Help us curate and collate the databases and standards useful for COVID-19 research. Our COVID-19 Collection is growing, but not yet complete. Join our community curatathon and tell us what's missing. Email contact@fairsharing.org to join!

FlyMine

General Information

FlyMine is an integrated database of genomic, expression and protein data for Drosophila, Anopheles and C. elegans. Integrating data makes it possible to run sophisticated data mining queries that span domains of biological knowledge.

Homepage https://www.flymine.org

Countries that developed this resource United Kingdom

Created in 2002

Taxonomic range

Anopheles gambiae

Caenorhabditis elegans

Drosophila melanogaster

Knowledge Domains

Subjects

How to cite this record FAIRsharing.org: FlyMine; FlyMine; DOI: https://doi.org/10.25504/FAIRsharing.rhpjhv; Last edited: Nov. 12, 2019, 9:26 a.m.; Last accessed: Apr 08 2020 8:08 a.m.

Publication for citation FlyMine: an integrated database for Drosophila and Anopheles genomics. Lyne R, Smith R, Rutherford K, Wakeling M, Varley A, Guillier F, Janssens H, Ji W, Mclaren P, North P, Rana D, Riley T, Sullivan J, Watkins X, Woodbridge M, Lilley K, Russell S, Ashburner M, Mizuguchi K, Micklem G.; Genome Biol ; 2007.

This record is maintained by julie and yochannah ORCID

Record updated: Nov. 11, 2019, 4:59 p.m. by yochannah.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.rhpjhv' by 'yochannah' at 16:59, 11 Nov 2019 (approved):

	'accessPoints' has been modified:
		Before:
			REST|http://www.flymine.org/flymine/api.do|Web Service Client (Perl, Python, Ruby, Java)
		After:
			REST|https://www.flymine.org/flymine/api.do|Web Service Client (Perl, Python, Ruby, Java)
		Added:
			REST|https://www.flymine.org/flymine/api.do|Web Service Client (Perl, Python, Ruby, Java)
		Removed:
			REST|http://www.flymine.org/flymine/api.do|Web Service Client (Perl, Python, Ruby, Java)

	'homepage' has been modified:
		Before: http://www.flymine.org
		After: https://www.flymine.org

Edits to 'https://fairsharing.org/FAIRsharing.rhpjhv' by 'The FAIRsharing Team' at 10:42, 13 Dec 2018 (approved):

	'supportLinks' has been modified:
		Before:
			blog|https://intermineorg.wordpress.com/
			help|https://tess.elixir-europe.org/materials/intermine-user-tutorial
			help|https://tess.elixir-europe.org/materials/intermine-user-manual
			help|https://intermineorg.wordpress.com/flymine/help/
			help|https://tess.elixir-europe.org/materials/flymine-intro-videos
			online documentation|http://www.flymine.org/flymine/dataCategories.do
			online documentation|https://intermineorg.wordpress.com/flymine/about/
			tess training|https://tess.elixir-europe.org/materials/flymine-intro-videos
		After:
			TeSS training|https://tess.elixir-europe.org/materials/flymine-intro-videos
			TeSS training|https://tess.elixir-europe.org/materials/intermine-user-tutorial
			TeSS training|https://tess.elixir-europe.org/materials/intermine-user-manual
			blog|https://intermineorg.wordpress.com/
			help|https://intermineorg.wordpress.com/flymine/help/
			online documentation|https://intermineorg.wordpress.com/flymine/about/
			online documentation|http://www.flymine.org/flymine/dataCategories.do
		Added:
			TeSS training|https://tess.elixir-europe.org/materials/flymine-intro-videos
			TeSS training|https://tess.elixir-europe.org/materials/intermine-user-tutorial
			TeSS training|https://tess.elixir-europe.org/materials/intermine-user-manual
		Removed:
			help|https://tess.elixir-europe.org/materials/intermine-user-tutorial
			help|https://tess.elixir-europe.org/materials/intermine-user-manual
			help|https://tess.elixir-europe.org/materials/flymine-intro-videos
			tess training|https://tess.elixir-europe.org/materials/flymine-intro-videos

Edits to 'https://fairsharing.org/FAIRsharing.rhpjhv' by 'The FAIRsharing Team' at 21:16, 12 Dec 2018 (approved):

	'supportLinks' has been modified:
		Before:
			blog|https://intermineorg.wordpress.com/
			help|https://tess.elixir-europe.org/materials/flymine-intro-videos
			help|https://intermineorg.wordpress.com/flymine/help/
			online documentation|https://intermineorg.wordpress.com/flymine/about/
			online documentation|http://www.flymine.org/flymine/dataCategories.do
			tess training|https://tess.elixir-europe.org/materials/intermine-user-tutorial
			tess training|https://tess.elixir-europe.org/materials/intermine-user-manual
		After:
			blog|https://intermineorg.wordpress.com/
			help|https://tess.elixir-europe.org/materials/intermine-user-tutorial
			help|https://tess.elixir-europe.org/materials/intermine-user-manual
			help|https://intermineorg.wordpress.com/flymine/help/
			help|https://tess.elixir-europe.org/materials/flymine-intro-videos
			online documentation|http://www.flymine.org/flymine/dataCategories.do
			online documentation|https://intermineorg.wordpress.com/flymine/about/
			tess training|https://tess.elixir-europe.org/materials/flymine-intro-videos
		Added:
			help|https://tess.elixir-europe.org/materials/intermine-user-tutorial
			help|https://tess.elixir-europe.org/materials/intermine-user-manual
			tess training|https://tess.elixir-europe.org/materials/flymine-intro-videos
		Removed:
			tess training|https://tess.elixir-europe.org/materials/intermine-user-tutorial
			tess training|https://tess.elixir-europe.org/materials/intermine-user-manual

Edits to 'https://fairsharing.org/FAIRsharing.rhpjhv' by 'The FAIRsharing Team' at 21:16, 12 Dec 2018 (approved):

	'related_databases' has been modified:
		Before:
			modMine
			MouseMine @ MGI
			RatMine
			WormMine
			YeastMine
			ZebrafishMine
			HumanMine
		After:
			FlyBase
			IntAct molecular interaction database
			modMine
			GenomeRNAi
			Berkeley Drosophila Genome Project EST database
			ArrayExpress
			Integrated resource of protein families, domains and functional sites
			Reactome - a curated knowledgebase of biological pathways
			Ensembl
			Homologene
			Biological General Repository for Interaction Datasets
			Protein ANalysis THrough Evolutionary Relationships: Classification of Genes and Proteins
			UniProt Knowledgebase
			miRBase Sequence Database
			MouseMine @ MGI
			Kyoto Encyclopedia of Genes and Genomes
			Online Mendelian Inheritance in Man
			RatMine
			WormMine
			YeastMine
			ZebrafishMine
			HumanMine
		Added:
			FlyBase
			IntAct molecular interaction database
			GenomeRNAi
			Berkeley Drosophila Genome Project EST database
			ArrayExpress
			Integrated resource of protein families, domains and functional sites
			Reactome - a curated knowledgebase of biological pathways
			Ensembl
			Homologene
			Biological General Repository for Interaction Datasets
			Protein ANalysis THrough Evolutionary Relationships: Classification of Genes and Proteins
			UniProt Knowledgebase
			miRBase Sequence Database
			Kyoto Encyclopedia of Genes and Genomes
			Online Mendelian Inheritance in Man
		Removed:

	'supportLinks' has been modified:
		Before:
			blog|https://intermineorg.wordpress.com/
			help|https://intermineorg.wordpress.com/flymine/help/
			online documentation|http://www.flymine.org/flymine/dataCategories.do
			online documentation|https://intermineorg.wordpress.com/flymine/about/
			tess training|https://tess.elixir-europe.org/materials/flymine-intro-videos
		After:
			blog|https://intermineorg.wordpress.com/
			help|https://tess.elixir-europe.org/materials/flymine-intro-videos
			help|https://intermineorg.wordpress.com/flymine/help/
			online documentation|https://intermineorg.wordpress.com/flymine/about/
			online documentation|http://www.flymine.org/flymine/dataCategories.do
			tess training|https://tess.elixir-europe.org/materials/intermine-user-tutorial
			tess training|https://tess.elixir-europe.org/materials/intermine-user-manual
		Added:
			help|https://tess.elixir-europe.org/materials/flymine-intro-videos
			tess training|https://tess.elixir-europe.org/materials/intermine-user-tutorial
			tess training|https://tess.elixir-europe.org/materials/intermine-user-manual
		Removed:
			tess training|https://tess.elixir-europe.org/materials/flymine-intro-videos

Edits to 'https://fairsharing.org/FAIRsharing.rhpjhv' by 'The FAIRsharing Team' at 14:44, 15 Nov 2018 (approved):

	'licences' has been modified:
		Before:
			GNU Lesser General Public License (LGPL) 2.1|https://www.gnu.org/licenses/lgpl-2.1.html|Data
		After:
			GNU Lesser General Public License (LGPL) 2.1|https://www.gnu.org/licenses/lgpl-2.1.html|Software
		Added:
			GNU Lesser General Public License (LGPL) 2.1|https://www.gnu.org/licenses/lgpl-2.1.html|Software
		Removed:
			GNU Lesser General Public License (LGPL) 2.1|https://www.gnu.org/licenses/lgpl-2.1.html|Data

	'supportLinks' has been modified:
		Before:
			blog|https://intermineorg.wordpress.com/
			help|https://intermineorg.wordpress.com/flymine/help/
			online documentation|http://www.flymine.org/flymine/dataCategories.do
			online documentation|https://intermineorg.wordpress.com/flymine/about/
			twitter|@intermineorg
		After:
			blog|https://intermineorg.wordpress.com/
			help|https://intermineorg.wordpress.com/flymine/help/
			online documentation|http://www.flymine.org/flymine/dataCategories.do
			online documentation|https://intermineorg.wordpress.com/flymine/about/
			tess training|https://tess.elixir-europe.org/materials/flymine-intro-videos
		Added:
			tess training|https://tess.elixir-europe.org/materials/flymine-intro-videos
		Removed:
			twitter|@intermineorg

Edits to 'https://fairsharing.org/FAIRsharing.rhpjhv' by 'The FAIRsharing Team' at 16:37, 07 Nov 2018 (approved):

	'supportLinks' has been modified:
		Before:
			blog|https://intermineorg.wordpress.com/
			contact form|http://www.flymine.org/flymine/mymine.do
			twitter|@intermineorg
		After:
			blog|https://intermineorg.wordpress.com/
			help|https://intermineorg.wordpress.com/flymine/help/
			online documentation|http://www.flymine.org/flymine/dataCategories.do
			online documentation|https://intermineorg.wordpress.com/flymine/about/
			twitter|@intermineorg
		Added:
			help|https://intermineorg.wordpress.com/flymine/help/
			online documentation|http://www.flymine.org/flymine/dataCategories.do
			online documentation|https://intermineorg.wordpress.com/flymine/about/
		Removed:
			contact form|http://www.flymine.org/flymine/mymine.do

	'dataProcesses' has been modified:
		Before:
			Perl
		After:
			Search within genomic regions
			Advanced Search (query builder)
			Search against a list
			Search via pre-defined queries
		Added:
			Search within genomic regions
			Advanced Search (query builder)
			Search against a list
			Search via pre-defined queries
		Removed:
			Perl

	'contact' has been modified:
		Before: Help desk
		After: FlyMine help desk

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

	'domains' has been modified:
		Before:
			Gene
			Life Science
		After:
			Gene
			Genomics
			Life Science
			Protein
			Protein interactions
		Added:
			Genomics
			Protein
			Protein interactions
		Removed:

	'accessPoints' has been modified:
		Before:
			REST|http://www.flymine.org/query/service/|RESTful
		After:
			REST|http://www.flymine.org/flymine/api.do|Web Service Client (Perl, Python, Ruby, Java)
		Added:
			REST|http://www.flymine.org/flymine/api.do|Web Service Client (Perl, Python, Ruby, Java)
		Removed:
			REST|http://www.flymine.org/query/service/|RESTful

	'tools' has been modified:
		Before:
			API Clients (Javascript, Python, Perl, Java, Ruby)|stable|http://intermine.readthedocs.io/en/latest/web-services/
		After:
		Added:
		Removed:
			API Clients (Javascript, Python, Perl, Java, Ruby)|stable|http://intermine.readthedocs.io/en/latest/web-services/

Edits to 'https://fairsharing.org/FAIRsharing.rhpjhv' by 'The FAIRsharing Team' at 17:26, 18 Aug 2016 (approved):

	'description' has been modified:
		Before: An integrated database for Drosophila genomics
		After: FlyMine is an integrated database of genomic, expression and protein data for Drosophila, Anopheles and C. elegans. Integrating data makes it possible to run sophisticated data mining queries that span domains of biological knowledge. Support links have changed:  Previous values: @intermineorg New values:  @intermineorg http://www.flymine.org/flymine/mymine.do Data processes have changed:  Previous values: New values:  Perl Organisations have changed:  Previous values: University of Cambridge|UK New values:  Cambridge Systems Biology Centre|University of Cambridge|UK National Human Genome Research Institute (NHGRI)|NIH The Wellcome Trust

In Collections

InterMine

Support

General

blog	InterMine blog
help	FlyMine Help
online documentation	About FlyMine
online documentation	Data Sources

Additional Information

Contact

FlyMine help desk

TeSS training resources

InterMine user manual

FlyMine intro videos

InterMine user tutorial

Tools

No tools defined

Access / Retrieve Data

Conditions of Use

Applies to: Database software

GNU Lesser General Public License (LGPL) 2.1

Data Access

Search within genomic regions	https://www.flymine.org/flymine/genomicRegionSearch.do
Advanced Search (query builder)	https://www.flymine.org/flymine/customQuery.do
Search against a list	https://www.flymine.org/flymine/bag.do
Search via pre-defined queries	https://www.flymine.org/flymine/templates.do

REST Web Services

Web Service Client (Perl, Python, Ruby, Java)

https://www.flymine.org/flymine/api.do

Publications

FlyMine: an integrated database for Drosophila and Anopheles genomics.

Lyne R, Smith R, Rutherford K, Wakeling M, Varley A, Guillier F, Janssens H, Ji W, Mclaren P, North P, Rana D, Riley T, Sullivan J, Watkins X, Woodbridge M, Lilley K, Russell S, Ashburner M, Mizuguchi K, Micklem G.
Genome Biol 2007

View Paper (PubMed)

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

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 julie and yochannah ORCID

Funds

The Wellcome Trust, UK (Charitable foundation)
National Human Genome Research Institute (NHGRI), Bethesda, MD, USA (Government body)

Maintains

Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK (University) Lead

FlyMine

We need your help!

Developed by

Contact Us

About FAIRsharing