From: Dawn F. <df...@ce...> - 2007-10-25 19:46:55
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Hi Aaron! ** Comments below=20 >>> "Aaron Gussman" <agu...@gm...> 10/25/07 16:36 >>> 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=3Ddetail&aid=3D1807500&group_= id=3D76834&atid=3D934923) should go.=20 ** Norman has been to the GO office a the EBI and is now editing EnvO...so = good timing. I'd like to see the Gemina terms in EnvO by the workshop and = we can work out any final issues there perhaps. 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. 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. ** I think we need to come back to this again at the next meeting (i.e. the= organism-associated branch and annotating with Organism+anatomy). I will = also post a second email about a Minimum Information Anatomy Ontology that = Jonathan Bard has recently circulated. Maybe this is a way forward? At lea= st you can check if it hold Gemina "Biological products" that deal with ana= tomy. 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? ** I say go for it if you want to in terms of content. Regardless of where= it sits, we need to start putting together some content - i.e. relevant li= nks, some text etc. Norman's friend who was going to do the design will st= ill that type of content so i think it would be a great idea to put togethe= r something. To be honest, something as simple as what OBI has as a front page would be = a real help - just consolidating the URLs for Term Tracker, SVN, mailinglis= t, workshops, case studies, workshop report would be a huge help. http://obi.sourceforge.net/ontologyInformation/ -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 W= iki > pages, the mailing list, the tracker, and the actual ontologies - at lea= st. > > 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...=20 > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.sourceforge.net/lists/listinfo/obo-envo=20 > or, via email, send a message with subject or body 'help' to > obo...@li...=20 > > You can reach the person managing the list at > obo...@li...=20 > > 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...=20 > Message-ID: <E1I...@sc...> > Content-Type: text/plain; charset=3D"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=3Ddetail&atid=3D934923&aid=3D180749= 7&group_id=3D76834=20 > > 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=3Ddetail&atid=3D934923&aid=3D180749= 7&group_id=3D76834=20 > > > > ------------------------------ > > 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...=20 > Message-ID: <E1I...@sc...> > Content-Type: text/plain; charset=3D"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=3Ddetail&atid=3D934923&aid=3D180749= 9&group_id=3D76834=20 > > 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 t= hey > 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=3Ddetail&atid=3D934923&aid=3D180749= 9&group_id=3D76834=20 > > > > ------------------------------ > > 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...=20 > Message-ID: <E1I...@sc...> > Content-Type: text/plain; charset=3D"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=3Ddetail&atid=3D934923&aid=3D180750= 0&group_id=3D76834=20 > > 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=3Ddetail&atid=3D934923&aid=3D180750= 0&group_id=3D76834=20 > > > > ------------------------------ > > 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...=20 > Message-ID: <E1I...@sc...> > Content-Type: text/plain; charset=3D"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=3Ddetail&atid=3D934923&aid=3D180751= 3&group_id=3D76834=20 > > 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=20 > > The CDC treats them as synonyms: > http://www.cdc.gov/ncidod/dvrd/spb/mnpages/glossary.htm=20 > > 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 wond= er > 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=3Ddetail&atid=3D934923&aid=3D180751= 3&group_id=3D76834=20 > > > > ------------------------------ > > 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...=20 > Message-ID: <E1I...@sc...> > Content-Type: text/plain; charset=3D"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=3Ddetail&atid=3D934923&aid=3D180751= 5&group_id=3D76834=20 > > 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=3Ddetail&atid=3D934923&aid=3D180751= 5&group_id=3D76834=20 > > > > ------------------------------ > > ------------------------------------------------------------------------- > 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/=20 > > ------------------------------ > > _______________________________________________ > Obo-envo mailing list > Obo...@li...=20 > https://lists.sourceforge.net/lists/listinfo/obo-envo=20 > > > 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. > > --=20 This message (and any attachments) is for the recipient only. 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