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HOGENOM

General Information

HOGENOM is a phylogenomic database providing families of homologous genes and associated phylogenetic trees (and sequence alignments) for a wide set sequenced organisms.

Homepage http://hogenom.univ-lyon1.fr/

Countries that developed this resource France

Created in 2008

Taxonomic range

Archaea

Bacteria

Eukaryota

Knowledge Domains

Subjects

How to cite this record FAIRsharing.org: HOGENOM; HOGENOM; DOI: https://doi.org/10.25504/FAIRsharing.qe8tz8; Last edited: Sept. 24, 2020, 2:23 p.m.; Last accessed: Sep 19 2021 5:43 p.m.

This record is maintained by penel

Record updated: Sept. 14, 2020, 11:53 a.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.qe8tz8' by 'The FAIRsharing Team' at 11:53, 14 Sep 2020 (approved):

	'standardsImplemented' has been modified:
		Before:
		After:
			Gene Ontology
		Added:
			Gene Ontology
		Removed:

	'related_databases' has been modified:
		Before:
		After:
			Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups
			Pfam
			ProtoNet
			Simple Modular Architecture Research Tool
			Gene3D
			Bgee DataBase for Gene Expression Evolution
			Integrated resource of protein families, domains and functional sites
			STRING
			Protein ANalysis THrough Evolutionary Relationships: Classification of Genes and Proteins
			PROSITE
			UniProt Knowledgebase
			Database of Orthologous Groups
			ModBase database of comparative protein structure models
			InParanoid
		Added:
			Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups
			Pfam
			ProtoNet
			Simple Modular Architecture Research Tool
			Gene3D
			Bgee DataBase for Gene Expression Evolution
			Integrated resource of protein families, domains and functional sites
			STRING
			Protein ANalysis THrough Evolutionary Relationships: Classification of Genes and Proteins
			PROSITE
			UniProt Knowledgebase
			Database of Orthologous Groups
			ModBase database of comparative protein structure models
			InParanoid
		Removed:

	'supportLinks' has been modified:
		Before:
			online documentation|http://doua.prabi.fr/databases/hogenom/home.php?contents=data
			online documentation|http://doua.prabi.fr/databases/hogenom/home.php?contents=methods
		After:
			help|http://hogenom.univ-lyon1.fr/about
			online documentation|http://hogenom.univ-lyon1.fr/doc
			online documentation|http://hogenom.univ-lyon1.fr/contents
		Added:
			help|http://hogenom.univ-lyon1.fr/about
			online documentation|http://hogenom.univ-lyon1.fr/doc
			online documentation|http://hogenom.univ-lyon1.fr/contents
		Removed:
			online documentation|http://doua.prabi.fr/databases/hogenom/home.php?contents=data
			online documentation|http://doua.prabi.fr/databases/hogenom/home.php?contents=methods

	'description' has been modified:
		Before: HOGENOM is a database of homologous genes from fully sequenced organisms (bacteria, archeae and eukarya). This collection references phylogenetic trees which can be retrieved using either UniProt accession numbers, or HOGENOM tree family identifier.
		After: HOGENOM is a phylogenomic database providing families of homologous genes and associated phylogenetic trees (and sequence alignments) for a wide set sequenced organisms.

	'licences' has been modified:
		Before:
			GNU General Public License (GPL) 3.0|https://www.gnu.org/licenses/gpl.html|Undefined
		After:
			CeCILL license|https://cecill.info/licences.fr.html|Data
		Added:
			CeCILL license|https://cecill.info/licences.fr.html|Data
		Removed:
			GNU General Public License (GPL) 3.0|https://www.gnu.org/licenses/gpl.html|Undefined

	'onto_disciplines' has been modified:
		Before:
			Life Science
			Phylogenetics
		After:
			Life Science
			Phylogenetics
			Phylogeny
		Added:
			Phylogeny
		Removed:

	'dataProcesses' has been modified:
		Before:
			Download, data access, ftp://pbil.univ-lyon1.fr/pub/hogenom/
			search, data access, http://pbil.univ-lyon1.fr/databases/hogenom/home.php?contents=query
		After:
			search, data access, http://hogenom.univ-lyon1.fr/query
		Added:
			search, data access, http://hogenom.univ-lyon1.fr/query
		Removed:
			Download, data access, ftp://pbil.univ-lyon1.fr/pub/hogenom/
			search, data access, http://pbil.univ-lyon1.fr/databases/hogenom/home.php?contents=query

	'homepage' has been modified:
		Before: http://pbil.univ-lyon1.fr/databases/hogenom.php
		After: http://hogenom.univ-lyon1.fr/

Edits to 'https://fairsharing.org/FAIRsharing.qe8tz8' by 'The FAIRsharing Team' at 07:45, 11 Dec 2016 (approved):

	'year' has been modified:
		Before: None
		After: 2008

Edits to 'https://fairsharing.org/FAIRsharing.qe8tz8' by 'The FAIRsharing Team' at 07:40, 11 Dec 2016 (approved):

	'name' has been modified:
		Before: The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms
		After: HOGENOM

In Collections

EOSC-Life

Support

General

help	http://hogenom.univ-lyon1.fr/about
online documentation	http://hogenom.univ-lyon1.fr/doc
online documentation	Information about the content

Additional Information

Contact

Simon Penel

Tools

No tools defined

Access / Retrieve Data

Conditions of Use

Applies to: Data use

CeCILL license

Data Access

http://hogenom.univ-lyon1.fr/query

Publications

Databases of homologous gene families for comparative genomics.

Penel S., Arigon AM., Dufayard JF., Sertier AS., Daubin V., Duret L., Gouy M., Perrière G.,
BMC Bioinformatics 2009

View Paper (PubMed) View Publication

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

Gene Ontology

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 penel

Funds

National Agency of Research (ANR), Paris, France (Government body)

Maintains

PBIL, Lyon, France

Grant Number(s)

ANR-08-EMER-011-03 (National Agency of Research (ANR), Paris, France)

HOGENOM

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