Systems Biology Ontology
Names
More detailed information about this field from each metasource.
Systems Biology Ontology
metasource: Fairsharing.org
version: FAIRsharing.org: SBO; Systems Biology Ontology; DOI: https://doi.org/10.25504/FAIRsharing.s19src; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
metasource: Biontology / Bioportal
version: 03:02:2018 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/SBO
SBO
metasource: Fairsharing.org
version: FAIRsharing.org: SBO; Systems Biology Ontology; DOI: https://doi.org/10.25504/FAIRsharing.s19src; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
metasource: Biontology / Bioportal
version: 03:02:2018 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/SBO
Names
More detailed information about this field from each metasource.
Systems Biology Ontology
metasource: Fairsharing.orgversion: FAIRsharing.org: SBO; Systems Biology Ontology; DOI: https://doi.org/10.25504/FAIRsharing.s19src; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
metasource: Biontology / Bioportal
version: 03:02:2018 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/SBO
SBO
metasource: Fairsharing.orgversion: FAIRsharing.org: SBO; Systems Biology Ontology; DOI: https://doi.org/10.25504/FAIRsharing.s19src; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
metasource: Biontology / Bioportal
version: 03:02:2018 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/SBO
Names
More detailed information about this field from each metasource.
Systems Biology Ontology
metasource: Fairsharing.orgversion: FAIRsharing.org: SBO; Systems Biology Ontology; DOI: https://doi.org/10.25504/FAIRsharing.s19src; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
metasource: Biontology / Bioportal
version: 03:02:2018 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/SBO
SBO
metasource: Fairsharing.orgversion: FAIRsharing.org: SBO; Systems Biology Ontology; DOI: https://doi.org/10.25504/FAIRsharing.s19src; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
metasource: Biontology / Bioportal
version: 03:02:2018 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/SBO
This source may no longer be available. No known URL could be resolved successfully.
The Systems Biology Ontology is a set of controlled, relational vocabularies of terms commonly used in Systems Biology, and in particular in computational modelling. It consists of seven orthogonal vocabularies defining: reaction participants roles (e.g. "substrate"), quantitative parameters (e.g. "Michaelis constant"), classification of mathematical expressions describing the system (e.g. "mass action rate law"), modelling framework used (e.g. "logical framework"), the nature of the entity (e.g. "macromolecule"), the type of interaction (e.g. "process"), as well as a branch to define the different types of metadata that may be present within a model. Use of such terms introduces a layer of semantic information into the standard description of a model, facilitating its interpretation and efficient reuse.
Description
More detailed information about this field from each metasource.
The Systems Biology Ontology is a set of controlled, relational vocabularies of terms commonly used in Systems Biology, and in particular in computational modelling. It consists of seven orthogonal vocabularies defining: reaction participants roles (e.g. "substrate"), quantitative parameters (e.g. "Michaelis constant"), classification of mathematical expressions describing the system (e.g. "mass action rate law"), modelling framework used (e.g. "logical framework"), the nature of the entity (e.g. "macromolecule"), the type of interaction (e.g. "process"), as well as a branch to define the different types of metadata that may be present within a model. Use of such terms introduces a layer of semantic information into the standard description of a model, facilitating its interpretation and efficient reuse.
metasource: Fairsharing.orgversion: FAIRsharing.org: SBO; Systems Biology Ontology; DOI: https://doi.org/10.25504/FAIRsharing.s19src; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
The Systems Biology Ontology is a set of controlled, relational vocabularies of terms commonly used in Systems Biology, and in particular in computational modeling. The ontology consists of six orthogonal vocabularies defining: the roles of reaction participants (eg. "substrate"), quantitative parameters (eg. "Michaelis constant"), a precise classification of mathematical expressions that describe the system (eg. "mass action rate law"), the modeling framework used (eg. "logical framework"), and a branch each to describe entity (eg. "macromolecule") and interaction (eg. "process") types, and a branch to define the different types of metadata that may be present within a model. SBO terms can be used to introduce a layer of semantic information into the standard description of a model, or to annotate the results of biochemical experiments in order to facilitate their efficient reuse. SBO is an Open Biomedical Ontologies (OBO) candidate ontology, and is free for use. More information about SBO can be found from the project FAQ, at http://www.ebi.ac.uk/sbo/ SBO is a project of the BioModels.net effort and is developed through community collaboration.
metasource: Biontology / Bioportalversion: 03:02:2018 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/SBO
Webpage:
http://www.ebi.ac.uk/sbo/Webpage
More detailed information about this field from each metasource.
http://www.ebi.ac.uk/sbo/
metasource: Fairsharing.orgversion: FAIRsharing.org: SBO; Systems Biology Ontology; DOI: https://doi.org/10.25504/FAIRsharing.s19src; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
Licence:
Name: Open Source Initiative Artistic license 2.0Licence name
More detailed information about this field from each metasource.
Open Source Initiative Artistic license 2.0
metasource: Fairsharing.orgversion: FAIRsharing.org: SBO; Systems Biology Ontology; DOI: https://doi.org/10.25504/FAIRsharing.s19src; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
Licence URL
More detailed information about this field from each metasource.
https://opensource.org/licenses/artistic-license-2.0.php
metasource: Fairsharing.orgversion: FAIRsharing.org: SBO; Systems Biology Ontology; DOI: https://doi.org/10.25504/FAIRsharing.s19src; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
Publications:
Publications
More detailed information about this field from each metasource.
Controlled vocabularies and semantics in systems biology
PMID: 22027554
metasource: Fairsharing.org
version: FAIRsharing.org: SBO; Systems Biology Ontology; DOI: https://doi.org/10.25504/FAIRsharing.s19src; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
Publications
More detailed information about this field from each metasource.
Controlled vocabularies and semantics in systems biology
PMID: 22027554
metasource: Fairsharing.org
version: FAIRsharing.org: SBO; Systems Biology Ontology; DOI: https://doi.org/10.25504/FAIRsharing.s19src; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
-
Controlled vocabularies and semantics in systems biology
PubMed citations: 103.
103 articles citing: Controlled vocabularies and semantics in systems biology
Exploring the evolution of biochemical models at the network level. PMID:35312734
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
Ten simple rules for creating reusable pathway models for computational analysis and visualization. PMID:34411100
Relating simulation studies by provenance-Developing a family of Wnt signaling models. PMID:34351901
Countering reproducibility issues in mathematical models with software engineering techniques: A case study using a one-dimensional mathematical model of the atrioventricular node. PMID:34280231
Curating and comparing 114 strain-specific genome-scale metabolic models of Staphylococcus aureus. PMID:34188046
First Genome-Scale Metabolic Model of Dolosigranulum pigrum Confirms Multiple Auxotrophies. PMID:33918864
SBGN Bricks Ontology as a tool to describe recurring concepts in molecular networks. PMID:33758926
Why and how to engage expert stakeholders in ontology development: insights from social and behavioural sciences. PMID:33757593
Converting disease maps into heavyweight ontologies: general methodology and application to Alzheimer's disease. PMID:33590873
Evaluating accessibility, usability and interoperability of genome-scale metabolic models for diverse yeasts species. PMID:33428734
Genome-scale metabolic reconstruction of the non-model yeast Issatchenkia orientalis SD108 and its application to organic acids production. PMID:33134082
The Synthetic Biology Open Language (SBOL) Version 3: Simplified Data Exchange for Bioengineering. PMID:33015004
Best Practices for Making Reproducible Biochemical Models. PMID:32853539
Computer-Aided Whole-Cell Design: Taking a Holistic Approach by Integrating Synthetic With Systems Biology. PMID:32850764
SBML Level 3: an extensible format for the exchange and reuse of biological models. PMID:32845085
Specifications of standards in systems and synthetic biology: status and developments in 2020. PMID:32598316
BpForms and BcForms: a toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks. PMID:32423472
MEMOTE for standardized genome-scale metabolic model testing. PMID:32123384
Organizing genome engineering for the gigabase scale. PMID:32019919
LePrimAlign: local entropy-based alignment of PPI networks to predict conserved modules. PMID:31874635
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
Communicating Structure and Function in Synthetic Biology Diagrams. PMID:31348656
ToxRefDB version 2.0: Improved utility for predictive and retrospective toxicology analyses. PMID:31340180
JigCell Model Connector: building large molecular network models from components. PMID:31303682
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019. PMID:31301675
Closing the gap between formats for storing layout information in systems biology. PMID:31273380
Quantitative evaluation of ontology design patterns for combining pathology and anatomy ontologies. PMID:30858527
How Sustainable are Biomedical Ontologies? PMID:30815087
BioLQM: A Java Toolkit for the Manipulation and Conversion of Logical Qualitative Models of Biological Networks. PMID:30510517
Harmonizing semantic annotations for computational models in biology. PMID:30462164
Identifying frequent patterns in biochemical reaction networks: a workflow. PMID:29992320
Tellurium notebooks-An environment for reproducible dynamical modeling in systems biology. PMID:29906293
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017. PMID:29596055
Control of primary metabolism by a virulence regulatory network promotes robustness in a plant pathogen. PMID:29379078
From word models to executable models of signaling networks using automated assembly. PMID:29175850
The bacterial interlocked process ONtology (BiPON): a systemic multi-scale unified representation of biological processes in prokaryotes. PMID:29169408
SABIO-RK: an updated resource for manually curated biochemical reaction kinetics. PMID:29092055
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016. PMID:28187405
Global open data management in metabolomics. PMID:28092796
phraSED-ML: A paraphrased, human-readable adaptation of SED-ML. PMID:27774871
Notions of similarity for systems biology models. PMID:27742665
A Resource Allocation Trade-Off between Virulence and Proliferation Drives Metabolic Versatility in the Plant Pathogen Ralstonia solanacearum. PMID:27732672
Guidelines for Reproducibly Building and Simulating Systems Biology Models. PMID:27429432
COMODI: an ontology to characterise differences in versions of computational models in biology. PMID:27401413
Qualitative dynamics semantics for SBGN process description. PMID:27306057
A physiome interoperability roadmap for personalized drug development. PMID:27051513
Reproducibility in Computational Neuroscience Models and Simulations. PMID:27046845
Challenges in horizontal model integration. PMID:26968798
ZBIT Bioinformatics Toolbox: A Web-Platform for Systems Biology and Expression Data Analysis. PMID:26882475
The evolution of standards and data management practices in systems biology. PMID:26700851
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
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
BioModels: Content, Features, Functionality, and Use. PMID:26225232
Overview of the Cancer Genetics and Pathway Curation tasks of BioNLP Shared Task 2013. PMID:26202570
JSBML 1.0: providing a smorgasbord of options to encode systems biology models. PMID:26079347
Automatising the analysis of stochastic biochemical time-series. PMID:26051821
Annotation-based feature extraction from sets of SBML models. PMID:25904997
Linking gene expression to phenotypes via pathway information. PMID:25901272
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
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
CSEO - the Cigarette Smoke Exposure Ontology. PMID:25093069
A dedicated database system for handling multi-level data in systems biology. PMID:25053973
Correlating information contents of gene ontology terms to infer semantic similarity of gene products. PMID:24963342
The cell behavior ontology: describing the intrinsic biological behaviors of real and model cells seen as active agents. PMID:24755304
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. PMID:24321545
Ontology of physics for biology: representing physical dependencies as a basis for biological processes. PMID:24295137
HuPSON: the human physiology simulation ontology. PMID:24267822
The Reactome pathway knowledgebase. PMID:24243840
Path2Models: large-scale generation of computational models from biochemical pathway maps. PMID:24180668
Function of dynamic models in systems biology: linking structure to behaviour. PMID:24103739
Computational models of the JAK1/2-STAT1 signaling. PMID:24069559
Metabolomics and systems pharmacology: why and how to model the human metabolic network for drug discovery. PMID:23892182
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
The systems biology simulation core algorithm. PMID:23826941
A method for integrating and ranking the evidence for biochemical pathways by mining reactions from text. PMID:23813008
Structure, function, and behaviour of computational models in systems biology. PMID:23721297
In silico modeling of shear-stress-induced nitric oxide production in endothelial cells through systems biology. PMID:23708369
Precise generation of systems biology models from KEGG pathways. PMID:23433509
Controlled vocabularies and ontologies in proteomics: overview, principles and practice. PMID:23429179
The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies. PMID:23398680
The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013. PMID:23180789
Data management strategies for multinational large-scale systems biology projects. PMID:23047157
LibKiSAO: a Java library for Querying KiSAO. PMID:23006857
Qualitative translation of relations from BioPAX to SBML qual. PMID:22923304
Nanoinformatics: a new area of research in nanomedicine. PMID:22866003
The Input Signal Step Function (ISSF), a standard method to encode input signals in SBML models with software support, applied to circadian clock models. PMID:22855577
Multiscale modeling and data integration in the virtual physiological rat project. PMID:22805979
Systems biology of fungal infection. PMID:22485108
Tav4SB: integrating tools for analysis of kinetic models of biological systems. PMID:22480273
Structure-based classification and ontology in chemistry. PMID:22480202
Scientific discovery as a combinatorial optimisation problem: how best to navigate the landscape of possible experiments? PMID:22252984
Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language. PMID:22172142
Tags:
Tags
More detailed information about this field from each metasource.
mathematical model
metasource: Fairsharing.org
version: FAIRsharing.org: SBO; Systems Biology Ontology; DOI: https://doi.org/10.25504/FAIRsharing.s19src; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
modeling and simulation
metasource: Fairsharing.org
version: FAIRsharing.org: SBO; Systems Biology Ontology; DOI: https://doi.org/10.25504/FAIRsharing.s19src; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
molecular interaction
metasource: Fairsharing.org
version: FAIRsharing.org: SBO; Systems Biology Ontology; DOI: https://doi.org/10.25504/FAIRsharing.s19src; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
pathway model
metasource: Fairsharing.org
version: FAIRsharing.org: SBO; Systems Biology Ontology; DOI: https://doi.org/10.25504/FAIRsharing.s19src; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
Tags
More detailed information about this field from each metasource.
mathematical model
metasource: Fairsharing.orgversion: FAIRsharing.org: SBO; Systems Biology Ontology; DOI: https://doi.org/10.25504/FAIRsharing.s19src; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
modeling and simulation
metasource: Fairsharing.orgversion: FAIRsharing.org: SBO; Systems Biology Ontology; DOI: https://doi.org/10.25504/FAIRsharing.s19src; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
molecular interaction
metasource: Fairsharing.orgversion: FAIRsharing.org: SBO; Systems Biology Ontology; DOI: https://doi.org/10.25504/FAIRsharing.s19src; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
pathway model
metasource: Fairsharing.orgversion: FAIRsharing.org: SBO; Systems Biology Ontology; DOI: https://doi.org/10.25504/FAIRsharing.s19src; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
mathematical model modeling and simulation molecular interaction pathway model
Need help integrating and/or managing biomedical data?