the key for mapping between ontology terms and the annotation file.

• Note: When you load Gene Association files, Cytoscape uses a special loader program designed only for Gene Association files. Because of this program, all attributes will be named automatically. Also, ontology IDs will be converted into term names and NCBI taxonomy ID will be converted into actual species name. However, for custom annotation files, those processes will not be applied. All ontology terms will be mapped as term IDs.