Species Naming Conventions

This page defines the standardized naming conventions for species in SPARCED, designed for compatibility with PEtab, SBML, and PCRE2.

General Principles

1. Uniqueness: Each species name must be unique across the model.

2. Readability: Names should be human-readable and concise, while avoiding ambiguity.

3. Compatibility: Naming conventions comply with PEtab, SBML, and PCRE2 standards.

4. Minimal Redundancy: Compartments are specified only if the species resides outside its “home” compartment (e.g., TGFb is extracellular by default).

Naming Structure

The general structure for species names is as follows:

[Modifiers][Residue&Position]_[BaseSpecies][__[AdditionalSpecies]][_Compartment]

Where:

• Modifiers: Prefixes indicating the modification state (e.g., p for phosphorylation, u for ubiquitination).

• Residue&Position: For species with specific post-translational modification (PTM) sites, denote the residue and its position (e.g., S15 for serine 15).

• BaseSpecies: The core species name (e.g., CyclinD, Cdk4).

• AdditionalSpecies: For complexes, additional species are concatenated using __ (double underscores).

• Compartment: The compartment is specified only when the species is outside its default “home” compartment.

Examples

1. Single Species with PTM:

   • pS15_TGFb_cytoplasm: TGFb phosphorylated at serine 15, located in the cytoplasm.

2. Two-Component Complex:

   • pS15_CyclinD__pT298_Cdk4_nucleus: CyclinD phosphorylated at serine 15 and Cdk4 phosphorylated at threonine 298, in the nucleus.

3. Multi-Component Complex:

   • pS15_CyclinD__pT298_Cdk4__pY104_EGFR_membrane: CyclinD, Cdk4, and EGFR phosphorylated at specific residues, forming a complex at the membrane.

Prefixes

The following table summarizes standard prefixes for species modifiers:

Prefixes for Species Modifiers

Prefix	Description	Example
p	Phosphorylation	pS15_TGFb
u	Ubiquitination	uK48_TGFbR1
m	Methylation	mK9_HistoneH3
a	Acetylation	aK27_HistoneH3
g	Glycosylation	gN100_EGFR
c	Cysteinylation	cC100_EGFR
i	Inactivated state	i_Cdk4
m	mRNA species of Gene names	m_CCND1

Suffixes

The following table summarizes compartment suffixes and their use cases:

Suffixes for Compartments

Suffix	Description
_extracellular	Species outside the cell.
_cytoplasm	Species in the cytoplasm.
_nucleus	Species in the nucleus.
_endosome	Species bound to a membrane.
_mitochondria	Species in the mitochondria.

Guidelines for Complexes

For complexes, each species is listed in order, separated by double underscores (__). If a component species has PTMs, these are specified as part of its name. Compartments are only appended to the entire complex name, not individual components.

Examples:

- Single PTM Complex: pS15_CyclinD__Cdk4_cytoplasm

- Multi-PTM Complex: pS15_CyclinD__pT298_Cdk4__pY104_EGFR_membrane

Potential Pitfalls

1. Ambiguity in Residue Position:

   • Always specify residues and positions for clarity in PTM names.

   • Example: Avoid p_CyclinD if pS15_CyclinD is more precise.

2. Complex Names Becoming Too Long:

   • Avoid redundancy in component names.

   • Use short, standard prefixes for PTMs. Look at synonyms on UniProt for inspiration.

3. Tool Compatibility:

   • Avoid special characters like parentheses () or symbols like & that might break tools.

Regex Validation

The following regular expression ensures compatibility with PEtab, SBML, and PCRE2:

^[a-zA-Z0-9_]+(__[a-zA-Z0-9_]+)*(_[a-zA-Z0-9_]+)?$

This regex enforces: - Alphanumeric names with underscores. - Double underscores (__) for complex species. - Optional compartment suffixes.

Automating Naming

To minimize errors and maintain consistency, consider automating the naming process with a script. Below is an example Python snippet for generating valid species names:

def generate_species_name(base, ptms=None, compartment=None):
    name = base
    if ptms:
        ptm_str = "__".join([f"{m}{r}" for m, r in ptms])
        name = f"{ptm_str}_{name}"
    if compartment:
        name = f"{name}_{compartment}"
    return name

# Example Usage
print(generate_species_name("CyclinD", ptms=[("pS", 15)], compartment="nucleus"))
# Output: pS15_CyclinD_nucleus

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