The BioGPS Blog from the Su Lab http://sulab.org A free extensible and customizable gene annotation portal, a complete resource for learning about gene and protein function Fri, 07 Jul 2017 20:52:35 +0000 en-US hourly 1 http://creativecommons.org/licenses/by-nc-sa/3.0/http://biogps.orghttp://sulab.org/wp-content/uploads/2011/05/biogps_logo_144px.pngBioGPS Blog from the Su Labbiogpshttps://feedburner.google.com A look back at 2016 for BioGPS http://feedproxy.google.com/~r/biogps/~3/SrMpdUG8IFQ/ http://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. The BioGPS spotlight...

Source

]]> http://sulab.org/2017/01/a-look-back-at-2016-for-biogps/feed/ 0 http://sulab.org/2017/01/a-look-back-at-2016-for-biogps/ MyGene.info 2016 Year-end review http://feedproxy.google.com/~r/biogps/~3/Ds3NZmoIaRY/ http://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...

Source

]]> http://sulab.org/2016/12/mygene-info-2016-year-end-review/feed/ 0 http://sulab.org/2016/12/mygene-info-2016-year-end-review/ BioGPS Spotlight on WormBase and WormMine http://feedproxy.google.com/~r/biogps/~3/F7-eGkVwcPQ/ http://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...

Source

]]> http://sulab.org/2016/09/biogps-spotlight-on-wormbase-and-wormmine/feed/ 0 http://sulab.org/2016/09/biogps-spotlight-on-wormbase-and-wormmine/ Functional gene constraint scores from ExAC now available from MyGene.info http://feedproxy.google.com/~r/biogps/~3/FFaHBeYItg4/ http://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, check...

Source

]]> http://sulab.org/2016/08/functional-gene-constraint-scores-from-exac-now-available-from-mygene-info/feed/ 0 http://sulab.org/2016/08/functional-gene-constraint-scores-from-exac-now-available-from-mygene-info/ BioGPS Spotlight on ZFIN and ZebraFishMine http://feedproxy.google.com/~r/biogps/~3/-edERCMbX4Y/ http://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...

Source

]]> http://sulab.org/2016/08/biogps-spotlight-on-zfin-and-zebrafishmine/feed/ 0 http://sulab.org/2016/08/biogps-spotlight-on-zfin-and-zebrafishmine/ New release: MyGene.info Python client updated to v3.0.0 http://feedproxy.google.com/~r/biogps/~3/PaIG2IiT2nI/ http://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. The mygene...

Source

]]> http://sulab.org/2016/08/new-release-mygene-info-python-client-updated-to-v3-0-0/feed/ 0 http://sulab.org/2016/08/new-release-mygene-info-python-client-updated-to-v3-0-0/ BioGPS Spotlight on RGD and RatMine http://feedproxy.google.com/~r/biogps/~3/GWdj-dJLFpQ/ http://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...

Source

]]> http://sulab.org/2016/08/biogps-spotlight-on-rgd-and-ratmine/feed/ 0 http://sulab.org/2016/08/biogps-spotlight-on-rgd-and-ratmine/ BioGPS Spotlight on HumanMine http://feedproxy.google.com/~r/biogps/~3/Q0PZlJcJxYc/ http://sulab.org/2016/07/biogps-spotlight-on-humanmine/#respond Fri, 22 Jul 2016 17:32:19 +0000 http://sulab.org/?p=6826 In our last spotlight we covered FlyMine, one of two mines maintained by the InterMine group at Cambridge University. This week’s spotlight is on HumanMine, the second of the two aforementioned mines. Yo Yehudi (developer), and Rachel Lyne (biologist) were kind enough to answer our questions for this post. In one tweet or less, introduce us to HumanMine: HumanMine integrates genomic data from 15+...

Source

]]> http://sulab.org/2016/07/biogps-spotlight-on-humanmine/feed/ 0 http://sulab.org/2016/07/biogps-spotlight-on-humanmine/ MyGene.info v3 API is out ! http://feedproxy.google.com/~r/biogps/~3/UD1Vky6P0BI/ http://sulab.org/2016/07/mygene-info-v3-api-is-out/#respond Thu, 07 Jul 2016 19:11:36 +0000 http://sulab.org/?guid=92084f10f7f20058ce9c8eb42f30e1ef We're proud to announce the next version of MyGene.info! This 3rd version brings new features, fixes some issues, and can be reached using URL http://mygene.info/v3. MyGene.info v2 will remain up and active while transitioning to v3. Stay tuned, we'll also post a step-by-step guide to

]]> We're proud to announce the next version of MyGene.info! This 3rd version brings new features, fixes some issues, and can be reached using URL http://mygene.info/v3. MyGene.info v2 will remain up and active while transitioning to v3. Stay tuned, we'll also post a step-by-step guide to migrate from v2 to v3. Here's a brief list of changes, we'll discuss some of them in depth in next posts: Refseq...

Source

]]> http://sulab.org/2016/07/mygene-info-v3-api-is-out/feed/ 0 http://sulab.org/2016/07/mygene-info-v3-api-is-out/ Help ensure BioGPS remains available http://feedproxy.google.com/~r/biogps/~3/_TmLWXu2v0o/ http://sulab.org/2016/06/help-ensure-biogps-remains-available/#comments Mon, 20 Jun 2016 21:18:46 +0000 http://sulab.org/?p=6737 2016.06.28 update- We need letters of support submitted by Friday, July 1st…please help! In the last two months, we focused on encouraging the user community to add and review more plugins. Since its humble beginnings, BioGPS has been a product of an amazing community of users–users who have extended its functionality with plugins, and aided its development with their letters of...

Source

]]> http://sulab.org/2016/06/help-ensure-biogps-remains-available/feed/ 7 http://sulab.org/2016/06/help-ensure-biogps-remains-available/