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Talk:BioMart

Latest comment: 8 years ago by Amkilpatrick in topic Removed list of sources/members
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Latest comment: 12 years ago3 comments3 people in discussion

Oh what a nightmare it has become to create a new page on Wikipedia.

--Tnabtaf (talk) 06:43, 24 November 2011 (UTC)Reply

Hi Tnabtaf,

Sounds like you need some help. It is best to create a new article in your own user space before copying it across to Wikipedia proper. In Wikipedia we don't mind articles that are very short or stubs as they're called. But it is not good to have clearly incomplete artiles with only headings. Anyway I'm sure we can soon get that fixed and move it across to mainspace. Please let me know if you have any questions and I'll try to help improve the article. Alexbateman (talk) 12:51, 24 November 2011 (UTC)Reply

Hi Tnabtaf, I have supplied a "non-free use rationale" for the logo, and re-added it to the infobox. --Magnus Manske (talk) 09:34, 25 November 2011 (UTC)Reply

Removed list of sources/members

edit
Latest comment: 8 years ago1 comment1 person in discussion

I removed the long list of sources and members during the transfer to article space and kept just a couple of the entries with wiki articles, I've copied the original list here just for the record....

Original Format

edit
Location Database Description Reference
Barcelona Supercomputing Center ICGC Catalogue of genomic abnormalities in cancer [1]
Barts Cancer Institute UK Pancreatic Expression Database Results from published literature [2]
Breast Cancer Campaign, UK and Ireland BCCTB Bioinformatics Portal Breast cancer tissue information NA
California Institute of Technology, US SpMart Sea urchin (Strongylocentrotus purpuratus) genome database [3]
Center for Mathematical Modeling and Center for Genome Regulation (CMM), Chile SalmonDB Genomic information for Atlantic salmon, rainbow trout, and related species [4]
Centre National de la Recherche Scientifique (CNRS), France Cildb Database for eukaryotic cilia and centriolar structures, integrating orthology relationships for 33 species with high throughput studies and OMIM [5]
Centre National de la Recherche Scientifique (CNRS), France ParameciumDB Paramecium genome database [6]
Cold Spring Harbor Laboratory (CSHL), US Gramene Agriculturally important grass genomes [7]
Cold Spring Harbor Laboratory (CSHL), US WormBase C. elegans and related nematode genomic information [8]
European Bioinformatics Institute (EBI), UK EMMA Mouse mutant strain information [9]
European Bioinformatics Institute (EBI), UK Ensembl Bacteria Genome databases for bacteria [10]
European Bioinformatics Institute (EBI), UK Ensembl Fungi Ensembl Fungi [10]
European Bioinformatics Institute (EBI), UK Ensembl Metazoa Ensembl Metazoa [10]
European Bioinformatics Institute (EBI), UK Ensembl Plants Ensembl Plants [10]
European Bioinformatics Institute (EBI), UK Ensembl Protists Ensembl Protists [10]
European Bioinformatics Institute (EBI), UK HGNC Repository of human gene nomenclature and associated resources [11]
European Bioinformatics Institute (EBI), UK InterPro Integrated database of predictive protein "signatures" used for the classification and automatic annotation of proteins and genomes [12]
European Bioinformatics Institute (EBI), UK PRIDE Repository for protein and peptide identifications [13]
European Bioinformatics Institute (EBI), UK UniProt Protein sequence and functional information [14]
Harwell Science and Innovation Campus (MRC Harwell), UK EuroPhenome Mouse phenotyping data [15]
Information Center for Bio-pharmacological Network (i-Pharm), South Korea i-Pharm Pharmacological network database consisting of three kinds of nodes: human diseases, drugs, and proteins [16]
Institut national de la santé et de la recherche médicale (Inserm), France GermOnLine Cross-species microarray expression database focusing on germline development, meiosis, and gametogenesis as well as the mitotic cell cycle [17]
Institut Nationale de Recherche Agronomique (INRA), Unité de Recherche en Génomique-Info (URGI), France GnpIS Genetic and Genomic Information System (GnpIS) [18]
International Potato Center (CIP), Peru Potato Database Potato and sweetpotato phenotypic and genomic information NA
Jackson Laboratory, US MGI Mouse genome features, locations, alleles, and orthologs [19]
Joint Genome Institute (JGI)/Center for Integrative Genomics (CIG), US Phytozome Comparative genomics of green plants [20]
Kazusa DNA Research Institute (Kazusa), Japan KazusaMart Cyanobase, rhizobia, and plant genome databases NA
Medical Research Council, Human Genetics Unit (MRC HGU), UK EMAGE In situ gene expression data in the mouse embryo [21]
Medical Research Council, Human Genetics Unit (MRC HGU), UK Euraexpress Transcriptome atlas database for mouse embryo [22]
National Center for Biotechnology Information (NCBI), US HapMap Multi-country effort to identify and catalog genetic similarities and differences in human beings [23]
Ontario Institute for Cancer Research (OICR), Canada Reactome Curated pathway annotation database [24]
Ontario Institute for Cancer Research (OICR), Canada ICGC Catalogue of genomic abnormalities in cancer [1]
Peking University, China Rice-Map Rice (japonica and indica) genome annotation database [25]
Peking University, China RhesusBase A knowledgebase for the monkey research community [26]
Queensland Centre for Medical Genomics, Australia ICGC Catalogue of genomic abnormalities in cancer [1]
University of California Los Angeles (UCLA), US SDxMart Saliva diagnostics for high-impact human diseases [27]
University of Leicester, UK GWAS Central GWAS Central provides a centralized compilation of summary level findings from genetic association studies, both large and small. [28]
INRA - French National Institute of Agricultural Research, France sigReannot Aquaculture and farm animal species microarray probes re-annotation [29]
University of Manchester, UK PepSeeker Database of proteome peptide identifications for investigating fragmentation patterns [30]
University of Notre Dame, US VectorBase Genome information for invertebrate vectors of human pathogens [31]
Universitat Pompeu Fabra (UPF), Spain IntOGen Integrated multidimensional data for the identification of genes and groups of genes involved in cancer development [32]
Universitat Pompeu Fabra (UPF), Spain Regulatory Genomics Group Predictive Models of Gene Regulation from High-Throughput Epigenomics Data [33]
University of Trento, Italy Atlas of UTR Regulatory Activity (AURA) Manually curated and comprehensive catalog of human UTRs and UTR regulatory annotations [34]
Wellcome Trust Sanger Institute (WTSI), UK COSMIC Somatic mutation information relating to human cancers [35]
Wellcome Trust Sanger Institute (WTSI), UK Ensembl Genome databases for vertebrates and other eukaryotic species [10]
Wellcome Trust Sanger Institute (WTSI), UK IKMC Data on mutant products (mice, ES cells and vectors) generated and made available by members of the International Knockout Mouse Consotium (IKMC) [36]
Wellcome Trust Sanger Institute (WTSI), UK VEGA Manual annotation of vertebrate genome sequences [37]
Wellcome Trust Sanger Institute (WTSI), UK WTSI Mouse Genetics Project Mouse phenotyping and expression data captured from mutant mouse lines [38]
Wellcome Trust Sanger Institute (WTSI), UK Rfam The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). [39]

New Format

edit
Mart Resource Description Host Reference
Atlas of UTR Regulatory Activity (AURA) Atlas of UTR Regulatory Activity Manually curated and comprehensive catalog of human UTRs and UTR regulatory annotations University of Trento, Italy [34]
BCCTB Bioinformatics Portal Breast Cancer Campaign Tissue Bank Breast cancer tissue information Breast Cancer Campaign, UK and Ireland NA
Cildb Cildb Database for eukaryotic cilia and centriolar structures, integrating orthology relationships for 33 species with high throughput studies and OMIM Centre National de la Recherche Scientifique (CNRS), France [5]
COSMIC Somatic mutation information relating to human cancers Wellcome Trust Sanger Institute (WTSI), UK [35]
EMAGE In situ gene expression data in the mouse embryo Medical Research Council, Human Genetics Unit (MRC HGU), UK [21]
EMMA Mouse mutant strain information European Bioinformatics Institute (EBI), UK [9]
Ensembl Genome databases for vertebrates and other eukaryotic species Wellcome Trust Sanger Institute (WTSI), UK [10]
Ensembl Bacteria Genome databases for bacteria European Bioinformatics Institute (EBI), UK [10]
Ensembl Fungi Ensembl Fungi European Bioinformatics Institute (EBI), UK [10]
Ensembl Metazoa Ensembl Metazoa European Bioinformatics Institute (EBI), UK [10]
Ensembl Plants Ensembl Plants European Bioinformatics Institute (EBI), UK [10]
Ensembl Protists Ensembl Protists European Bioinformatics Institute (EBI), UK [10]
Euraexpress Transcriptome atlas database for mouse embryo Medical Research Council, Human Genetics Unit (MRC HGU), UK [22]
EuroPhenome Mouse phenotyping data Harwell Science and Innovation Campus (MRC Harwell), UK [15]
GermOnLine Cross-species microarray expression database focusing on germline development, meiosis, and gametogenesis as well as the mitotic cell cycle Institut national de la santé et de la recherche médicale (Inserm), France [17]
GnpIS Genetic and Genomic Information System (GnpIS) Institut Nationale de Recherche Agronomique (INRA), Unité de Recherche en Génomique-Info (URGI), France [18]
Gramene Agriculturally important grass genomes Cold Spring Harbor Laboratory (CSHL), US [7]
GWAS Central GWAS Central provides a centralized compilation of summary level findings from genetic association studies, both large and small. University of Leicester, UK [28]
HapMap Multi-country effort to identify and catalog genetic similarities and differences in human beings National Center for Biotechnology Information (NCBI), US [23]
HGNC Repository of human gene nomenclature and associated resources European Bioinformatics Institute (EBI), UK [11]
i-Pharm Pharmacological network database consisting of three kinds of nodes: human diseases, drugs, and proteins Information Center for Bio-pharmacological Network (i-Pharm), South Korea [16]
ICGC Catalogue of genomic abnormalities in cancer Barcelona Supercomputing Center [1]
ICGC Catalogue of genomic abnormalities in cancer Ontario Institute for Cancer Research (OICR), Canada [1]
ICGC Catalogue of genomic abnormalities in cancer Queensland Centre for Medical Genomics, Australia [1]
IKMC Data on mutant products (mice, ES cells and vectors) generated and made available by members of the International Knockout Mouse Consotium (IKMC) Wellcome Trust Sanger Institute (WTSI), UK [36]
InterPro Integrated database of predictive protein "signatures" used for the classification and automatic annotation of proteins and genomes European Bioinformatics Institute (EBI), UK [12]
IntOGen Integrated multidimensional data for the identification of genes and groups of genes involved in cancer development Universitat Pompeu Fabra (UPF), Spain [32]
KazusaMart Cyanobase, rhizobia, and plant genome databases Kazusa DNA Research Institute (Kazusa), Japan NA
MGI Mouse genome features, locations, alleles, and orthologs Jackson Laboratory, US [19]
Pancreatic Expression Database Results from published literature Barts Cancer Institute UK [2]
ParameciumDB Paramecium genome database Centre National de la Recherche Scientifique (CNRS), France [6]
PepSeeker Database of proteome peptide identifications for investigating fragmentation patterns University of Manchester, UK [30]
Phytozome Comparative genomics of green plants Joint Genome Institute (JGI)/Center for Integrative Genomics (CIG), US [20]
Potato Database Potato and sweetpotato phenotypic and genomic information International Potato Center (CIP), Peru NA
PRIDE Repository for protein and peptide identifications European Bioinformatics Institute (EBI), UK [13]
Reactome Curated pathway annotation database Ontario Institute for Cancer Research (OICR), Canada [24]
Regulatory Genomics Group Predictive Models of Gene Regulation from High-Throughput Epigenomics Data Universitat Pompeu Fabra (UPF), Spain [33]
Rfam The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). Wellcome Trust Sanger Institute (WTSI), UK [39]
RhesusBase A knowledgebase for the monkey research community Peking University, China [26]
Rice-Map Rice (japonica and indica) genome annotation database Peking University, China [25]
SalmonDB Genomic information for Atlantic salmon, rainbow trout, and related species Center for Mathematical Modeling and Center for Genome Regulation (CMM), Chile [4]
SDxMart Saliva diagnostics for high-impact human diseases University of California Los Angeles (UCLA), US [27]
sigReannot Aquaculture and farm animal species microarray probes re-annotation INRA - French National Institute of Agricultural Research, France [29]
SpMart Sea urchin (Strongylocentrotus purpuratus) genome database California Institute of Technology, US [3]
UniProt Protein sequence and functional information European Bioinformatics Institute (EBI), UK [14]
VectorBase Genome information for invertebrate vectors of human pathogens University of Notre Dame, US [31]
VEGA Manual annotation of vertebrate genome sequences Wellcome Trust Sanger Institute (WTSI), UK [37]
WormBase C. elegans and related nematode genomic information Cold Spring Harbor Laboratory (CSHL), US [8]
WTSI Mouse Genetics Project Mouse phenotyping and expression data captured from mutant mouse lines Wellcome Trust Sanger Institute (WTSI), UK [38]
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  21. ^ a b Stevenson P, Richardson L, Venkataraman S, Yang Y, Baldock R (2011). "The BioMart interface to the eMouseAtlas gene expression database EMAGE". Database (Oxford). 2011: bar029. doi:10.1093/database/bar029. PMC 3263595. PMID 21930504.{{cite journal}}: CS1 maint: multiple names: authors list (link)
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--Amkilpatrick (talk) 15:30, 14 July 2016 (UTC)Reply

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