Pathway/Chain Report

Overview

Pathway/Chain Reports contain details about pathways and chains involved in signaling. Pathways reflect canonical pathways for specific signaling molecules (mostly ligands or receptors) and are made up of one or more chains. Chains are sets of consequent reactions; in other words, the reactions contain common molecules. For a detailed explantion of pathways and chains, click here.

Each Pathway Report is similarly organized and comprises different blocks for properties curated and references cited in the Report. Other BKL Reports mentioned in the Pathway Report are hyperlinked to the corresponding Reports. For example, individual reactions that comprise the pathway are listed on the Pathway Report, with links to their corresponding Reaction Reports.

Pathway Reports may be accessed through the BKL Tools or through hyperlinks on BKL reports. A visualization of the signaling pathways is accessible in the BKL Pathfinder. The pathway views can be customized, enabling expansion at any point of interest. These pathway representations have their counterparts in the hand-drawn pathway maps, which are interactive and contain more condensed information but are static.


Anatomy of a Pathway/Chain Report

The general structure of a Pathway/Chain Report is described below. Since the format is slightly different for a chain versus a pathway, examples of both are provided. The first image shows an example of a Chain, and the second shows an example of a Pathway. For details about chains and pathways, click here.

  • Access help by clicking the help menu  help  and clicking the Drug report help link.

  • Navigate to the desired section of the report by opening the table of contents  toc

Points of navigation within the report are indicated by the following visual cues.

  • Links to additional reports within the BKL are presented as regular text links.

  • Links to external resources are indicated by a blue bubble, such as the PubMedID link shown here:  external link  .

  • Links to display additional text within the page are indicated by a yellow bubble, such as the show abstract link shown here:  expand content  .
  • Links providing an option to send data to another tool within the BKL are indicated by a gray bubble, such as the Pathfinder link shown here:  download content  .


Anatomy of a Chain Report

Chains consist of multiple reactions and are assembled to build pathways. In the Chain Report, each reaction and molecule are listed, and the pathway assembled from the chain is indicated.

Pathway Information Describes the characteristics of the chain. help
Type
Identifies whether report describes a chain or a pathway. If the sequence of reactions that comprise the chain has been reported by one primary paper, the chain is labelled as an evidence chain. Chains that comprise metabolic pathway steps are labelled metabolic chains. Click here for more details about chains.
Pathways
Indicates the pathway the chain is associated with, with hyperlinks to the corresponding Pathway Report.
Reactions
Identifies the reactions associated with the chain, with hyperlinks to the corresponding Reaction Reports. Also identifies the effect of the reaction. For information about effects, click here. The reactions are displayed in a cascade view of all reactions the pathway/chain consists of. The level of indentation and the gray lines indicate subsequent reactions. Square brackets and italic reaction names depict the second occurrence of a reaction in a cascade. When the mouse pointer is moved over a reaction, its precursor reactions are highlighted in red.
Molecules
Lists the molecules associated with the chain, with hyperlinks to the corresponding Locus, Family, Complex, or Small Molecule Reports. Click [show] to display the molecules and [hide] (not displayed here) to remove molecules from view.

Annotations Displays free-text annotations added by curators to provide additional details about the chain.  
This block displays comments from the curator, regarding particular function, mechanisms...etc., separated by topic. For a list of topics covered in Annotations, click here.

References Displays list of references cited in the Pathway/Chain Report.  
This block gives the full citations, with titles, that correspond to the PubMed identifiers displayed. When a PubMed identifier is not available, the Medline identifier is displayed. When neither a PubMed nor Medline identifier is available, a BIOBASE-specific number is assigned preceded by a "P". Nearly all of the reference numbers are hyperlinked to the Entrez database where the abstracts may be read. All references cited in the annotations and properties section are listed, and other references known to contain information about the protein may also be listed. The first five references are shown, click [ more ...] to view all references, and view abstracts via webservice, by additionally clicking the [+] which appears.




Anatomy of a Pathway Report

Pathways consist of multiple chains of reactions. In the Pathway Report, each chain is listed, with its corresponding reactions and molecules.

Pathway Information Describes the characteristics of the pathway. help
Type
Identifies whether report describes a chain or a pathway.
Chain
Lists all chains associated with the pathway, with hyperlinks to the corresponding Chain Report.
Reactions
Identifies the reactions associated with the particular chain in the pathway, with hyperlinks to the corresponding Reaction Reports. Also identifies the effect of the reaction. For information about effects, click here. The reactions are displayed in a cascade view of all reactions the pathway/chain consists of. The level of indentation and the gray lines indicate subsequent reactions. Square brackets and italic reaction names depict the second occurrence of a reaction in a cascade. When the mouse pointer is moved over a reaction, its precursor reactions are highlighted in red.
Molecules
Lists the molecules associated with the particular chain in the pathway, with hyperlinks to the corresponding Locus, Family, Complex, or Small Molecule Reports. Click [show] to display the molecules and [hide] (not displayed here) to remove molecules from view.

Annotations Displays free-text annotations added by curators to provide additional details about the pathway.  
This block displays comments from the curator, regarding particular function, mechanisms...etc., separated by topic. For a list of topics covered in Annotations, click here.

References Displays list of references cited in the Pathway/Chain Report.  
This block gives the full citations, with titles, that correspond to the PubMed identifiers displayed. When a PubMed identifier is not available, the Medline identifier is displayed. When neither a PubMed nor Medline identifier is available, a BIOBASE-specific number is assigned preceded by a "P". Nearly all of the reference numbers are hyperlinked to the Entrez database where the abstracts may be read. All references cited in the annotations and properties section are listed, and other references known to contain information about the protein may also be listed. The first five references are shown, click [ more ...] to view all references. View abstracts via webservice, by additionally clicking the [+] which appears.

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