libAnnotationSBML: a library for exploiting SBML annotations
Open accessAbstract
Summary: The Systems Biology Markup Language (SBML) is an established community XML format for the markup of biochemical models. With the introduction of SBML level 2 version 3, specific model entities, such as species or reactions, can now be annotated using ontological terms. These annotations, which are encoded using the resource description framework (RDF), provide the facility to specify definite terms to individual components, allowing software to unambiguously identify such components and thus link the models to existing data resources. libSBML is an application programming interface library for the manipulation of SBML files. While libSBML provides the facilities for reading and writing such annotations from and to models, it is beyond the scope of libSBML to provide interpretation of these terms. The libAnnotationSBML library introduced here acts as a layer on top of libSBML linking SBML annotations to the web services that describe these ontological terms. Two applications that use this library are described: SbmlSynonymExtractor finds name synonyms of SBML model entities and SbmlReactionBalancer checks SBML files to determine whether specifed reactions are elementally balanced. Availability: http://mcisb.sourceforge.net/ Contact: neil.swainston@manchester.ac.uk
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
KEGG: Kyoto Encyclopedia of Genes and Genomes
Kanehisa, M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.27 · Cited by 37,077 · see citing works
KEGG: Kyoto Encyclopedia of Genes and Genomes
Ogata, H., Goto, S., Sato, K., Fujibuchi, W., Bono, H., & Kanehisa, M. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.1.29 · Cited by 31,232 · see citing works
The Universal Protein Resource (UniProt)
Bairoch, A. (2004) · Nucleic Acids Research · doi:10.1093/nar/gki070 · Cited by 3,774 · see citing works
Hucka, M., Finney, A., Sauro, H. M., Bolouri, H., Doyle, J. C., Kitano, H., Arkin, A. P., Bornstein, B. J., Bray, D., Cornish-Bowden, A., et al. (2003) · Bioinformatics · doi:10.1093/bioinformatics/btg015 · Cited by 3,060 · see citing works
Self-citationChEBI: a database and ontology for chemical entities of biological interest
Degtyarenko, K. N., de Matos, P., Ennis, M., Hastings, J., Zbinden, M., McNaught, A., Alcántara, R., Darsow, M., Guedj, M., & Ashburner, M. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm791 · Cited by 1,130 · see citing works
The Universal Protein Resource (UniProt)
The UniProt Consortium (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm895 · Cited by 824 · see citing works
Minimum information requested in the annotation of biochemical models (MIRIAM)
Novère, N. L., Finney, A., Hucka, M., Bhalla, U. S., Campagne, F., Collado-Vides, J., Crampin, E. J., Halstead, M., Klipp, E., Mendes, P., et al. (2005) · Nature Biotechnology · doi:10.1038/nbt1156 · Cited by 622 · see citing works
Self-citationHerrgård, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Blüthgen, N., Borger, S., Costenoble, R., Heinemann, M., et al. (2008) · Nature Biotechnology · doi:10.1038/nbt1492 · Cited by 588 · see citing works
Self-citationLibSBML: an API Library for SBML
Bornstein, B. J., Keating, S. M., Jouraku, A., & Hucka, M. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn051 · Cited by 373 · see citing works
MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology
Laibe, C., & Novère, N. G. L. (2007) · BMC Systems Biology · doi:10.1186/1752-0509-1-58 · Cited by 102 · see citing works
SBMLmerge, a system for combining biochemical network models.
Schulz, M., Uhlendorf, J., Klipp, E., & Liebermeister, W. (2006) · PubMed · Cited by 48 · see citing works
The markup is the model: Reasoning about systems biology models in the Semantic Web era
Kell, D. B., & Mendes, P. (2007) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2007.10.023 · Cited by 31 · see citing works
Self-citation
Flagged first, then by citations
Cited by
Sorted by citations
A community-driven global reconstruction of human metabolism
Thiele, I., Swainston, N., Fleming, R. M. T., Hoppe, A., Sahoo, S., Aurich, M. K., Haraldsdottir, H., Mo, M. L., Rolfsson, O., Stobbe, M. D., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2488 · Cited by 1,019 · see citing works
Self-citationLi, C., Donizelli, M., Rodriguez, N., Dharuri, H., Endler, L., Chelliah, V., Li, L., He, E., Henry, A., Stefan, M. I., et al. (2010) · BMC Systems Biology · doi:10.1186/1752-0509-4-92 · Cited by 597 · see citing works
Controlled vocabularies and semantics in systems biology
Courtot, M., Juty, N., Knüpfer, C., Waltemath, D., Zhukova, A., Dräger, A., Dumontier, M., Finney, A., Golebiewski, M., Hastings, J., et al. (2011) · Molecular Systems Biology · doi:10.1038/msb.2011.77 · Cited by 316 · see citing works
“Web applications such as Saint (Lister et al , 2009) and libraries such as libAnnotationSBML (Swainston and Mendes, 2009) can be used to suggest and add appropriate biological annotations, including SBO terms, to models.”
MethodSelf-citationPath2Models: large-scale generation of computational models from biochemical pathway maps
Büchel, F., Rodríguez, N., Swainston, N., Wrzodek, C., Czauderna, T., Keller, R., Mittag, F., Schubert, M., Glont, M., Golebiewski, M., et al. (2013) · BMC Systems Biology · doi:10.1186/1752-0509-7-116 · Cited by 173 · see citing works
Self-citationA model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes
Smallbone, K., Messiha, H. L., Carroll, K. M., Winder, C. L., Malys, N., Dunn, W. B., Murabito, E., Swainston, N., Dada, J. O., Khan, F., et al. (2013) · FEBS Letters · doi:10.1016/j.febslet.2013.06.043 · Cited by 147 · see citing works
Self-citationA ‘rule of 0.5’ for the metabolite-likeness of approved pharmaceutical drugs
O’Hagan, S., Swainston, N., Handl, J., & Kell, D. B. (2014) · Metabolomics · doi:10.1007/s11306-014-0733-z · Cited by 101 · see citing works
Self-citationThe SuBliMinaL Toolbox: automating steps in the reconstruction of metabolic networks
Swainston, N., B, K. S. A., Mendes, P., Kell, D. B., & Paton, N. W. (2011) · Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics · doi:10.1515/jib-2011-186 · Cited by 97 · see citing works
Self-citationIntegrating systems biology models and biomedical ontologies
Hoehndorf, R., Dumontier, M., Gennari, J. H., Wimalaratne, S., de Bono, B., Cook, D. L., & Gkoutos, G. V. (2011) · BMC Systems Biology · doi:10.1186/1752-0509-5-124 · Cited by 59 · see citing works
biochem4j: Integrated and extensible biochemical knowledge through graph databases
Swainston, N., Batista-Navarro, R., Carbonell, P., Dobson, P. D., Dunstan, M. S., Jervis, A. J., Vinaixa, M., Williams, A. R., Ananiadou, S., Faulon, J., et al. (2017) · PLoS ONE · doi:10.1371/journal.pone.0179130 · Cited by 44 · see citing works
Self-citationAn analysis of a ‘community-driven’ reconstruction of the human metabolic network
Swainston, N., Mendes, P., & Kell, D. B. (2013) · Metabolomics · doi:10.1007/s11306-013-0564-3 · Cited by 41 · see citing works
Self-citationSystematic integration of experimental data and models in systems biology
Li, P., Dada, J. O., Jameson, D., Spasić, ., Swainston, N., Carroll, K. M., Dunn, W. B., Khan, F., Malys, N., Messiha, H. L., et al. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-582 · Cited by 36 · see citing works
Self-citationAdapting modeling and simulation credibility standards to computational systems biology
Tatka, L. T., Smith, L. P., Hellerstein, J. L., & Sauro, H. M. (2023) · Journal of Translational Medicine · doi:10.1186/s12967-023-04290-5 · Cited by 25 · see citing works
libChEBI: an API for accessing the ChEBI database
Swainston, N., Hastings, J., Dekker, A., Muthukrishnan, V., May, J. W., Steinbeck, C., & Mendes, P. (2016) · Journal of Cheminformatics · doi:10.1186/s13321-016-0123-9 · Cited by 25 · see citing works
Self-citationAnnotation of SBML Models Through Rule-Based Semantic IntegrationPreprint
Lister, A., Lord, P., Pocock, M., & Wipat, A. (2009) · Nature Precedings · doi:10.1038/npre.2009.3286.1 · Cited by 25 · see citing works
Enzyme kinetics informatics: from instrument to browser
Swainston, N., Golebiewski, M., Messiha, H., Malys, N., Kania, R., Kengne, S., Krebs, O., Mir, S., Sauer-Danzwith, H., Smallbone, K., et al. (2010) · The FEBS Journal · doi:10.1111/j.1742-4658.2010.07778.x · Cited by 24 · see citing works
Self-citationSaint: a lightweight integration environment for model annotation
Lister, A. L., Pocock, M. R., Taschuk, M. L., & Wipat, A. (2009) · Bioinform. · doi:10.1093/bioinformatics/btp523 · Cited by 25 · see citing works
Misirli, G., Cavaliere, M., Waites, W., Pocock, M. R., Madsen, C., Gilfellon, O., Honorato-Zimmer, R., Zuliani, P., Danos, V., & Wipat, A. (2015) · Bioinform. · doi:10.1093/bioinformatics/btv660 · Cited by 21 · see citing works
Krause, F., Schulz, M., Swainston, N., & Liebermeister, W. (2011) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/b978-0-12-385118-5.00019-0 · Cited by 13 · see citing works
Self-citationCheminformatics and Bioinformatics at the Interface with Systems Biology
Kaushik, A. C., Mehmood, A., Wei, D., Nawab, S., Sahi, S., & Kumar, A. (2023) · Royal Society of Chemistry eBooks · doi:10.1039/9781839166037 · Cited by 7 · see citing works
Stanford, N., Scharm, M., Dobson, P. D., Golebiewski, M., Hucka, M., Kothamachu, V. B., Nickerson, D. P., Owen, S., Pahle, J., Wittig, U., et al. (2019) · Methods in molecular biology · doi:10.1007/978-1-4939-9736-7_17 · Cited by 7 · see citing works
Self-citationLachor, P., Puszyński, K., & Polański, A. (2014) · Biotechnologia · doi:10.5114/bta.2011.46543 · Cited by 5 · see citing works
Cheminformatics for genome-scale metabolic reconstructions
May, J. W. (2015) · Apollo (University of Cambridge) · doi:10.17863/cam.15987 · Cited by 6 · see citing works
Genome-scale model management and comparison.
Pabinger, S., & Trajanoski, Z. (2013) · Methods in molecular biology · doi:10.1007/978-1-62703-299-5_1 · Cited by 4 · see citing works
Data Formats for Systems Biology and Quantitative Modeling
Golebiewski, M. (2019) · Encyclopedia of Bioinformatics and Computational Biology · doi:10.1016/b978-0-12-809633-8.20471-8 · Cited by 6 · see citing works
Annotations for Rule-Based Models
Cavaliere, M., Danos, V., Honorato-Zimmer, R., & Waites, W. (2018) · Methods in molecular biology · doi:10.1007/978-1-4939-9102-0_13 · Cited by 1 · see citing works
Data Model Standardization for Synthetic Biomolecular Circuits and Systems
Galdzicki, M., Chandran, D., Gennari, J. H., & Sauro, H. M. (2011) · Springer eBooks · doi:10.1007/978-1-4419-6766-4_13 · Cited by 1 · see citing works
Controlled Vocabularies and Semantics in Systems Biology
(2023) · Royal Society of Chemistry eBooks · doi:10.1039/9781839166037-00136 · Cited by 1 · see citing works
Waltemath, D. (2011) · Ros Dok Rostocker Dokumentenserver (Universitätsbibliothek Rostock) · doi:10.18453/rosdok_id00000903
Data Formats for Systems Biology, Systems Medicine and Computational Modeling
Golebiewski, M., & Mayer, G. (2024) · Elsevier eBooks · doi:10.1016/b978-0-323-95502-7.00164-0
- Authors
- Swainston, N., & Mendes, P.
- Affiliations
- University of Manchester (GB)
- Corresponding author
- Swainston, Neil
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2009-06-26
- Volume
- 25
- Issue
- 17
- Pages
- 2292-2293
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- PMC
- PMC2734318
- OpenAlex
- W2146744007
- Cited by
- 29
- References
- 12
- Citations by year
- 2024: 1 · 2023: 3 · 2019: 2 · 2018: 1 · 2017: 1 · 2016: 1 · 2015: 2 · 2014: 2 · 2013: 5
- FWCI
- 1.47
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Bioinformatics (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Research Explorer (The University of Manchester) (submittedVersion)
- Funders
- Engineering and Physical Sciences Research Council
- Biotechnology and Biological Sciences Research Council
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biomedical Text Mining and Ontologies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- SBML, RDF, libSBML, web services
- MeSH terms
- Programming Languages, Computational Biology, Systems Biology
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
