modMine
Homepage http://intermine.modencode.org/
Developed in Canada , United Kingdom , United States
Created in 2008
Taxonomic range
Knowledge Domains BETA
Subjects BETA
How to cite this record FAIRsharing.org: modMine; modMine; DOI: https://doi.org/10.25504/FAIRsharing.ekzmjp; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Feb 16 2019 9:09 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;
Record updated: Dec. 12, 2018, 9:33 p.m. by The FAIRsharing Team.
FAQ | modMine FAQ |
online documentation | modMine Quick Start Guide |
Additional Information
Contact | Gos Micklem |
TeSS training resources
Query Builder | http://intermine.modencode.org/release-33/customQuery.do |
Conditions of Use
Applies to: Database softwareData 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 |
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., Dosé 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., Rätsch 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
Reporting Guidelines
No guidelines defined
Terminology Artifacts
Models and Formats
- FASTA Sequence Format
- FASTQ Sequence and Sequence Quality Format
- Nimblegen Design File Format
- Affymetrix Raw Intensity Format
- microarray track data Browser Extensible Data Format
- Binary Probe Map Format
- NimbleGen Gene Description
- Gene Transfer Format
- Generic Feature Format Version 3
- Sequence Alignment Map
- Browser Extensible Data Format
- Binary Alignment Map Format
- Standard Flowgram Format
- Wiggle Track Format
Identifier Schemas
No identifier schema standards defined
Metrics
No metrics standards defined
This record is not implemented by any policy.
Record Maintainer
Funds
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