PgmNr M5110: What’s New in Mouse Genome Informatics (MGI)?

Authors:
J. Richardson; J. Kadin; M. Ringwald; J. Blake; C. Bult; J. T. Eppig; MGI Team


Institutes
The Jackson Laboratory, Bar Harbor, ME.


Abstract:

Newly implemented in MGI in the last year: (1) MGI Gene Pages, the most frequently viewed pages in MGI are re-designed, including a new human disease table showing OMIM diseases with the human causitive gene, and human diseases modeled in mice with mutations in the gene being viewed, and Grid displays providing overviews of phenotypes, functional annotations, and embryonic gene expression in tissues [see poster Blake et al];  (2) Improvements to the Recombinase search, allowing users more specific parameter searching and providing autocomplete fields. The results summary also allows filtering and sorting of the data returned;  (3) GO tables are enhanced to include a Category column from a GO slim subset of terms and a Context column providing details of the conditions used in the experiment [see poster Christie et al];  (4) MGI's Mouse dbSNP Query is re-designed to vastly improve performance. Users can now filter results by funtional class and re-order columns to reposition strains of interest. [see poster Law et al];  (5) A Batch Search utility has been added to the Gene Expression (GXD) Query to facilitate searches with lists of gene symbols or IDs. GXD searches return a tissue-by-gene matrix view as part of its multi-tabbed data summary [see poster Smith et al & Shaw et al].

MGI also is working with model organisms on collaborative projects: (1) A project to port individual organism InterMine instances (in MGI’s case, MouseMine) to a shared Cloud environment to make accessibility across model organisms more transparent for users.  (2) A project including MGI, RGD (Rat Genome Database) and DO (Disease Ontology) to enhance and improve DO depth and structure so that it can support disease annotations from mouse and rat.  (3) A project including MGI and Wormbase to test and improve Textpresso as a literature triage tool that could save significant curator time in screening biomedical literature.

MGI also recently completed a major upgrade to its software infrastructure, porting nearly 200 tables in the database to Postgres and rewriting data loads, software for curation, and scripts supporting the web interface. Most MGI software now resides on the Jackson Laboratory server cloud. As a result we have improved the stability and speed of MGI and simplified future maintenance. Supported by NIH grants HG000330, HG002273, HD064299.