InterMine
Names
More detailed information about this field from each metasource.
InterMine
metasource: Fairsharing.org
version: FAIRsharing.org: InterMine; InterMine; DOI: https://doi.org/10.25504/FAIRsharing.DXjTQ8; Last edited: June 10, 2021, 11:55 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:57.432616
intermine
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:57.432616
Names
More detailed information about this field from each metasource.
InterMine
metasource: Fairsharing.orgversion: FAIRsharing.org: InterMine; InterMine; DOI: https://doi.org/10.25504/FAIRsharing.DXjTQ8; Last edited: June 10, 2021, 11:55 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:57.432616
intermine
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:26:57.432616
Names
More detailed information about this field from each metasource.
InterMine
metasource: Fairsharing.orgversion: FAIRsharing.org: InterMine; InterMine; DOI: https://doi.org/10.25504/FAIRsharing.DXjTQ8; Last edited: June 10, 2021, 11:55 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:57.432616
intermine
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:26:57.432616
InterMine was formed in 2002 at the University of Cambridge, originally as a Drosophila-dedicated resource, before expanding to become organism-agnostic, enabling a large range of organisations around the world to create their own InterMines. There are many instances of InterMine installations, relating to particular model organisms. These can be searched individually or via a cross-Mine search function.
Description
More detailed information about this field from each metasource.
InterMine was formed in 2002 at the University of Cambridge, originally as a Drosophila-dedicated resource, before expanding to become organism-agnostic, enabling a large range of organisations around the world to create their own InterMines. There are many instances of InterMine installations, relating to particular model organisms. These can be searched individually or via a cross-Mine search function.
metasource: Fairsharing.orgversion: FAIRsharing.org: InterMine; InterMine; DOI: https://doi.org/10.25504/FAIRsharing.DXjTQ8; Last edited: June 10, 2021, 11:55 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
Open source data warehouse built specifically for the integration and analysis of complex biological data. It enables the creation of biological databases accessed by sophisticated web query tools. Parsers are provided for integrating data from many common biological data sources and formats, and there is a framework for adding your own data.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:26:57.432616
Webpage:
http://intermine.org/Webpage
More detailed information about this field from each metasource.
http://intermine.org/
metasource: Fairsharing.orgversion: FAIRsharing.org: InterMine; InterMine; DOI: https://doi.org/10.25504/FAIRsharing.DXjTQ8; Last edited: June 10, 2021, 11:55 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
http://www.intermine.org
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:26:57.432616
Licence:
Name: LGPL-2.1Licence name
More detailed information about this field from each metasource.
Publications:
Publications
More detailed information about this field from each metasource.
InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data
PMID: 23023984
metasource: Fairsharing.org
version: FAIRsharing.org: InterMine; InterMine; DOI: https://doi.org/10.25504/FAIRsharing.DXjTQ8; Last edited: June 10, 2021, 11:55 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:57.432616
InterMine: extensive web services for modern biology
PMID: 24753429
metasource: Fairsharing.org
version: FAIRsharing.org: InterMine; InterMine; DOI: https://doi.org/10.25504/FAIRsharing.DXjTQ8; Last edited: June 10, 2021, 11:55 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:57.432616
Publications
More detailed information about this field from each metasource.
InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data
PMID: 23023984
metasource: Fairsharing.org
version: FAIRsharing.org: InterMine; InterMine; DOI: https://doi.org/10.25504/FAIRsharing.DXjTQ8; Last edited: June 10, 2021, 11:55 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:57.432616
InterMine: extensive web services for modern biology
PMID: 24753429
metasource: Fairsharing.org
version: FAIRsharing.org: InterMine; InterMine; DOI: https://doi.org/10.25504/FAIRsharing.DXjTQ8; Last edited: June 10, 2021, 11:55 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:57.432616
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InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data
PubMed citations: 113.
113 articles citing: InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data
HumanMine: advanced data searching, analysis and cross-species comparison. PMID:35820040
Construction of Multiscale Genome-Scale Metabolic Models: Frameworks and Challenges. PMID:35625648
Zebrafish information network, the knowledgebase for Danio rerio research. PMID:35166825
Gene family evolution underlies cell-type diversification in the hypothalamus of teleosts. PMID:34824389
Genome-wide approaches delineate the additive, epistatic, and pleiotropic nature of variants controlling fatty acid composition in peanut (Arachis hypogaea L.). PMID:34751378
Hymenoptera Genome Database: new genomes and annotation datasets for improved go enrichment and orthologue analyses. PMID:34747465
Mouse Genome Informatics (MGI): latest news from MGD and GXD. PMID:34698891
A PostgreSQL Tripal solution for large-scale genotypic and phenotypic data. PMID:34389844
Two isoforms of the essential C. elegans Argonaute CSR-1 differentially regulate sperm and oocyte fertility. PMID:34329465
Planarian Anatomy Ontology: a resource to connect data within and across experimental platforms. PMID:34318308
The GEnetic Syntax Score: a genetic risk assessment implementation tool grading the complexity of coronary artery disease-rationale and design of the GESS study. PMID:34103005
Advantages of using graph databases to explore chromatin conformation capture experiments. PMID:33902433
DDK regulates replication initiation by controlling the multiplicity of Cdc45-GINS binding to Mcm2-7. PMID:33616038
Signalling pathways and mechanistic cues highlighted by transcriptomic analysis of primordial, primary, and secondary ovarian follicles in domestic cat. PMID:33514822
The human O-GlcNAcome database and meta-analysis. PMID:33479245
Elucidating the network features and evolutionary attributes of intra- and interspecific protein-protein interactions between human and pathogenic bacteria. PMID:33420198
Towards a unified open access dataset of molecular interactions. PMID:33262342
MaizeMine: A Data Mining Warehouse for the Maize Genetics and Genomics Database. PMID:33193550
FlyRNAi.org-the database of the Drosophila RNAi screening center and transgenic RNAi project: 2021 update. PMID:33104800
Nucleoporin TPR is an integral component of the TREX-2 mRNA export pathway. PMID:32917881
COVID-WAREHOUSE: A Data Warehouse of Italian COVID-19, Pollution, and Climate Data. PMID:32756428
Genome-wide investigation of gene-cancer associations for the prediction of novel therapeutic targets in oncology. PMID:32612205
Differential regulation of lineage commitment in human and mouse primed pluripotent stem cells by the nucleosome remodelling and deacetylation complex. PMID:32535494
Loss-of-function variants in C3ORF52 result in localized autosomal recessive hypotrichosis. PMID:32336749
DNA methylation QTL analysis identifies new regulators of human longevity. PMID:32160291
A population genomics appraisal suggests independent dispersals for bitter and sweet manioc in Brazilian Amazonia. PMID:31993081
Faint gray bands in Drosophila melanogaster polytene chromosomes are formed by coding sequences of housekeeping genes. PMID:31820086
Investigating the energy crisis in Alzheimer disease using transcriptome study. PMID:31811163
ILF3 contributes to the establishment of the antiviral type I interferon program. PMID:31701124
The TargetMine Data Warehouse: Enhancement and Updates. PMID:31649722
Bovine Genome Database: new annotation tools for a new reference genome. PMID:31647100
Chemogenomic study of gemcitabine using Saccharomyces cerevisiae as model cell-molecular insights about chemoresistance. PMID:31515725
Transgenerational Self-Reconstruction of Disrupted Chromatin Organization After Exposure To An Environmental Stressor in Mice. PMID:31506492
Tripal v3: an ontology-based toolkit for construction of FAIR biological community databases. PMID:31328773
Core transcriptional signatures of phase change in the migratory locust. PMID:31292921
From observing to predicting single-cell structure and function with high-throughput/high-content microscopy. PMID:31243141
Predicting Metabolism from Gene Expression in an Improved Whole-Genome Metabolic Network Model of Danio rerio. PMID:31216234
GeneNoteBook, a collaborative notebook for comparative genomics. PMID:31199463
Application of image-based phenotyping tools to identify QTL for in-field winter survival of winter wheat (Triticum aestivum L.). PMID:31177292
NetR and AttR, Two New Bioinformatic Tools to Integrate Diverse Datasets into Cytoscape Network and Attribute Files. PMID:31159440
Hidden in plain sight: what remains to be discovered in the eukaryotic proteome? PMID:30938578
RepetDB: a unified resource for transposable element references. PMID:30719103
InterMineR: an R package for InterMine databases. PMID:30668641
HPV, tumour metabolism and novel target identification in head and neck squamous cell carcinoma. PMID:30655616
Integrated omics profiling reveals novel patterns of epigenetic programming in cancer-associated myofibroblasts. PMID:30624614
Agronomic Linked Data (AgroLD): A knowledge-based system to enable integrative biology in agronomy. PMID:30500839
BioGraph: a web application and a graph database for querying and analyzing bioinformatics resources. PMID:30458802
MaizeGDB 2018: the maize multi-genome genetics and genomics database. PMID:30407532
A pan-cancer analysis of driver gene mutations, DNA methylation and gene expressions reveals that chromatin remodeling is a major mechanism inducing global changes in cancer epigenomes. PMID:30400878
MitoMiner v4.0: an updated database of mitochondrial localization evidence, phenotypes and diseases. PMID:30398659
Dysregulated gene expression predicts tumor aggressiveness in African-American prostate cancer patients. PMID:30397274
Arena-Idb: a platform to build human non-coding RNA interaction networks. PMID:30367585
ZFLNC: a comprehensive and well-annotated database for zebrafish lncRNA. PMID:30335154
AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. PMID:30239679
Cell surface nucleolin interacts with and internalizes Bothrops asper Lys49 phospholipase A2 and mediates its toxic activity. PMID:30006575
Loss of tumor suppressor IGFBP4 drives epigenetic reprogramming in hepatic carcinogenesis. PMID:29992318
Remodeling of the Acetylproteome by SIRT3 Manipulation Fails to Affect Insulin Secretion or β Cell Metabolism in the Absence of Overnutrition. PMID:29972782
Genomic atlas of the human plasma proteome. PMID:29875488
TelNet - a database for human and yeast genes involved in telomere maintenance. PMID:29776332
Using WormBase: A Genome Biology Resource for Caenorhabditis elegans and Related Nematodes. PMID:29761466
Mapping the tumour human leukocyte antigen (HLA) ligandome by mass spectrometry. PMID:29658117
JAMI: a Java library for molecular interactions and data interoperability. PMID:29642846
Analysis of Combined Transcriptomes Identifies Gene Modules that Differentially Respond to Pathogenic Stimulation of Vascular Smooth Muscle and Endothelial Cells. PMID:29321689
Chromatin state changes during neural development revealed by in vivo cell-type specific profiling. PMID:29273756
ComplexViewer: visualization of curated macromolecular complexes. PMID:29036573
Mouse Genome Informatics (MGI) Resource: Genetic, Genomic, and Biological Knowledgebase for the Laboratory Mouse. PMID:28838066
Early-onset torsion dystonia: a novel high-throughput yeast genetic screen for factors modifying protein levels of torsinAΔE. PMID:28768697
A Drosophila model for toxicogenomics: Genetic variation in susceptibility to heavy metal exposure. PMID:28732062
Gene2Function: An Integrated Online Resource for Gene Function Discovery. PMID:28663344
Identifying Cell Subpopulations and Their Genetic Drivers from Single-Cell RNA-Seq Data Using a Biclustering Approach. PMID:28657835
Knowledge Discovery in Biological Databases for Revealing Candidate Genes Linked to Complex Phenotypes. PMID:28609292
CHOmine: an integrated data warehouse for CHO systems biology and modeling. PMID:28605771
Interactive Toxicogenomics: Gene set discovery, clustering and analysis in Toxygates. PMID:28469246
Protein and Genetic Composition of Four Chromatin Types in Drosophila melanogaster Cell Lines. PMID:28367077
Curated protein information in the Saccharomyces genome database. PMID:28365727
Integrative Comparison of mRNA Expression Patterns in Breast Cancers from Caucasian and Asian Americans with Implications for Precision Medicine. PMID:28069798
TBro: visualization and management of de novo transcriptomes. PMID:28025338
The Genome Conformation As an Integrator of Multi-Omic Data: The Example of Damage Spreading in Cancer. PMID:27895661
Chado use case: storing genomic, genetic and breeding data of Rosaceae and Gossypium crops in Chado. PMID:26989146
An integrative data analysis platform for gene set analysis and knowledge discovery in a data warehouse framework. PMID:26989145
Mouse genome database 2016. PMID:26578600
WormBase 2016: expanding to enable helminth genomic research. PMID:26578572
PlanMine--a mineable resource of planarian biology and biodiversity. PMID:26578570
Hymenoptera Genome Database: integrating genome annotations in HymenopteraMine. PMID:26578564
Legume information system (LegumeInfo.org): a key component of a set of federated data resources for the legume family. PMID:26546515
Bovine Genome Database: new tools for gleaning function from the Bos taurus genome. PMID:26481361
Mouse Genome Informatics (MGI): reflecting on 25 years. PMID:26238262
Anatomy of BioJS, an open source community for the life sciences. PMID:26153621
toxoMine: an integrated omics data warehouse for Toxoplasma gondii systems biology research. PMID:26130662
Cross-organism analysis using InterMine. PMID:26097192
ZFIN, The zebrafish model organism database: Updates and new directions. PMID:26097180
MouseMine: a new data warehouse for MGI. PMID:26092688
dictyBase 2015: Expanding data and annotations in a new software environment. PMID:26088819
The mouse gene expression database: New features and how to use them effectively. PMID:26045019
Clinical decision support systems for improving diagnostic accuracy and achieving precision medicine. PMID:25834725
Web resources for model organism studies. PMID:25707592
The BioJS article collection of open source components for biological data visualisation. PMID:25580221
Araport: the Arabidopsis information portal. PMID:25414324
esyN: network building, sharing and publishing. PMID:25181461
Mining a database of single amplified genomes from Red Sea brine pool extremophiles-improving reliability of gene function prediction using a profile and pattern matching algorithm (PPMA). PMID:24778629
InterMine: extensive web services for modern biology. PMID:24753429
What's that gene (or protein)? Online resources for exploring functions of genes, transcripts, and proteins. PMID:24723265
Obesity-associated variants within FTO form long-range functional connections with IRX3. PMID:24646999
BioJS DAGViewer: A reusable JavaScript component for displaying directed graphs. PMID:24627804
INDIGO - INtegrated data warehouse of microbial genomes with examples from the red sea extremophiles. PMID:24324765
WormBase 2014: new views of curated biology. PMID:24194605
Astrogenomics: big data, old problems, old solutions? PMID:23953643
metabolicMine: an integrated genomics, genetics and proteomics data warehouse for common metabolic disease research. PMID:23935057
Cloud-based uniform ChIP-Seq processing tools for modENCODE and ENCODE. PMID:23875683
Tuning the dials of Synthetic Biology. PMID:23704788
InterMOD: integrated data and tools for the unification of model organism research. PMID:23652793
The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies. PMID:23398680
The YeastGenome app: the Saccharomyces Genome Database at your fingertips. PMID:23396302 -
InterMine: extensive web services for modern biology
PubMed citations: 58.
58 articles citing: InterMine: extensive web services for modern biology
HumanMine: advanced data searching, analysis and cross-species comparison. PMID:35820040
Tumor Heterogeneity and Molecular Characteristics of Glioblastoma Revealed by Single-Cell RNA-Seq Data Analysis. PMID:35327982
Zebrafish information network, the knowledgebase for Danio rerio research. PMID:35166825
Clin.iobio: A Collaborative Diagnostic Workflow to Enable Team-Based Precision Genomics. PMID:35055388
Doing Genetic and Genomic Biology Using the Legume Information System and Associated Resources. PMID:35037201
Hymenoptera Genome Database: new genomes and annotation datasets for improved go enrichment and orthologue analyses. PMID:34747465
Translating synthetic natural language to database queries with a polyglot deep learning framework. PMID:34531510
Two isoforms of the essential C. elegans Argonaute CSR-1 differentially regulate sperm and oocyte fertility. PMID:34329465
Planarian Anatomy Ontology: a resource to connect data within and across experimental platforms. PMID:34318308
Signalling pathways and mechanistic cues highlighted by transcriptomic analysis of primordial, primary, and secondary ovarian follicles in domestic cat. PMID:33514822
MaizeMine: A Data Mining Warehouse for the Maize Genetics and Genomics Database. PMID:33193550
The Zebrafish Information Network: major gene page and home page updates. PMID:33170210
Genenames.org: the HGNC and VGNC resources in 2021. PMID:33152070
FlyRNAi.org-the database of the Drosophila RNAi screening center and transgenic RNAi project: 2021 update. PMID:33104800
The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals. PMID:33037820
Machado: Open source genomics data integration framework. PMID:32930331
TargetDB: A target information aggregation tool and tractability predictor. PMID:32877430
A population genomics appraisal suggests independent dispersals for bitter and sweet manioc in Brazilian Amazonia. PMID:31993081
Galaxy External Display Applications: closing a dataflow interoperability loop. PMID:31959996
Investigating the energy crisis in Alzheimer disease using transcriptome study. PMID:31811163
The TargetMine Data Warehouse: Enhancement and Updates. PMID:31649722
WormBase: a modern Model Organism Information Resource. PMID:31642470
Patterns and Constraints in the Evolution of Sperm Individualization Genes in Insects, with an Emphasis on Beetles. PMID:31590243
Wavelet-Based Genomic Signal Processing for Centromere Identification and Hypothesis Generation. PMID:31214244
NetR and AttR, Two New Bioinformatic Tools to Integrate Diverse Datasets into Cytoscape Network and Attribute Files. PMID:31159440
The genome of cowpea (Vigna unguiculata [L.] Walp.). PMID:31017340
Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. PMID:30944313
UTAP: User-friendly Transcriptome Analysis Pipeline. PMID:30909881
GenCoNet - A Graph Database for the Analysis of Comorbidities by Gene Networks. PMID:30864352
RepetDB: a unified resource for transposable element references. PMID:30719103
TogoGenome/TogoStanza: modularized Semantic Web genome database. PMID:30624651
BioGraph: a web application and a graph database for querying and analyzing bioinformatics resources. PMID:30458802
MitoMiner v4.0: an updated database of mitochondrial localization evidence, phenotypes and diseases. PMID:30398659
Complex Portal 2018: extended content and enhanced visualization tools for macromolecular complexes. PMID:30357405
Addressing Global Ruminant Agricultural Challenges Through Understanding the Rumen Microbiome: Past, Present, and Future. PMID:30319557
Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data. PMID:30115101
Oak genome reveals facets of long lifespan. PMID:29915331
Using WormBase: A Genome Biology Resource for Caenorhabditis elegans and Related Nematodes. PMID:29761466
Update notifications for the BioCyc collection of databases. PMID:29220477
Xenbase: a genomic, epigenomic and transcriptomic model organism database. PMID:29059324
Mouse Genome Informatics (MGI) Resource: Genetic, Genomic, and Biological Knowledgebase for the Laboratory Mouse. PMID:28838066
GenomeHubs: simple containerized setup of a custom Ensembl database and web server for any species. PMID:28605774
Lotus Base: An integrated information portal for the model legume Lotus japonicus. PMID:28008948
The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species. PMID:27899636
The life cycle of a genome project: perspectives and guidelines inspired by insect genome projects. PMID:27006757
An integrative data analysis platform for gene set analysis and knowledge discovery in a data warehouse framework. PMID:26989145
AnGeLi: A Tool for the Analysis of Gene Lists from Fission Yeast. PMID:26635866
The Saccharomyces Genome Database: Advanced Searching Methods and Data Mining. PMID:26631124
Bovine Genome Database: new tools for gleaning function from the Bos taurus genome. PMID:26481361
MitoMiner v3.1, an update on the mitochondrial proteomics database. PMID:26432830
Allele, phenotype and disease data at Mouse Genome Informatics: improving access and analysis. PMID:26162703
Mouse Genome Database: From sequence to phenotypes and disease models. PMID:26150326
Application of comparative biology in GO functional annotation: the mouse model. PMID:26141960
toxoMine: an integrated omics data warehouse for Toxoplasma gondii systems biology research. PMID:26130662
Cross-organism analysis using InterMine. PMID:26097192
MouseMine: a new data warehouse for MGI. PMID:26092688
Shared resources, shared costs--leveraging biocuration resources. PMID:25776020
Araport: the Arabidopsis information portal. PMID:25414324
Tags:
Tags
More detailed information about this field from each metasource.
data model
metasource: Fairsharing.org
version: FAIRsharing.org: InterMine; InterMine; DOI: https://doi.org/10.25504/FAIRsharing.DXjTQ8; Last edited: June 10, 2021, 11:55 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
data storage
metasource: Fairsharing.org
version: FAIRsharing.org: InterMine; InterMine; DOI: https://doi.org/10.25504/FAIRsharing.DXjTQ8; Last edited: June 10, 2021, 11:55 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
knowledge representation
metasource: Fairsharing.org
version: FAIRsharing.org: InterMine; InterMine; DOI: https://doi.org/10.25504/FAIRsharing.DXjTQ8; Last edited: June 10, 2021, 11:55 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
data integration and warehousing
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:57.432616
rare diseases
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:57.432616
Tags
More detailed information about this field from each metasource.
data model
metasource: Fairsharing.orgversion: FAIRsharing.org: InterMine; InterMine; DOI: https://doi.org/10.25504/FAIRsharing.DXjTQ8; Last edited: June 10, 2021, 11:55 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
data storage
metasource: Fairsharing.orgversion: FAIRsharing.org: InterMine; InterMine; DOI: https://doi.org/10.25504/FAIRsharing.DXjTQ8; Last edited: June 10, 2021, 11:55 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
knowledge representation
metasource: Fairsharing.orgversion: FAIRsharing.org: InterMine; InterMine; DOI: https://doi.org/10.25504/FAIRsharing.DXjTQ8; Last edited: June 10, 2021, 11:55 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
data integration and warehousing
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:26:57.432616
rare diseases
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:26:57.432616
data model data storage knowledge representation data integration and warehousing rare diseases
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