Component Details

Pathway component details are displayed in the Details panel. Details of the components are displayed by:
  • Clicking and Selecting a pathway or its component in the browser.
  • Selecting show details option from the context menu that is displayed by right clicking on a pathway title or its component in the browser.
  • Clicking on a pathway component on the diagram.
For example below Figures show a way to navigate browser and display protein details.
To get Protein Details, expand the pathway node from the pathway tree navigate to the protein of interest. Click on the protein or Right click on the selected protein and and select 'show protein details'. Protein gets marked with an overlay ( customizable by user by overlay options) on the pathway diagram and also pop-open the details panel (shown in Figure 2) showing the information about the protein.

Figure 1


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Information about ‘Details panel’

Component Type = Pathway

Tab name

Description

Data provenance

Summary

Displays summary about the pathway viewed

iPAVS added annotations + information from respective data sources to which pathway belong.

For list of data sources see here

Contributed

IPAVS allows users to submit functional annotations. See document about ‘community contribution’ to read about how you can contribute.

The contributed annotations are verified by IPAVS team for accuracy and completeness and will make it available in this tab along with appropriate authorship attribution.

Individuals of the Community

Sub/Related Pathway

Displays pathways having parent-child contains relationship (e.g. Main- pathway and sub-pathway (sub-network)). Example RB pathway provides one main map and several functional modules which they extracted from the main map using an algorithm. Such small modules are considered as sub-pathways.

 

Pathways that are considered to be related

For example: Wnt signaling pathway and Wnt signaling pathway in hypertrophy are considered to be related pathway. In other words related pathways may have several similar common components.

Currently available only for some of the IPAVS pathways and Rb pathway database

Pathway Xref

Manually annotated for iPAVS team. Pathways iPAVS considered to be equivalent by curator to pathways in other external databases or web resources.

 

Currently available only for IPAVS pathways

Proteins

List of all the proteins and Genes belonging to the pathway

Information from respective data sources to which pathway belong.

 

Synonyms/Aliases are obtained from Uniprot database

Interaction(Conversion)

List of all the pathway interaction of type Conversion(See BioPax for details)

See mapping between the CellDesigner-SBML and BioPax

information from respective data sources to which pathway belong

Interaction(Control)

List of all the pathway interaction of type Control (See BioPax for details)

See mapping between the CellDesigner-SBML and BioPax

information from respective data sources to which pathway belong

Complexes

List of biomolecular complexes

information from respective data sources to which pathway belong

Publication

List of publication for the pathway

PMIDS are obtained from

respective data sources to which pathway belong

 

Publication Details like Citation, Title are populated from NCBI Pubmed database

 

Component Type = Protein/Gene /RNA

Tab name

Description

Data provenance

Summary

Displays summary about the pathway viewed

IPAVS meta data +

Information from respective data sources to which pathway belong.

For list of data sources see here + Uniprot

Contributed

IPAVS allows users to submit functional annotations. See document about ‘community contribution’ to read about how you can contribute.

The contributed annotations are verified by IPAVS team for accuracy and completeness and will make it available in this tab along with appropriate authorship attribution.

Individuals of the Community

Function

Gene / Protein functions

Uniprot database

Go Annotation

Ontology Categories and Evidence given as Pubmed IDs

Gene Ontology Annotation Database

DBXref

Links to pages giving details of the protein and genes on the external database

The Xref list was collated from several sources including Uniprot database, EBI-IPI and PIR

Pathways

List of pathways for all the data sources to which integrated to which the protein or gene belongs to.

Information from pathway sources

Complexes

List of complexes in which the protein/gene/rna is a member. The list includes complexes along with the pathways in which they participate. Same complex in two different pathways are listed distinctly.

Information from pathway sources

Biochemical Reactions

List of all the pathway interaction of type Conversion(See BioPax for details)

 

See details here Cell Designer documentation.

Example: Interaction of type complex formation, transport, state transition, transcription, tanslation and truncation belongs to this type

Information from pathway sources

Control Reactions

Interactions of type Modification, enzyme reactions belongs to this category.

(See BioPax ,  Cell Designer documentation for details)

 

Information from pathway sources

Enzyme Interactions &

Physical Interactions

Currently not available. We will get it working soon

Protein-protein databases, Protein –DNA database

e.g. IntAct, Biogrid, HPRD etc.

Other Interaction

Indirect interactions ( e.g. known transitions omitted and unknown transitions). For more details refer to SBGN process diagram notations or Cell Designer documentation.

Information from pathway sources

Publication

If a protein is annotated with an evidence by the source database. The information about the cited publication will be provided here

NCBI - Pubmed




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