Note that you're going to need a github account to write to anything that Jeff sets up for you; so you might as well just fork https://github.com/SCILHS/scilhs-ontology and add the code to your fork. If you want to contribute it back upstream, the norm is to do a pull request.
If you prefer to just attach a .zip file to a message to gpc-dev, that would be a place to start. -- Dan ________________________________ From: Pedersen, Jay G [jay.peder...@unmc.edu] Sent: Monday, April 24, 2017 10:06 PM To: Klann, Jeffrey G.; Dan Connolly Cc: Hubert Hickman; Russ Waitman; gpc-dev@listserv.kumc.edu; Michael Prittie; Campbell, James R Subject: Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient Hi, A "contrib" repo in SCILHS works for me. It gives me a place to put this ... and a place for you to take a look at it, etc. Jay Pedersen, M.A. Department of Pathology/Microbiology University of Nebraska Medical Center 985900 Nebraska Medical Center Omaha NE 68198-5900 402-559-9487<tel:402-559-9593> (office) 402-739-3496<tel:402-350-7851> (mobile) ________________________________ From: Klann, Jeffrey G. <jeff.kl...@mgh.harvard.edu> Sent: Monday, April 24, 2017 9:58:00 PM To: Pedersen, Jay G; Dan Connolly Cc: Hubert Hickman; Russ Waitman; gpc-dev@listserv.kumc.edu; Michael Prittie; Campbell, James R Subject: Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient Might make more sense for you guys to have your own GitHub for the time being, and we could link to it. Or if you prefer, I’d be happy to set up a “contrib” repo in SCILHS that you could commit to. Thanks, Jeff Klann From: "Pedersen, Jay G" <jay.peder...@unmc.edu> Date: Monday, April 24, 2017 at 10:28 PM To: Dan Connolly <dconno...@kumc.edu> Cc: Hubert Hickman <huhick...@nebraskamed.com>, Russ Waitman <rwait...@kumc.edu>, "gpc-dev@listserv.kumc.edu" <gpc-dev@listserv.kumc.edu>, Jeffrey KLANN <jeff.kl...@mgh.harvard.edu>, Michael Prittie <mprit...@kumc.edu>, "Campbell, James R" <campb...@unmc.edu> Subject: Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient Hi, I wasn't sure where to put the code in github. I believe we are glad to share the code, which is written in python and uses web services from the NLM and an input file with history information of RxNorm codes received from the NLM. Where would be the appropriate spot to put that? I thought it was supposed to go to the SCILHS github. Jay Pedersen, M.A. Department of Pathology/Microbiology University of Nebraska Medical Center 985900 Nebraska Medical Center Omaha NE 68198-5900 402-559-9487<tel:402-559-9593> (office) 402-739-3496<tel:402-350-7851> (mobile) ________________________________ From: Dan Connolly <dconno...@kumc.edu> Sent: Monday, April 24, 2017 8:56:13 PM To: Pedersen, Jay G Cc: Hubert Hickman; Russ Waitman; gpc-dev@listserv.kumc.edu; Klann, Jeffrey G.; Michael Prittie; Campbell, James R Subject: Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient Yes, it's on babel. But Jim wrote that you were sharing it via git as well. Not so? On Apr 24, 2017 7:44 PM, "Pedersen, Jay G" <jay.peder...@unmc.edu> wrote: Hi, The Medication ontology exists in BABEL, at folder UNMC: SCILHS, in the Medications subfolder. I tried it moments ago, and it still opened VERY slow. So ... I include links to a couple of pictures taken from BABEL that shows the metadata -- from the VA class level through the RxNorm code level for ingredients and orderable drugs down to the NDC code level for packaged drugs. The 'VA class' hierarchy is the first subfolder of Medications, and we also have a second which has the ingredients in alphabetical order. We have a folder for letters A through Z. Taking any of these folders lists the ingredients which start with that letter, and underneath of ingredients lie the orderable drugs and the drug packages. Links to BABEL pictures of SCILHS Medications Ontology (NOTE: there are quite a rows for modifiers (blue dot rows), that repeat at each level, and can be hidden by modifying their C_VISUALATTRIBUTES if they don't apply at any particular site): https://dl.dropboxusercontent.com/u/5167630/UNMC_SCILHS_MEDS_p1.png [https://dl.dropboxusercontent.com/u/5167630/UNMC_SCILHS_MEDS_p1.png] https://dl.dropboxusercontent.com/u/5167630/UNMC_SCILHS_MEDS_p2.png [https://dl.dropboxusercontent.com/u/5167630/UNMC_SCILHS_MEDS_p2.png] Jay Pedersen, M.A. Department of Pathology/Microbiology University of Nebraska Medical Center 985900 Nebraska Medical Center Omaha NE 68198-5900 402-559-9487<tel:402-559-9593> (office) 402-739-3496<tel:402-350-7851> (mobile) ________________________________ From: Klann, Jeffrey G. <jeff.kl...@mgh.harvard.edu> Sent: Monday, April 24, 2017 11:15:23 AM To: gpc-dev@listserv.kumc.edu; Pedersen, Jay G; Campbell, James R; huhick...@nebraskamed.com; dconno...@kumc.edu; rwait...@kumc.edu Cc: mprit...@kumc.edu Subject: Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient Yes, I have not seen it either. Please point us to it, thanks. On 4/24/17, 11:59 AM, "GPC Informatics" <d...@madmode.com> wrote: #280: Medication ontology orgainzed by ingredient -------------------------+---------------------------- Reporter: preeder | Owner: jay.pedersen Type: enhancement | Status: assigned Priority: major | Milestone: snow-shrine-2 Component: data-stds | Resolution: Keywords: all-sites | Blocked By: 568, 592 Blocking: | -------------------------+---------------------------- Comment (by dconnolly): Campbell writes Wednesday, April 12, 2017 6:27 PM > Jay is pushing a copy along with documentation up to your GITHUB site for you and the SCILHS community to comment. Jay, point us to the results of that push? URL? commit hash? -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/280#comment:25> gpc-informatics <http://informatics.gpcnetwork.org/> Greater Plains Network - Informatics The information in this e-mail is intended only for the person to whom it is addressed. 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