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ModelSEED Biochemistry Database

General Information

For over 10 years, ModelSEED has been a primary resource for the construction of draft genome-scale metabolic models based on annotated microbial or plant genomes. The ModelSEED biochemistry database is the foundation of the biochemical data underlying ModelSEED and KBase. The The ModelSEED biochemistry database (i) includes compartmentalization, transport reactions, charged molecules and proton balancing on reactions; (ii) is extensible by the user community, with all data stored in GitHub; and (iii) designed as a biochemical ‘Rosetta Stone’ to facilitate comparison and integration of annotations from many different tools and databases. The database was constructed by combining chemical data from many resources, applying standard transformations, identifying redundancies and computing thermodynamic properties. The ModelSEED biochemistry is continually tested using flux balance analysis to ensure the biochemical network is modeling-ready and capable of simulating diverse phenotypes.

Homepage https://modelseed.org/biochem

Countries that developed this resource Denmark , Switzerland , United States

Created in 2020

Taxonomic range

Bacteria

Fungi

Plantae

Knowledge Domains

Subjects

User-defined Tags

Genome Scale Metabolic Model

How to cite this record FAIRsharing.org: ModelSEED Biochemistry Database; ModelSEED Biochemistry Database; DOI: https://doi.org/10.25504/FAIRsharing.Ql6K87; Last edited: Feb. 4, 2021, 2:48 p.m.; Last accessed: Oct 27 2021 6:22 p.m.

This record is maintained by seaver

Record added: Oct. 15, 2020, 9:07 p.m.
Record updated: Feb. 4, 2021, 1:23 p.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.Ql6K87' by 'The FAIRsharing Team' at 13:23, 04 Feb 2021 (approved):

	'onto_domains' has been modified:
		Before:
			Data retrieval
			Mathematical model
			Pathway or network prediction
			Prediction and recognition
			Reaction data
			genome
			modeling and simulation objective
			network model
		After:
			Data retrieval
			Mathematical model
			Prediction and recognition
			Reaction data
			genome
			modeling and simulation objective
			network model
		Added:
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			Pathway or network prediction

Edits to 'https://fairsharing.org/FAIRsharing.Ql6K87' by 'The FAIRsharing Team' at 13:22, 04 Feb 2021 (approved):

	'related_databases' has been modified:
		Before:
			US Department of Energy Systems Biology Knowledgebase
		After:
			MetaCyc
			Kyoto Encyclopedia of Genes and Genomes
			US Department of Energy Systems Biology Knowledgebase
			Phytozome
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			MetaCyc
			Kyoto Encyclopedia of Genes and Genomes
			Phytozome
		Removed:

	'supportLinks' has been modified:
		Before:
			forum|https://github.com/ModelSEED/ModelSEEDDatabase/issues
			online documentation|https://modelseed.org/about
		After:
			forum|https://github.com/ModelSEED/ModelSEEDDatabase/issues
			online documentation|https://modelseed.org/about
			online documentation|https://github.com/ModelSEED/ModelSEEDDatabase
		Added:
			online documentation|https://github.com/ModelSEED/ModelSEEDDatabase
		Removed:

	'description' has been modified:
		Before: For over 10 years, ModelSEED has been a primary resource for the construction of draft genome-scale metabolic models based on annotated microbial or plant genomes. Now being released, the biochemistry database serves as the foundation of biochemical data underlying ModelSEED and KBase. The biochemistry database embodies several properties that, taken together, distinguish it from other published biochemistry resources by: (i) including compartmentalization, transport reactions, charged molecules and proton balancing on reactions; (ii) being extensible by the user community, with all data stored in GitHub; and (iii) design as a biochemical ?Rosetta Stone? to facilitate comparison and integration of annotations from many different tools and databases. The database was constructed by combining chemical data from many resources, applying standard transformations, identifying redundancies and computing thermodynamic properties. The ModelSEED biochemistry is continually tested using flux balance analysis to ensure the biochemical network is modeling-ready and capable of simulating diverse phenotypes. Ontologies can be designed to aid in comparing and reconciling metabolic reconstructions that differ in how they represent various metabolic pathways. ModelSEED now includes 33,978 compounds and 36,645 reactions, available as a set of extensible files on GitHub, and available to search at https://modelseed.org and KBase.
		After: For over 10 years, ModelSEED has been a primary resource for the construction of draft genome-scale metabolic models based on annotated microbial or plant genomes. The ModelSEED biochemistry database is the foundation of the biochemical data underlying ModelSEED and KBase. The The ModelSEED biochemistry database (i) includes compartmentalization, transport reactions, charged molecules and proton balancing on reactions; (ii) is extensible by the user community, with all data stored in GitHub; and (iii) designed as a biochemical ?Rosetta Stone? to facilitate comparison and integration of annotations from many different tools and databases. The database was constructed by combining chemical data from many resources, applying standard transformations, identifying redundancies and computing thermodynamic properties. The ModelSEED biochemistry is continually tested using flux balance analysis to ensure the biochemical network is modeling-ready and capable of simulating diverse phenotypes.  

	'onto_disciplines' has been modified:
		Before:
			Biochemistry
			Life Science
		After:
			Biochemistry
			Data Integration
			Life Science
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			Data Integration
		Removed:

	'dataProcesses' has been modified:
		Before:
			Browse & search reactions, data access, https://modelseed.org/biochem/reactions
			Browse & search compounds, data access, https://modelseed.org/biochem/compounds
			ModelSEED Biochemistry Database v1.1.1, data versioning, https://github.com/ModelSEED/ModelSEEDDatabase/tree/v1.1.1
		After:
			Browse & search reactions, data access, https://modelseed.org/biochem/reactions
			Browse & search compounds, data access, https://modelseed.org/biochem/compounds
			Data Versions, data versioning, https://github.com/ModelSEED/ModelSEEDDatabase/releases
		Added:
			Data Versions, data versioning, https://github.com/ModelSEED/ModelSEEDDatabase/releases
		Removed:
			ModelSEED Biochemistry Database v1.1.1, data versioning, https://github.com/ModelSEED/ModelSEEDDatabase/tree/v1.1.1

	'onto_domains' has been modified:
		Before:
			Data retrieval
			Pathway or network prediction
			Reaction data
		After:
			Data retrieval
			Mathematical model
			Pathway or network prediction
			Prediction and recognition
			Reaction data
			genome
			modeling and simulation objective
			network model
		Added:
			Mathematical model
			Prediction and recognition
			genome
			modeling and simulation objective
			network model
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.Ql6K87' by 'The FAIRsharing Team' at 16:06, 09 Nov 2020 (approved):

	'onto_disciplines' has been modified:
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			Biochemistry
		After:
			Biochemistry
			Life Science
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			Life Science
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	'onto_domains' has been modified:
		Before:
			Data retrieval
		After:
			Data retrieval
			Pathway or network prediction
			Reaction data
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			Pathway or network prediction
			Reaction data
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Edits to 'https://fairsharing.org/FAIRsharing.Ql6K87' by 'seaver' at 15:49, 21 Oct 2020 (approved):

	'dataProcesses' has been modified:
		Before:
			Browse & search reactions, data access, https://modelseed.org/biochem/reactions
			Browse & search subsystems, data access, https://modelseed.org/genomes/Annotations
			plant models, data access, https://modelseed.org/genomes/Plants
			Browse & search compounds, data access, https://modelseed.org/biochem/compounds
			Browse & search media, data access, https://modelseed.org/list-media/
			ModelSEED v2.6.1, data versioning, https://modelseed.org/about/version
		After:
			Browse & search reactions, data access, https://modelseed.org/biochem/reactions
			Browse & search compounds, data access, https://modelseed.org/biochem/compounds
			ModelSEED Biochemistry Database v1.1.1, data versioning, https://github.com/ModelSEED/ModelSEEDDatabase/tree/v1.1.1
		Added:
			ModelSEED Biochemistry Database v1.1.1, data versioning, https://github.com/ModelSEED/ModelSEEDDatabase/tree/v1.1.1
		Removed:
			Browse & search subsystems, data access, https://modelseed.org/genomes/Annotations
			plant models, data access, https://modelseed.org/genomes/Plants
			Browse & search media, data access, https://modelseed.org/list-media/
			ModelSEED v2.6.1, data versioning, https://modelseed.org/about/version

Edits to 'https://fairsharing.org/FAIRsharing.Ql6K87' by 'The FAIRsharing Team' at 15:45, 20 Oct 2020 (approved):

	'supportLinks' has been modified:
		Before:
			forum|https://github.com/ModelSEED/ModelSEEDDatabase/issues
		After:
			forum|https://github.com/ModelSEED/ModelSEEDDatabase/issues
			online documentation|https://modelseed.org/about
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			online documentation|https://modelseed.org/about
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	'dataProcesses' has been modified:
		Before:
		After:
			Browse & search reactions, data access, https://modelseed.org/biochem/reactions
			Browse & search subsystems, data access, https://modelseed.org/genomes/Annotations
			plant models, data access, https://modelseed.org/genomes/Plants
			Browse & search compounds, data access, https://modelseed.org/biochem/compounds
			Browse & search media, data access, https://modelseed.org/list-media/
			ModelSEED v2.6.1, data versioning, https://modelseed.org/about/version
		Added:
			Browse & search reactions, data access, https://modelseed.org/biochem/reactions
			Browse & search subsystems, data access, https://modelseed.org/genomes/Annotations
			plant models, data access, https://modelseed.org/genomes/Plants
			Browse & search compounds, data access, https://modelseed.org/biochem/compounds
			Browse & search media, data access, https://modelseed.org/list-media/
			ModelSEED v2.6.1, data versioning, https://modelseed.org/about/version
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.Ql6K87' by 'The FAIRsharing Team' at 14:46, 20 Oct 2020 (approved):

	'licences' has been modified:
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			Creative Commons Attribution Non-Commercial License|http://creativecommons.org/licenses/by-nc/4.0/|Data
		After:
			Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)|https://creativecommons.org/licenses/by-nc/4.0/|Data
		Added:
			Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)|https://creativecommons.org/licenses/by-nc/4.0/|Data
		Removed:
			Creative Commons Attribution Non-Commercial License|http://creativecommons.org/licenses/by-nc/4.0/|Data

	'miriam_id' has been modified:
		Before: None
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Edits to 'https://fairsharing.org/FAIRsharing.Ql6K87' by 'The FAIRsharing Team' at 13:44, 19 Oct 2020 (approved):

	'doi' has been modified:
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	'miriam_id' has been modified:
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Support

General

forum	ModelSEED Biochemistry GitHub Issues
online documentation	About
online documentation	GitHub Project

Additional Information

Contact

Samuel Seaver ORCID

Tools

No tools defined

Access / Retrieve Data

Conditions of Use

Applies to: Data use

Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)

Data Versioning

Data Versions

https://github.com/ModelSEED/ModelSEEDDatabase/releases

Data Access

Browse & search reactions	https://modelseed.org/biochem/reactions
Browse & search compounds	https://modelseed.org/biochem/compounds

REST Web Services

Apache SOLR instance serving the biochemistry data

https://modelseed.org/solr

Publications

The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes

Samuel M D Seaver, Filipe Liu, Qizhi Zhang et al.
Nucleic Acids Research 2020

View Paper (PubMed) View Publication

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

No semantic standards defined

Models and Formats

No syntax standards defined

Identifier Schemas

No identifier schema standards defined

Metrics

No metrics standards defined

Related Databases

Implementing Policies

This record is not implemented by any policy.

Credit

Record Maintainer

This record is maintained by seaver

Funds

United States Department of Energy, Office of Science, USA (Government body)
National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, USA (Government body)
National Science Foundation (NSF), USA (Government body)
European Union's Horizon 2020 research and innovation programme (Government body)

Maintains

Argonne National Laboratory, Lemont, IL, USA (Government body) Lead

Undefined

Lawrence Berkeley National Laboratory (LBNL), CA, USA (Government body)
Lawrence Livermore National Laboratory (LLNL), USA (Lab)
Oak Ridge National Laboratory, USA (Government body)
Hope College, Holland, MI (University)
Mayo Clinic, Rochester, USA (Research institute)
Institute of Molecular Systems Biology, Zürich, Switzerland
Technical University of Denmark, Denmark (University)

Grant Number(s)

686070 (DD-DeCaF) (European Union's Horizon 2020 research and innovation programme)
DE-AC02–05CH11231 (United States Department of Energy, Office of Science, USA)
DE-AC02–06CH11357 (United States Department of Energy, Office of Science, USA)
DE-AC05–00OR22725 (United States Department of Energy, Office of Science, USA)
DE-AC52–07NA27344 (United States Department of Energy, Office of Science, USA)
GEPR-1444202 (National Science Foundation (NSF), USA)
MCB-1716285 (National Science Foundation (NSF), USA)
R01CA179243 (National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, USA)

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