Hi Mike, Thank you very much the relevant link. I will have a look and let you know if I have any questions.
With best regards, Abu On Wed, 6 Mar 2019 at 22:40, Michael Duncan <mjsdun...@gmail.com> wrote: > hi abu, sorry for the delay in responding. most current work on opencog > based bioinformatics is happening in the context of singularitynet services > (see here <https://github.com/MOZI-AI>). much of the current agi-bio > repo is outdated but i'm slowly getting it up to speed. the *biosciences* > module does need to be built and installed with the opencog stack to > provide the custom atomtypes "GeneNode" and "MoleculeNode". > *knowledge-import/SNET* has the scripts that generate the atomspace used > by the service (GO, reactome, and bioGRID) plus the small molecule pathway > database which has a non-commercial license. this repo > <https://github.com/MOZI-AI/annotation-scheme> has the scheme code used > by the service for you to experiment with, while the service (which can be > built to run in a local docker container) includes a browser based network > visualization that is importable into cytoscape. > > please post specific code questions as issues in the appropriate github > repo or more general questions here in the google groups so we can most > effectively respond to your questions and suggestions. > > looking forward to your feedback! > mike > > On Friday, March 1, 2019 at 6:41:12 PM UTC-5, Abu Naser wrote: >> >> Hi Ben, >> >> Thank your for responding my queries. I will try to find the papers and >> guessing you are one of the authors of the papers. It would be very useful >> for me if I could get Bioinfromatics related toy examples to play around, >> which will help me to get to know the opencog code. Hope Mike will point me >> to one of those example code. >> >> With kind regards, >> >> Abu >> >> On Fri, 1 Mar 2019 at 23:14, Ben Goertzel <b...@goertzel.org> wrote: >> >>> There are two pieces to what we've been doing w/ OpenCog for >>> bioinformatics >>> >>> 1) supervised classification of genomics datasets (e.g. SNPs, gene >>> expression) using MOSES >>> >>> 2) integration of various ontologies into the Atomspace, import of >>> MOSES classification models into the Atomspace, and use of PLN >>> reasoning (currently on a pretty ad hoc, human guided basis) to do >>> inference based on this combined data >>> >>> There are publications on both of these things, though I don't have >>> time to dig up the URL right now, and Mike can point you to the >>> code... >>> >>> ben >>> >>> On Sat, Mar 2, 2019 at 5:51 AM Linas Vepstas <linasv...@gmail.com> >>> wrote: >>> > >>> > Hi, >>> > >>> > Opencog has many parts to it.There is an agi-bio part for >>> bioinformatics but it seems slim, and I think the main part of that system >>> is somewhere else. I'm hoping Mike Duncan can respond in more detail. >>> > >>> > --linas >>> > >>> > On Fri, Mar 1, 2019 at 1:15 PM Abu Naser <nase...@gmail.com> wrote: >>> >> >>> >> Hello Everyone, >>> >> >>> >> I have just installed opencog on Ubuntu. I am a biologist and wish to >>> use opencog for solving biological problems. I have been wondering whether >>> there is any tutorial related to Bioinformatics. Please let me know. >>> >> >>> >> With best regards, >>> >> >>> >> Abu >>> >> >>> >> -- >>> >> You received this message because you are subscribed to the Google >>> Groups "opencog" group. >>> >> To unsubscribe from this group and stop receiving emails from it, >>> send an email to opencog+u...@googlegroups.com. >>> >> To post to this group, send email to ope...@googlegroups.com. >>> >> Visit this group at https://groups.google.com/group/opencog. >>> >> To view this discussion on the web visit >>> https://groups.google.com/d/msgid/opencog/b91a8dda-25db-48ea-80ed-776fed30dea6%40googlegroups.com >>> . >>> >> For more options, visit https://groups.google.com/d/optout. >>> > >>> > >>> > >>> > -- >>> > cassette tapes - analog TV - film cameras - you >>> > >>> > -- >>> > You received this message because you are subscribed to the Google >>> Groups "opencog" group. >>> > To unsubscribe from this group and stop receiving emails from it, send >>> an email to opencog+u...@googlegroups.com. >>> > To post to this group, send email to ope...@googlegroups.com. >>> > Visit this group at https://groups.google.com/group/opencog. >>> > To view this discussion on the web visit >>> https://groups.google.com/d/msgid/opencog/CAHrUA34wuXH1z%3DiDwE9_HX7%2BN04SPyTHjzSp8hKPR6%2Bgih1rXA%40mail.gmail.com >>> . >>> > For more options, visit https://groups.google.com/d/optout. >>> >>> >>> >>> -- >>> Ben Goertzel, PhD >>> http://goertzel.org >>> >>> "Listen: This world is the lunatic's sphere, / Don't always agree >>> it's real. / Even with my feet upon it / And the postman knowing my >>> door / My address is somewhere else." -- Hafiz >>> >>> -- >>> You received this message because you are subscribed to the Google >>> Groups "opencog" group. >>> To unsubscribe from this group and stop receiving emails from it, send >>> an email to opencog+u...@googlegroups.com. >>> To post to this group, send email to ope...@googlegroups.com. >>> Visit this group at https://groups.google.com/group/opencog. >>> To view this discussion on the web visit >>> https://groups.google.com/d/msgid/opencog/CACYTDBe4hX_MK2x2wXRmZ6ZiVqGO5Q48FC%3DJoyPYWAUYOv3VBQ%40mail.gmail.com >>> . >>> For more options, visit https://groups.google.com/d/optout. >>> >> -- > You received this message because you are subscribed to the Google Groups > "opencog" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to opencog+unsubscr...@googlegroups.com. > To post to this group, send email to opencog@googlegroups.com. > Visit this group at https://groups.google.com/group/opencog. > To view this discussion on the web visit > https://groups.google.com/d/msgid/opencog/8272dfa7-e76e-4fb0-8682-22f9d20bbe72%40googlegroups.com > <https://groups.google.com/d/msgid/opencog/8272dfa7-e76e-4fb0-8682-22f9d20bbe72%40googlegroups.com?utm_medium=email&utm_source=footer> > . > For more options, visit https://groups.google.com/d/optout. > -- You received this message because you are subscribed to the Google Groups "opencog" group. To unsubscribe from this group and stop receiving emails from it, send an email to opencog+unsubscr...@googlegroups.com. To post to this group, send email to opencog@googlegroups.com. Visit this group at https://groups.google.com/group/opencog. To view this discussion on the web visit https://groups.google.com/d/msgid/opencog/CAMw3wdi2PD2xbg4KrRXzRTJc31wGycNkrL%2B77Me6SKTrZNAS6A%40mail.gmail.com. For more options, visit https://groups.google.com/d/optout.
