Check, annotate, merge and compare SBML models using their semantic (MIRIAM / identifiers.org) annotations – from the command line or in the browser.
What it does
| Annotate | list, search, add and remove annotations; annotate elements automatically by name |
| Check | missing and duplicate annotations, atom balance of reactions |
| Merge | join models: elements with the same annotations become one, with a report of all differences |
| Match | find corresponding elements of two models, using relations between database entries |
| Similarity | compare whole models by their annotations |
| View | picture of the reaction network |
Installation
Needs Python 3.10 or newer; for network pictures also Graphviz.
git clone https://github.com/liebermeister/semanticsbml-3.git cd semanticsbml-3/semanticsbml3 python3 -m venv .venv .venv/bin/pip install -e . .venv/bin/semanticsbml build-database # once: builds the annotation database .venv/bin/semanticsbml gui # browser interface .venv/bin/semanticsbml merge A.xml B.xml -o AB.xml # command line .venv/bin/semanticsbml --help
build-database downloads current versions of ChEBI, the Gene Ontology, SBO
and the identifiers.org registry (about 90 MB). Details on all commands are in the
manual.
History
semanticSBML was developed 2005–2011 at the Max Planck Institute for Molecular Genetics and Humboldt University Berlin (Falko Krause, Marvin Schulz, Jannis Uhlendorf, Wolfram Liebermeister, Anselm Helbig, Timo Lubitz, Stefan Stiller, Gady Goldsobel, Claudia Beck). semanticSBML 3 is a port of its core to current Python, made in 2026. The program is in an alpha state.
References
- Krause F., Uhlendorf J., Lubitz T., Schulz M., Klipp E., Liebermeister W. (2010). Annotation and merging of SBML models with semanticSBML. Bioinformatics 26(3), 421–422. [Article]
- Schulz M., Krause F., Le Novère N., Klipp E., Liebermeister W. (2011). Retrieval, alignment, and clustering of computational models based on semantic annotations. Molecular Systems Biology 7, 512. [Article]
semanticSBML 3 is free software under the GNU General Public License, version 3.