Minimum information requested in the annotation of biochemical models (MIRIAM)
Open accessAbstract
Most of the published quantitative models in biology are lost for the community because they are either not made available or they are insufficiently characterized to allow them to be reused. The lack of a standard description format, lack of stringent reviewing and authors' carelessness are the main causes for incomplete model descriptions. With today's increased interest in detailed biochemical models, it is necessary to define a minimum quality standard for the encoding of those models. We propose a set of rules for curating quantitative models of biological systems. These rules define procedures for encoding and annotating models represented in machine-readable form. We believe their application will enable users to (i) have confidence that curated models are an accurate reflection of their associated reference descriptions, (ii) search collections of curated models with precision, (iii) quickly identify the biological phenomena that a given curated model or model constituent represents and (iv) facilitate model reuse and composition into large subcellular models.
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In systems biology, MIRIAM and MIASE are two community standards used for documenting simulation models and corresponding simulation experiments.
“In the case of systems biology, the “Minimum Information Requested in the Annotation of Biochemical Models (MIRIAM)” [7] and the “Minimum Information About a Simulation Experiment (MIASE)” [8] are two community standards used for documenting simulation models and corresponding simulation experiments.”
From Relating simulation studies by provenance—Developing a family of Wnt signaling models (2021) · cites this paper as [7]
Along with MIRIAM guidelines, MIASE compliance guarantees that the simulation experiment is true to the intention of the original authors and is reproducible.
“Along with MIRIAM [36] guidelines, MIASE compliance guarantees that the simulation experiment is true to the intention of the original authors and is reproducible.”
From Adapting modeling and simulation credibility standards to computational systems biology (2023) · cites this paper as [36]
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“” Although we do not intend to establish what this would be, annotation standards could start with those described in the minimum information requested in the annotation of biochemical models.(19) Checklists are typically required for the description of experimental data and methods,(20) and similar checklists could b…”
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“In the case of systems biology, the “Minimum Information Requested in the Annotation of Biochemical Models (MIRIAM)” [7] and the “Minimum Information About a Simulation Experiment (MIASE)” [8] are two community standards used for documenting simulation models and corresponding simulation experiments.”
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- Authors
- Novère, N. L., Finney, A., Hucka, M., Bhalla, U. S., Campagne, F., Collado-Vides, J., Crampin, E. J., Halstead, M., Klipp, E., Mendes, P., Nielsen, P., Sauro, H., Shapiro, B., Snoep, J. L., Spence, H. D., & Wanner, B. L.
- Affiliations
- California Institute of Technology (US)
- Tata Institute of Fundamental Research (IN)
- Cornell University (US)
- University of Auckland (NZ)
- Max Planck Society (DE)
- Virginia Tech (US)
- Keck Graduate Institute (US)
- Stellenbosch University (ZA)
- GlaxoSmithKline (United Kingdom) (GB)
- Purdue University West Lafayette (US)
- ORCID
- Venue
- Nature Biotechnology
- Published
- 2005-12
- Volume
- 23
- Issue
- 12
- Pages
- 1509-1515
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- OpenAlex
- W2020561965
- Cited by
- 622
- References
- 45
- Citations by year
- 2026: 14 · 2025: 11 · 2024: 21 · 2023: 25 · 2022: 19 · 2021: 27 · 2020: 23 · 2019: 20 · 2018: 27 · 2017: 18 · 2016: 32 · 2015: 40 · 2014: 26 · 2013: 53 · 2012: 13
- FWCI
- 12.59
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- public-domain
- www.springer.com/tdm (tdm)
- Locations
- Nature Biotechnology (publishedVersion, public-domain)
- PubMed (publishedVersion)
- CaltechAUTHORS (California Institute of Technology) (submittedVersion)
- Max Planck Institute for Plasma Physics (submittedVersion)
- Research Explorer (The University of Manchester) (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion, other-oa)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Social Sciences › Decision Sciences › Information Systems and Management › Scientific Computing and Data Management
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
- Keywords
- Miriam, model curation, model reuse
- MeSH terms
- Biochemistry, Cell Physiological Phenomena, Documentation, Models, Biological, Terminology as Topic, Databases, Factual, Information Storage and Retrieval, Guidelines as Topic, Information Dissemination
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.
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