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| March 15, 2013 |
- MouseMine represents a new generation of access to MGI data. Powered by InterMine, MouseMine offers flexible querying, numerous predefined query templates, a point-and-click interface for building your own queries or modifying a template, iterative refinement of results, built-in enrichment analysis, downloading in multiple formats, forwarding to Galaxy, linking to other model organism Mines, and more.
- MouseMine:
- currently contains genetic, genomic and annotation data (function,
phenotype, disease) from MGI
- offers many useful "canned" queries, plus point-and-click query editing
- supports links to any object's detail page or to any query results page
- allows any query result to be downloaded (text, xml, json) or
forwarded to Galaxy
- supports uploading and manipulating lists of objects
- provides web service access to all of the above functions
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| January 31, 2013 |
- MGI now integrates phenotype data from high-throughput phenotyping centers with curated data from scientific publications, providing comprehensive comparative phenotypes for mouse mutants. Current data sets include those from the Wellcome Trust Sanger Institute (WTSI) and the Europhenome (EuPh) data. This integration allows specific comparisons between different Center data interpretations and is a model for future MGI data integration from the International Mouse Phenotyping Consortium (IMPC). All data on the MGI website are refreshed weekly.
- MGI Allele Summary Pages have been streamlined, concatinating biological systems where phenotypes have been detected while removing the details of each genotype examined. In addition, Allele Detail pages have been redesigned for clarity and performance, and to display results from these high-throughput phenotyping centers. Sex-specific phenotype data also are easier to discover.
- For an example, see this MGI Allele Detail page.
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| December 6, 2012 |
- MGI mouse genome coordinates are now updated to NCBI Mouse Build 38 (GRCm38.p1). For Mus musculus Build GRCm38.p1 statistics, see The Genome Reference Consortium web site.
- Temporarily, there is a discrepancy between genome coordinates for mouse SNPs, which are derived from an earlier NCBI build of the mouse genome, and genes and markers, whose coordinates are derived from the current build. (see details).
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| August, 30 2012 |
- The Gene Expression Data Query form has been re-designed to add new search functions and make it easier to use. In addition to gene function (Gene Ontology) terms, you can now use phenotype or disease terms to define gene sets of interest in expression searches. Auto fill lists for these categories and for anatomical structure searches make it easier to find the appropriate search terms. In addition to Theiler stage, age is now available as a search parameter.
- The mechanisms behind the searches and their returned data summaries have been entirely re-designed. The most noticeable improvement will be the speed of the return. Each search will now return a page with tabbed summaries for the assay results, assays, and genes matching your parameters. Most columns on these summaries are sortable. New columns have been added to provide additional context. The figure links on the assay results tab provide direct access to images of data. Export features have been added to the assay results and genes tabs, allowing results to be downloaded in text or spreadsheet format. The genes list can be forwarded to the MGI batch query to allow you to search for additional information, such as the function, phenotype and/or disease terms associated with the genes of interest.
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| June 29, 2012 |
- The Gene Expression Database (GXD) is pleased to announce that additional RNA in situ hybridization data from the GenePaint database are now available at accession number J:122989. The GenePaint data set in MGI now includes:
- over 289,300 RNA in situ hybridization results at E14.5
- 2,958 genes
- 24,984 images
- Some useful links for querying subsets of data in GXD and MGI are:
- If you are interested in submitting your data to GXD, please see our guidelines for submitting expression data to the Gene Expression Database or contact GEN@jax.org for further information.
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| April 11, 2012 |
- The Reference and Gene Expression Literature Search Forms' author and journal fields now contain an autocomplete feature. When you start typing an author name or a journal abbreviation, you are offered a list of appropriate choices. The Reference search results can now be sorted, and filtered by author, journal, year and curated data. Reference search results can now be exported as tab-delimited text files.
- The International Mouse Strain Resource (IMSR) now allows you to filter your search results by Stock State (live mice, embryo, sperm, ES cell) Type (inbred, mutant stock, recombinant inbred) Provider and Mutation (spontaneous, gene trap, targeted). Search results can now be sorted by strain name or provider and can be exported in tab-delimited text or Excel formats.
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