From: Thomas, P. <pdt...@us...> - 2011-10-24 18:18:58
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Here's the link to the ftp directory for the files with pairwise orthologs across the GO Reference Genomes: ftp://ftp.pantherdb.org/ortholog Paul. On 10/24/11 5:59 AM, "Richard Smith" <ri...@fl...> wrote: >Hi all, >I can see the reference proteomes for download but only a link to >InParanoid for orthologs. Have other methods been used on the >reference proteomes and is there a plan for a blessed set of >ortholog predictions? > >At InterMine we're working with several MODs and interoperability >between the Mines is a big part of the project. We would like to >load in the most widely accepted ortholog predictions. > >As Josh says, Alex is working on an InterMine implementation of the >GMOD REST API, which will be available for the MODs that are >deploying InterMine instances (SGD, RGD, ZFIN, WormBase, MGI). > > >Thanks, >Richard. > > >On 20/10/2011 21:30, Suzanna Lewis wrote: >> Yes, Ben is absolutely right. For more information you can look here: >>http://www.ebi.ac.uk/reference_proteomes/ >> >> And of course we really want to hear from all of you. Involvement and >>feedback are really wanted! >> >> I think the phylogenetic trees GO is using are soon to be available >>programmatically, if not today then certainly by the end of the year. >>the new GO architecture (all the behind the scenes stuff) is all >>services based. >> >> -S >> >> On Oct 20, 2011, at 11:04 AM, Benjamin Hitz wrote: >> >>> Hi gmod. Hope everyone had a good time in Toronto; sorry I couldn't >>>make it. >>> Kalpana gave us a report on the meeting and something stuck out at us >>>that I though we should follow up on - the discussion on MOD >>>interoperation by Josh Goodman. >>> >>> There were no notes to confirm, but message we received back at SGD >>>was that it was difficult for MODs to communicate without some common >>>ortholog discussion. >>> I know there is not a huge overlap in meeting attendees between GMOD >>>meeting and GO consortium meetings, BUT all the major and most minor >>>mods are part of GO - and GO has essentially "solved" this problem, or >>>at least has decided on common protein sets and a set of orthologs >>>across model organisms. I am not personally part of this GO >>>subproject, but certainly we should work together with GO on this. >>> >>> We are planning to re-do SGD's software in the next couple years and I >>>would like to use whatever GMOD common REST API (and I suppose might as >>>well implement SADI as well) from the beginning... whatever that API >>>happens to be. Oh, but I can 99% guarentee we won't use CHADO - and I >>>know worm, mouse, zfin, etc. don't either, so we should think about >>>generic implemention of the REST API (as a group) >>> >>> Ben >>> -- >>> Ben Hitz >>> Senior Scientific Programmer ** Saccharomyces Genome Database ** GO >>>Consortium >>> Stanford University ** hi...@st... >>> >>> >>> >>> >>> >>> >>>------------------------------------------------------------------------ >>>------ >>> The demand for IT networking professionals continues to grow, and the >>> demand for specialized networking skills is growing even more rapidly. >>> Take a complimentary Learning@Cisco Self-Assessment and learn >>> about Cisco certifications, training, and career opportunities. >>> http://p.sf.net/sfu/cisco-dev2dev >>> _______________________________________________ >>> Gmod-devel mailing list >>> Gmo...@li... >>> https://lists.sourceforge.net/lists/listinfo/gmod-devel >> >> >> >>------------------------------------------------------------------------- >>----- >> The demand for IT networking professionals continues to grow, and the >> demand for specialized networking skills is growing even more rapidly. >> Take a complimentary Learning@Cisco Self-Assessment and learn >> about Cisco certifications, training, and career opportunities. >> http://p.sf.net/sfu/cisco-dev2dev >> _______________________________________________ >> Gmod-devel mailing list >> Gmo...@li... >> https://lists.sourceforge.net/lists/listinfo/gmod-devel >> > |