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HAMAP database of microbial protein families

Abbreviation:HAMAP

General Information

HAMAP is a system, based on manual protein annotation, that identifies and semi-automatically annotates proteins that are part of well-conserved families or subfamilies: the HAMAP families. HAMAP is based on manually created family rules and is applied to bacterial, archaeal and plastid-encoded proteins.

Homepage https://hamap.expasy.org/

Countries that developed this resource Switzerland

Created in 2008

Taxonomic range

All

Knowledge Domains

Subjects

How to cite this record FAIRsharing.org: HAMAP; HAMAP database of microbial protein families; DOI: https://doi.org/10.25504/FAIRsharing.63m4ss; Last edited: April 20, 2021, 9:26 a.m.; Last accessed: Apr 21 2021 5:32 p.m.

This record is maintained by alanbridge

Record updated: April 20, 2021, 9:26 a.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.63m4ss' by 'The FAIRsharing Team' at 09:26, 20 Apr 2021 (not approved):

	'licences' has been modified:
		Before:
			Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)|https://creativecommons.org/licenses/by-nc/4.0/|Data
			Open Data Commons (ODC) Public Domain Dedication and Licence (PDDL) 1.0|http://opendatacommons.org/licenses/pddl/1.0/|Data
			Academic use||Data
			Attribution required||Data
			No commercial use without permission||Data
		After:
			Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)|https://creativecommons.org/licenses/by-nc/4.0/|Data
			Open Data Commons (ODC) Public Domain Dedication and Licence (PDDL) 1.0|http://opendatacommons.org/licenses/pddl/1.0/|Data
			Expasy Academic use|https://www.expasy.org/terms-of-use|Data
			Expasy Attribution required|https://www.expasy.org/terms-of-use|Data
			Expasy No commercial use without permission|https://www.expasy.org/terms-of-use|Data
		Added:
			Expasy Academic use|https://www.expasy.org/terms-of-use|Data
			Expasy Attribution required|https://www.expasy.org/terms-of-use|Data
			Expasy No commercial use without permission|https://www.expasy.org/terms-of-use|Data
		Removed:
			Academic use||Data
			Attribution required||Data
			No commercial use without permission||Data

Edits to 'https://fairsharing.org/FAIRsharing.63m4ss' by 'The FAIRsharing Team' at 17:19, 10 Mar 2021 (approved):

	'homepage' has been modified:
		Before: http://us.expasy.org/sprot/hamap/
		After: https://hamap.expasy.org/

	'standardsImplemented' has been modified:
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			Gene Ontology
			FASTA Sequence Format
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			Gene Ontology
			FASTA Sequence Format
			Bioschemas
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			Bioschemas
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	'tools' has been modified:
		Before:
			analyze||http://hamap.expasy.org/hamap_scan.html
			browse||http://hamap.expasy.org/proteomes.html
		After:
			analyze||http://hamap.expasy.org/hamap_scan.html
		Added:
		Removed:
			browse||http://hamap.expasy.org/proteomes.html

	'dataProcesses' has been modified:
		Before:
			automated annotation;manual curation, data curation, 
			Download, data access, ftp://ftp.expasy.org/databases/hamap/
		After:
			Automated annotation ; manual curation, data curation, 
			Download, data access, ftp://ftp.expasy.org/databases/hamap/
			Browse annotation rules, data access, https://hamap.expasy.org/cgi-bin/unirule/unirule_browse.cgi?browse=description&context=HAMAP
			Browse proteomes, data access, http://hamap.expasy.org/proteomes.html
		Added:
			Automated annotation ; manual curation, data curation, 
			Browse annotation rules, data access, https://hamap.expasy.org/cgi-bin/unirule/unirule_browse.cgi?browse=description&context=HAMAP
			Browse proteomes, data access, http://hamap.expasy.org/proteomes.html
		Removed:
			automated annotation;manual curation, data curation,

Edits to 'https://fairsharing.org/FAIRsharing.63m4ss' by 'The FAIRsharing Team' at 09:50, 21 Nov 2018 (approved):

	'domains' has been modified:
		Before:
			Life Science
			Protein
			Sequence annotation
		After:
			Amino acid sequence
			Life Science
			Protein
			Sequence annotation
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			Amino acid sequence
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Edits to 'https://fairsharing.org/FAIRsharing.63m4ss' by 'The FAIRsharing Team' at 09:20, 04 Aug 2018 (approved):

	'supportLinks' has been modified:
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			help|http://hamap.expasy.org/unirule/unirule.html
			online documentation|http://hamap.expasy.org/hamap_doc.html
		After:
			contact form|https://hamap.expasy.org/contact
			help|http://hamap.expasy.org/unirule/unirule.html
			online documentation|http://hamap.expasy.org/hamap_doc.html
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			contact form|https://hamap.expasy.org/contact
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.63m4ss' by 'The FAIRsharing Team' at 19:27, 02 Sep 2016 (approved):

	'contactName' has been modified:
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			Alan Bridge
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In Collections

Bioschemas

Support

General

contact form	https://hamap.expasy.org/contact
help	http://hamap.expasy.org/unirule/unirule. ...
online documentation	http://hamap.expasy.org/hamap_doc.html

Additional Information

Contact

Alan Bridge ORCID

Tools

analyze

http://hamap.expasy.org/hamap_scan.html

Access / Retrieve Data

Conditions of Use

Applies to: Data use

Data Curation

Automated annotation ; manual curation

No link recorded

Data Access

Download	ftp://ftp.expasy.org/databases/hamap/
Browse annotation rules	https://hamap.expasy.org/cgi-bin/unirule/unirule_browse.cgi?browse=des ...
Browse proteomes	http://hamap.expasy.org/proteomes.html

Publications

HAMAP in 2013, new developments in the protein family classification and annotation system.

Pedruzzi I., Rivoire C., Auchincloss AH., Coudert E., Keller G., de Castro E., Baratin D., Cuche BA., Bougueleret L., Poux S., Redaschi N., Xenarios I., Bridge A.,
Nucleic Acids Res. 2013

View Paper (PubMed) View Publication

HAMAP in 2015: updates to the protein family classification and annotation system.

Pedruzzi I,Rivoire C,Auchincloss AH,Coudert E,Keller G,de Castro E,Baratin D,Cuche BA,Bougueleret L,Poux S,Redaschi N,Xenarios I,Bridge A
Nucleic Acids Res 2014

View Paper (PubMed) View Publication

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

Gene Ontology

Models and Formats

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 alanbridge

Funds

U.S. National Library of Medicine (Government body)
Swiss National Sciences Foundation (SNCF) (Government body)
State Secretariat for Education, Research and Innovation SERI (Government body)
National Institutes of Health (NIH), Bethesda, MD, USA (Government body)

Maintains

Swiss Institute of Bioinformatics (SIB) (Research institute)

Grant Number(s)

JRP09 (Swiss National Sciences Foundation (SNCF))
JRP13 (Swiss National Sciences Foundation (SNCF))
U41HG006104 (U.S. National Library of Medicine)

HAMAP database of microbial protein families

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