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Using Phenotype Ontologies in GVF

Abbreviation: GVF Guidelines

General Information

This guideline describes a set of best practices when using phenotype ontologies to annotate genomic variant files using Genome Variation Format (GVF) and the Sequence Ontology.

Homepage http://www.sequenceontology.org/so_wiki/index.php/Using_Phenotype_Ontologies_in_GVF

Countries that developed this resource United States

Created in 2009

Taxonomic range

Homo sapiens

Knowledge Domains

Subjects

How to cite this record FAIRsharing.org: GVF Guidelines; Using Phenotype Ontologies in GVF; DOI: https://doi.org/10.25504/FAIRsharing.h1v36j; Last edited: Feb. 13, 2020, 2:56 p.m.; Last accessed: Sep 23 2020 1:45 p.m.

This record is maintained by keilbeck

Record updated: Feb. 13, 2020, 2:55 p.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.h1v36j' by 'The FAIRsharing Team' at 14:55, 13 Feb 2020 (approved):

	'related_standards' has been modified:
		Before:
		After:
			Sequence Ontology
			Genome Variation Format
			Human Phenotype Ontology
			Disease Ontology
			Online Mendelian Inheritance in Man Ontology
			Systematized Nomenclature of Medicine-Clinical Terms
			International Classification of Diseases Version 9 - Clinical Modification
			Mammalian Phenotype Ontology
		Added:
			Sequence Ontology
			Genome Variation Format
			Human Phenotype Ontology
			Disease Ontology
			Online Mendelian Inheritance in Man Ontology
			Systematized Nomenclature of Medicine-Clinical Terms
			International Classification of Diseases Version 9 - Clinical Modification
			Mammalian Phenotype Ontology
		Removed:

	'description' has been modified:
		Before: This guideline describes a set of best practices when using phenotype ontologies to annotate genomic variant files using GVF.
		After: This guideline describes a set of best practices when using phenotype ontologies to annotate genomic variant files using Genome Variation Format (GVF) and the Sequence Ontology.

Edits to 'https://fairsharing.org/FAIRsharing.h1v36j' by 'The FAIRsharing Team' at 18:00, 09 Feb 2020 (approved):

	'organizations' has been modified:
		Before:
			Biotechnology and Biological Sciences Research Council (BBSRC), UK|https://bbsrc.ukri.org|Funds
			The Monarch Initiative|http://monarchinitiative.org/|Funds
			Sequence Ontology Administrators|http://www.sequenceontology.org/|Maintains
			National Institutes of Health (NIH), Bethesda, MD, USA|http://www.nih.gov|Funds
			National Human Genome Research Institute (NHGRI), Bethesda, MD, USA|http://www.genome.gov/|Funds
		After:
			Biotechnology and Biological Sciences Research Council (BBSRC), UK|https://bbsrc.ukri.org|Funds
			The Monarch Initiative|http://monarchinitiative.org/|Funds
			National Institutes of Health (NIH), Bethesda, MD, USA|http://www.nih.gov|Funds
			National Human Genome Research Institute (NHGRI), Bethesda, MD, USA|http://www.genome.gov/|Funds
			Sequence Ontology Administrators|http://www.sequenceontology.org/|Maintains
			U.S. National Library of Medicine|https://www.nlm.nih.gov/|Funds
		Added:
			U.S. National Library of Medicine|https://www.nlm.nih.gov/|Funds
		Removed:

	'miriam_id' has been modified:
		Before: None
		After: 

	'contactORCID' has been modified:
		Before: 
		After: 0000-0002-0831-6427

	'dataProcesses' has been modified:
		Before:
		After:
			Using Phenotype Ontologies in Human GVF
			Non-human phenotype annotation
		Added:
			Using Phenotype Ontologies in Human GVF
			Non-human phenotype annotation
		Removed:

Support

No support information provided.

Additional Information

Contact

Karen Eilbeck ORCID

Tools

No tools defined

Schemas

No XSD schemas defined

Access / Retrieve Data

Conditions of Use

Data Access

Using Phenotype Ontologies in Human GVF	http://www.sequenceontology.org/so_wiki/index.php/Using_Phenotype_Onto ...
Non-human phenotype annotation	http://www.sequenceontology.org/so_wiki/index.php/Non-human_phenotype_ ...

Publications

Integrating phenotype ontologies across multiple species.

Mungall CJ,Gkoutos GV,Smith CL,Haendel MA,Lewis SE,Ashburner M
Genome Biol 2010

View Paper (PubMed) View Publication

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

Models and Formats

Genome Variation Format

Identifier Schemas

No identifier schema standards defined

Metrics

No metrics standards defined

Related Databases (0)

No Related Databases

Implementing Policies

This record is not implemented by any policy.

Credit

Record Maintainer

This record is maintained by keilbeck

Funds

Biotechnology and Biological Sciences Research Council (BBSRC), UK (Government body)
The Monarch Initiative (Consortium)
National Human Genome Research Institute (NHGRI), Bethesda, MD, USA (Government body)
U.S. National Library of Medicine (Government body)
National Institutes of Health (NIH), Bethesda, MD, USA (Government body)

Maintains

Sequence Ontology Administrators (Consortium)

Grant Number(s)

BG/G004358/1 (Biotechnology and Biological Sciences Research Council (BBSRC), UK)
HG000330 (National Human Genome Research Institute (NHGRI), Bethesda, MD, USA)
U54 HG004028 (U.S. National Library of Medicine)

Using Phenotype Ontologies in GVF

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