The BioGPS Blog from the Su Lab https://sulab.org A free extensible and customizable gene annotation portal, a complete resource for learning about gene and protein function Wed, 31 Oct 2018 16:08:13 +0000 en-US hourly 1 No trick, this new plugin is quite the treat https://sulab.org/2018/10/no-trick-this-new-plugin-is-quite-the-treat/ https://sulab.org/2018/10/no-trick-this-new-plugin-is-quite-the-treat/#respond Wed, 31 Oct 2018 16:08:13 +0000 http://sulab.org/?p=16170 Check out the new PanDrugs plugin from @pandrugs_cnio–the clean design neatly and intuitively provides information on drugs that relate to your gene of interest. Thanks to the good folks at Centro Nacional de Investigaciones Oncologicas, this awesome new resource is available on BioGPS. Speaking of BioGPS–just so we’re not confused with the other ‘BioGPS’ tools that came after us–BioGPS stands...

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]]> https://sulab.org/2018/10/no-trick-this-new-plugin-is-quite-the-treat/feed/ 0 Gene Wiki Data, BioThings, Mark2Cure, & more! A review of 2017 in the Su Lab https://sulab.org/2018/01/gene-wiki-data-biothings-mark2cure-more-a-review-of-2017-in-the-su-lab/ https://sulab.org/2018/01/gene-wiki-data-biothings-mark2cure-more-a-review-of-2017-in-the-su-lab/#respond Mon, 01 Jan 2018 08:00:56 +0000 http://sulab.org/?p=15857 Rather than summarize the 2017 progress on in each project in separate, project-specific posts, I’m putting it all in once post this year for one important reason–recruitment! As with any academic research group, we expect to see a number of our talented team members move on to bigger and better things. 2017 did not disappoint (well, it was disappointing to lose such talent, but we’re also happy...

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]]> https://sulab.org/2018/01/gene-wiki-data-biothings-mark2cure-more-a-review-of-2017-in-the-su-lab/feed/ 0 BioGPS Spotlight on the Sheep Gene Expression Atlas https://sulab.org/2017/11/biogps-spotlight-on-the-sheep-gene-expression-atlas/ https://sulab.org/2017/11/biogps-spotlight-on-the-sheep-gene-expression-atlas/#respond Mon, 06 Nov 2017 15:00:06 +0000 http://sulab.org/?p=15835 In BioGPS, there are a number of Intermine–based model organism plugins (and to a lesser extent model organism data sets) which allow users to explore gene expression in organisms typically studied in biomedical research. Model organisms such as mice, rats, flies, worms, zebra fish, etc. have well-annotated genomes and a lot of well-established tools for further exploring and contributing to the...

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]]> https://sulab.org/2017/11/biogps-spotlight-on-the-sheep-gene-expression-atlas/feed/ 0 A look back at 2016 for BioGPS https://sulab.org/2017/01/a-look-back-at-2016-for-biogps/ https://sulab.org/2017/01/a-look-back-at-2016-for-biogps/#respond Thu, 05 Jan 2017 15:30:02 +0000 http://sulab.org/?p=15552 BioGPS opened 2016 with a publication in Nucleic Acids Research, right after the New Year holiday. Throughout the year, new designs for the site were being created, reviewed, adjusted, reviewed, adjusted, and more review/adjustments in anticipation of a site redesign for 2017. A Plugin registration Blitz was held in March and April; followed by a Plugin Review Blitz in May.

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]]> https://sulab.org/2017/01/a-look-back-at-2016-for-biogps/feed/ 0 MyGene.info 2016 Year-end review https://sulab.org/2016/12/mygene-info-2016-year-end-review/ https://sulab.org/2016/12/mygene-info-2016-year-end-review/#respond Tue, 27 Dec 2016 15:00:00 +0000 http://sulab.org/?guid=96a2ef2ac6b0195d1ede140ffdb131e8 It has been a busy year for the MyGene.info team as they worked to apply the lessons they learned in building MyGene.info and MyVariant.info towards a BioThings framework, and the generation of additional services. At this rate, 2017 is on track to be a very interesting year. In 2016, aside from all the BioThings improvements happening behind-the-scenes, MyGene.info saw a number of improvements...

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]]> https://sulab.org/2016/12/mygene-info-2016-year-end-review/feed/ 0 BioGPS Spotlight on WormBase and WormMine https://sulab.org/2016/09/biogps-spotlight-on-wormbase-and-wormmine/ https://sulab.org/2016/09/biogps-spotlight-on-wormbase-and-wormmine/#respond Fri, 02 Sep 2016 14:25:18 +0000 http://sulab.org/?p=15288 If worms are your model organism of choice, you’re probably already familiar with WormBase. WormBase was founded in 2000 and is a multi-institutional consortium led by Paul Sternberg of the California Institute of Technology (CalTech), Paul Kersey of the European Bioinformatics Institute (EBI), Matt Berriman of the Wellcome Trust Sanger Institute, and Lincoln Stein of the Ontario Institute for...

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]]> https://sulab.org/2016/09/biogps-spotlight-on-wormbase-and-wormmine/feed/ 0 Functional gene constraint scores from ExAC now available from MyGene.info https://sulab.org/2016/08/functional-gene-constraint-scores-from-exac-now-available-from-mygene-info/ https://sulab.org/2016/08/functional-gene-constraint-scores-from-exac-now-available-from-mygene-info/#respond Thu, 25 Aug 2016 17:17:00 +0000 http://sulab.org/?guid=5888689abb6d08ced2b4d775d181e67b With the publication of a new paper in Nature, the Exome Aggregation Consortium (ExAC) has received some much deserved attention on their open data/open access practice. ExAC variant annotation data has been available for awhile through MyVariant.info; however, their functional gene constraint data doesn't fit well into MyVariant.

]]> With the publication of a new paper in Nature, the Exome Aggregation Consortium (ExAC) has received some much deserved attention on their open data/open access practice. ExAC variant annotation data has been available for awhile through MyVariant.info; however, their functional gene constraint data doesn’t fit well into MyVariant.info model. Speaking of ExAC annotations in MyVariant.info...

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]]> https://sulab.org/2016/08/functional-gene-constraint-scores-from-exac-now-available-from-mygene-info/feed/ 0 BioGPS Spotlight on ZFIN and ZebraFishMine https://sulab.org/2016/08/biogps-spotlight-on-zfin-and-zebrafishmine/ https://sulab.org/2016/08/biogps-spotlight-on-zfin-and-zebrafishmine/#respond Fri, 19 Aug 2016 15:56:28 +0000 http://sulab.org/?p=15257 The Zebrafish Model Organism Database (ZFIN) has served the scientific community for over twenty years. As with the Rat Genome Database, which was previously featured in our Spotlight series, ZFIN also manages an InterMine-based resource called ZebrafishMine. The ZFIN team is based at University of Oregon, and their data curation manager, Doug Howe, has kindly answered our questions about this...

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]]> https://sulab.org/2016/08/biogps-spotlight-on-zfin-and-zebrafishmine/feed/ 0 New release: MyGene.info Python client updated to v3.0.0 https://sulab.org/2016/08/new-release-mygene-info-python-client-updated-to-v3-0-0/ https://sulab.org/2016/08/new-release-mygene-info-python-client-updated-to-v3-0-0/#respond Thu, 18 Aug 2016 18:13:00 +0000 http://sulab.org/?guid=f186054f8a3fc5132b1927cdcb5af7a1 A few weeks ago, we released MyGene.info v3 API, which brings changes to exon field data structure and added accession version numbers to refseq and accession fields, along with some other back-compatible changes.

Our Python client mygene module is now updated to use our v3 API as the default.

]]> A few weeks ago, we released MyGene.info v3 API, which brings changes to exon field data structure and added accession version numbers to refseq and accession fields, along with some other back-compatible changes. Our Python client mygene module is now updated to use our v3 API as the default. We increased its version from v2.3.0 to v3.0.0, just to match the underlying API version.

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]]> https://sulab.org/2016/08/new-release-mygene-info-python-client-updated-to-v3-0-0/feed/ 0 BioGPS Spotlight on RGD and RatMine https://sulab.org/2016/08/biogps-spotlight-on-rgd-and-ratmine/ https://sulab.org/2016/08/biogps-spotlight-on-rgd-and-ratmine/#respond Fri, 05 Aug 2016 16:25:47 +0000 http://sulab.org/?p=13609 RatMine is one of several InterMine-based resources available as plugins in BioGPS. Unlike FlyMine and HumanMine (which are run by the InterMine team), RatMine is one of several resources available in the Rat Genome Database (RGD) offered by the Biomedical Informatics Program at the Medical College of Wisconsin. The Rat Genome Database is a well-respected and established resource for rat...

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