From: Norman M. <mor...@cs...> - 2007-10-26 12:56:18
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I've been working through some of the terms that Aaron submitted. I've suggested that we have a skype chat on Monday afternoon to work through them further since Aaron has some bandwidth at the moment. There are some interesting questions that arise that should probably be followed through on the tracker... watch that space :-) Chris Mungall wrote: > On Oct 25, 2007, at 8:36 AM, Aaron Gussman wrote: > > >> Hi Dawn, >> I'm not entirely sure where the Gemina "biological products" >> terms I added to the tracker ( http://sourceforge.net/tracker/ >> index.php?func=detail&aid=1807500&group_id=76834&atid=934923) >> should go. In Gemina, we are using them to describe human anatomy >> and most of the terms are too specific to be considered common to >> all organisms/animals. >> > > Is the full list on the tracker? > > >> I'm trying to remember what was discussed at the meeting, and I >> want to say the agreement was to use cross products for >> environments that are anatomy+organism. >> > > unfortunately we don't have a comprehensive enough species-neutral > anatomy ontology. You can use FMA for the human terms, but for wool, > bird feces, cow rumen etc it would seem reasonable to have a small > set in envo for now. When the appropriate external ontologies are in > place we can obsolete these and add replaced_by tags pointing at the > appropriate terms. > > Seems like a sensible course of action... >> I'd be happy to throw together a quick webpage with basic EnvO >> info. I'm not sure if www.envoc.org can be made to point to a >> website hosted at the sourceforge site though, since there's not a >> dedicated envo project, it's under obo. Maybe someone on the list >> can confirm/deny the ability to host at sourceforge or offer >> hosting services? >> > > we can set up something such as http://obo.sf.net/envoc; or do we > need a dedicated host? We can do this at berkeley I believe > The "physical" hosting of the www.envoc.org website is something I hope to discuss with the coordination committee on Tuesday 30th Oct. Will feedback the decision to this list... > >> -Aaron >> >> On 10/5/07, Dawn Field <df...@ce...> wrote: Aaron - these look >> like good additions and in the right places. Many thanks. I need >> 'discharge' and 'effluent' from ear :-) as I start to look at >> GOLD...so now that this is moving and can start submitting some >> too. Do we want human-associated or did you just mean 'organism- >> associated'. As in any species could have the things listed by >> GEMINA for humans. >> >> Norman - are you going to take care of this? The latest version >> of EnvO is committed right? This isn't coming through the tracker >> though is it? It should, right? >> >> We need to link up all the bits of the infrastructure now...A >> simple page at the HomePage URL would be really helpful - to >> contain a link to the Wiki pages, the mailing list, the tracker, >> and the actual ontologies - at least. >> >> Anyone willing to do this - prior to knowing whether Norman's >> collegue will take this on in the long run? >> >> I assume it could just be uploaded to the sourceforge site? >> >> Dawn >> >> >>>>> obo...@li... 10/4/07 20:07 >>> >>>>> >> Send Obo-envo mailing list submissions to >> obo...@li... >> >> To subscribe or unsubscribe via the World Wide Web, visit >> https://lists.sourceforge.net/lists/listinfo/obo-envo >> or, via email, send a message with subject or body 'help' to >> obo...@li... >> >> You can reach the person managing the list at >> obo...@li... >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Obo-envo digest..." >> >> >> Today's Topics: >> >> 1. [ obo-Environmental Ontology (EnvO) term requests-1807497 ] >> environmental substances in Gemina (SourceForge.net ) >> 2. [ obo-Environmental Ontology (EnvO) term requests-1807499 ] >> foods in Gemina (SourceForge.net) >> 3. [ obo-Environmental Ontology (EnvO) term requests-1807500 ] >> biological products in Gemina ( SourceForge.net) >> 4. [ obo-Environmental Ontology (EnvO) term requests-1807513 ] >> vehicles in Gemina (SourceForge.net) >> 5. [ obo-Environmental Ontology (EnvO) term requests-1807515 ] >> vomit under animal waste ( SourceForge.net) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Thu, 04 Oct 2007 06:18:46 -0700 >> From: "SourceForge.net" < no...@so...> >> Subject: [Obo-envo] [ obo-Environmental Ontology (EnvO) term >> requests-1807497 ] environmental substances in Gemina >> To: no...@so... >> Message-ID: <E1I...@sc...> >> Content-Type: text/plain; charset="UTF-8" >> >> Environmental Ontology (EnvO) term requests item #1807497, was >> opened at 2007-10-04 09:18 >> Message generated for change (Tracker Item Submitted) made by Item >> Submitter >> You can respond by visiting: >> https://sourceforge.net/tracker/? >> func=detail&atid=934923&aid=1807497&group_id=76834 >> >> Please note that this message will contain a full copy of the >> comment thread, >> including the initial issue submission, for this request, >> not just the latest update. >> Category: None >> Group: None >> Status: Open >> Resolution: None >> Priority: 5 >> Private: No >> Submitted By: Aaron Gussman (agussman) >> Assigned to: Nobody/Anonymous (nobody) >> Summary: environmental substances in Gemina >> >> Initial Comment: >> We would like to have the following terms from Gemina's ontology >> incorporated into EnvO. I think they would be placed under >> "environmental substance": >> air/droplet nuclei >> soil/aquatic sediment >> soil/surface soil >> >> >> ---------------------------------------------------------------------- >> >> You can respond by visiting: >> https://sourceforge.net/tracker/? >> func=detail&atid=934923&aid=1807497&group_id=76834 >> >> >> >> ------------------------------ >> >> Message: 2 >> Date: Thu, 04 Oct 2007 06:20:55 -0700 >> From: "SourceForge.net " <no...@so...> >> Subject: [Obo-envo] [ obo-Environmental Ontology (EnvO) term >> requests-1807499 ] foods in Gemina >> To: no...@so... >> Message-ID: <E1I...@sc...> >> Content-Type: text/plain; charset="UTF-8" >> >> Environmental Ontology (EnvO) term requests item #1807499, was >> opened at 2007-10-04 09:20 >> Message generated for change (Tracker Item Submitted) made by Item >> Submitter >> You can respond by visiting: >> https://sourceforge.net/tracker/? >> func=detail&atid=934923&aid=1807499&group_id=76834 >> >> Please note that this message will contain a full copy of the >> comment thread, >> including the initial issue submission, for this request, >> not just the latest update. >> Category: None >> Group: None >> Status: Open >> Resolution: None >> Priority: 5 >> Private: No >> Submitted By: Aaron Gussman (agussman) >> Assigned to: Nobody/Anonymous (nobody) >> Summary: foods in Gemina >> >> Initial Comment: >> The following are terms from the Gemina ontology we'd like to have >> incorporated into EnvO (slashes indicate parentage in Gemina). I >> think they would be added under "food": >> food/beverage >> beverage/apple cider (no cider, but an apple juice) >> apple cider/unpasteurized apple cider >> orange juice >> orange juice/unpasteurized orange juice >> cheese/unpasteurized cheese >> dairy product/egg >> milk/breast milk >> milk/unpasteurized milk >> dessert >> dessert/cake >> dessert/cake/cake icing >> dessert/chocolate >> dessert/custard >> beef/ground beef >> meat/poultry >> poultry/duck >> poultry/goose >> poultry/turkey >> food/mushroom >> food/plant >> plant/bean >> fruit/cantaloupe >> plant/peanut >> vegetable/spinach >> salad/potato salad >> salad/salad dressing >> seafood/clam >> seafood/oyster >> seafood/shellfish >> >> >> ---------------------------------------------------------------------- >> >> You can respond by visiting: >> https://sourceforge.net/tracker/? >> func=detail&atid=934923&aid=1807499&group_id=76834 >> >> >> >> ------------------------------ >> >> Message: 3 >> Date: Thu, 04 Oct 2007 06:23:01 -0700 >> From: "SourceForge.net" <no...@so...> >> Subject: [Obo-envo] [ obo-Environmental Ontology (EnvO) term >> requests-1807500 ] biological products in Gemina >> To: no...@so... >> Message-ID: < E1I...@sc...> >> Content-Type: text/plain; charset="UTF-8" >> >> Environmental Ontology (EnvO) term requests item #1807500, was >> opened at 2007-10-04 09:23 >> Message generated for change (Tracker Item Submitted) made by Item >> Submitter >> You can respond by visiting: >> https://sourceforge.net/tracker/? >> func=detail&atid=934923&aid=1807500&group_id=76834 >> >> Please note that this message will contain a full copy of the >> comment thread, >> including the initial issue submission, for this request, >> not just the latest update. >> Category: None >> Group: None >> Status: Open >> Resolution: None >> Priority: 5 >> Private: No >> Submitted By: Aaron Gussman (agussman) >> Assigned to: Nobody/Anonymous (nobody) >> Summary: biological products in Gemina >> >> Initial Comment: >> The following terms were listed under Gemina's "biological >> products" node. It looks like the equivalent place to put (most >> of) them in EnvO would under human-associated habitat. >> >> biological product >> biological product/animal product >> biological product/animal product/hide >> biological product/animal product/wool >> biological product/blood >> biological product/body fluid >> biological product/bone meal >> biological product/excreta/feces/wild bird feces >> biological product/excreta/sweat >> biological product/gastrointestinal tract >> biological product/gastrointestinal tract/intestine >> biological product/genitalia >> biological product/hair >> biological product/organ >> biological product/oronasal secretion >> biological product/reproductive tract >> biological product/respiratory tract >> biological product/saliva >> biological product/tissue >> biological product/urinary tract >> >> ---------------------------------------------------------------------- >> >> You can respond by visiting: >> https://sourceforge.net/tracker/? >> func=detail&atid=934923&aid=1807500&group_id=76834 >> >> >> >> ------------------------------ >> >> Message: 4 >> Date: Thu, 04 Oct 2007 06:36:27 -0700 >> From: "SourceForge.net " <no...@so...> >> Subject: [Obo-envo] [ obo-Environmental Ontology (EnvO) term >> requests-1807513 ] vehicles in Gemina >> To: no...@so... >> Message-ID: <E1I...@sc...> >> Content-Type: text/plain; charset="UTF-8" >> >> Environmental Ontology (EnvO) term requests item #1807513, was >> opened at 2007-10-04 09:36 >> Message generated for change (Tracker Item Submitted) made by Item >> Submitter >> You can respond by visiting: >> https://sourceforge.net/tracker/? >> func=detail&atid=934923&aid=1807513&group_id=76834 >> >> Please note that this message will contain a full copy of the >> comment thread, >> including the initial issue submission, for this request, >> not just the latest update. >> Category: None >> Group: None >> Status: Open >> Resolution: None >> Priority: 5 >> Private: No >> Submitted By: Aaron Gussman (agussman) >> Assigned to: Nobody/Anonymous (nobody) >> Summary: vehicles in Gemina >> >> Initial Comment: >> In Gemina we had a term "vehicle" with a number of children terms. >> In googling around it's not really clear what the distinction >> should be, if any, between a "vehicle" and a "fomite". >> >> This page distinguishes them on the basis of if they are routinely >> taken into the body (vehicles) or not (fomites): http:// >> www.mansfield.ohio-state.edu/~sabedon/biol2050.htm#fomite >> >> The CDC treats them as synonyms: >> http://www.cdc.gov/ncidod/dvrd/spb/mnpages/glossary.htm >> >> In our thinking, our fomites are vehicles, but not all vehicles are >> fomites (but I am less sure of this distinction now). >> >> In the existing EnvO, the closest thing I can find to a parent term >> to our terms is "mesoscopic feature". I'm not entirely sure that >> it is the best term, though, based off the definition. Looking at >> it's children, I wonder if maybe this could be changed to vehicle/ >> fomite, with abiotic and biotic children? >> >> At any rate, the terms we'd like to have added are: >> vehicle >> vehicle/bedding >> vehicle/cell culture >> vehicle/fomite >> fomite/cloth >> feature/product >> fomite/needle >> fomite/nesting material >> fomite/umbrella >> >> >> ---------------------------------------------------------------------- >> >> You can respond by visiting: >> https://sourceforge.net/tracker/? >> func=detail&atid=934923&aid=1807513&group_id=76834 >> >> >> >> ------------------------------ >> >> Message: 5 >> Date: Thu, 04 Oct 2007 06:37:46 -0700 >> From: "SourceForge.net " <no...@so...> >> Subject: [Obo-envo] [ obo-Environmental Ontology (EnvO) term >> requests-1807515 ] vomit under animal waste >> To: no...@so... >> Message-ID: <E1I...@sc...> >> Content-Type: text/plain; charset="UTF-8" >> >> Environmental Ontology (EnvO) term requests item #1807515, was >> opened at 2007-10-04 09:37 >> Message generated for change (Tracker Item Submitted) made by Item >> Submitter >> You can respond by visiting: >> https://sourceforge.net/tracker/? >> func=detail&atid=934923&aid=1807515&group_id=76834 >> >> Please note that this message will contain a full copy of the >> comment thread, >> including the initial issue submission, for this request, >> not just the latest update. >> Category: None >> Group: None >> Status: Open >> Resolution: None >> Priority: 5 >> Private: No >> Submitted By: Aaron Gussman (agussman) >> Assigned to: Nobody/Anonymous (nobody) >> Summary: vomit under animal waste >> >> Initial Comment: >> Can we add "vomit" to EnvO under the "animal waste" term? >> >> ---------------------------------------------------------------------- >> >> You can respond by visiting: >> https://sourceforge.net/tracker/? >> func=detail&atid=934923&aid=1807515&group_id=76834 >> >> >> >> ------------------------------ >> >> ---------------------------------------------------------------------- >> --- >> This SF.net email is sponsored by: Splunk Inc. >> Still grepping through log files to find problems? Stop. >> Now Search log events and configuration files using AJAX and a >> browser. >> Download your FREE copy of Splunk now >> http://get.splunk.com/ >> >> ------------------------------ >> >> _______________________________________________ >> Obo-envo mailing list >> Obo...@li... >> https://lists.sourceforge.net/lists/listinfo/obo-envo >> >> >> End of Obo-envo Digest, Vol 2, Issue 1 >> ************************************** >> >> -- >> This message (and any attachments) is for the recipient only. NERC >> is subject to the Freedom of Information Act 2000 and the contents >> of this email and any reply you make may be disclosed by NERC unless >> it is exempt from release under the Act. Any material supplied to >> NERC may be stored in an electronic records management system. >> >> >> ---------------------------------------------------------------------- >> --- >> This SF.net email is sponsored by: Splunk Inc. >> Still grepping through log files to find problems? Stop. >> Now Search log events and configuration files using AJAX and a >> browser. >> Download your FREE copy of Splunk now >> http://get.splunk.com/ >> _______________________________________________ >> Obo-envo mailing list >> Obo...@li... >> https://lists.sourceforge.net/lists/listinfo/obo-envo >> > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. > Still grepping through log files to find problems? Stop. > Now Search log events and configuration files using AJAX and a browser. > Download your FREE copy of Splunk now >> http://get.splunk.com/ > _______________________________________________ > Obo-envo mailing list > Obo...@li... > https://lists.sourceforge.net/lists/listinfo/obo-envo > -- Dr Norman Morrison NEBC Omic Data Standards Coordinator (http://nebc.nox.ac.uk/) Room LF8, School of Computer Science, Kilburn Building, University of Manchester, Oxford Road, MANCHESTER, UK. M13 9PL. 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