Help:Tutorial:Step 3 old
From WikiPathways
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| - | A good way to start drawing the pathway is to add the proteins. On a WikiPathways pathway, all biological entities with an annotation are stored as a | + | A good way to start drawing the pathway is to add the proteins. On a WikiPathways pathway, all biological entities with an annotation are stored as a Data Node. A Data Node can have different types, in this case, we choose the type ''GeneProduct''. To add a gene product, click the {{TutorialImage|newgeneproduct.gif}} button, followed by clicking on the drawing area on the location that you want the element to be added. Repeat this to add 6 gene-products. You pathway now looks something like this: |
{|class=prettytable | {|class=prettytable | ||
|{{TutorialImage|step3.png}} | |{{TutorialImage|step3.png}} | ||
|} | |} | ||
| - | === Annotating | + | === Annotating Data Nodes === |
{{TutorialVideo|qhXzAlRh8RY|360|Annotate a datanode}} | {{TutorialVideo|qhXzAlRh8RY|360|Annotate a datanode}} | ||
| - | Now you are going to annotate the | + | Now you are going to annotate the Data Nodes and set a proper text label. Data Nodes can be annotated using an identifier from one of the available datasources. A pathway with annotated Data Nodes has several advantages: |
| - | * Detailed information about the entity is directly available in the [[Help:Tutorial#Used terms and abbreviations| | + | * Detailed information about the entity is directly available in the [[Help:Tutorial#Used terms and abbreviations|'''Backpage''' panel]] |
* The pathway page provides direct links to extended info at the annotation datasource website (e.g. [http://www.ensembl.org Ensembl]) | * The pathway page provides direct links to extended info at the annotation datasource website (e.g. [http://www.ensembl.org Ensembl]) | ||
* The pathway can be used for computational analysis, e.g. visualization with GenMAPP, or statistics with Eu.gene or MAPPFinder | * The pathway can be used for computational analysis, e.g. visualization with GenMAPP, or statistics with Eu.gene or MAPPFinder | ||
| - | To annotate a | + | To annotate a Data Node, go to the annotations tab in the properties dialog, by double-clicking the Data Node or choosing '''Properties''' from the right-click menu. Below is a screenshot of the annotation dialog: |
{| | {| | ||
|{{TutorialImage|datanode_annotation.png}} | |{{TutorialImage|datanode_annotation.png}} | ||
|} | |} | ||
| - | In this dialog, you need to set the identifier, | + | In this dialog, you need to set the identifier, database and a text label that will be displayed on the pathway. You can manually fill in these values or search in the synonym database. To search for an annotation, enter a search term and press the search button. If the identifier you are looking for is found, select the identifier/datasource from the results list and the text label, identifier and database fields will be automatically completed. The text in the '''Text label''' field will be displayed on the pathway and doesn't affect the annotation. |
| - | After annotating a | + | After annotating a Data Node, you can click on the Data Node to see whether it's correctly annotated. If the identifier can be found in the database, the annotation info will show up in the ' 'Backpage' ' tab of the side panel: |
{|class=prettytable | {|class=prettytable | ||
|{{TutorialImage|backpage.png}} | |{{TutorialImage|backpage.png}} | ||
Revision as of 22:59, 27 May 2014
The proteins of the circadian clock pathway
| Adding a gene-product |
This pathway is formed by interactions between the following proteins:
| Name | Identifier | Database |
|---|---|---|
| Bmal1 | ENSMUSG00000055116 | Ensembl |
| Clock | ENSMUSG00000029238 | Ensembl |
| Cry1 | 12952 | Entrez Gene |
| Cry2 | 12953 | Entrez Gene |
| Per1 | ENSMUSG00000020893 | Ensembl |
| Per2 | ENSMUSG00000055866 | Ensembl |
A good way to start drawing the pathway is to add the proteins. On a WikiPathways pathway, all biological entities with an annotation are stored as a Data Node. A Data Node can have different types, in this case, we choose the type GeneProduct. To add a gene product, click the 
button, followed by clicking on the drawing area on the location that you want the element to be added. Repeat this to add 6 gene-products. You pathway now looks something like this:
|
Annotating Data Nodes
| Annotate a datanode |
Now you are going to annotate the Data Nodes and set a proper text label. Data Nodes can be annotated using an identifier from one of the available datasources. A pathway with annotated Data Nodes has several advantages:
- Detailed information about the entity is directly available in the Backpage panel
- The pathway page provides direct links to extended info at the annotation datasource website (e.g. Ensembl)
- The pathway can be used for computational analysis, e.g. visualization with GenMAPP, or statistics with Eu.gene or MAPPFinder
To annotate a Data Node, go to the annotations tab in the properties dialog, by double-clicking the Data Node or choosing Properties from the right-click menu. Below is a screenshot of the annotation dialog:
|
In this dialog, you need to set the identifier, database and a text label that will be displayed on the pathway. You can manually fill in these values or search in the synonym database. To search for an annotation, enter a search term and press the search button. If the identifier you are looking for is found, select the identifier/datasource from the results list and the text label, identifier and database fields will be automatically completed. The text in the Text label field will be displayed on the pathway and doesn't affect the annotation.
After annotating a Data Node, you can click on the Data Node to see whether it's correctly annotated. If the identifier can be found in the database, the annotation info will show up in the ' 'Backpage' ' tab of the side panel:
|
Note: If you try to search for Bmal1, you'll notice that it is not found. This is because this particular gene has two synonymous names (Bmal1 and Arntl1), but only the latter is stored in the internal database. However, since we have a valid Ensembl ID we can still annotate this gene manually. Just fill out the Ensembl ID and Bmal1 in the right fields. You can check the backpage to confirm that the manual entry is cross-referenced.
