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PIR SuperFamily

Abbreviation:PIRSF

General Information

The PIR SuperFamily concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships.

Homepage https://proteininformationresource.org/pirwww/dbinfo/pirsf.shtml

Countries that developed this resource United States

Created in 1984

Taxonomic range

All

Knowledge Domains

Subjects

How to cite this record FAIRsharing.org: PIRSF; PIR SuperFamily; DOI: https://doi.org/10.25504/FAIRsharing.vssch2; Last edited: April 20, 2020, 3:38 p.m.; Last accessed: Sep 21 2020 1:39 p.m.

Record updated: April 20, 2020, 3:38 p.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.vssch2' by 'The FAIRsharing Team' at 15:38, 20 Apr 2020 (approved):

	'homepage' has been modified:
		Before: http://pir.georgetown.edu/pirwww/dbinfo/pirsf.shtml
		After: https://proteininformationresource.org/pirwww/dbinfo/pirsf.shtml

	'supportLinks' has been modified:
		Before:
			FAQ|http://pir.georgetown.edu/pirwww/support/faq.shtml
			help|http://pir.georgetown.edu/pirwww/support/help.shtml
		After:
			training|https://proteininformationresource.org/pirwww/about/doc/tutorials/pirsftutorial.ppt
		Added:
			training|https://proteininformationresource.org/pirwww/about/doc/tutorials/pirsftutorial.ppt
		Removed:
			FAQ|http://pir.georgetown.edu/pirwww/support/faq.shtml
			help|http://pir.georgetown.edu/pirwww/support/help.shtml

	'tools' has been modified:
		Before:
			BLAST||http://pir.georgetown.edu/pirwww/search/blast.shtml
		After:
		Added:
		Removed:
			BLAST||http://pir.georgetown.edu/pirwww/search/blast.shtml

	'dataProcesses' has been modified:
		Before:
			Download
			search
			advanced search
			Scan
			Batch Retrieval
			Text search
		After:
			Download
			advanced search
			Scan
			Batch Retrieval
		Added:
		Removed:
			search
			Text search

	'onto_domains' has been modified:
		Before:
			protein
			structure
		After:
			Sequence cluster
			protein
			structure
		Added:
			Sequence cluster
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.vssch2' by 'The FAIRsharing Team' at 13:48, 15 Jan 2019 (approved):

	'organizations' has been modified:
		Before:
			National Institutes of Health (NIH), Bethesda, MD, USA|http://www.nih.gov|Funds
			Georgetown University Medical Center , Georgetown University, Washington DC, USA|https://gumc.georgetown.edu/|Maintains
			PIR|http://pir.georgetown.edu|Maintains
			University of Delaware, USA|http://www.udel.edu|Maintains
			European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK|https://www.ebi.ac.uk/|Maintains
			European Commission under FP7 Grant Agreement|http://ec.europa.eu/research/fp7/index_en.cfm?pg=documents|Undefined
		After:
			National Institutes of Health (NIH), Bethesda, MD, USA|http://www.nih.gov|Funds
			Georgetown University Medical Center , Georgetown University, Washington DC, USA|https://gumc.georgetown.edu/|Maintains
			PIR|http://pir.georgetown.edu|Maintains
			University of Delaware, USA|http://www.udel.edu|Maintains
			European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK|https://www.ebi.ac.uk/|Maintains
			European Commission under FP7 Grant Agreement|http://ec.europa.eu/research/fp7/index_en.cfm?pg=documents|Funds
		Added:
			European Commission under FP7 Grant Agreement|http://ec.europa.eu/research/fp7/index_en.cfm?pg=documents|Funds
		Removed:
			European Commission under FP7 Grant Agreement|http://ec.europa.eu/research/fp7/index_en.cfm?pg=documents|Undefined

Edits to 'https://fairsharing.org/FAIRsharing.vssch2' by 'The FAIRsharing Team' at 13:47, 15 Jan 2019 (approved):

	'organizations' has been modified:
		Before:
			Georgetown University, DC, USA|http://gumc.georgetown.edu|Maintains
			PIR|http://pir.georgetown.edu/pirwww/about/sponsor.shtml|Maintains
			University of Delaware, USA|http://www.udel.edu|Maintains
			European Commission under FP7 Grant Agreement|http://ec.europa.eu/research/fp7/index_en.cfm?pg=documents|Undefined
			Swiss Institute of Bioinformatics (SIB)|http://www.sib.swiss/|Maintains
			National Institutes of Health (NIH), Bethesda, MD, USA|http://www.nih.gov|Funds
		After:
			National Institutes of Health (NIH), Bethesda, MD, USA|http://www.nih.gov|Funds
			Georgetown University Medical Center , Georgetown University, Washington DC, USA|https://gumc.georgetown.edu/|Maintains
			PIR|http://pir.georgetown.edu|Maintains
			University of Delaware, USA|http://www.udel.edu|Maintains
			European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK|https://www.ebi.ac.uk/|Maintains
			European Commission under FP7 Grant Agreement|http://ec.europa.eu/research/fp7/index_en.cfm?pg=documents|Undefined
		Added:
			Georgetown University Medical Center , Georgetown University, Washington DC, USA|https://gumc.georgetown.edu/|Maintains
			PIR|http://pir.georgetown.edu|Maintains
			European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK|https://www.ebi.ac.uk/|Maintains
		Removed:
			Georgetown University, DC, USA|http://gumc.georgetown.edu|Maintains
			PIR|http://pir.georgetown.edu/pirwww/about/sponsor.shtml|Maintains
			Swiss Institute of Bioinformatics (SIB)|http://www.sib.swiss/|Maintains

	'supportLinks' has been modified:
		Before:
			FAQ|http://pir.georgetown.edu/pirwww/support/faq.shtml
			help|http://pir.georgetown.edu/pirwww/support/help.shtml
			training|http://pir.georgetown.edu/pirwww/about/doc/tutorials/iproclasstutorial.ppt
		After:
			FAQ|http://pir.georgetown.edu/pirwww/support/faq.shtml
			help|http://pir.georgetown.edu/pirwww/support/help.shtml
		Added:
		Removed:
			training|http://pir.georgetown.edu/pirwww/about/doc/tutorials/iproclasstutorial.ppt

Edits to 'https://fairsharing.org/FAIRsharing.vssch2' by 'The FAIRsharing Team' at 16:02, 05 Aug 2018 (approved):

	'related_databases' has been modified:
		Before:
			ProtoNet
		After:
			ProtoNet
			UniProt Knowledgebase
		Added:
			UniProt Knowledgebase
		Removed:

	'name' has been modified:
		Before: PIRSF; a whole-protein classification database
		After: PIR SuperFamily

	'dataProcesses' has been modified:
		Before:
			Download
			search
			advanced search
		After:
			Download
			search
			advanced search
			Scan
			Batch Retrieval
			Text search
		Added:
			Scan
			Batch Retrieval
			Text search
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.vssch2' by 'The FAIRsharing Team' at 21:12, 04 Oct 2016 (approved):

	'contactName' has been modified:
		Before:
			
		After:
			General contact
		Added:
		Removed:

Support

General

training

Tutorial (PPT)

Additional Information

Contact

General contact

Tools

No tools defined

Access / Retrieve Data

Conditions of Use

Applies to: Data use

Attribution required
Open Data Commons (ODC) Public Domain Dedication and Licence (PDDL) 1.0

Data Release

Download

ftp://ftp.pir.georgetown.edu/databases/pirsf/

Data Access

advanced search	http://research.bioinformatics.udel.edu/peptidematch/index.jsp
Scan	https://proteininformationresource.org/pirwww/search/pirsfscan.shtml
Batch Retrieval	https://proteininformationresource.org/pirwww/search/batch_sf.shtml

Publications

PIRSF: family classification system at the Protein Information Resource.

Wu CH., Nikolskaya A., Huang H., Yeh LS., Natale DA., Vinayaka CR., Hu ZZ., Mazumder R., Kumar S., Kourtesis P., Ledley RS., Suzek BE., Arminski L., Chen Y., Zhang J., Cardenas JL., Chung S., Castro-Alvear J., Dinkov G., Barker WC.,
Nucleic Acids Res. 2004

View Paper (PubMed)

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

No semantic standards defined

Models and Formats

FASTA Sequence Format

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 in need of a maintainer. If you login, you'll be able to claim this record.

Funds

European Commission under FP7 Grant Agreement (Government body)
National Institutes of Health (NIH), Bethesda, MD, USA (Government body)

Maintains

Georgetown University Medical Center , Georgetown University, Washington DC, USA (University)
PIR (Research institute) Lead
University of Delaware, USA (University)
European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK (Research institute)

PIR SuperFamily

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