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.

modMine

General Information

modMine is an integrated web resource of data and tools to browse and search modENCODE data and experimental details, download results and access the GBrowse genome browser.

Homepage http://intermine.modencode.org/

Countries that developed this resource Canada , United Kingdom , United States

Created in 2008

Taxonomic range

Caenorhabditis elegans

Drosophila ananassae

Drosophila melanogaster

Drosophila mojavensis

Drosophila pseudoobscura

Drosophila simulans

Drosophila virilis

Drosophila yakuba

Knowledge Domains

Subjects

How to cite this record FAIRsharing.org: modMine; modMine; DOI: https://doi.org/10.25504/FAIRsharing.ekzmjp; Last edited: June 22, 2021, 11:56 a.m.; Last accessed: Sep 18 2021 3:03 p.m.

Publication for citation modMine: flexible access to modENCODE data Contrino S, Smith RN, Butano D, Carr A, Hu F, Lyne R, Rutherford K, Kalderimis A, Sullivan J, Carbon S, Kephart ET, Lloyd P, Stinson EO, Washington NL, Perry MD, Ruzanov P, Zha Z, Lewis SE, Stein LD, Micklem G.; Nucleic Acids Res. ; 2012; 10.1093/nar/gkr921;

This record is maintained by sergio and InterMineTeam

Record updated: June 15, 2021, 1:34 p.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.ekzmjp' by 'The FAIRsharing Team' at 13:34, 15 Jun 2021 (approved):

	'supportLinks' has been modified:
		Before:
			FAQ|http://www.modencode.org/publications/faq/
			online documentation|http://www.modencode.org/quickstart/
			tess training|https://tess.elixir-europe.org/materials/intermine-user-tutorial
			tess training|https://tess.elixir-europe.org/materials/intermine-user-manual
		After:
			FAQ|http://www.modencode.org/publications/faq/
			TeSS training|https://tess.elixir-europe.org/materials/intermine-user-tutorial
			TeSS training|https://tess.elixir-europe.org/materials/intermine-user-manual
			online documentation|http://www.modencode.org/quickstart/
		Added:
			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/intermine-user-tutorial
			tess training|https://tess.elixir-europe.org/materials/intermine-user-manual

	'publications' has been modified:
		Before:
			Unlocking the secrets of the genome.|Celniker SE., Dillon LA., Gerstein MB., Gunsalus KC., Henikoff S., Karpen GH., Kellis M., Lai EC., Lieb JD., MacAlpine DM., Micklem G., Piano F., Snyder M., Stein L., White KP., Waterston RH., |Nature|2009
			Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project.|Gerstein MB., Lu ZJ., Van Nostrand EL., Cheng C., Arshinoff BI., Liu T., Yip KY., Robilotto R., Rechtsteiner A., Ikegami K., Alves P., Chateigner A., Perry M., Morris M., Auerbach RK., Feng X., Leng J., Vielle A., Niu W., Rhrissorrakrai K., Agarwal A., Alexander RP., Barber G., Brdlik CM., Brennan J., Brouillet JJ., Carr A., Cheung MS., Clawson H., Contrino S., Dannenberg LO., Dernburg AF., Desai A., Dick L., Dos AC., Du J., Egelhofer T., Ercan S., Euskirchen G., Ewing B., Feingold EA., Gassmann R., Good PJ., Green P., Gullier F., Gutwein M., Guyer MS., Habegger L., Han T., Henikoff JG., Henz SR., Hinrichs A., Holster H., Hyman T., Iniguez AL., Janette J., Jensen M., Kato M., Kent WJ., Kephart E., Khivansara V., Khurana E., Kim JK., Kolasinska-Zwierz P., Lai EC., Latorre I., Leahey A., Lewis S., Lloyd P., Lochovsky L., Lowdon RF., Lubling Y., Lyne R., MacCoss M., Mackowiak SD., Mangone M., McKay S., Mecenas D., Merrihew G., Miller DM., Muroyama A., Murray JI., Ooi SL., Pham H., Phippen T., Preston EA., Rajewsky N., Rtsch G., Rosenbaum H., Rozowsky J., Rutherford K., Ruzanov P., Sarov M., Sasidharan R., Sboner A., Scheid P., Segal E., Shin H., Shou C., Slack FJ., Slightam C., Smith R., Spencer WC., Stinson EO., Taing S., Takasaki T., Vafeados D., Voronina K., Wang G., Washington NL., Whittle CM., Wu B., Yan KK., Zeller G., Zha Z., Zhong M., Zhou X., Ahringer J., Strome S., Gunsalus KC., Micklem G., Liu XS., Reinke V., Kim SK., Hillier LW., Henikoff S., Piano F., Snyder M., Stein L., Lieb JD., Waterston RH., |Science|2010
			Identification of functional elements and regulatory circuits by Drosophila modENCODE.|Roy S., Ernst J., Kharchenko PV., Kheradpour P., Negre N., Eaton ML., Landolin JM., Bristow CA., Ma L., Lin MF., Washietl S., Arshinoff BI., Ay F., Meyer PE., Robine N., Washington NL., Di Stefano L., Berezikov E., Brown CD., Candeias R., Carlson JW., Carr A., Jungreis I., Marbach D., Sealfon R., Tolstorukov MY., Will S., Alekseyenko AA., Artieri C., Booth BW., Brooks AN., Dai Q., Davis CA., Duff MO., Feng X., Gorchakov AA., Gu T., Henikoff JG., Kapranov P., Li R., MacAlpine HK., Malone J., Minoda A., Nordman J., Okamura K., Perry M., Powell SK., Riddle NC., Sakai A., Samsonova A., Sandler JE., Schwartz YB., Sher N., Spokony R., Sturgill D., van Baren M., Wan KH., Yang L., Yu C., Feingold E., Good P., Guyer M., Lowdon R., Ahmad K., Andrews J., Berger B., Brenner SE., Brent MR., Cherbas L., Elgin SC., Gingeras TR., Grossman R., Hoskins RA., Kaufman TC., Kent W., Kuroda MI., Orr-Weaver T., Perrimon N., Pirrotta V., Posakony JW., Ren B., Russell S., Cherbas P., Graveley BR., Lewis S., Micklem G., Oliver B., Park PJ., Celniker SE., Henikoff S., Karpen GH., Lai EC., MacAlpine DM., Stein LD., White KP., Kellis M., |Science|2010
			modMine: flexible access to modENCODE data|Contrino S, Smith RN, Butano D, Carr A, Hu F, Lyne R, Rutherford K, Kalderimis A, Sullivan J, Carbon S, Kephart ET, Lloyd P, Stinson EO, Washington NL, Perry MD, Ruzanov P, Zha Z, Lewis SE, Stein LD, Micklem G.|Nucleic Acids Res.|2012
		After:
			Unlocking the secrets of the genome.|Celniker SE., Dillon LA., Gerstein MB., Gunsalus KC., Henikoff S., Karpen GH., Kellis M., Lai EC., Lieb JD., MacAlpine DM., Micklem G., Piano F., Snyder M., Stein L., White KP., Waterston RH., |Nature|2009
			Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project.|Gerstein MB., et al.|Science|2010
			Identification of functional elements and regulatory circuits by Drosophila modENCODE.|Roy S., et al.|Science|2010
			modMine: flexible access to modENCODE data|Contrino S, Smith RN, Butano D, Carr A, Hu F, Lyne R, Rutherford K, Kalderimis A, Sullivan J, Carbon S, Kephart ET, Lloyd P, Stinson EO, Washington NL, Perry MD, Ruzanov P, Zha Z, Lewis SE, Stein LD, Micklem G.|Nucleic Acids Res.|2012
		Added:
			Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project.|Gerstein MB., et al.|Science|2010
			Identification of functional elements and regulatory circuits by Drosophila modENCODE.|Roy S., et al.|Science|2010
		Removed:
			Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project.|Gerstein MB., Lu ZJ., Van Nostrand EL., Cheng C., Arshinoff BI., Liu T., Yip KY., Robilotto R., Rechtsteiner A., Ikegami K., Alves P., Chateigner A., Perry M., Morris M., Auerbach RK., Feng X., Leng J., Vielle A., Niu W., Rhrissorrakrai K., Agarwal A., Alexander RP., Barber G., Brdlik CM., Brennan J., Brouillet JJ., Carr A., Cheung MS., Clawson H., Contrino S., Dannenberg LO., Dernburg AF., Desai A., Dick L., Dos AC., Du J., Egelhofer T., Ercan S., Euskirchen G., Ewing B., Feingold EA., Gassmann R., Good PJ., Green P., Gullier F., Gutwein M., Guyer MS., Habegger L., Han T., Henikoff JG., Henz SR., Hinrichs A., Holster H., Hyman T., Iniguez AL., Janette J., Jensen M., Kato M., Kent WJ., Kephart E., Khivansara V., Khurana E., Kim JK., Kolasinska-Zwierz P., Lai EC., Latorre I., Leahey A., Lewis S., Lloyd P., Lochovsky L., Lowdon RF., Lubling Y., Lyne R., MacCoss M., Mackowiak SD., Mangone M., McKay S., Mecenas D., Merrihew G., Miller DM., Muroyama A., Murray JI., Ooi SL., Pham H., Phippen T., Preston EA., Rajewsky N., Rtsch G., Rosenbaum H., Rozowsky J., Rutherford K., Ruzanov P., Sarov M., Sasidharan R., Sboner A., Scheid P., Segal E., Shin H., Shou C., Slack FJ., Slightam C., Smith R., Spencer WC., Stinson EO., Taing S., Takasaki T., Vafeados D., Voronina K., Wang G., Washington NL., Whittle CM., Wu B., Yan KK., Zeller G., Zha Z., Zhong M., Zhou X., Ahringer J., Strome S., Gunsalus KC., Micklem G., Liu XS., Reinke V., Kim SK., Hillier LW., Henikoff S., Piano F., Snyder M., Stein L., Lieb JD., Waterston RH., |Science|2010
			Identification of functional elements and regulatory circuits by Drosophila modENCODE.|Roy S., Ernst J., Kharchenko PV., Kheradpour P., Negre N., Eaton ML., Landolin JM., Bristow CA., Ma L., Lin MF., Washietl S., Arshinoff BI., Ay F., Meyer PE., Robine N., Washington NL., Di Stefano L., Berezikov E., Brown CD., Candeias R., Carlson JW., Carr A., Jungreis I., Marbach D., Sealfon R., Tolstorukov MY., Will S., Alekseyenko AA., Artieri C., Booth BW., Brooks AN., Dai Q., Davis CA., Duff MO., Feng X., Gorchakov AA., Gu T., Henikoff JG., Kapranov P., Li R., MacAlpine HK., Malone J., Minoda A., Nordman J., Okamura K., Perry M., Powell SK., Riddle NC., Sakai A., Samsonova A., Sandler JE., Schwartz YB., Sher N., Spokony R., Sturgill D., van Baren M., Wan KH., Yang L., Yu C., Feingold E., Good P., Guyer M., Lowdon R., Ahmad K., Andrews J., Berger B., Brenner SE., Brent MR., Cherbas L., Elgin SC., Gingeras TR., Grossman R., Hoskins RA., Kaufman TC., Kent W., Kuroda MI., Orr-Weaver T., Perrimon N., Pirrotta V., Posakony JW., Ren B., Russell S., Cherbas P., Graveley BR., Lewis S., Micklem G., Oliver B., Park PJ., Celniker SE., Henikoff S., Karpen GH., Lai EC., MacAlpine DM., Stein LD., White KP., Kellis M., |Science|2010

Edits to 'https://fairsharing.org/FAIRsharing.ekzmjp' by 'The FAIRsharing Team' at 21:33, 12 Dec 2018 (approved):

	'supportLinks' has been modified:
		Before:
			FAQ|http://www.modencode.org/publications/faq/
			online documentation|http://www.modencode.org/quickstart/
		After:
			FAQ|http://www.modencode.org/publications/faq/
			online documentation|http://www.modencode.org/quickstart/
			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:

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

Edits to 'https://fairsharing.org/FAIRsharing.ekzmjp' by 'The FAIRsharing Team' at 11:02, 21 Nov 2018 (approved):

	'domains' has been modified:
		Before:
			Binding site
			Chromatin immunoprecipitation - DNA microarray (ChIP-chip)
			Chromatin immunoprecipitation - DNA sequencing (ChIP-seq)
			Citation
			DNA sequence data
			Gene Ontology (GO) enrichment
			Gene model annotation
			Life Science
			Orthologous
			Phenotype
			Prediction and recognition
			Protein
			Protein domain
		After:
			Binding site
			Chromatin immunoprecipitation - DNA microarray (ChIP-chip)
			Chromatin immunoprecipitation - DNA sequencing (ChIP-seq)
			Citation
			Computational predictions
			DNA sequence data
			Gene Ontology (GO) enrichment
			Gene model annotation
			Life Science
			Orthologous
			Phenotype
			Protein
			Protein domain
		Added:
			Computational predictions
		Removed:
			Prediction and recognition

Edits to 'https://fairsharing.org/FAIRsharing.ekzmjp' by 'The FAIRsharing Team' at 10:52, 21 Nov 2018 (approved):

	'domains' has been modified:
		Before:
			Binding site
			Chromatin immunoprecipitation - DNA microarray (ChIP-chip)
			Chromatin immunoprecipitation - DNA sequencing (ChIP-seq)
			Citation
			Gene Ontology (GO) enrichment
			Gene model annotation
			Life Science
			Orthologous
			Phenotype
			Prediction and recognition
			Protein
			Protein domain
		After:
			Binding site
			Chromatin immunoprecipitation - DNA microarray (ChIP-chip)
			Chromatin immunoprecipitation - DNA sequencing (ChIP-seq)
			Citation
			DNA sequence data
			Gene Ontology (GO) enrichment
			Gene model annotation
			Life Science
			Orthologous
			Phenotype
			Prediction and recognition
			Protein
			Protein domain
		Added:
			DNA sequence data
		Removed:

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

Edits to 'https://fairsharing.org/FAIRsharing.ekzmjp' 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

Edits to 'https://fairsharing.org/FAIRsharing.ekzmjp' by 'The FAIRsharing Team' at 12:28, 14 Nov 2018 (approved):

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

Edits to 'https://fairsharing.org/FAIRsharing.ekzmjp' by 'The FAIRsharing Team' at 12:27, 14 Nov 2018 (approved):

	'organizations' has been modified:
		Before:
			Lawrence Berkeley National Laboratory|http://www.lbl.gov/about/|Maintains
			InterMine, System Biology Centre, Cambridge, United Kingdom|http://intermine.org/|Maintains
			US National Institute of General Medical Sciences, (NIGMS)|http://www.nigms.nih.gov|Funds
			Wellcome Trust, UK|http://www.wellcome.ac.uk|Funds
			National Human Genome Research Institute|http://www.genome.gov/|Funds
		After:
			US National Institute of General Medical Sciences, (NIGMS)|http://www.nigms.nih.gov|Funds
			Wellcome Trust, UK|http://www.wellcome.ac.uk|Funds
			National Human Genome Research Institute|http://www.genome.gov/|Funds
			Lawrence Berkeley National Laboratory|http://www.lbl.gov/about/|Maintains
			InterMine, System Biology Centre, Cambridge, United Kingdom|http://intermine.org/|Maintains
			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:

	'supportLinks' has been modified:
		Before:
			online documentation|http://www.modencode.org/quickstart/
		After:
			FAQ|http://www.modencode.org/publications/faq/
			online documentation|http://www.modencode.org/quickstart/
		Added:
			FAQ|http://www.modencode.org/publications/faq/
		Removed:

	'description' has been modified:
		Before: modMine is an integrated web resource of data & tools to browse and search modENCODE data and experimental details, download results and access the GBrowse genome browser.
		After: modMine is an integrated web resource of data and tools to browse and search modENCODE data and experimental details, download results and access the GBrowse genome browser.

	'dataProcesses' has been modified:
		Before:
			quarterly release
			required metadata for experiment results
			access to historical files available
			Browse
			file download(txt,XML,CSV)
			SQL database dump
		After:
			quarterly release
			required metadata for experiment results
			access to historical files available
			Browse
			file download(txt,XML,CSV)
			SQL database dump
			Search via Templates
			Search Against a List
			Search Within Genomic Regions
		Added:
			Search via Templates
			Search Against a List
			Search Within Genomic Regions
		Removed:

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

	'accessPoints' has been modified:
		Before:
			REST|http://intermine.modencode.org/release-32/api.do|rest
		After:
			REST|http://intermine.modencode.org/release-33/api.do|Web Service Client (Perl, Python, Ruby, Java)
		Added:
			REST|http://intermine.modencode.org/release-33/api.do|Web Service Client (Perl, Python, Ruby, Java)
		Removed:
			REST|http://intermine.modencode.org/release-32/api.do|rest

	'tools' has been modified:
		Before:
			InterMine||http://intermine.org/
			Query Builder||http://intermine.modencode.org/release-33/customQuery.do
		After:
			Query Builder||http://intermine.modencode.org/release-33/customQuery.do
		Added:
		Removed:
			InterMine||http://intermine.org/

In Collections

RDA Covid-19 WG Resources

InterMine

Support

General

FAQ	modMine FAQ
online documentation	modMine Quick Start Guide

Additional Information

Contact

Gos Micklem

TeSS training resources

InterMine user tutorial

InterMine user manual

Tools

Query Builder

http://intermine.modencode.org/release-33/customQuery.do

Access / Retrieve Data

Conditions of Use

Applies to: Database software

GNU Lesser General Public License (LGPL) 2.1

Data Versioning

access to historical files available

No link recorded

Data Release

quarterly release

No link recorded

Data Curation

required metadata for experiment results

No link recorded

Data Access

file download(txt,XML,CSV)	No link recorded
SQL database dump	No link recorded
Browse	http://intermine.modencode.org/release-33/projectsSummary.do
Search via Templates	http://intermine.modencode.org/release-33/templates.do
Search Against a List	http://intermine.modencode.org/release-33/bag.do
Search Within Genomic Regions	http://intermine.modencode.org/release-33/spanUploadOptions.do

REST Web Services

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

http://intermine.modencode.org/release-33/api.do

Publications

Unlocking the secrets of the genome.

Celniker SE., Dillon LA., Gerstein MB., Gunsalus KC., Henikoff S., Karpen GH., Kellis M., Lai EC., Lieb JD., MacAlpine DM., Micklem G., Piano F., Snyder M., Stein L., White KP., Waterston RH.,
Nature 2009

View Paper (PubMed) View Publication

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project.

Gerstein MB., et al.
Science 2010

View Paper (PubMed) View Publication

Identification of functional elements and regulatory circuits by Drosophila modENCODE.

Roy S., et al.
Science 2010

View Paper (PubMed) View Publication

modMine: flexible access to modENCODE data

Contrino S, Smith RN, Butano D, Carr A, Hu F, Lyne R, Rutherford K, Kalderimis A, Sullivan J, Carbon S, Kephart ET, Lloyd P, Stinson EO, Washington NL, Perry MD, Ruzanov P, Zha Z, Lewis SE, Stein LD, Micklem G.
Nucleic Acids Res. 2012

View Paper (PubMed) View Publication

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 sergio and InterMineTeam

Funds

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

Maintains

Lawrence Berkeley National Laboratory (LBNL), CA, USA (Government body)
InterMine, System Biology Centre, Cambridge, UK (Consortium)
Department of Genetics, University of Cambridge, UK (University) Lead

modMine

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