Reaction Report

Overview

Reaction Reports contain details about the individual reactions that comprise signaling pathways. "Reaction" is a term used in BKL to describe all kinds of interactions between signaling entities (molecules or genes) in signaling or regulatory events. The characteristics of each interaction, in other words the effect of the interaction, are defined by an effect term that appears on the Reaction Report. Reactions as processes are not physical entities like molecules, yet they are the central point in a signal transduction database. By representing reactions between molecules as separate Reaction Reports, it becomes possible to store their properties and annotate them. Since many reactions in signal transduction are catalyzed, and most catalyzed reactions are quasi-unidirectional, all reactions stored in the database are by default unidirectional. Equilibrium reactions, however, are identified as "reversible" on the Reaction Report. 

Four basic types of reactions are descibed: molecular evidence, pathway step, decomposition, and semantic. These reaction types are summarized in the table below.

*An illustration of semantic and mechanistic notations is shown in Figure 1. Detailed information about semantic and mechanistic reactions can be found here.

Figure 1. Semantic and Mechanistic Reactions Semantic reactions (small, light squares) go from SoS to Ras and from Ras to Raf, implying that each of the molecules has two states, one "inactive" state for receiving signals and an "active" state for transducing signals. Mechanistic reactions (slightly darker, bigger squares) are pathway steps and assign states explicitly to the molecules.

Please note: Molecular evidence, pathway step, and semantic reactions can be specified as direct or indirect.

Please note: Metabolic reactions are curated at the pathway step level only. They are assigned pathway step metabolic.

Please note: Additional details about the data model can be found in the following reference:
Choi C, Crass T, Kel A, Kel-Margoulis O, Krull M, Pistor S, Potapov A, Voss N, Wingender E. (2004) Consistent re-modeling of signaling pathways and its implementation in the TRANSPATH database, Genome Inf Ser 15:244-254. [Abstract]

Each Reaction Report is similarly organized and comprises different blocks for properties curated and references cited in the Report. When additional details are provided, the property blocks contain links to detailed Property Reports. Other BKL Reports mentioned in the Reaction Report are hyperlinked to the corresponding Reports. For example, individual components of the reaction are listed on the Reaction Report, with links to their corresponding Locus, Family, Complex, or Small Molecule Reports.

Reaction Reports may be accessed through the BKL Tools or through hyperlinks on BKL reports.

Anatomy of a Reaction Report

The general structure of a Reaction Report is described below. A reaction report will show several reactions, if the selected reaction is part of the reaction hierarchy. In addition to the selected and highlighted reaction, its parents and children in the hierarchy will be displayed. An overview is given in the navigator, while detailed information about the reactions is shown below in the data sections.

• Access help by clicking the help menu    and clicking the Drug report help link.
  
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• Navigate to the desired section of the report by opening the table of contents  

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.
  
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• Links to external resources are indicated by a blue bubble, such as the PubMedID link shown here:    .
  
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• Links to display additional text within the page are indicated by a yellow bubble, such as the show abstract link shown here:    .
  
• 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:    .
  
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Semantic Reaction Information Describes the characteristics of the semantic-level reactions associated with the reaction. RX#### Identifies a semantic-level reaction that is associated with the reaction of the page, with hyperlinks to the corresponding Locus, Small Molecule, Family, or Complex Reports and the cited PubMed reference. Click here for detailed information about semantic-level reactions. If a curator has added comments regarding particular functions or mechanisms that provide additional detail about the reaction, a [Comments] link appears, hyperlinked to a list of comments, or Annotations, for the reaction. For a list of topics covered in Comments, click here. Note: Each semantic reaction associated with the Reaction Report is displayed in an individual block on the Report. Effect Describes the effect(s) of the semantic reaction and identifies the reaction as direct or indirect. Click here for a list of Effect terms.

Pathway Step Reaction Information Describes the characteristics of the pathway step-level reactions associated with the reaction.   RX#### Identifies a pathway step-level reaction that is associated with the reaction of the page, with hyperlinks to the corresponding Locus, Small Molecule, Family, or Complex Reports and the cited PubMed reference. Click here for detailed information about pathway step-level reactions. If a curator has added comments regarding particular functions or mechanisms that provide additional detail about the reaction, a [Comments] link appears, hyperlinked to a list of comments, or Annotations, for the reaction. For a list of topics covered in Comments, click here. Note: Each pathway step reaction associated with the Reaction Report is displayed in an individual block on the Report. Effect Describes the effect(s) of the pathway step reaction and identifies the reaction as direct or indirect. Click here for a list of Effect terms. Pathways:Chains Lists pathways or chains the pathway step-level reaction is associated with, with hyperlinks to the corresponding Pathway/Chain Reports.

Molecular Evidence Reaction Information Describes the characteristics of the molecular evidence-level reactions associated with the reaction.   RX#### Identifies a molecular evidence-level reaction that is associated with the reaction of the page, with hyperlinks to the corresponding Locus, Small Molecule, Family, or Complex Reports and the cited PubMed reference. Click here for detailed information about molecular evidence-level reactions. If a curator has added comments regarding particular functions or mechanisms that provide additional detail about the reaction, a [Comments] link appears, hyperlinked to a list of comments, or Annotations, for the reaction. For a list of topics covered in Comments, click here. Note: Each unique molecular evidence reaction associated with the Reaction Report is displayed in an individual block on the Report. Effect Describes the effect(s) of the molecular evidence reaction and identifies the reaction as direct or indirect. Click here for a list of Effect terms. Quality Indicates the reliability of the experiment performed to identify the reaction, according to the TRANSPATH quality matrix. Click here for additional details about how combinations of materials and methods are associated with quality scores. Experimental Source Indicates the source (cell line) for the material used in the experiment that identified the molecular evidence reaction. Details about the experimental source are accessible by clicking on [details], which opens a Property Report. Note that in cases where multiple experiments have identified the exact same reaction, the blocks that contains the Experimental Source, Material, Method, and PMID eppear for each representative experiment. Material Provides additional detail about the material used in the experiment that identified the molecular evidence reaction. Click here for additional details about experimental materials. Method Indicates the method used to identify the reaction. Click here for additional details about experimental methods. PMID Lists the PubMed identifier for the reference cited for the molecular evidence reaction, hyperlinked to the PubMed abstract.

Decomposition Reaction Information Describes the characteristics of the decomposition reactions associated with the pathway step reaction.   RX#### Identifies a decomposition reaction that is associated with the pathway step reaction of the page, with hyperlinks to the corresponding Locus, Small Molecule, Family, or Complex Reports and the cited PubMed reference. Click here for detailed information about decomposition and pathway step reactions. If a curator has added comments regarding particular functions or mechanisms that provide additional detail about the reaction, a [Comments] link appears, hyperlinked to a list of comments, or Annotations, for the reaction. For a list of topics covered in Comments, click here. Note: Each decomposition reaction associated with the Reaction Report is displayed in an individual block on the Report. Effect Describes the effect(s) of the decomposition reaction and identifies the reaction as direct or indirect. Click here for a list of Effect terms.

References Displays list of references cited in the Reaction 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.