PD2AF 1.0 Specification

1. Identifying active entities
2. Posttranslational modification (activation and deactivation)
3. Metabolic reactions
4. Empty set (production, degradation, transcription, translation)
5. Heterocomplex association and dissociation
6. Multimerisation
7. Translocation and transport
8. Hidden inhibition

This page offers the specification of the conversion rules. That includes identification of active entities and the translation of Process Description (PD) expressions to Activity Flow (AF) expressions. For each case we ensured that the converter translates exactly as shown: each left-hand diagram (PD) transforms into the corresponding right-hand diagram (AF).

Letter code used for human-readable rule identifiers: A - active; AS - association; AE - active entity; CURM - currency metabolites; CAT - catalysis; CATR - catalysis, reversible process; COMPL - complex; CONS - consumption; DEGR - degradation; DIS - dissociation; ES - empty set; HIDINH - hidden inhibition; I - incactive; INH - inhibition; INHR - inhibition, reverisible process; LO - logical operator; M - metabolite; MOD - modulation; MULT - multimerisation; N - named; NCURM - noncurrency metabolites; NSTI - necessery stimulation; STI - stimulation; TRANS - transport; TRSCR - transcription; TRSL - tranaslation.

Light green used to highlight active entities.

1. Identifying active entities

The following rules are used for identifying active entities in the context of Process Description maps. Then, in other rules, the status of the entities active vs. inactive is used for adequate conversion. An entity is identified as active if it is marked as “active” in a state variable, or has an outgoing regulatory arc (modulation, stimulation, catalysis, inhibition, necessery stimiulation), or has a consumption arc, or has a logic arc (input to a logical operator).

In graphical visualisatin of these rules we use unspecified entity to show that different types of entities can be in its place such as macromolecule (protein), simple chemical (metabolite), nucleic acid feature (gene, mRNA) or complex.

1.1 PD2AF:AE-A (0.1 act)

GML

1.2 PD2AF:AE-MOD (0.2 mod)

GML

1.3 PD2AF:AE-STI (0.3 stim)

GML

1.4 PD2AF:AE-CAT (0.4 cat)

GML

1.5 PD2AF:AE-INH (0.5 inh)

GML

1.6 PD2AF:AE-NSTI (0.6 nstim)

GML

1.7 PD2AF:AE-LO (NEW)

GML


2. Posttranslational modification (activation and deactivation)

Associated terms: SBO:0000182 conversion, GO:0036211 protein modification process, GO:0140096 catalytic activity, acting on a protein

2.1 PD2AF:I-STI-I (1.1 i-sti-i)

SBGN-ML    Newt SBGN-ML    Newt


2.2 PD2AF:I-CAT-I (1.2 i-cat-i)

SBGN-ML    Newt SBGN-ML    Newt


2.3 PD2AF:I-NSTI-I (1.3 i-nsti-i)

SBGN-ML    Newt SBGN-ML    Newt


2.4 PD2AF:I-MOD-I (1.4 i-mod-i)

SBGN-ML    Newt SBGN-ML    Newt


2.5 PD2AF:I-INH-I (1.5 i-inh-i)

SBGN-ML    Newt SBGN-ML    Newt


2.6 PD2AF:I-STI-A (1.6 i-sti-a)

GML    SBGN-ML    Newt SBGN-ML    Newt


2.7 PD2AF:I-CAT-A (1.7 i-cat-a)

GML    SBGN-ML    Newt SBGN-ML    Newt


2.8 PD2AF:I-NSTI-A (1.8 i-nsti-a)

WARNING: Rare or wrong representation of a signalling event.

SBGN-ML    Newt SBGN-ML    Newt


2.9 PD2AF:I-MOD-A (1.9 i-mod-a)

SBGN-ML    Newt SBGN-ML    Newt


2.10 PD2AF:I-INH-A (1.10 i-inh-a)

SBGN-ML    Newt SBGN-ML    Newt


2.11 PD2AF:A-STI-I (1.11 a-sti-i)

SBGN-ML    Newt SBGN-ML    Newt


2.12 PD2AF:A-CAT-I (1.12 a-cat-i)

SBGN-ML    Newt SBGN-ML    Newt


2.13 PD2AF:A-NSTI-I (1.13 a-nsti-i)

WARNING: Rare or wrong representation of a signalling event.

SBGN-ML    Newt SBGN-ML    Newt


2.14 PD2AF:A-MOD-I (1.14 a-mod-i)

SBGN-ML    Newt SBGN-ML    Newt


2.15 PD2AF:A-INH-I (1.15 a-inh-i)

SBGN-ML    Newt SBGN-ML    Newt


2.16 PD2AF:A-STI-A (1.16 a-sti-a)

GML    SBGN-ML    Newt SBGN-ML    Newt


2.17 PD2AF:A-CAT-A (1.17 a-cat-a)

SBGN-ML    Newt SBGN-ML    Newt


2.18 PD2AF:A-NSTI-A (1.18 a-nsti-a)

WARNING: Rare or wrong representation of a signalling event.

SBGN-ML    Newt SBGN-ML    Newt


2.19 PD2AF:A-MOD-A (1.19 a-mod-a)

SBGN-ML    Newt SBGN-ML    Newt


2.20 PD2AF:A-INH-A (1.20 a-inh-a)

SBGN-ML    Newt SBGN-ML    Newt


2.21 PD2AF:CURM Currency metabolites (9.1 Currency metabolites 1)

GML    SBGN-ML    Newt SBGN-ML    Newt


2.22 PD2AF:NCURM Noncurrency metabolites (9.2 Noncurrency metabolites 1)

COMMENT: Modified represetnation in Activity Flow: demerging arcs from the logical operator (not available in the current version of the SBGN standard).

GML    SBGN-ML    Newt GML    SBGN-ML    Newt




2.23 PD2AF:A-CATR-A (1.27 a-catr-a)

WARNING: Rare or wrong representation of a signalling event.

GML    SBGN-ML    Newt GML    SBGN-ML    Newt


2.24 PD2AF:I-CATR-A (1.28 a-catr-i)

WARNING: Rare or wrong representation of a signalling event.

GML    SBGN-ML    Newt GML    SBGN-ML    Newt


2.25 PD2AF:I-INHR-A (AF OUTPUT CORRECTED) (1.29 i-inhr-a)

WARNING: Rare or wrong representation of a signalling event.

GML    SBGN-ML    Newt GML    SBGN-ML    Newt


3. Metabolic reactions

Associated terms: GO:0008152 metabolic process

3.1 PD2AF:M-CAT-M (1.22 m-cat-m)

GML    SBGN-ML    Newt GML    SBGN-ML    Newt


3.2 PD2AF:M-STI-M (1.21 m-sti-m)

SBGN-ML    Newt GML    SBGN-ML    Newt


3.3 PD2AF:M-NSTI-M (1.23 m-nsti-m)

WARNING: Rare or wrong representation of a metabolic event.

SBGN-ML    Newt GML    SBGN-ML    Newt


3.4 PD2AF:M-MOD-M (1.24 m-mod-m)

WARNING: Rare or wrong representation of a metabolic event.

SBGN-ML    Newt GML    SBGN-ML    Newt


3.5 PD2AF:M-INH-M (AF OUTPUT CORRECTED) (1.25 m-inh-m)

SBGN-ML    Newt GML    SBGN-ML    Newt


3.6 PD2AF:M-CATR-M (1.30 m-catr-m)

SBGN-ML    Newt GML    SBGN-ML    Newt


3.7 PD2AF:M-INHR-M (AF OUTPUT CORRECTED) (1.31 m-inhr-m)

SBGN-ML    Newt GML    SBGN-ML    Newt


4. Empty set (production, degradation, transcription, translation)

This section describes processes with an empty set that represents an external pool of entities and is used when we do not need or wish or have enough information to represent specific entities. For example, for the production of a protein, we do not represent all the amino acids and other metabolites used.

Associated terms: SBO:0000179 degradation

4.1 PD2AF:ES-STI (2.1 ss-sti-i)

SBGN-ML    Newt SBGN-ML    Newt


4.2 PD2AF:ES-DEGR-STI (2.2 i-sti-ss)

SBGN-ML    Newt SBGN-ML    Newt


4.3 PD2AF:ES-DEGR-CAT (2.3 a-cat-ss)

SBGN-ML    Newt SBGN-ML    Newt


4.4 PD2AF:ES-DEGR-INH (2.4 a-inh-ss)

SBGN-ML    Newt SBGN-ML    Newt


4.5 PD2AF:ES-TRSCR Trancscription (NEW)

GML    SBGN-ML    Newt GML    SBGN-ML    Newt


4.6 PD2AF:ES-TRSL Translation (NEW)

GML    SBGN-ML    Newt GML    SBGN-ML    Newt




5. Heterocomplex association and dissociation

Associated terms: SBO:0000177 non-covalent binding, SBO:0000180 dissociation, GO:0005488 binding

5.1 PD2AF:COMPL-AS-N Heterocomplex association (named complex)

GML    SBGN-ML    Newt GML    SBGN-ML    Newt


5.2 PD2AF:COMPL-AS Heterocomplex association (unnamed complex)

SGML    SBGN-ML    Newt GML    SBGN-ML    Newt


5.3 PD2AF:COMPL-AS-CAT (5.3 Regulated heterocomplex association)

SBGN-ML    Newt SBGN-ML    Newt


5.4 PD2AF:COMPL-DIS (5.4 Heterocomplex dissociation)

SBGN-ML    Newt SBGN-ML    Newt




6. Multimerisation

X = 2; Y = dimer X = 7; Y = heptamer X = 12; Y = dodecamer X = 17; Y = heptadecamer
X = 3; Y = trimer X = 8; Y = octamer X = 13; Y = tridecamer X = 18; Y = octadecamer
X = 4; Y = tetramer X = 9; Y = nonamer X = 14; Y = tetradecamer X = 19; Y = nonadecamer
X = 5; Y = pentamer X = 10; Y = decamer X = 15; Y = pentadecamer X = 20; Y = eicosamer
X = 6; Y = hexamer X = 11; Y = undecamer X = 16; Y = hexadecamer X = 21; Y = 21-mer


6.1 PD2AF:MULT Multimerisation

GML    SBGN-ML    Newt SBGN-ML    Newt


6.2 PD2AF:MULT-STI Multimerisation regulated

GML    SBGN-ML    Newt GML    SBGN-ML    Newt




7. Translocation and transport

Associated terms: SBO:0000185 tranlocation reaction, SBO:0000655 transport reaction, GO:0006810 transport

7.1 PD2AF:TRANS (4.1 Translocation 1)

SBGN-ML    Newt SBGN-ML    Newt


7.1 PD2AF:TRANS-STI (4.2 Transport)

SBGN-ML    Newt SBGN-ML    Newt




8. Hidden inhibition

8.1 PD2AF:HIDINH1 (6.1 Hidden inhibition 1)

SBGN-ML    Newt SBGN-ML    Newt


8.2 PD2AF:HIDINH2 (6.2 Hidden inhibition 2)

This is a combination of rules 8.1 and 2.7

SBGN-ML    Newt SBGN-ML    Newt