Third-party databases and tools

refineGEMs connects to, queries, and in some cases redistributes selected data from external databases and tools. This page summarises the expected citations and the licence or terms that are relevant for use of these resources. Redistribution notices are also collected in the repository-level THIRD_PARTY_LICENSES.md file.

Important

This page is a documentation aid for users and maintainers, not legal advice. Users remain responsible for checking the current upstream terms, especially for commercial use or redistribution of downloaded database content.

Databases

Resource	Use in refineGEMs	Licence or terms	Citation
BiGG Models	Local BiGG metabolite and reaction tables are shipped in the internal database and BiGG identifiers are used for media export, mapping, and model curation.	Free for educational, research, and non-profit purposes if the BiGG copyright notice and licence text are retained. Commercial use requires a separate agreement with UC San Diego.	King et al.[1]
ChEBI	ChEBI is queried for compound names, formulae, charges, and identifiers.	ChEBI data are available under CC BY 4.0 and governed by EMBL-EBI terms of use.	Hastings et al.[2]
KEGG	KEGG is queried for genes, enzymes, reactions, compounds, and pathway annotations. Released refineGEMs files should contain only KEGG identifiers or annotations, not cached KEGG records or KEGG database exports.	Academic users may use the KEGG website freely. KEGG is not a public database for non-academic use; non-academic use and service provision require the appropriate KEGG licence.	Kanehisa and Goto[3]
MetaNetX / MNXref	MetaNetX identifiers and mapping tables are used for reaction and metabolite mapping, including gap-filling.	MetaNetX data are CC BY 4.0 unless otherwise noted. MNXref records sourced from external databases may remain subject to the original database restrictions.	Moretti et al.[4]
ModelSEED	Local ModelSEED compound data are shipped in the internal database and used for charge and formula comparison.	ModelSEED data are CC BY 4.0 unless otherwise noted. Records derived from external resources may remain subject to the original resource restrictions.	Henry et al.[5]

Tools

Tool	Use in refineGEMs	Licence or terms	Citation
BOFdat	Called to generate selected biomass objective function coefficients from experimental input data.	Distributed as open-source software under the MIT licence; check the installed upstream or forked package for the exact licence text.	Lachance et al.[6]
MassChargeCuration (MCC)	Called to curate metabolite masses and charges.	Distributed as free software under the GNU LGPL-3.0 licence.	Mostolizadeh et al.[7]
MEMOTE	Used to run model consistency tests and generate MEMOTE reports. Some consistency helper functions are imported for internal checks, and biomass-normalisation code in refineGEMs was adapted from MEMOTE.	Distributed under the Apache-2.0 licence.	Lieven et al.[8]
SBOannotator	Called to assign SBO terms to SBML model entities.	Distributed as free software under the GNU GPL-3.0 licence. This affects users who install or redistribute the optional SBOannotator-dependent functionality.	Leonidou et al.[9]

Compliance notes for maintainers

The internal SQLite database currently redistributes BiGG and ModelSEED-derived tables. When these tables are updated, preserve the upstream licence notices, record the source version or download date, and keep this page in sync.

The refineGEMs source code is distributed under the MIT licence. Bundled third-party data, database identifiers, and connected external tools remain under their own licences or terms, as listed above and in THIRD_PARTY_LICENSES.md.

KEGG-dependent functionality should be documented and implemented as online queries through the user-accessed KEGG services. Avoid bundling KEGG data in released artefacts unless the project has confirmed that the intended release and user base are covered by an appropriate KEGG licence.

Because ModelSEED and MetaNetX aggregate data from other resources, downstream use may need to follow the original source terms for specific records. Preserve provenance columns and identifiers where possible so users can trace records back to their source database.

[1]

Zachary A. King, Justin Lu, Andreas Dräger, Philip Miller, Stephen Federowicz, Joshua A. Lerman, Ali Ebrahim, Bernhard O. Palsson, and Nathan E. Lewis. Bigg models: a platform for integrating, standardizing and sharing genome-scale models. Nucleic Acids Research, 44(D1):D515–D522, 2016. URL: https://doi.org/10.1093/nar/gkv1049, doi:10.1093/nar/gkv1049.

[2]

Janna Hastings, Gareth Owen, Adriano Dekker, Marcus Ennis, Namrata Kale, Venkatesh Muthukrishnan, Steve Turner, Neil Swainston, Pedro Mendes, and Christoph Steinbeck. Chebi in 2016: improved services and an expanding collection of metabolites. Nucleic Acids Research, 44(D1):D1214–D1219, 2016. URL: https://doi.org/10.1093/nar/gkv1031, doi:10.1093/nar/gkv1031.

[3]

Minoru Kanehisa and Susumu Goto. Kegg: kyoto encyclopedia of genes and genomes. Nucleic Acids Research, 28(1):27–30, 2000. URL: https://doi.org/10.1093/nar/28.1.27, doi:10.1093/nar/28.1.27.

[4]

Sébastien Moretti, Van Du Tran, Federico Mehl, Mark Ibberson, and Marco Pagni. Metanetx/mnxref: unified namespace for metabolites and biochemical reactions in the context of metabolic models. Nucleic Acids Research, 49(D1):D570–D574, 2021. URL: https://doi.org/10.1093/nar/gkaa992, doi:10.1093/nar/gkaa992.

[5]

Christopher S. Henry, Matthew DeJongh, Aaron A. Best, Paul M. Frybarger, Ben Linsay, and Rick L. Stevens. High-throughput generation, optimization and analysis of genome-scale metabolic models. Nature Biotechnology, 28:977–982, 2010. URL: https://doi.org/10.1038/nbt.1672, doi:10.1038/nbt.1672.

[6]

Jean-Christophe Lachance, Colton J. Lloyd, Jonathan M. Monk, Laurence Yang, Anand V. Sastry, Yousef Seif, Bernhard O. Palsson, Adam M. Feist, and Zachary A. King. Bofdat: generating biomass objective functions for genome-scale metabolic models from experimental data. PLOS Computational Biology, 15(4):e1006971, 2019. URL: https://doi.org/10.1371/journal.pcbi.1006971, doi:10.1371/journal.pcbi.1006971.

[7]

Reihaneh Mostolizadeh, Finn Mier, and Andreas Dräger. Mcc: automated mass and charge curation at the genome scale applied to <i>c. tuberculostearicum</i>. Microbiology Spectrum, 14(2):e03200–24, 2026. URL: https://journals.asm.org/doi/abs/10.1128/spectrum.03200-24, doi:10.1128/spectrum.03200-24.

[8]

Christian Lieven, Moritz E. Beber, Brett G. Olivier, and others. Memote for standardized genome-scale metabolic model testing. Nature Biotechnology, 38:272–276, 2020. URL: https://doi.org/10.1038/s41587-020-0446-y, doi:10.1038/s41587-020-0446-y.

[9]

Nantia Leonidou, Elisabeth Fritze, Alina Renz, and Andreas Dräger. Sboannotator: a python tool for the automated assignment of systems biology ontology terms. Bioinformatics, 2023. URL: https://doi.org/10.1093/bioinformatics/btad437, doi:10.1093/bioinformatics/btad437.