SBGN bricks dictionary
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Metabolic networks
| Biological event | SBGN brick | Description |
|---|---|---|
| CATALYSIS
associated GO terms: GO:0008152, GO:0044238, GO:0003824 | ||
| PD |  | Irreversible reaction with 1 substrate and 1 product
The enzyme catalyzes an irreversible (metabolic) process which consumes the substrate (S1) and produces the product (P1). The enzyme is a protein, therefore represented as a ‘macromolecule’. Substrate and product of the biochemical reaction are represented by ‘simple chemicals’. The consumption of S1 is represented by the consumption arc. The production arc represents the synthesis of P1. |
 | Irreversible reaction with 2 substrates and 1 product
The enzyme catalyzes an irreversible (metabolic) process which consumes two substrates (S1 and S2) and produces the product (P1). The enzyme is a protein, therefore represented as a ‘macromolecule’. Substrates and product of the biochemical reaction are represented by ‘simple chemicals’. The consumption of S1and S2 is represented by the consumption arc. The production arc represents the synthesis of P1. | |
 | Irreversible reaction with 1 substrate and 2 products
The enzyme catalyzes an irreversible (metabolic) process which consumes the substrate (S1) and produces two products (P1 and P2). The enzyme is a protein, therefore represented as a ‘macromolecule’. Substrate and products of the biochemical reaction are represented by ‘simple chemicals’. The consumption of S1 is represented by the consumption arc. The production arc represents the synthesis of P1 and P2. | |
 | Irreversible reaction with 2 substrates and 2 products
The enzyme catalyzes an irreversible (metabolic) process which consumes two substrates (S1 and S2) and produces two products (P1 and P2). The enzyme is a protein, therefore represented as a ‘macromolecule’. Substrates and products of the biochemical reaction are represented by ‘simple chemicals’. The consumption of S1 and S2 is represented by the consumption arc. The production arc represents the synthesis of P1 and P2. | |
 | Reversible reaction with 1 substrate and 1 product
The enzyme catalyzes a reversible (metabolic) process which consumes the substrate (S1) and produces the product (P1). The enzyme is a protein, therefore represented as a ‘macromolecule’. Substrate and product of the biochemical reaction are represented by ‘simple chemicals’. Reversibility of this reaction is represented by the consumption/production arc for reversible reactions. | |
 | Reversible reaction with 2 substrates and 2 products
The enzyme catalyzes a reversible (metabolic) process which consumes two substrates (S1 and S2) and produces two products (P1 and P2). The enzyme is a protein, therefore represented as a ‘macromolecule’. Substrates and products of the biochemical reaction are represented by ‘simple chemicals’. Reversibility of this reaction is represented by the consumption/production arc for reversible reactions. | |
| ER | Not applicable | ER does not consider temporal aspects and is therefore less applicable for the representation of metabolic networks. |
| AF |  | Irreversible reaction with 1 substrate and 1 product
The activities of the enzyme and the substrate (S1) transform into the activity of the product (P1). Both substrate and product activities are marked by the ‘simple chemical’ unit of information. The enzyme activity is represented using the ‘macromolecule’ unit of information. The use of the ‘positive influence’ arc indicates the production of P1 as a result of the enzyme and substrate activities. ‘Logic arcs’ resulting in the logical operator ‘AND’ represent the combined activities of S1 and enzyme. |
 | Irreversible reaction with 2 substrates and 1 product
The activities of the enzyme and two substrates (S1 and S2) transform into the activity of the product (P1). All substrate and product activities are marked by the ‘simple chemical’ unit of information. The enzyme activity is represented using the ‘macromolecule’ unit of information. The use of the ‘positive influence’ arc indicates the production of P1 as a result of the enzyme and substrates activities. ‘Logic arcs’ resulting in the logical operator ‘AND’ represent the combined activities of S1, S2 and enzyme. | |
| Other types of biochemical reactions
Not suitable because of intricate representations with multiple logical operators based on the number of products. |
Signaling networks
| Biological event | SBGN brick | Description |
|---|---|---|
| PROTEIN PHOSPHORYLATION
associated GO terms: GO:0006468,GO:0003824 | ||
| PD |  | A kinase protein catalyzes an irreversible reaction which consumes unphosphorylated protein X and ATP and produces phosphorylated protein X and ADP. All proteins involved are represented by macromolecules and ‘state variables’ are used to indicate the phosphorylation state. ATP and ADP are represented as ‘simple chemicals’. |
| ER |  | A kinase entity stimulates the assignment of a phosphorylated state to a target protein entity (X). The assignment is represented using the ‘assignment’ arc. The phosphate is represented using a ‘variable value’ with the label ‘P’. The ‘state variable’ at the target protein indicates the phosphorylation site. |
| AF |  | The kinase activity positively influences the activity of a phosphorylated protein (X-P). Both activities are marked by the ‘macromolecule’ unit of information. The information about the phosphorylated state can be indicated by the label. No state variables exist in AF and the ‘unit of information’ auxiliary unit is used to represent the nature of the entity (here a ‘macromolecule’). |
Protein-protein-interaction networks
| Biological event | SBGN brick | Description |
|---|---|---|
| COMPLEX FORMATION (PROTEINS) associated GO terms: GO:0006461 | ||
| PD |  | Two ‚macromolecule‘ entities X and Y form the complex X_Y. Complex formation is represented using the ‘association’ process node with ingoing consumption and outgoing production arcs. The ‘complex’ glyph surrounds subunits X and Y. |
| ER |  | The interaction between the entities X and Y results in the assignment of the value ’true’ to the state variable ‘existence’ of the X_Y entity. The complex identity is indicated using the label X_Y. |
| AF |  | The activity X together with the activity Y stimulates the activity X_Y. X and Y are macromolecules as displayed using the ‘macromolecule’ unit of information. The identity of X_Y as a complex is represented using the ‘complex’ unit of information. |
| COMPLEX DISSOCIATION
associated GO terms: GO:0043241 | ||
| PD |  | A complex of two ‘macromolecule’ entities X and Y breaks down into X and Y. The ‘complex’ glyph surrounds the X and Y entities. Complex breakdown is represented using the ‘dissociation’ process node with ingoing consumption and outgoing production arcs. |
| ER |  | The entity X_Y, representing a complex of X and Y, stimulates the assignment of the value ‘true’ to the existence of both two entities X and Y. ‘True’ is indicated using a ‘variable value’ with the label ‘T’. |
| AF |  | The activity X_Y stimulates the activities X and Y. The identity of X_Y as a complex is represented using the ‘complex’ unit of information. X and Y are macromolecules as displayed using the ‘macromolecule’ unit of information. |
| OLIGOMERIZATION/ HOMODIMERIZATION associated GO terms: GO:0035786 | ||
| PD |  | The ‘macromolecule’ X, which is phosphorylated at two residues undergoes homodimerization, a process which consumes 2 entities X and produces the ‘multimer’ X. The number of 2 monomers is given as additional information ‘N:2’. |
| ER |  | Two entities X stimulate the assignment of the value ‘true’ to the existence of entity XX. The cardinality is represented using the ‘unit of information’ with the label giving the number of entities (in this case two). The homodimer identity is indicated by the label XX. Both entities, X and XX, are phosphorylated at two residues indicated using another ‘unit of information’ with the label indicating the phosphorylation site. |
| AF |  | The activity of X-2P stimulates the activity of XX-2P. Both activities are phosphorylated at two residues (indicated by suffix -2P in the label). The complex identity of XX-2P is represented using the ‘complex’ unit of information. Cardinality cannot be represented in AF. The process of homodimerization is indicated by the labels X-2P and XX-2P. |
Gene regulatory networks
| Biological event | SBGN brick | Description |
|---|---|---|
| REGULATION OF TRANSCRIPTION
associated GO terms: GO:0006355 GO:0065004 GO:0009299 GO:0006351 | ||
| PD |  | Direct regulation of a target gene by a transcription factor (promoter binding)
During direct gene regulation the transcription factor (TF) builds a complex with the target gene promoter. The TF protein is a ‘macromolecule’ with the material type protein (mt:prot) whereas the gene promoter is given as a ‘nucleic acid feature’ with the conceptual type ‘gene’ (ct:gene). The complex of both regulator and target gene promoter/DNA triggers the `process` of transcription. The connecting arc ‘necessary stimulation’ is applied to indicate that the stimulation by the regulator-target-complex is necessary for the transcription process to take place. The target gene messenger as a product of the transcription process is represented by a ‘nucleic acid feature’ with the conceptual type ‘mRNA’ (ct:mRNA). The ‘unspecified source’ symbol is used to represent the large number of substrates of a transcription process (e.g. trinucleotides). |
 | Regulation of a target gene by a transcription factor (without knowledge about promoter binding)
A transcription factor (TF) protein together with a target gene promoter X triggers the `process` of transcription. Direct binding of the TF to the target gene promoter has not been experimentally verified, therefore the logical operator ‘AND’ is used to describe the yet unspecified interaction between TF and target gene. The TF protein is a macromolecule of the material type 'protein' (mt:prot) whereas the gene promoter is given as a ‘nucleic acid feature’ with the conceptual type 'gene' (ct:gene). The connecting arc ‘necessary stimulation’ is applied to indicate that the stimulation by both regulator and target is necessary for the transcription process to take place. The target gene messenger as a product of the transcription process is represented by a ‘nucleic acid feature’ with the conceptual type ‘mRNA’ (ct:mRNA). The ‘unspecified source’ symbol is used to represent the large number of substrates of a transcription process (i.e. trinucleotides). | |
| ER |  | A transcription factor (TF) entity interacts with a target gene genomic DNA entity X. Only if this interaction exists, the existence of the target gene mRNA entity becomes true. ‘True’ is indicated using a ‘variable value’ with the label ‘T’. The connecting arc ‘necessary stimulation’ is applied to indicate that the interaction of regulator and target is necessary for the transcription to take place. All entities carry units of information with the label indicating the material (mt:prot) or conceptual types (ct:gene, ct:mRNA). |
| AF |  | Direct regulation of a target gene by a transcription factor (promoter binding)
The activities of a transcription factor (TF) and its target gene DNA X form a complex TF-X indicating the experimentally verified promoter binding of the TF. The complex identity of TF-X is represented using the ‘complex’ unit of information. This complex necessarily stimulates the activity of the target gene mRNA X. The identities of genomic fragment of DNA or RNA as ‘nucleic acid features’ is represented by the shape of the unit of information and the conceptual types (ct:gene, ct:mRNA) as label in the unit of information. The connecting arc ‘necessary stimulation’ is applied to indicate that the stimulation by both the activities of TF and target gene DNA is necessary for the target gene mRNA activity. |
 | Regulation of a target gene by a transcription factor (without knowledge about promoter binding)
The activities of a transcription factor (TF) and its target gene DNA necessarily stimulate the activity of the target gene mRNA. The identities of genomic fragment of DNA or RNA as ‘nucleic acid features’ is represented by the shape of the unit of information and the conceptual types as label in the unit of information. The connecting arc ‘necessary stimulation’ is applied to indicate that the stimulation by both the activities of TF and target gene DNA is necessary for the target gene mRNA activity. | |
| TRANSLATION
associated GO terms: GO:0006412 | ||
| PD |  | The mRNA of gene X essentially stimulates the translation process leading to the production of the corresponding protein X. The transcript is given as a ‘nucleic acid feature’ with the conceptual type ‘mRNA’ (ct:mRNA) whereas the corresponding protein is a macromolecule of the material type ‘protein’ (mt:prot). The connecting arc ‘necessary stimulation’ is applied to indicate that the stimulation by the mRNA is necessary for the translation process to take place. The 'unspecified source' symbol is used to represent the large number of substrates of the translation process (i.e. amino acids). |
| ER |  | The entity X with the conceptual type ‚mRNA‘ essentially stimulates the assignment of the value ‘true’ to the existence of entity X with the material type ‘protein’ (mt:prot). The connecting arc ‘necessary stimulation’ is applied to indicate that the stimulation by the mRNA is necessary for the translation process to take place. |
| AF |  | The activity of X with the ‚nucleic acid feature‘ unit of information with the conceptual type 'mRNA' (ct:mRNA) essentially stimulates the activity X with the ‚macromolecule‘ unit of information and the material type 'protein' (mt:prot). The connecting arc ‘necessary stimulation’ is applied to indicate that the stimulation by the mRNA is necessary for the translation process to take place. |
Networks of functional genomics
| Biological event | SBGN brick | Description |
|---|---|---|
| FUNCTIONAL RELATIONSHIP
associated GO terms: GO:0008150 any Biological Process | ||
| PD | Not applicable | As a special feature, AF enables the conceptual representation of biological events with a low level of knowledge or detail. This is especially suitable for the representation of networks of functional genomics with the focus on interactions between genes and biological processes without mechanistic details. A direct translation of the corresponding AF brick to PD or ER is not possible because it requires a higher level of knowledge. |
| ER | Not applicable | As a special feature, AF enables the conceptual representation of biological events with a low level of knowledge or detail. This is especially suitable for the representation of networks of functional genomics with the focus on interactions between genes and biological processes without mechanistic details. A direct translation of the corresponding AF brick to PD or ER is not possible because it requires a higher level of knowledge. |
| AF |  | Any kind of biological event X (such as changing developmental or environmental conditions) is represented using the ‘pertubation’ glyph and positively influences the species E (in any way). Species E in turn positively influences another biological event Y, represented using the ‘phenotype’ glyph. |
Others
| Biological event | SBGN brick | Description |
|---|---|---|
| COMPARTMENTATION/ TRANSPORT associated GO terms: GO:0006810 | ||
| PD |  | Passive transport (diffusion)
The ‚macromolecule‘ X in the cytosol serves as the substrate of a process leading to the production of the macromolecule X in the nucleus. This process describes the passive transport of X from one compartment to the other. The two macromolecules X do not carry the clone marker because the containing compartment is part of their identity. |
 | Active transport (transporter, channel)
The ‚macromolecule‘ X in the cytosol serves as the substrate of a process leading to the production of the macromolecule X in the nucleus. This process is stimulated by the ‘macromolecule’ Y which is located within the nuclear membrane and represents the transporter protein. Cytosolic, membrane and nuclear localization are represented using the ‘compartment’ glyph with the corresponding label. The two macromolecules X do not carry the clone marker because the containing compartment is part of their identity. | |
| ER |  | Compartmentation/Passive transport (diffusion)
The variable value ‘nucleus’ is assigned to the entity X. No compartment glyphs exist in ER. Therefore the location of entities is represented using the special state variables 'location' and the assigned variable values. ER does not represent temporal aspects, this brick does not show the transport of X from one to another compartment but rather shows the compartment X is located in. |
 | Compartmentation/Active transport (transporter, channel)
The entity Y stimulates the assignment of the value ‘nucleus’ to the state variable ‘location’ of entity X. The location is indicated using a ‘variable value’ with the label ‘nucleus’. No compartment glyphs exist in ER. Therefore the location of entities is represented using the special state variables 'location' and the assigned variable values. ER does not represent temporal aspects, this brick does not show the Y-mediated transport of X from one to another compartment. It rather shows the influence of Y on the location of X. | |
| AF |  | Passive transport (diffusion)
The activity X in the cytosol stimulates the activity X in the nucleus. This process describes the passive transport of X from one compartment to the other. Cytosolic and nuclear localization are represented using the ‘compartment’ glyph with the corresponding label. |
 | Active transport (transporter, channel)
The activity X in the cytosol and the activity Y in the nuclear membrane stimulate the activity X in the nucleus. This process describes the active transport of X from one compartment to the other. Different localizations are represented using the ‘compartment’ glyph with the corresponding label. ‘Logic arcs’ resulting in the logical operator ‘AND’ represent the combined activities of X and Y. |