tabularqual 0.1.6

TabularQual converter

Convert between spreadsheets (XLSX, CSV) and SBML-qual for logical models (Boolean and multi-valued).

Note: the format is specified here.

---

Install

pip install tabularqual

Or install from source:

git clone https://github.com/sys-bio/TabularQual.git
cd TabularQual
python3.11 -m venv .venv
source .venv/bin/activate
python -m pip install --upgrade pip
python -m pip install -e .

Python 3.11 or newer is required. For the optional FastAPI server, install .[api]; for release development, install .[test,release,api].

---

Usage

TabularQual can be used as a web app, a Python package, or via the command line (CLI).

Web App

No installation required — open in your browser:

Launch Web App

For large networks the Streamlit cloud may hit resource limits. Run locally instead:

streamlit run app.py

Python API

from tabularqual import convert_spreadsheet_to_sbml, convert_sbml_to_spreadsheet

# Spreadsheet to SBML  (accepts XLSX file, CSV folder, or CSV prefix)
stats = convert_spreadsheet_to_sbml("Model.xlsx", "Model.sbml")

# SBML to Spreadsheet (XLSX)
stats = convert_sbml_to_spreadsheet("Model.sbml", "Model.xlsx")

# SBML to CSV files
stats = convert_sbml_to_spreadsheet("Model.sbml", "Model", output_csv=True)

Both functions return a stats dict:

{
    "species":                 int,
    "transitions":             int,
    "interactions":            int,
    "warnings":                list[str],   # all messages produced
    "validation_errors":       list[str],   # annotation identifier issues
    "total_validation_errors": int,
    "created_files":           list[str],   # output file paths
}

See python_api_example.py for a working example covering multi-valued models and other options.

CLI

Spreadsheet → SBML

# XLSX input (output defaults to same name with .sbml extension)
to-sbml examples/ToyExample.xlsx

# CSV directory
to-sbml examples/ToyExample_csv/

# CSV prefix (looks for Model_Species.csv, Model_Transitions.csv, etc.)
to-sbml Model

SBML → Spreadsheet

# XLSX output (default)
to-table examples/ToyExample.sbml

# CSV output (creates ToyExample_Species.csv, ToyExample_Transitions.csv, etc.)
to-table examples/ToyExample.sbml --csv

Options

to-sbml INPUT [OUTPUT]

Option	Description
--inter-anno	Include annotations from the Interactions sheet in SBML
--trans-anno	Include annotations from the Transitions sheet in SBML
--use-name	Rules/targets use species Names instead of IDs (see below)
--no-validate	Skip annotation identifier validation

to-table INPUT [OUTPUT]

Option	Description
--csv	Write CSV files instead of a single XLSX workbook
--colon-format	Use colon notation in rules (A:2 instead of A >= 2)
--use-name	Write species Names in rules/targets instead of IDs
--template PATH	Custom template file for README/Appendix sheets (XLSX only)
--no-validate	Skip annotation identifier validation

---

Spreadsheet Format

The spreadsheet consists of up to four sheets. Sheet names and column headers must match exactly (case-sensitive).

Sheet	Required	Required columns
Model	No	—
Species	Yes	Species_ID or Name
Transitions	Yes	Target, Rule
Interactions	No	Target, Source

Additional sheets (e.g. README, Appendix) and columns are silently ignored.

See the specification, the template spreadsheet and examples for details.

---

Transition Rules Syntax

The Rule column accepts Boolean and comparison expressions; spaces are ignored during parsing. See the transition-rule syntax guide for full details including operator precedence and multi-valued model conventions.

Symbol	Meaning	Example
&	AND	A & B
|	OR	A | B
!	NOT	!A
^	XOR	A ^ B
()	Grouping	(A & B) | C
A:2	A ≥ 2 (threshold)	multi-valued only
!A:2	A < 2	multi-valued only
>= <= > < = == !=	Comparison operators	A >= 2
TRUE / FALSE	Fixed active / inactive	constant rule
2	Fixed at level 2	constant rule (multi-valued)
"name"	Name with spaces or special characters	"p53 protein" & B

Examples

A & B                      # Both A and B active (level ≥ 1)
A | (D & !C)               # A active, or D active and C inactive
A ^ B                      # Exactly one of A or B active (XOR)
A:2 | B < 1                # A at level 2+, or B inactive
!CI:2 & !Cro:3             # CI below level 2 AND Cro below level 3
(A & B) | (!C & D != 1)    # Complex grouped expression
FALSE                      # Target always inactive

Multi-valued models: each result level gets its own row in the Transitions sheet with a different Level value. Rows with the same Target are merged into one SBML Transition with multiple function terms.

When importing SBML-qual, the tool follows spec §5.1: symbolic threshold <ci> references in MathML are replaced with their thresholdLevel values, and Boolean simplification is applied (e.g. A >= 1 → A, A < 1 → !A).

---

Species Names in Rules

By default, Target and Rule columns reference species by ID (Species_ID). Passing --use-name (CLI) or checking "Rules use species Names" (web app / use_name=True in Python) switches to Name-based references.

Names with spaces or special characters must be enclosed in double quotes in rules:

"p53 protein" & MDM2
"NF-κB complex" | IKK

Duplicate names are automatically disambiguated with numeric suffixes. Given:

Species_ID	Name
GeneA	Kinase
GeneB	Kinase

The first occurrence keeps the original name; subsequent ones get _1, _2, ...:

Kinase & Kinase_1    # refers to GeneA and GeneB respectively

Fallback: if any species lack a Name when --use-name is active, a warning is issued and IDs are used instead.

---

Validation

SId Format

Model_ID, Species_ID, Transitions_ID, and Compartment must conform to SBML SId rules:

• Start with a letter or underscore
• Contain only letters, digits, and underscores
• No spaces, slashes, or other special characters

Invalid IDs are cleaned automatically: special characters → _, leading digit → prepend _, duplicates → append _1, _2, ... A warning is shown for each correction.

Example: PI3K/AKT-pathway → PI3K_AKT_pathway

Controlled vocabulary

Field	Valid values
Species Type	Input, Internal, Output
Interaction Sign	positive, negative, dual, unknown
Relation (Species)	is, hasVersion, isVersionOf, isDescribedBy, hasPart, isPartOf, hasProperty, isPropertyOf, encodes, isEncodedBy, isHomologTo, occursIn, hasTaxon
Relation (Transitions / Interactions)	same list as above; defaults to isDescribedBy

All values are accepted case-insensitively and normalised to their canonical form.

Annotation identifiers

Compact identifiers (prefix:accession, e.g. uniprot:P19838) are resolved to https://identifiers.org/ URLs in SBML. Optionally validate that identifiers actually exist through sbmlutils:

Common ChEBI variants such as chebi:35305 are normalized to the canonical CHEBI:35305 form before validation.

pip install sbmlutils>=0.9.6
# then run without --no-validate (the default)

---

Examples

File	Description
examples/ToyExample.xlsx	Small Boolean model
examples/ToyExample_multivalue.xlsx	Multi-valued variant of the toy model
examples/Faure2006/Faure2006.xlsx	Fauré 2006 mammalian cell-cycle (Boolean)
examples/ThieffryThomas1995/ThieffryThomas1995_multivalue.xlsx	Thieffry & Thomas 1995 λ phage (multi-valued)