Minimal Information Required In the Annotation of Models
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Minimal Information Required In the Annotation of Models
metasource: Fairsharing.org
version: FAIRsharing.org: MIRIAM; Minimal Information Required In the Annotation of Models; DOI: https://doi.org/10.25504/FAIRsharing.ap169a; Last edited: June 22, 2021, 2:27 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
MIRIAM
metasource: Fairsharing.org
version: FAIRsharing.org: MIRIAM; Minimal Information Required In the Annotation of Models; DOI: https://doi.org/10.25504/FAIRsharing.ap169a; Last edited: June 22, 2021, 2:27 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
Names
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Minimal Information Required In the Annotation of Models
metasource: Fairsharing.orgversion: FAIRsharing.org: MIRIAM; Minimal Information Required In the Annotation of Models; DOI: https://doi.org/10.25504/FAIRsharing.ap169a; Last edited: June 22, 2021, 2:27 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
MIRIAM
metasource: Fairsharing.orgversion: FAIRsharing.org: MIRIAM; Minimal Information Required In the Annotation of Models; DOI: https://doi.org/10.25504/FAIRsharing.ap169a; Last edited: June 22, 2021, 2:27 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
Names
More detailed information about this field from each metasource.
Minimal Information Required In the Annotation of Models
metasource: Fairsharing.orgversion: FAIRsharing.org: MIRIAM; Minimal Information Required In the Annotation of Models; DOI: https://doi.org/10.25504/FAIRsharing.ap169a; Last edited: June 22, 2021, 2:27 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
MIRIAM
metasource: Fairsharing.orgversion: FAIRsharing.org: MIRIAM; Minimal Information Required In the Annotation of Models; DOI: https://doi.org/10.25504/FAIRsharing.ap169a; Last edited: June 22, 2021, 2:27 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
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The Minimal Information Required In the Annotation of Models (MIRIAM), initiated by the BioModels.net effort, is a set of guidelines for the consistent annotation and curation of computational models in biology. It is suitable for use with any structured format for computational models.
Description
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The Minimal Information Required In the Annotation of Models (MIRIAM), initiated by the BioModels.net effort, is a set of guidelines for the consistent annotation and curation of computational models in biology. It is suitable for use with any structured format for computational models.
metasource: Fairsharing.orgversion: FAIRsharing.org: MIRIAM; Minimal Information Required In the Annotation of Models; DOI: https://doi.org/10.25504/FAIRsharing.ap169a; Last edited: June 22, 2021, 2:27 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
Webpage:
http://co.mbine.org/standards/miriamWebpage
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http://co.mbine.org/standards/miriam
metasource: Fairsharing.orgversion: FAIRsharing.org: MIRIAM; Minimal Information Required In the Annotation of Models; DOI: https://doi.org/10.25504/FAIRsharing.ap169a; Last edited: June 22, 2021, 2:27 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
Licence:
Name: Creative Commons Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)Licence name
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Creative Commons Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
metasource: Fairsharing.orgversion: FAIRsharing.org: MIRIAM; Minimal Information Required In the Annotation of Models; DOI: https://doi.org/10.25504/FAIRsharing.ap169a; Last edited: June 22, 2021, 2:27 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
Licence URL
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https://creativecommons.org/licenses/by-sa/4.0/
metasource: Fairsharing.orgversion: FAIRsharing.org: MIRIAM; Minimal Information Required In the Annotation of Models; DOI: https://doi.org/10.25504/FAIRsharing.ap169a; Last edited: June 22, 2021, 2:27 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
Publications:
Publications
More detailed information about this field from each metasource.
Minimum information requested in the annotation of biochemical models (MIRIAM)
PMID: 16333295
metasource: Fairsharing.org
version: FAIRsharing.org: MIRIAM; Minimal Information Required In the Annotation of Models; DOI: https://doi.org/10.25504/FAIRsharing.ap169a; Last edited: June 22, 2021, 2:27 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
Identifiers.org and MIRIAM Registry: community resources to provide persistent identification
PMID: 22140103
metasource: Fairsharing.org
version: FAIRsharing.org: MIRIAM; Minimal Information Required In the Annotation of Models; DOI: https://doi.org/10.25504/FAIRsharing.ap169a; Last edited: June 22, 2021, 2:27 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology
PMID: 18078503
metasource: Fairsharing.org
version: FAIRsharing.org: MIRIAM; Minimal Information Required In the Annotation of Models; DOI: https://doi.org/10.25504/FAIRsharing.ap169a; Last edited: June 22, 2021, 2:27 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
Publications
More detailed information about this field from each metasource.
Minimum information requested in the annotation of biochemical models (MIRIAM)
PMID: 16333295
metasource: Fairsharing.org
version: FAIRsharing.org: MIRIAM; Minimal Information Required In the Annotation of Models; DOI: https://doi.org/10.25504/FAIRsharing.ap169a; Last edited: June 22, 2021, 2:27 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
Identifiers.org and MIRIAM Registry: community resources to provide persistent identification
PMID: 22140103
metasource: Fairsharing.org
version: FAIRsharing.org: MIRIAM; Minimal Information Required In the Annotation of Models; DOI: https://doi.org/10.25504/FAIRsharing.ap169a; Last edited: June 22, 2021, 2:27 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology
PMID: 18078503
metasource: Fairsharing.org
version: FAIRsharing.org: MIRIAM; Minimal Information Required In the Annotation of Models; DOI: https://doi.org/10.25504/FAIRsharing.ap169a; Last edited: June 22, 2021, 2:27 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
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Minimum information requested in the annotation of biochemical models (MIRIAM)
PubMed citations: 203.
203 articles citing: Minimum information requested in the annotation of biochemical models (MIRIAM)
Reinforcing Interdisciplinary Collaborations to Unravel the Astrocyte "Calcium Code". PMID:35543801
High-Quality Genome-Scale Reconstruction of Corynebacterium glutamicum ATCC 13032. PMID:34867870
Humans and machines in biomedical knowledge curation: hypertrophic cardiomyopathy molecular mechanisms' representation. PMID:34600580
Relating simulation studies by provenance-Developing a family of Wnt signaling models. PMID:34351901
CFTR Lifecycle Map-A Systems Medicine Model of CFTR Maturation to Predict Possible Active Compound Combinations. PMID:34299207
Scientific and regulatory evaluation of mechanistic in silico drug and disease models in drug development: Building model credibility. PMID:34102034
Ten steps to investigate a cellular system with mathematical modeling. PMID:33983922
Constructing and analysing dynamic models with modelbase v1.2.3: a software update. PMID:33879053
Genome-scale metabolic reconstruction of the non-model yeast Issatchenkia orientalis SD108 and its application to organic acids production. PMID:33134082
Metadata Stewardship in Nanosafety Research: Community-Driven Organisation of Metadata Schemas to Support FAIR Nanoscience Data. PMID:33076428
A practical guide to mechanistic systems modeling in biology using a logic-based approach. PMID:33064138
SBML Level 3: an extensible format for the exchange and reuse of biological models. PMID:32845085
Community standards to facilitate development and address challenges in metabolic modeling. PMID:32845080
Application of data science in risk assessment and early warning. PMID:32626466
The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE). PMID:32598315
Setting the basis of best practices and standards for curation and annotation of logical models in biology-highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop. PMID:32313939
RA-map: building a state-of-the-art interactive knowledge base for rheumatoid arthritis. PMID:32311035
MEMOTE for standardized genome-scale metabolic model testing. PMID:32123384
Non-Viral in Vitro Gene Delivery: It is Now Time to Set the Bar! PMID:32098191
BioModels-15 years of sharing computational models in life science. PMID:31701150
Rational Design and Methods of Analysis for the Study of Short- and Long-Term Dynamic Responses of Eukaryotic Systems. PMID:31602619
Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices. PMID:31602618
ModelBricks-modules for reproducible modeling improving model annotation and provenance. PMID:31602314
A systematic assessment of current genome-scale metabolic reconstruction tools. PMID:31391098
The Design of FluxML: A Universal Modeling Language for 13C Metabolic Flux Analysis. PMID:31178829
Reproducibility of Quantitative Systems Pharmacology Models: Current Challenges and Future Opportunities. PMID:30697975
Best Practices to Maximize the Use and Reuse of Quantitative and Systems Pharmacology Models: Recommendations From the United Kingdom Quantitative and Systems Pharmacology Network. PMID:30667172
Harmonizing semantic annotations for computational models in biology. PMID:30462164
"Reproducible" Research in Mathematical Sciences Requires Changes in our Peer Review Culture and Modernization of our Current Publication Approach. PMID:30232583
BioModelKit - An Integrative Framework for Multi-Scale Biomodel-Engineering. PMID:30205646
Reproducible Research Using Biomodels. PMID:30191472
Minimum information reporting in bio-nano experimental literature. PMID:30190620
Identifying frequent patterns in biochemical reaction networks: a workflow. PMID:29992320
Development and validation of an updated computational model of Streptomyces coelicolor primary and secondary metabolism. PMID:29973148
The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks. PMID:29971009
Contextualising manufacturing data for lifecycle decision-making. PMID:29911681
Challenges in Reproducibility, Replicability, and Comparability of Computational Models and Tools for Neuronal and Glial Networks, Cells, and Subcellular Structures. PMID:29765315
Evolution of computational models in BioModels Database and the Physiome Model Repository. PMID:29650016
Rational cell culture optimization enhances experimental reproducibility in cancer cells. PMID:29445172
From word models to executable models of signaling networks using automated assembly. PMID:29175850
A Protocol for Generating and Exchanging (Genome-Scale) Metabolic Resource Allocation Models. PMID:28878200
MINERVA-a platform for visualization and curation of molecular interaction networks. PMID:28725475
Network analyses based on comprehensive molecular interaction maps reveal robust control structures in yeast stress response pathways. PMID:28725465
Reproducibility and Comparability of Computational Models for Astrocyte Calcium Excitability. PMID:28270761
FAIRDOMHub: a repository and collaboration environment for sharing systems biology research. PMID:27899646
Harnessing Big Data for Systems Pharmacology. PMID:27814027
Where next for the reproducibility agenda in computational biology? PMID:27422148
Logical Modeling and Dynamical Analysis of Cellular Networks. PMID:27303434
SBtab: a flexible table format for data exchange in systems biology. PMID:27153616
The Human Physiome: how standards, software and innovative service infrastructures are providing the building blocks to make it achievable. PMID:27051515
A physiome interoperability roadmap for personalized drug development. PMID:27051513
The systems biology format converter. PMID:27044654
Challenges in horizontal model integration. PMID:26968798
Models and Simulations as a Service: Exploring the Use of Galaxy for Delivering Computational Models. PMID:26958881
libChEBI: an API for accessing the ChEBI database. PMID:26933452
Methodological challenges and analytic opportunities for modeling and interpreting Big Healthcare Data. PMID:26918190
The Cardiac Electrophysiology Web Lab. PMID:26789753
The evolution of standards and data management practices in systems biology. PMID:26700851
Towards improved genome-scale metabolic network reconstructions: unification, transcript specificity and beyond. PMID:26615025
Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization. PMID:26559508
Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions. PMID:26528569
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core. PMID:26528564
SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks. PMID:26452770
Databases for multilevel biophysiology research available at Physiome.jp. PMID:26441671
BioModels: Content, Features, Functionality, and Use. PMID:26225232
The gastrin and cholecystokinin receptors mediated signaling network: a scaffold for data analysis and new hypotheses on regulatory mechanisms. PMID:26205660
SEEK: a systems biology data and model management platform. PMID:26160520
HEPNet: A Knowledge Base Model of Human Energy Pool Network for Predicting the Energy Availability Status of an Individual. PMID:26053019
The role of markup for enabling interoperability in health informatics. PMID:26042043
Reconstructing genome-scale metabolic models with merlin. PMID:25845595
Combining computational models, semantic annotations and simulation experiments in a graph database. PMID:25754863
Current state of genome-scale modeling in filamentous fungi. PMID:25700817
Quantitative and logic modelling of molecular and gene networks. PMID:25645874
Integration of a constraint-based metabolic model of Brassica napus developing seeds with (13)C-metabolic flux analysis. PMID:25566296
Transparency in metabolic network reconstruction enables scalable biological discovery. PMID:25562137
Improving collaboration by standardization efforts in systems biology. PMID:25538939
Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently. PMID:25503938
COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project. PMID:25494900
BioModels: ten-year anniversary. PMID:25414348
Plant metabolic modeling: achieving new insight into metabolism and metabolic engineering. PMID:25344492
MOSBIE: a tool for comparison and analysis of rule-based biochemical models. PMID:25253680
Genome scale modeling in systems biology: algorithms and resources. PMID:24822031
MEMOSys 2.0: an update of the bioinformatics database for genome-scale models and genomic data. PMID:24532766
A framework for different levels of integration of computational models into web-based virtual patients. PMID:24463466
Multi-scale computational models of the airways to unravel the pathophysiological mechanisms in asthma and chronic obstructive pulmonary disease (AirPROM). PMID:24427517
Pathway Commons at virtual cell: use of pathway data for mathematical modeling. PMID:24273241
Path2Models: large-scale generation of computational models from biochemical pathway maps. PMID:24180668
Toward an integrated software platform for systems pharmacology. PMID:24150748
Rule-based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems. PMID:24123887
A comprehensive map of the influenza A virus replication cycle. PMID:24088197
An online model composition tool for system biology models. PMID:24006914
Reconstruction and validation of a genome-scale metabolic model for the filamentous fungus Neurospora crassa using FARM. PMID:23935467
Version 6 of the consensus yeast metabolic network refines biochemical coverage and improves model performance. PMID:23935056
An analysis of a 'community-driven' reconstruction of the human metabolic network. PMID:23888127
A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes. PMID:23831062
A method for integrating and ranking the evidence for biochemical pathways by mining reactions from text. PMID:23813008
In silico modeling of shear-stress-induced nitric oxide production in endothelial cells through systems biology. PMID:23708369
Biographer: web-based editing and rendering of SBGN compliant biochemical networks. PMID:23574737
The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum. PMID:23555215
Chaste: an open source C++ library for computational physiology and biology. PMID:23516352
A community-driven global reconstruction of human metabolism. PMID:23455439
Precise generation of systems biology models from KEGG pathways. PMID:23433509
Programming biological models in Python using PySB. PMID:23423320
Qualitative translation of relations from BioPAX to SBML qual. PMID:22923304
Reverse engineering biomolecular systems using -omic data: challenges, progress and opportunities. PMID:22833495
DIPSBC--data integration platform for systems biology collaborations. PMID:22568834
OREMPdb: a semantic dictionary of computational pathway models. PMID:22536973
Propagating semantic information in biochemical network models. PMID:22289386
Reconstruction of Arabidopsis metabolic network models accounting for subcellular compartmentalization and tissue-specificity. PMID:22184215
Identifiers.org and MIRIAM Registry: community resources to provide persistent identification. PMID:22140103
SABIO-RK--database for biochemical reaction kinetics. PMID:22102587
PathCase-SB architecture and database design. PMID:22070889
Software for systems biology: from tools to integrated platforms. PMID:22048662
Controlled vocabularies and semantics in systems biology. PMID:22027554
Dupuytren's: a systems biology disease. PMID:21943049
The RICORDO approach to semantic interoperability for biomedical data and models: strategy, standards and solutions. PMID:21878109
Approaches for the study of cancer: towards the integration of genomics, proteomics and metabolomics. PMID:21865133
Integrating systems biology models and biomedical ontologies. PMID:21835028
Retrieval, alignment, and clustering of computational models based on semantic annotations. PMID:21772260
A metabolic model of the mitochondrion and its use in modelling diseases of the tricarboxylic acid cycle. PMID:21714867
KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats. PMID:21700675
JSBML: a flexible Java library for working with SBML. PMID:21697129
Modeling signal transduction leading to synaptic plasticity: evaluation and comparison of five models. PMID:21559300
Minimum Information About a Simulation Experiment (MIASE). PMID:21552546
Automated ensemble modeling with modelMaGe: analyzing feedback mechanisms in the Sho1 branch of the HOG pathway. PMID:21483474
CytoSolve: A Scalable Computational Method for Dynamic Integration of Multiple Molecular Pathway Models. PMID:21423324
Towards interoperable reporting standards for omics data: hopes and hurdles. PMID:21347181
Meeting Report from the Second "Minimum Information for Biological and Biomedical Investigations" (MIBBI) workshop. PMID:21304730
Model annotation for synthetic biology: automating model to nucleotide sequence conversion. PMID:21296753
MEMOSys: Bioinformatics platform for genome-scale metabolic models. PMID:21276275
Integrated multilaboratory systems biology reveals differences in protein metabolism between two reference yeast strains. PMID:21266995
Software that goes with the flow in systems biology. PMID:21114874
Systematic integration of experimental data and models in systems biology. PMID:21114840
Further developments towards a genome-scale metabolic model of yeast. PMID:21029416
Towards a unifying, systems biology understanding of large-scale cellular death and destruction caused by poorly liganded iron: Parkinson's, Huntington's, Alzheimer's, prions, bactericides, chemical toxicology and others as examples. PMID:20967426
A comprehensive molecular interaction map of the budding yeast cell cycle. PMID:20865008
In silico models of cancer. PMID:20836040
Using views of Systems Biology Cloud: application for model building. PMID:20730508
Integration of metabolic databases for the reconstruction of genome-scale metabolic networks. PMID:20712863
Ranked retrieval of Computational Biology models. PMID:20701772
Annotation of SBML models through rule-based semantic integration. PMID:20626923
The metabolic network of Synechocystis sp. PCC 6803: systemic properties of autotrophic growth. PMID:20616194
Multiple ontologies in action: composite annotations for biosimulation models. PMID:20601121
BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. PMID:20587024
Imaging and modeling of myocardial metabolism. PMID:20559785
PINT: Pathways INtegration Tool. PMID:20538652
PathText: a text mining integrator for biological pathway visualizations. PMID:20529930
Reconstruction and validation of RefRec: a global model for the yeast molecular interaction network. PMID:20498836
Model composition for macromolecular regulatory networks. PMID:20431147
Payao: a community platform for SBML pathway model curation. PMID:20371497
Mathematical modeling-guided evaluation of biochemical, developmental, environmental, and genotypic determinants of essential oil composition and yield in peppermint leaves. PMID:20147490
Simulating plant metabolic pathways with enzyme-kinetic models. PMID:20118273
Towards a genome-scale kinetic model of cellular metabolism. PMID:20109182
The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services. PMID:20047655
The 2010 Nucleic Acids Research Database Issue and online Database Collection: a community of data resources. PMID:19965766
Current progress in patient-specific modeling. PMID:19955236
BioModels.net Web Services, a free and integrated toolkit for computational modelling software. PMID:19939940
The challenges of informatics in synthetic biology: from biomolecular networks to artificial organisms. PMID:19906839
KEGGconverter: a tool for the in-silico modelling of metabolic networks of the KEGG Pathways database. PMID:19814801
An editor for pathway drawing and data visualization in the Biopathways Workbench. PMID:19799790
Saint: a lightweight integration environment for model annotation. PMID:19734151
Towards reproducible descriptions of neuronal network models. PMID:19662159
libAnnotationSBML: a library for exploiting SBML annotations. PMID:19561017
Consistent design schematics for biological systems: standardization of representation in biological engineering. PMID:19493898
Web services at the European Bioinformatics Institute-2009. PMID:19435877
CycSim--an online tool for exploring and experimenting with genome-scale metabolic models. PMID:19420054
CellML metadata standards, associated tools and repositories. PMID:19380315
Designing and encoding models for synthetic biology. PMID:19364720
Multiscale models of angiogenesis. PMID:19349248
GetBonNie for building, analyzing and sharing rule-based models. PMID:19321734
SBML2L(A)T(E)X: conversion of SBML files into human-readable reports. PMID:19307240
Advances in semantic representation for multiscale biosimulation: a case study in merging models. PMID:19209710
How to deal with large models? PMID:19156132
Iron behaving badly: inappropriate iron chelation as a major contributor to the aetiology of vascular and other progressive inflammatory and degenerative diseases. PMID:19133145
PyMOOSE: Interoperable Scripting in Python for MOOSE. PMID:19129924
Genome-scale models of bacterial metabolism: reconstruction and applications. PMID:19067749
Microcirculation and the physiome projects. PMID:19051119
Virtual Cell modelling and simulation software environment. PMID:19045830
Bridging biological ontologies and biosimulation: the ontology of physics for biology. PMID:18999003
A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. PMID:18846089
Standards and ontologies in computational systems biology. PMID:18793134
MIFlowCyt: the minimum information about a Flow Cytometry Experiment. PMID:18752282
Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. PMID:18688244
Programming with models: modularity and abstraction provide powerful capabilities for systems biology. PMID:18647734
Minimal information: an urgent need to assess the functional reliability of recombinant proteins used in biological experiments. PMID:18647423
The model repository of the models of infectious disease agent study. PMID:18632331
The signaling petri net-based simulator: a non-parametric strategy for characterizing the dynamics of cell-specific signaling networks. PMID:18463702
A comprehensive modular map of molecular interactions in RB/E2F pathway. PMID:18319725
A systems biology approach identifies the biochemical mechanisms regulating monoterpenoid essential oil composition in peppermint. PMID:18287058
LibSBML: an API library for SBML. PMID:18252737
MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology. PMID:18078503
Sensitivity analysis of intracellular signaling pathway kinetics predicts targets for stem cell fate control. PMID:17616983
Pathogen profiling for disease management and surveillance. PMID:17487146
Computational biology of cardiac myocytes: proposed standards for the physiome. PMID:17449822
Cell size at S phase initiation: an emergent property of the G1/S network. PMID:17432928
SBMLeditor: effective creation of models in the Systems Biology Markup language (SBML). PMID:17341299
Parameter estimate of signal transduction pathways. PMID:17118160
Model storage, exchange and integration. PMID:17118155
Mathematical modeling of intracellular signaling pathways. PMID:17118154
cPath: open source software for collecting, storing, and querying biological pathways. PMID:17101041
Data standards for flow cytometry. PMID:16901228
Dry work in a wet world: computation in systems biology. PMID:16820781
BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. PMID:16381960 -
Identifiers.org and MIRIAM Registry: community resources to provide persistent identification
PubMed citations: 87.
87 articles citing: Identifiers.org and MIRIAM Registry: community resources to provide persistent identification
Providing Adverse Outcome Pathways from the AOP-Wiki in a Semantic Web Format to Increase Usability and Accessibility of the Content. PMID:35388368
ELIXIR biovalidator for semantic validation of life science metadata. PMID:35380605
High-Quality Genome-Scale Reconstruction of Corynebacterium glutamicum ATCC 13032. PMID:34867870
Specifications of standards in systems and synthetic biology: status and developments in 2021. PMID:34674411
COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. PMID:34664389
An updated genome-scale metabolic network reconstruction of Pseudomonas aeruginosa PA14 to characterize mucin-driven shifts in bacterial metabolism. PMID:34625561
Integrated human/SARS-CoV-2 metabolic models present novel treatment strategies against COVID-19. PMID:34353886
Curating and comparing 114 strain-specific genome-scale metabolic models of Staphylococcus aureus. PMID:34188046
ELIXIR: Providing a Sustainable Infrastructure for Life Science Data at European Scale. PMID:34175941
BENZ WS: the Bologna ENZyme Web Server for four-level EC number annotation. PMID:33963861
A resource to explore the discovery of rare diseases and their causative genes. PMID:33947870
First Genome-Scale Metabolic Model of Dolosigranulum pigrum Confirms Multiple Auxotrophies. PMID:33918864
Genome-scale metabolic reconstruction of the non-model yeast Issatchenkia orientalis SD108 and its application to organic acids production. PMID:33134082
Executable biochemical space for specification and analysis of biochemical systems. PMID:32915842
Publishing reproducible dynamic kinetic models. PMID:32793969
Specifications of standards in systems and synthetic biology: status and developments in 2020. PMID:32598316
A comprehensive genome-scale model for Rhodosporidium toruloides IFO0880 accounting for functional genomics and phenotypic data. PMID:31720216
Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices. PMID:31602618
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019. PMID:31301675
Re-curation and rational enrichment of knowledge graphs in Biological Expression Language. PMID:31225582
MINERVA API and plugins: opening molecular network analysis and visualization to the community. PMID:31074494
Metabolic Modeling of Pectobacterium parmentieri SCC3193 Provides Insights into Metabolic Pathways of Plant Pathogenic Bacteria. PMID:30959803
NBDC RDF portal: a comprehensive repository for semantic data in life sciences. PMID:30576482
Agronomic Linked Data (AgroLD): A knowledge-based system to enable integrative biology in agronomy. PMID:30500839
Harmonizing semantic annotations for computational models in biology. PMID:30462164
A data citation roadmap for scientific publishers. PMID:30457573
Integration among databases and data sets to support productive nanotechnology: Challenges and recommendations. PMID:30246165
Sustainable data and metadata management at the BD2K-LINCS Data Coordination and Integration Center. PMID:29917015
Biomedical Informatics on the Cloud: A Treasure Hunt for Advancing Cardiovascular Medicine. PMID:29700073
Community-driven roadmap for integrated disease maps. PMID:29688273
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017. PMID:29596055
LAILAPS-QSM: A RESTful API and JAVA library for semantic query suggestions. PMID:29529024
Biotea: semantics for Pubmed Central. PMID:29312824
From word models to executable models of signaling networks using automated assembly. PMID:29175850
Data Portal for the Library of Integrated Network-based Cellular Signatures (LINCS) program: integrated access to diverse large-scale cellular perturbation response data. PMID:29140462
Using semantics for representing experimental protocols. PMID:29132408
BioModels: expanding horizons to include more modelling approaches and formats. PMID:29106614
biochem4j: Integrated and extensible biochemical knowledge through graph databases. PMID:28708831
Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data. PMID:28662064
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016. PMID:28187405
Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins. PMID:27927232
Bio-TDS: bioscience query tool discovery system. PMID:27924016
The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants. PMID:27842607
Harnessing Big Data for Systems Pharmacology. PMID:27814027
The health care and life sciences community profile for dataset descriptions. PMID:27602295
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. PMID:27374120
Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources. PMID:27336457
Generation of open biomedical datasets through ontology-driven transformation and integration processes. PMID:27255189
DisGeNET-RDF: harnessing the innovative power of the Semantic Web to explore the genetic basis of diseases. PMID:27153650
SBtab: a flexible table format for data exchange in systems biology. PMID:27153616
RegenBase: a knowledge base of spinal cord injury biology for translational research. PMID:27055827
The systems biology format converter. PMID:27044654
Challenges in horizontal model integration. PMID:26968798
Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization. PMID:26559508
BiGG Models: A platform for integrating, standardizing and sharing genome-scale models. PMID:26476456
SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks. PMID:26452770
Data integration in biological research: an overview. PMID:26336651
BioModels: Content, Features, Functionality, and Use. PMID:26225232
Human metabolic atlas: an online resource for human metabolism. PMID:26209309
Achieving human and machine accessibility of cited data in scholarly publications. PMID:26167542
From Peer-Reviewed to Peer-Reproduced in Scholarly Publishing: The Complementary Roles of Data Models and Workflows in Bioinformatics. PMID:26154165
Visualisation of BioPAX Networks using BioLayout Express (3D). PMID:25949802
KaBOB: ontology-based semantic integration of biomedical databases. PMID:25903923
Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative. PMID:25759811
Combining computational models, semantic annotations and simulation experiments in a graph database. PMID:25754863
Computationally Modeling Lipid Metabolism and Aging: A Mini-review. PMID:25750699
OpenCOR: a modular and interoperable approach to computational biology. PMID:25705192
SPARQL-enabled identifier conversion with Identifiers.org. PMID:25638809
Integration of a constraint-based metabolic model of Brassica napus developing seeds with (13)C-metabolic flux analysis. PMID:25566296
Improving collaboration by standardization efforts in systems biology. PMID:25538939
COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project. PMID:25494900
The DDBJ Japanese Genotype-phenotype Archive for genetic and phenotypic human data. PMID:25477381
BioModels: ten-year anniversary. PMID:25414348
BioModels linked dataset. PMID:25182954
Guidelines for managing data and processes in bone and cartilage tissue engineering. PMID:24564199
BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. PMID:24495517
The EBI RDF platform: linked open data for the life sciences. PMID:24413672
Path2Models: large-scale generation of computational models from biochemical pathway maps. PMID:24180668
Variation Ontology for annotation of variation effects and mechanisms. PMID:24162187
NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps. PMID:24099179
Metingear: a development environment for annotating genome-scale metabolic models. PMID:23766418
Biotea: RDFizing PubMed Central in support for the paper as an interface to the Web of Data. PMID:23734622
Structure, function, and behaviour of computational models in systems biology. PMID:23721297
The MetaboLights repository: curation challenges in metabolomics. PMID:23630246
Towards the collaborative curation of the registry underlying Identifiers.org. PMID:23584831
Precise generation of systems biology models from KEGG pathways. PMID:23433509
VarioML framework for comprehensive variation data representation and exchange. PMID:23031277 -
MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology
PubMed citations: 42.
42 articles citing: MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology
Best Practices for Making Reproducible Biochemical Models. PMID:32853539
Re-curation and rational enrichment of knowledge graphs in Biological Expression Language. PMID:31225582
CiliateGEM: an open-project and a tool for predictions of ciliate metabolic variations and experimental condition design. PMID:30497359
Modelling pyruvate dehydrogenase under hypoxia and its role in cancer metabolism. PMID:29134060
Metabolic modeling to identify engineering targets for Komagataella phaffii: The effect of biomass composition on gene target identification. PMID:28691262
Harnessing Big Data for Systems Pharmacology. PMID:27814027
SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks. PMID:26452770
Implementation of linked data in the life sciences at BioHackathon 2011. PMID:25973165
OpenCOR: a modular and interoperable approach to computational biology. PMID:25705192
Improving collaboration by standardization efforts in systems biology. PMID:25538939
Towards the collaborative curation of the registry underlying Identifiers.org. PMID:23584831
LibKiSAO: a Java library for Querying KiSAO. PMID:23006857
AbsIDconvert: an absolute approach for converting genetic identifiers at different granularities. PMID:22967011
Reverse engineering biomolecular systems using -omic data: challenges, progress and opportunities. PMID:22833495
A tool for multi-scale modelling of the renal nephron. PMID:22670210
AlzPathway: a comprehensive map of signaling pathways of Alzheimer's disease. PMID:22647208
Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language. PMID:22172142
Identifiers.org and MIRIAM Registry: community resources to provide persistent identification. PMID:22140103
Identifying and relating biological concepts in the Catalogue of Life. PMID:22004596
Empowering industrial research with shared biomedical vocabularies. PMID:21963522
The RICORDO approach to semantic interoperability for biomedical data and models: strategy, standards and solutions. PMID:21878109
Semantic-JSON: a lightweight web service interface for Semantic Web contents integrating multiple life science databases. PMID:21632604
Current trends and new challenges of databases and web applications for systems driven biological research. PMID:21423387
The Biomolecular Interaction Network Database in PSI-MI 2.5. PMID:21233089
Further developments towards a genome-scale metabolic model of yeast. PMID:21029416
The BioPAX community standard for pathway data sharing. PMID:20829833
Ranked retrieval of Computational Biology models. PMID:20701772
Annotation of SBML models through rule-based semantic integration. PMID:20626923
BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. PMID:20587024
Semantic integration of data on transcriptional regulation. PMID:20427517
Snazer: the simulations and networks analyzer. PMID:20056001
BioModels.net Web Services, a free and integrated toolkit for computational modelling software. PMID:19939940
The challenges of informatics in synthetic biology: from biomolecular networks to artificial organisms. PMID:19906839
XML-based approaches for the integration of heterogeneous bio-molecular data. PMID:19828083
An editor for pathway drawing and data visualization in the Biopathways Workbench. PMID:19799790
BioGateway: a semantic systems biology tool for the life sciences. PMID:19796395
Saint: a lightweight integration environment for model annotation. PMID:19734151
libAnnotationSBML: a library for exploiting SBML annotations. PMID:19561017
CellML metadata standards, associated tools and repositories. PMID:19380315
Designing and encoding models for synthetic biology. PMID:19364720
How to deal with large models? PMID:19156132
Complexity and modularity of intracellular networks: a systematic approach for modelling and simulation. PMID:19045831
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annotation
metasource: Fairsharing.org
version: FAIRsharing.org: MIRIAM; Minimal Information Required In the Annotation of Models; DOI: https://doi.org/10.25504/FAIRsharing.ap169a; Last edited: June 22, 2021, 2:27 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
chemical entity
metasource: Fairsharing.org
version: FAIRsharing.org: MIRIAM; Minimal Information Required In the Annotation of Models; DOI: https://doi.org/10.25504/FAIRsharing.ap169a; Last edited: June 22, 2021, 2:27 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
enzymatic reaction
metasource: Fairsharing.org
version: FAIRsharing.org: MIRIAM; Minimal Information Required In the Annotation of Models; DOI: https://doi.org/10.25504/FAIRsharing.ap169a; Last edited: June 22, 2021, 2:27 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
mathematical model
metasource: Fairsharing.org
version: FAIRsharing.org: MIRIAM; Minimal Information Required In the Annotation of Models; DOI: https://doi.org/10.25504/FAIRsharing.ap169a; Last edited: June 22, 2021, 2:27 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
modeling and simulation
metasource: Fairsharing.org
version: FAIRsharing.org: MIRIAM; Minimal Information Required In the Annotation of Models; DOI: https://doi.org/10.25504/FAIRsharing.ap169a; Last edited: June 22, 2021, 2:27 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
pathway model
metasource: Fairsharing.org
version: FAIRsharing.org: MIRIAM; Minimal Information Required In the Annotation of Models; DOI: https://doi.org/10.25504/FAIRsharing.ap169a; Last edited: June 22, 2021, 2:27 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
protein
metasource: Fairsharing.org
version: FAIRsharing.org: MIRIAM; Minimal Information Required In the Annotation of Models; DOI: https://doi.org/10.25504/FAIRsharing.ap169a; Last edited: June 22, 2021, 2:27 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
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annotation
metasource: Fairsharing.orgversion: FAIRsharing.org: MIRIAM; Minimal Information Required In the Annotation of Models; DOI: https://doi.org/10.25504/FAIRsharing.ap169a; Last edited: June 22, 2021, 2:27 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
chemical entity
metasource: Fairsharing.orgversion: FAIRsharing.org: MIRIAM; Minimal Information Required In the Annotation of Models; DOI: https://doi.org/10.25504/FAIRsharing.ap169a; Last edited: June 22, 2021, 2:27 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
enzymatic reaction
metasource: Fairsharing.orgversion: FAIRsharing.org: MIRIAM; Minimal Information Required In the Annotation of Models; DOI: https://doi.org/10.25504/FAIRsharing.ap169a; Last edited: June 22, 2021, 2:27 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
mathematical model
metasource: Fairsharing.orgversion: FAIRsharing.org: MIRIAM; Minimal Information Required In the Annotation of Models; DOI: https://doi.org/10.25504/FAIRsharing.ap169a; Last edited: June 22, 2021, 2:27 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
modeling and simulation
metasource: Fairsharing.orgversion: FAIRsharing.org: MIRIAM; Minimal Information Required In the Annotation of Models; DOI: https://doi.org/10.25504/FAIRsharing.ap169a; Last edited: June 22, 2021, 2:27 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
pathway model
metasource: Fairsharing.orgversion: FAIRsharing.org: MIRIAM; Minimal Information Required In the Annotation of Models; DOI: https://doi.org/10.25504/FAIRsharing.ap169a; Last edited: June 22, 2021, 2:27 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
protein
metasource: Fairsharing.orgversion: FAIRsharing.org: MIRIAM; Minimal Information Required In the Annotation of Models; DOI: https://doi.org/10.25504/FAIRsharing.ap169a; Last edited: June 22, 2021, 2:27 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
chemical entity enzymatic reaction mathematical model modeling and simulation pathway model protein
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