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Enzyme Structure Function Ontology

Abbreviation: ESFO

General Information

The ESFO provides a new paradigm for organizing enzyme sequence, structure, and function information, whereby specific elements of enzyme sequence and structure are mapped to specific conserved aspects of function, thus facilitating the functional annotation of uncharacterized enzymes. The ESFO helps prevent misannotation by emphasizing annotation of enzymes only at the level of functional granularity warranted by available information. The archive is a static snapshot of the data in the SFLD as of April 2019, and will not be updated

Homepage http://sfld.rbvi.ucsf.edu/

Countries that developed this resource United States

Created in 2016

Taxonomic range

All

Knowledge Domains

Subjects

How to cite this record FAIRsharing.org: ESFO; Enzyme Structure Function Ontology; DOI: https://doi.org/10.25504/FAIRsharing.9y3gv0; Last edited: Dec. 18, 2019, 11:16 a.m.; Last accessed: Jul 10 2020 10:22 a.m.

Publication for citation Biocuration in the structure-function linkage database: the anatomy of a superfamily. Holliday GL,Brown SD,Akiva E,Mischel D,Hicks MA,Morris JH,Huang CC,Meng EC,Pegg SC,Ferrin TE,Babbitt PC; Database (Oxford) ; 2017; 10.1093/database/bax006;

Record added: Oct. 24, 2017, 9:41 a.m.
Record updated: Dec. 16, 2019, 2:01 p.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.9y3gv0' by 'The FAIRsharing Team' at 14:01, 16 Dec 2019 (approved):

	'supportLinks' has been modified:
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			training|http://sfld.rbvi.ucsf.edu/django/web/tutorial_links/
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			training|http://sfld.rbvi.ucsf.edu/django/web/tutorial_links/

Edits to 'https://fairsharing.org/FAIRsharing.9y3gv0' by 'The FAIRsharing Team' at 14:00, 16 Dec 2019 (approved):

	'organizations' has been modified:
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			Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, USA|https://bts.ucsf.edu/|Maintains
			Human Longevity, Inc, San Diego, USA|https://www.humanlongevity.com/|Maintains
			Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, USA|https://pharmchem.ucsf.edu/|Maintains
			Gladstone Institutes|https://gladstone.org/|Maintains
			California Institute for Quantitative Biosciences, University of California, San Francisco, USA|https://vcresearch.berkeley.edu/research-unit/california-institute-quantitative-biosciences|Maintains
		Added:
			Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, USA|https://bts.ucsf.edu/|Maintains
			Human Longevity, Inc, San Diego, USA|https://www.humanlongevity.com/|Maintains
			Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, USA|https://pharmchem.ucsf.edu/|Maintains
			Gladstone Institutes|https://gladstone.org/|Maintains
			California Institute for Quantitative Biosciences, University of California, San Francisco, USA|https://vcresearch.berkeley.edu/research-unit/california-institute-quantitative-biosciences|Maintains
		Removed:

	'description' has been modified:
		Before: The ESFO provides a new paradigm for organizing enzyme sequence, structure, and function information, whereby specific elements of enzyme sequence and structure are mapped to specific conserved aspects of function, thus facilitating the functional annotation of uncharacterized enzymes. The ESFO helps prevent misannotation by emphasizing annotation of enzymes only at the level of functional granularity warranted by available information.
		After: The ESFO provides a new paradigm for organizing enzyme sequence, structure, and function information, whereby specific elements of enzyme sequence and structure are mapped to specific conserved aspects of function, thus facilitating the functional annotation of uncharacterized enzymes. The ESFO helps prevent misannotation by emphasizing annotation of enzymes only at the level of functional granularity warranted by available information. The archive is a static snapshot of the data in the SFLD as of April 2019, and will not be updated

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			United States
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			United States
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			Life Science
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			Enzymology
			Life Science
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			Enzymology
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	'onto_domains' has been modified:
		Before:
			Annotation
			DNA sequence
			Sequence alignment
			enzyme
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			Annotation
			DNA sequence
			Function analysis
			Protein structure
			Sequence alignment
			Structure
			enzyme
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			Function analysis
			Protein structure
			Structure
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	'related_standards' has been modified:
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			Enzyme Mechanism Ontology
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			Enzyme Mechanism Ontology
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	'publications' has been modified:
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			Biocuration in the structure-function linkage database: the anatomy of a superfamily.|Holliday GL,Brown SD,Akiva E,Mischel D,Hicks MA,Morris JH,Huang CC,Meng EC,Pegg SC,Ferrin TE,Babbitt PC|Database (Oxford)|2017
		Added:
			Biocuration in the structure-function linkage database: the anatomy of a superfamily.|Holliday GL,Brown SD,Akiva E,Mischel D,Hicks MA,Morris JH,Huang CC,Meng EC,Pegg SC,Ferrin TE,Babbitt PC|Database (Oxford)|2017
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Edits to 'https://fairsharing.org/FAIRsharing.9y3gv0' by 'The FAIRsharing Team' at 10:43, 21 Nov 2018 (approved):

	'domains' has been modified:
		Before:
			Annotation
			Enzyme
			Sequence alignment
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			Annotation
			DNA sequence data
			Enzyme
			Life Science
			Sequence alignment
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			DNA sequence data
			Life Science
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	'miriam_id' has been modified:
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		After: None

Edits to 'https://fairsharing.org/FAIRsharing.9y3gv0' by 'The FAIRsharing Team' at 21:56, 05 Aug 2018 (approved):

	'domains' has been modified:
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		After:
			Annotation
			DNA sequence
			Enzyme
			Sequence alignment
		Added:
			Annotation
			DNA sequence
			Enzyme
			Sequence alignment
		Removed:

	'supportLinks' has been modified:
		Before:
		After:
			training|http://sfld.rbvi.ucsf.edu/django/web/tutorial_links/
		Added:
			training|http://sfld.rbvi.ucsf.edu/django/web/tutorial_links/
		Removed:

	'miriam_id' has been modified:
		Before: None
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In Collections

RDA Covid-19 WG Resources

Support

No support information provided.

Additional Information

Contact

Shoshana Brown

External Links

Bioportal

http://bioportal.bioontology.org/ontologies/ESFO

Tools

No tools defined

Schemas

No XSD schemas defined

Access / Retrieve Data

Conditions of Use

Publications

Biocuration in the structure-function linkage database: the anatomy of a superfamily.

Holliday GL,Brown SD,Akiva E,Mischel D,Hicks MA,Morris JH,Huang CC,Meng EC,Pegg SC,Ferrin TE,Babbitt PC
Database (Oxford) 2017

View Paper (PubMed) View Publication

ESFO Ontology Display

View in BioPortal.

Disclaimer: This widget assumes the availability of the ontology resources in the NCBO BioPortal.

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

Enzyme Mechanism Ontology

Models and Formats

No syntax standards defined

Identifier Schemas

No identifier schema standards defined

Metrics

No metrics standards defined

Related Databases (2)

Mechanism, Annotation and Classification in Enzymes
MACiE is an electronic database of well-characterised enzymatic reactions. MACiE is the result of more than three years' collaboration between the Mitchell and Murray-Rust groups in the Unilever Centre and Prof. Janet Thornton at the European Bioinformatics Institute. The database contains the reaction mechanisms for 100 individual enzymes; this includes the overall reactions and the multiple steps that constitute them.

Structure Function Linkage Database Archive
Structure Function Linkage Database (SFLD) is a database of enzymes classified by linking sequences to chemical function. A hierachical systems is used to classify enzymes by family or superfamily other category levels include functional domain, subgroup and suprafamily. The archive does not contain the interactive functionality found in the original SFLD, such as search capabilities. Instead, the archive is a static snapshot of the data in the SFLD as of April 2019, and will not be updated.

Implementing Policies

This record is not implemented by any policy.

Credit

Record Maintainer

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Maintains

Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, USA (University)
Human Longevity, Inc, San Diego, USA (Company)
Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, USA (University)
Gladstone Institutes (Government body)
California Institute for Quantitative Biosciences, University of California, San Francisco, USA (Research institute)

Enzyme Structure Function Ontology

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