Update in progress: note to all users. FAIRsharing is always available for you to search and discover databases, standards and data policies. However, for producers of these resources who maintain or wish to add new records, please note that editing is disabled until September while we migrate our data to our new, improved system. Read our blog post or get in touch with us for more details.

HumanMine

General Information

HumanMine integrates many types of data for Homo sapiens and Mus musculus. Users can run flexible queries, export results and analyse lists of data.

Homepage https://www.humanmine.org/

Countries that developed this resource United Kingdom

Taxonomic range

Homo sapiens

Mus musculus

Knowledge Domains

Subjects

How to cite this record FAIRsharing.org: HumanMine; HumanMine; DOI: https://doi.org/10.25504/FAIRsharing.RJ99Pj; Last edited: March 10, 2021, 8:51 p.m.; Last accessed: Jul 29 2021 6:58 a.m.

This record is maintained by InterMineTeam

Record added: Nov. 19, 2018, 1:03 p.m.
Record updated: March 10, 2021, 8:51 p.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.RJ99Pj' by 'The FAIRsharing Team' at 20:51, 10 Mar 2021 (approved):

	'standardsImplemented' has been modified:
		Before:
			Human Phenotype Ontology
		After:
			Human Phenotype Ontology
			Bioschemas
		Added:
			Bioschemas
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.RJ99Pj' by 'The FAIRsharing Team' at 20:50, 10 Mar 2021 (approved):

	'standardsImplemented' has been modified:
		Before:
		After:
			Human Phenotype Ontology
		Added:
			Human Phenotype Ontology
		Removed:

	'related_databases' has been modified:
		Before:
			Integrated resource of protein families, domains and functional sites
			Reactome - a curated knowledgebase of biological pathways
			HUGO Gene Nomenclature Committee
			Human Protein Atlas
			Rat Genome Database
			Mouse Genome Database - a Mouse Genome Informatics (MGI) Resource
			PubMed
			Biological General Repository for Interaction Datasets
			Protein ANalysis THrough Evolutionary Relationships: Classification of Genes and Proteins
			UniProt Knowledgebase
			FlyMine
			MouseMine @ MGI
			Kyoto Encyclopedia of Genes and Genomes
			ClinVar
			Online Mendelian Inheritance in Man
			RatMine
			WormMine
			GTEx Portal
			YeastMine
			ZebrafishMine
			InterMine
		After:
			IntAct molecular interaction database
			Integrated resource of protein families, domains and functional sites
			Reactome - a curated knowledgebase of biological pathways
			HUGO Gene Nomenclature Committee
			Human Protein Atlas
			Rat Genome Database
			Mouse Genome Database - a Mouse Genome Informatics (MGI) Resource
			PubMed
			Biological General Repository for Interaction Datasets
			Protein ANalysis THrough Evolutionary Relationships: Classification of Genes and Proteins
			UniProt Knowledgebase
			FlyMine
			MouseMine @ MGI
			Kyoto Encyclopedia of Genes and Genomes
			ClinVar
			Online Mendelian Inheritance in Man
			RatMine
			WormMine
			GTEx Portal
			YeastMine
			ZebrafishMine
			Genome-Wide Association Studies Catalog
			InterMine
		Added:
			IntAct molecular interaction database
			Genome-Wide Association Studies Catalog
		Removed:

	'description' has been modified:
		Before: HumanMine integrates many types of data for Homo sapiens and Mus musculus. You can run flexible queries, export results and analyse lists of data.
		After: HumanMine integrates many types of data for Homo sapiens and Mus musculus. Users can run flexible queries, export results and analyse lists of data.

	'onto_disciplines' has been modified:
		Before:
			Genomics
			Life Science
		After:
			Biology
			Genomics
		Added:
			Biology
		Removed:
			Life Science

	'contact' has been modified:
		Before: 
		After: General Information

	'publications' has been modified:
		Before:
		After:
			InterMine: extensive web services for modern biology.|Kalderimis A,Lyne R,Butano D,Contrino S,Lyne M,Heimbach J,Hu F,Smith R,Stepan R,Sullivan J,Micklem G|Nucleic Acids Res|2014
		Added:
			InterMine: extensive web services for modern biology.|Kalderimis A,Lyne R,Butano D,Contrino S,Lyne M,Heimbach J,Hu F,Smith R,Stepan R,Sullivan J,Micklem G|Nucleic Acids Res|2014
		Removed:

	'tools' has been modified:
		Before:
		After:
			Android App||https://play.google.com/store/apps/details?id=org.intermine.app
			Apple App||https://apps.apple.com/us/app/intermine-gene-search/id1271710231
		Added:
			Android App||https://play.google.com/store/apps/details?id=org.intermine.app
			Apple App||https://apps.apple.com/us/app/intermine-gene-search/id1271710231
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.RJ99Pj' by 'yochannah' at 11:47, 12 Nov 2019 (approved):

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

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

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

	'organizations' has been modified:
		Before:
			Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK|http://www.sysbiol.cam.ac.uk|Maintains
		After:
			Department of Genetics, University of Cambridge, UK|https://www.gen.cam.ac.uk/|Maintains
		Added:
			Department of Genetics, University of Cambridge, UK|https://www.gen.cam.ac.uk/|Maintains
		Removed:
			Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK|http://www.sysbiol.cam.ac.uk|Maintains

Edits to 'https://fairsharing.org/FAIRsharing.RJ99Pj' by 'The FAIRsharing Team' at 21:22, 12 Dec 2018 (approved):

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

Edits to 'https://fairsharing.org/FAIRsharing.RJ99Pj' by 'The FAIRsharing Team' at 13:04, 19 Nov 2018 (approved):

	'related_databases' has been modified:
		Before:
			Integrated resource of protein families, domains and functional sites
			Reactome - a curated knowledgebase of biological pathways
			HUGO Gene Nomenclature Committee 
			Human Protein Atlas
			Rat Genome Database
			 Mouse Genome Database - a Mouse Genome Informatics (MGI) Resource
			PubMed
			Biological General Repository for Interaction Datasets
			Protein ANalysis THrough Evolutionary Relationships: Classification of Genes and Proteins
			UniProt Knowledgebase
			Kyoto Encyclopedia of Genes and Genomes
			ClinVar
			Online Mendelian Inheritance in Man
		After:
			Integrated resource of protein families, domains and functional sites
			Reactome - a curated knowledgebase of biological pathways
			HUGO Gene Nomenclature Committee 
			Human Protein Atlas
			Rat Genome Database
			 Mouse Genome Database - a Mouse Genome Informatics (MGI) Resource
			PubMed
			Biological General Repository for Interaction Datasets
			Protein ANalysis THrough Evolutionary Relationships: Classification of Genes and Proteins
			UniProt Knowledgebase
			FlyMine
			MouseMine @ MGI
			Kyoto Encyclopedia of Genes and Genomes
			ClinVar
			Online Mendelian Inheritance in Man
			RatMine
			WormMine
			YeastMine
			ZebrafishMine
		Added:
			FlyMine
			MouseMine @ MGI
			RatMine
			WormMine
			YeastMine
			ZebrafishMine
		Removed:

In Collections

Bioschemas

InterMine

Support

General

blog	HumanMine blog posts
online documentation	Data Categories

Additional Information

Contact

General Information

TeSS training resources

InterMine user tutorial

InterMine user manual

Tools

Android App	https://play.google.com/store/apps/details?id=org.intermine.app
Apple App	https://apps.apple.com/us/app/intermine-gene-search/id1271710231

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.humanmine.org/humanmine/genomicRegionSearch.do
Advanced Search (Query Builder)	https://www.humanmine.org/humanmine/customQuery.do
Search Against A List	https://www.humanmine.org/humanmine/bag.do
Search Via Pre-Defined Queries	https://www.humanmine.org/humanmine/templates.do

REST Web Services

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

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

Publications

InterMine: extensive web services for modern biology.

Kalderimis A,Lyne R,Butano D,Contrino S,Lyne M,Heimbach J,Hu F,Smith R,Stepan R,Sullivan J,Micklem G
Nucleic Acids Res 2014

View Paper (PubMed) View Publication

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

Human Phenotype Ontology

Models and Formats

Bioschemas

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 InterMineTeam

Maintains

Department of Genetics, University of Cambridge, UK (University) Lead

HumanMine

We need your help!

Developed by

Contact Us

About FAIRsharing