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From: Hogan, W. R <WR...@ua...> - 2012-12-12 21:20:24
|
If those URIs are unambiguous as to nation vs. territory, then yes. Bill From: Hilmar Lapp <hl...@ne...<mailto:hl...@ne...>> Date: Wednesday, December 12, 2012 2:05 PM To: William Hogan <WR...@ua...<mailto:WR...@ua...>> Cc: Chris Mungall <cjm...@lb...<mailto:cjm...@lb...>>, OBO Environmental Ontology <obo...@li...<mailto:obo...@li...>>, Mathias Brochhausen <MBr...@ua...<mailto:MBr...@ua...>> Subject: Re: [Obo-envo] [obo-admin] OBO namespace ID and PURL If it's primarily the URI that you need, any reason you can't use one from DBpedia or Freebase? Do we really have to create yet another set of URIs to be maintained for that? Plus, there'll probably be many more places on the data web that will link to the DBpedia URI than to a GEO URI. -hilmar On Dec 12, 2012, at 11:51 AM, Hogan, William R wrote: The United States has been one entity since the Constitution was ratified. However, the territory it controls has undergone dramatic changes. We need one URI for the United States as a nation. We need a separate, distinct URI for its current territorial boundaries. My understanding is GAZ has the URI for the territory. We created a URI for the nation. Bill From: Chris Mungall <cjm...@lb...<mailto:cjm...@lb...>> Date: Wednesday, December 12, 2012 10:47 AM To: William Hogan <WR...@ua...<mailto:WR...@ua...>> Cc: Mathias Brochhausen <MBr...@ua...<mailto:MBr...@ua...>>, OBO Environmental Ontology <obo...@li...<mailto:obo...@li...>>, Michael Ashburner <ma...@ge...<mailto:ma...@ge...>> Subject: Re: [obo-admin] OBO namespace ID and PURL [following up on obo-envo] I believe that in GAZ counties are purely administrative, but there are many cases where there are both administrative and non-administrative entities overlapping or occupying the same space. On Dec 12, 2012, at 8:39 AM, Hogan, William R wrote: When GAZ refers to Adams County, Colorado, is it referring to the organization or the territory? We need URI's for both. Nations declare war, you are located in geographical regions, but the two are different entities (nation vs. its territory). Bill From: Chris Mungall <cjm...@lb...<mailto:cjm...@lb...>> Date: Wednesday, December 12, 2012 10:34 AM To: William Hogan <WR...@ua...<mailto:WR...@ua...>> Cc: Mathias Brochhausen <MBr...@ua...<mailto:MBr...@ua...>>, "obo...@li...<mailto:obo...@li...>" <obo...@li...<mailto:obo...@li...>>, Melanie Courtot <mco...@gm...<mailto:mco...@gm...>>, "obo...@fr...<mailto:obo...@fr...>" <obo...@fr...<mailto:obo...@fr...>>, OBO Environmental Ontology <obo...@li...<mailto:obo...@li...>> Subject: Re: [obo-admin] OBO namespace ID and PURL ENVO has classes like rock, hill, mine, mountain, dirt, first-order administrative division, etc GAZ represents specific instances of these, like Iron Mountain Mine, USA, California, etc So I think you should use a combination of both. There a couple of issues with the OWL version of GAZ, we can follow up on the obo-envo list, you can subscribe here: https://lists.sourceforge.net/lists/listinfo/obo-envo On Dec 12, 2012, at 8:17 AM, Hogan, William R wrote: If you're referring to GAZ, the difference is that we are referring to geopolitical entities like nations, states etc. not the territory that they control. I've received emails in the past, that explicitly state GAZ is only talking about rocks, trees, hills, mountains, dirt, lakes, et cetera. Not the nations that own them. Sent from my iPhone On Dec 12, 2012, at 10:11 AM, "Chris Mungall" <cjm...@lb...<mailto:cjm...@lb...>> wrote: Why not just use the relevant subset of ENVO? Re: namespace although we only require uniqueness of ID space within OBO, I would discourage clashes with commonly used bioinformatics resources On Dec 12, 2012, at 7:41 AM, Brochhausen, Mathias wrote: Hi, To allow representation of geographical entities we have created a BFO-based ontology of geographical entities, GEO. We would like to ask for the OBO namespace GEO for the Geographical Entity Ontology. In addition, we ask for the following PURLs: http://purl.obolibrary.org/obo/geo/ http://purl.obolibrary.org/obo/geo.owl Here is the information about our ontology: Title: Geographical Entity Ontology - Short description: An ontology of geographical entities implemented in Web Ontology Language 2 (OWL2) and based on Basic Formal Ontology (BFO). The developers aim to adhere to the OBO Foundry principles. - Download link: https://ge-ontology.googlecode.com/svn/releases/2012-12-12/geo.owl - Home page: https://code.google.com/p/ge-ontology/ - Contact: Mathias Brochhausen (mbrochhausen) and Bill Hogan (hoganwr) Thanks, Mathias -- Mathias Brochhausen Ph.D. M.A. Assistant Professor Division of Biomedical Informatics University of Arkansas of Medical Sciences 4301 West Markham Slot #782 Little Rock, AR 72205 501.603.1765 (phone) 501.526.5964 (fax) Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. ------------------------------------------------------------------------------ LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d_______________________________________________ Obo-envo mailing list Obo...@li...<mailto:Obo...@li...> https://lists.sourceforge.net/lists/listinfo/obo-envo -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org<http://informatics.nescent.org> : =========================================================== Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. |
From: Hilmar L. <hl...@ne...> - 2012-12-12 20:06:06
|
If it's primarily the URI that you need, any reason you can't use one from DBpedia or Freebase? Do we really have to create yet another set of URIs to be maintained for that? Plus, there'll probably be many more places on the data web that will link to the DBpedia URI than to a GEO URI. -hilmar On Dec 12, 2012, at 11:51 AM, Hogan, William R wrote: > The United States has been one entity since the Constitution was ratified. > > However, the territory it controls has undergone dramatic changes. > > We need one URI for the United States as a nation. > > We need a separate, distinct URI for its current territorial boundaries. My understanding is GAZ has the URI for the territory. We created a URI for the nation. > > Bill > > From: Chris Mungall <cjm...@lb...> > Date: Wednesday, December 12, 2012 10:47 AM > To: William Hogan <WR...@ua...> > Cc: Mathias Brochhausen <MBr...@ua...>, OBO Environmental Ontology <obo...@li...>, Michael Ashburner <ma...@ge...> > Subject: Re: [obo-admin] OBO namespace ID and PURL > > [following up on obo-envo] > > I believe that in GAZ counties are purely administrative, but there are many cases where there are both administrative and non-administrative entities overlapping or occupying the same space. > > On Dec 12, 2012, at 8:39 AM, Hogan, William R wrote: > >> When GAZ refers to Adams County, Colorado, is it referring to the organization or the territory? We need URI's for both. Nations declare war, you are located in geographical regions, but the two are different entities (nation vs. its territory). >> >> Bill >> >> From: Chris Mungall <cjm...@lb...> >> Date: Wednesday, December 12, 2012 10:34 AM >> To: William Hogan <WR...@ua...> >> Cc: Mathias Brochhausen <MBr...@ua...>, "obo...@li..." <obo...@li...>, Melanie Courtot <mco...@gm...>, "obo...@fr..." <obo...@fr...>, OBO Environmental Ontology <obo...@li...> >> Subject: Re: [obo-admin] OBO namespace ID and PURL >> >> >> ENVO has classes like rock, hill, mine, mountain, dirt, first-order administrative division, etc >> >> GAZ represents specific instances of these, like Iron Mountain Mine, USA, California, etc >> >> So I think you should use a combination of both. >> >> There a couple of issues with the OWL version of GAZ, we can follow up on the obo-envo list, you can subscribe here: https://lists.sourceforge.net/lists/listinfo/obo-envo >> >> >> On Dec 12, 2012, at 8:17 AM, Hogan, William R wrote: >> >>> If you're referring to GAZ, the difference is that we are referring to geopolitical entities like nations, states etc. not the territory that they control. I've received emails in the past, that explicitly state GAZ is only talking about rocks, trees, hills, mountains, dirt, lakes, et cetera. Not the nations that own them. >>> >>> Sent from my iPhone >>> >>> On Dec 12, 2012, at 10:11 AM, "Chris Mungall" <cjm...@lb...> wrote: >>> >>>> >>>> Why not just use the relevant subset of ENVO? >>>> >>>> Re: namespace although we only require uniqueness of ID space within OBO, I would discourage clashes with commonly used bioinformatics resources >>>> >>>> On Dec 12, 2012, at 7:41 AM, Brochhausen, Mathias wrote: >>>> >>>>> Hi, >>>>> >>>>> To allow representation of geographical entities we have created a BFO-based ontology of geographical entities, GEO. >>>>> >>>>> We would like to ask for the OBO namespace GEO for the Geographical Entity Ontology. >>>>> >>>>> In addition, we ask for the following PURLs: >>>>> >>>>> http://purl.obolibrary.org/obo/geo/ >>>>> >>>>> http://purl.obolibrary.org/obo/geo.owl >>>>> >>>>> Here is the information about our ontology: >>>>> >>>>> Title: Geographical Entity Ontology >>>>> - Short description: An ontology of geographical entities implemented in Web Ontology Language 2 (OWL2) and based on Basic Formal Ontology (BFO). The developers aim to adhere to the OBO Foundry principles. >>>>> - Download link: https://ge-ontology.googlecode.com/svn/releases/2012-12-12/geo.owl >>>>> - Home page: https://code.google.com/p/ge-ontology/ >>>>> - Contact: Mathias Brochhausen (mbrochhausen) and Bill Hogan (hoganwr) >>>>> >>>>> Thanks, >>>>> Mathias >>>>> >>>>> -- >>>>> Mathias Brochhausen Ph.D. M.A. >>>>> Assistant Professor >>>>> Division of Biomedical Informatics >>>>> University of Arkansas of Medical Sciences >>>>> 4301 West Markham Slot #782 >>>>> Little Rock, AR 72205 >>>>> 501.603.1765 (phone) >>>>> 501.526.5964 (fax) >>>>> Confidentiality Notice: This e-mail message, including any attachments, >>>>> is for the sole use of the intended recipient(s) and may contain >>>>> confidential and privileged information. Any unauthorized review, >>>>> use, disclosure or distribution is prohibited. If you are not the >>>>> intended recipient, please contact the sender by reply >>>>> e-mail and destroy all copies of the original message. >>>> >>> Confidentiality Notice: This e-mail message, including any attachments, >>> is for the sole use of the intended recipient(s) and may contain >>> confidential and privileged information. Any unauthorized review, >>> use, disclosure or distribution is prohibited. If you are not the >>> intended recipient, please contact the sender by reply >>> e-mail and destroy all copies of the original message. >> >> Confidentiality Notice: This e-mail message, including any attachments, >> is for the sole use of the intended recipient(s) and may contain >> confidential and privileged information. Any unauthorized review, >> use, disclosure or distribution is prohibited. If you are not the >> intended recipient, please contact the sender by reply >> e-mail and destroy all copies of the original message. > > Confidentiality Notice: This e-mail message, including any attachments, > is for the sole use of the intended recipient(s) and may contain > confidential and privileged information. Any unauthorized review, > use, disclosure or distribution is prohibited. If you are not the > intended recipient, please contact the sender by reply > e-mail and destroy all copies of the original message. > ------------------------------------------------------------------------------ > LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial > Remotely access PCs and mobile devices and provide instant support > Improve your efficiency, and focus on delivering more value-add services > Discover what IT Professionals Know. Rescue delivers > http://p.sf.net/sfu/logmein_12329d2d_______________________________________________ > Obo-envo mailing list > Obo...@li... > https://lists.sourceforge.net/lists/listinfo/obo-envo -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
From: Hogan, W. R <WR...@ua...> - 2012-12-12 16:51:18
|
The United States has been one entity since the Constitution was ratified. However, the territory it controls has undergone dramatic changes. We need one URI for the United States as a nation. We need a separate, distinct URI for its current territorial boundaries. My understanding is GAZ has the URI for the territory. We created a URI for the nation. Bill From: Chris Mungall <cjm...@lb...<mailto:cjm...@lb...>> Date: Wednesday, December 12, 2012 10:47 AM To: William Hogan <WR...@ua...<mailto:WR...@ua...>> Cc: Mathias Brochhausen <MBr...@ua...<mailto:MBr...@ua...>>, OBO Environmental Ontology <obo...@li...<mailto:obo...@li...>>, Michael Ashburner <ma...@ge...<mailto:ma...@ge...>> Subject: Re: [obo-admin] OBO namespace ID and PURL [following up on obo-envo] I believe that in GAZ counties are purely administrative, but there are many cases where there are both administrative and non-administrative entities overlapping or occupying the same space. On Dec 12, 2012, at 8:39 AM, Hogan, William R wrote: When GAZ refers to Adams County, Colorado, is it referring to the organization or the territory? We need URI's for both. Nations declare war, you are located in geographical regions, but the two are different entities (nation vs. its territory). Bill From: Chris Mungall <cjm...@lb...<mailto:cjm...@lb...>> Date: Wednesday, December 12, 2012 10:34 AM To: William Hogan <WR...@ua...<mailto:WR...@ua...>> Cc: Mathias Brochhausen <MBr...@ua...<mailto:MBr...@ua...>>, "obo...@li...<mailto:obo...@li...>" <obo...@li...<mailto:obo...@li...>>, Melanie Courtot <mco...@gm...<mailto:mco...@gm...>>, "obo...@fr...<mailto:obo...@fr...>" <obo...@fr...<mailto:obo...@fr...>>, OBO Environmental Ontology <obo...@li...<mailto:obo...@li...>> Subject: Re: [obo-admin] OBO namespace ID and PURL ENVO has classes like rock, hill, mine, mountain, dirt, first-order administrative division, etc GAZ represents specific instances of these, like Iron Mountain Mine, USA, California, etc So I think you should use a combination of both. There a couple of issues with the OWL version of GAZ, we can follow up on the obo-envo list, you can subscribe here: https://lists.sourceforge.net/lists/listinfo/obo-envo On Dec 12, 2012, at 8:17 AM, Hogan, William R wrote: If you're referring to GAZ, the difference is that we are referring to geopolitical entities like nations, states etc. not the territory that they control. I've received emails in the past, that explicitly state GAZ is only talking about rocks, trees, hills, mountains, dirt, lakes, et cetera. Not the nations that own them. Sent from my iPhone On Dec 12, 2012, at 10:11 AM, "Chris Mungall" <cjm...@lb...<mailto:cjm...@lb...>> wrote: Why not just use the relevant subset of ENVO? Re: namespace although we only require uniqueness of ID space within OBO, I would discourage clashes with commonly used bioinformatics resources On Dec 12, 2012, at 7:41 AM, Brochhausen, Mathias wrote: Hi, To allow representation of geographical entities we have created a BFO-based ontology of geographical entities, GEO. We would like to ask for the OBO namespace GEO for the Geographical Entity Ontology. In addition, we ask for the following PURLs: http://purl.obolibrary.org/obo/geo/ http://purl.obolibrary.org/obo/geo.owl Here is the information about our ontology: Title: Geographical Entity Ontology - Short description: An ontology of geographical entities implemented in Web Ontology Language 2 (OWL2) and based on Basic Formal Ontology (BFO). The developers aim to adhere to the OBO Foundry principles. - Download link: https://ge-ontology.googlecode.com/svn/releases/2012-12-12/geo.owl - Home page: https://code.google.com/p/ge-ontology/ - Contact: Mathias Brochhausen (mbrochhausen) and Bill Hogan (hoganwr) Thanks, Mathias -- Mathias Brochhausen Ph.D. M.A. Assistant Professor Division of Biomedical Informatics University of Arkansas of Medical Sciences 4301 West Markham Slot #782 Little Rock, AR 72205 501.603.1765 (phone) 501.526.5964 (fax) Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. |
From: Chris M. <cjm...@lb...> - 2012-12-12 16:48:31
|
[following up on obo-envo] I believe that in GAZ counties are purely administrative, but there are many cases where there are both administrative and non-administrative entities overlapping or occupying the same space. On Dec 12, 2012, at 8:39 AM, Hogan, William R wrote: > When GAZ refers to Adams County, Colorado, is it referring to the organization or the territory? We need URI's for both. Nations declare war, you are located in geographical regions, but the two are different entities (nation vs. its territory). > > Bill > > From: Chris Mungall <cjm...@lb...> > Date: Wednesday, December 12, 2012 10:34 AM > To: William Hogan <WR...@ua...> > Cc: Mathias Brochhausen <MBr...@ua...>, "obo...@li..." <obo...@li...>, Melanie Courtot <mco...@gm...>, "obo...@fr..." <obo...@fr...>, OBO Environmental Ontology <obo...@li...> > Subject: Re: [obo-admin] OBO namespace ID and PURL > > > ENVO has classes like rock, hill, mine, mountain, dirt, first-order administrative division, etc > > GAZ represents specific instances of these, like Iron Mountain Mine, USA, California, etc > > So I think you should use a combination of both. > > There a couple of issues with the OWL version of GAZ, we can follow up on the obo-envo list, you can subscribe here: https://lists.sourceforge.net/lists/listinfo/obo-envo > > > On Dec 12, 2012, at 8:17 AM, Hogan, William R wrote: > >> If you're referring to GAZ, the difference is that we are referring to geopolitical entities like nations, states etc. not the territory that they control. I've received emails in the past, that explicitly state GAZ is only talking about rocks, trees, hills, mountains, dirt, lakes, et cetera. Not the nations that own them. >> >> Sent from my iPhone >> >> On Dec 12, 2012, at 10:11 AM, "Chris Mungall" <cjm...@lb...> wrote: >> >>> >>> Why not just use the relevant subset of ENVO? >>> >>> Re: namespace although we only require uniqueness of ID space within OBO, I would discourage clashes with commonly used bioinformatics resources >>> >>> On Dec 12, 2012, at 7:41 AM, Brochhausen, Mathias wrote: >>> >>>> Hi, >>>> >>>> To allow representation of geographical entities we have created a BFO-based ontology of geographical entities, GEO. >>>> >>>> We would like to ask for the OBO namespace GEO for the Geographical Entity Ontology. >>>> >>>> In addition, we ask for the following PURLs: >>>> >>>> http://purl.obolibrary.org/obo/geo/ >>>> >>>> http://purl.obolibrary.org/obo/geo.owl >>>> >>>> Here is the information about our ontology: >>>> >>>> Title: Geographical Entity Ontology >>>> - Short description: An ontology of geographical entities implemented in Web Ontology Language 2 (OWL2) and based on Basic Formal Ontology (BFO). The developers aim to adhere to the OBO Foundry principles. >>>> - Download link: https://ge-ontology.googlecode.com/svn/releases/2012-12-12/geo.owl >>>> - Home page: https://code.google.com/p/ge-ontology/ >>>> - Contact: Mathias Brochhausen (mbrochhausen) and Bill Hogan (hoganwr) >>>> >>>> Thanks, >>>> Mathias >>>> >>>> -- >>>> Mathias Brochhausen Ph.D. M.A. >>>> Assistant Professor >>>> Division of Biomedical Informatics >>>> University of Arkansas of Medical Sciences >>>> 4301 West Markham Slot #782 >>>> Little Rock, AR 72205 >>>> 501.603.1765 (phone) >>>> 501.526.5964 (fax) >>>> Confidentiality Notice: This e-mail message, including any attachments, >>>> is for the sole use of the intended recipient(s) and may contain >>>> confidential and privileged information. Any unauthorized review, >>>> use, disclosure or distribution is prohibited. If you are not the >>>> intended recipient, please contact the sender by reply >>>> e-mail and destroy all copies of the original message. >>> >> Confidentiality Notice: This e-mail message, including any attachments, >> is for the sole use of the intended recipient(s) and may contain >> confidential and privileged information. Any unauthorized review, >> use, disclosure or distribution is prohibited. If you are not the >> intended recipient, please contact the sender by reply >> e-mail and destroy all copies of the original message. > > Confidentiality Notice: This e-mail message, including any attachments, > is for the sole use of the intended recipient(s) and may contain > confidential and privileged information. Any unauthorized review, > use, disclosure or distribution is prohibited. If you are not the > intended recipient, please contact the sender by reply > e-mail and destroy all copies of the original message. |
From: Chris M. <cjm...@lb...> - 2012-12-12 16:48:17
|
[follow ups on the obo-envo list] On Dec 12, 2012, at 8:39 AM, Hogan, William R wrote: > When GAZ refers to Adams County, Colorado, is it referring to the organization or the territory? We need URI's for both. Nations declare war, you are located in geographical regions, but the two are different entities (nation vs. its territory). > > Bill > > From: Chris Mungall <cjm...@lb...> > Date: Wednesday, December 12, 2012 10:34 AM > To: William Hogan <WR...@ua...> > Cc: Mathias Brochhausen <MBr...@ua...>, "obo...@li..." <obo...@li...>, Melanie Courtot <mco...@gm...>, "obo...@fr..." <obo...@fr...>, OBO Environmental Ontology <obo...@li...> > Subject: Re: [obo-admin] OBO namespace ID and PURL > > > ENVO has classes like rock, hill, mine, mountain, dirt, first-order administrative division, etc > > GAZ represents specific instances of these, like Iron Mountain Mine, USA, California, etc > > So I think you should use a combination of both. > > There a couple of issues with the OWL version of GAZ, we can follow up on the obo-envo list, you can subscribe here: https://lists.sourceforge.net/lists/listinfo/obo-envo > > > On Dec 12, 2012, at 8:17 AM, Hogan, William R wrote: > >> If you're referring to GAZ, the difference is that we are referring to geopolitical entities like nations, states etc. not the territory that they control. I've received emails in the past, that explicitly state GAZ is only talking about rocks, trees, hills, mountains, dirt, lakes, et cetera. Not the nations that own them. >> >> Sent from my iPhone >> >> On Dec 12, 2012, at 10:11 AM, "Chris Mungall" <cjm...@lb...> wrote: >> >>> >>> Why not just use the relevant subset of ENVO? >>> >>> Re: namespace although we only require uniqueness of ID space within OBO, I would discourage clashes with commonly used bioinformatics resources >>> >>> On Dec 12, 2012, at 7:41 AM, Brochhausen, Mathias wrote: >>> >>>> Hi, >>>> >>>> To allow representation of geographical entities we have created a BFO-based ontology of geographical entities, GEO. >>>> >>>> We would like to ask for the OBO namespace GEO for the Geographical Entity Ontology. >>>> >>>> In addition, we ask for the following PURLs: >>>> >>>> http://purl.obolibrary.org/obo/geo/ >>>> >>>> http://purl.obolibrary.org/obo/geo.owl >>>> >>>> Here is the information about our ontology: >>>> >>>> Title: Geographical Entity Ontology >>>> - Short description: An ontology of geographical entities implemented in Web Ontology Language 2 (OWL2) and based on Basic Formal Ontology (BFO). The developers aim to adhere to the OBO Foundry principles. >>>> - Download link: https://ge-ontology.googlecode.com/svn/releases/2012-12-12/geo.owl >>>> - Home page: https://code.google.com/p/ge-ontology/ >>>> - Contact: Mathias Brochhausen (mbrochhausen) and Bill Hogan (hoganwr) >>>> >>>> Thanks, >>>> Mathias >>>> >>>> -- >>>> Mathias Brochhausen Ph.D. M.A. >>>> Assistant Professor >>>> Division of Biomedical Informatics >>>> University of Arkansas of Medical Sciences >>>> 4301 West Markham Slot #782 >>>> Little Rock, AR 72205 >>>> 501.603.1765 (phone) >>>> 501.526.5964 (fax) >>>> Confidentiality Notice: This e-mail message, including any attachments, >>>> is for the sole use of the intended recipient(s) and may contain >>>> confidential and privileged information. Any unauthorized review, >>>> use, disclosure or distribution is prohibited. If you are not the >>>> intended recipient, please contact the sender by reply >>>> e-mail and destroy all copies of the original message. >>> >> Confidentiality Notice: This e-mail message, including any attachments, >> is for the sole use of the intended recipient(s) and may contain >> confidential and privileged information. Any unauthorized review, >> use, disclosure or distribution is prohibited. If you are not the >> intended recipient, please contact the sender by reply >> e-mail and destroy all copies of the original message. > > Confidentiality Notice: This e-mail message, including any attachments, > is for the sole use of the intended recipient(s) and may contain > confidential and privileged information. Any unauthorized review, > use, disclosure or distribution is prohibited. If you are not the > intended recipient, please contact the sender by reply > e-mail and destroy all copies of the original message. |
From: Hogan, W. R <WR...@ua...> - 2012-12-12 16:39:56
|
When GAZ refers to Adams County, Colorado, is it referring to the organization or the territory? We need URI's for both. Nations declare war, you are located in geographical regions, but the two are different entities (nation vs. its territory). Bill From: Chris Mungall <cjm...@lb...<mailto:cjm...@lb...>> Date: Wednesday, December 12, 2012 10:34 AM To: William Hogan <WR...@ua...<mailto:WR...@ua...>> Cc: Mathias Brochhausen <MBr...@ua...<mailto:MBr...@ua...>>, "obo...@li...<mailto:obo...@li...>" <obo...@li...<mailto:obo...@li...>>, Melanie Courtot <mco...@gm...<mailto:mco...@gm...>>, "obo...@fr...<mailto:obo...@fr...>" <obo...@fr...<mailto:obo...@fr...>>, OBO Environmental Ontology <obo...@li...<mailto:obo...@li...>> Subject: Re: [obo-admin] OBO namespace ID and PURL ENVO has classes like rock, hill, mine, mountain, dirt, first-order administrative division, etc GAZ represents specific instances of these, like Iron Mountain Mine, USA, California, etc So I think you should use a combination of both. There a couple of issues with the OWL version of GAZ, we can follow up on the obo-envo list, you can subscribe here: https://lists.sourceforge.net/lists/listinfo/obo-envo On Dec 12, 2012, at 8:17 AM, Hogan, William R wrote: If you're referring to GAZ, the difference is that we are referring to geopolitical entities like nations, states etc. not the territory that they control. I've received emails in the past, that explicitly state GAZ is only talking about rocks, trees, hills, mountains, dirt, lakes, et cetera. Not the nations that own them. Sent from my iPhone On Dec 12, 2012, at 10:11 AM, "Chris Mungall" <cjm...@lb...<mailto:cjm...@lb...>> wrote: Why not just use the relevant subset of ENVO? Re: namespace although we only require uniqueness of ID space within OBO, I would discourage clashes with commonly used bioinformatics resources On Dec 12, 2012, at 7:41 AM, Brochhausen, Mathias wrote: Hi, To allow representation of geographical entities we have created a BFO-based ontology of geographical entities, GEO. We would like to ask for the OBO namespace GEO for the Geographical Entity Ontology. In addition, we ask for the following PURLs: http://purl.obolibrary.org/obo/geo/ http://purl.obolibrary.org/obo/geo.owl Here is the information about our ontology: Title: Geographical Entity Ontology - Short description: An ontology of geographical entities implemented in Web Ontology Language 2 (OWL2) and based on Basic Formal Ontology (BFO). The developers aim to adhere to the OBO Foundry principles. - Download link: https://ge-ontology.googlecode.com/svn/releases/2012-12-12/geo.owl - Home page: https://code.google.com/p/ge-ontology/ - Contact: Mathias Brochhausen (mbrochhausen) and Bill Hogan (hoganwr) Thanks, Mathias -- Mathias Brochhausen Ph.D. M.A. Assistant Professor Division of Biomedical Informatics University of Arkansas of Medical Sciences 4301 West Markham Slot #782 Little Rock, AR 72205 501.603.1765 (phone) 501.526.5964 (fax) Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. |
From: Chris M. <cjm...@lb...> - 2012-12-12 16:35:50
|
ENVO has classes like rock, hill, mine, mountain, dirt, first-order administrative division, etc GAZ represents specific instances of these, like Iron Mountain Mine, USA, California, etc So I think you should use a combination of both. There a couple of issues with the OWL version of GAZ, we can follow up on the obo-envo list, you can subscribe here: https://lists.sourceforge.net/lists/listinfo/obo-envo On Dec 12, 2012, at 8:17 AM, Hogan, William R wrote: > If you're referring to GAZ, the difference is that we are referring to geopolitical entities like nations, states etc. not the territory that they control. I've received emails in the past, that explicitly state GAZ is only talking about rocks, trees, hills, mountains, dirt, lakes, et cetera. Not the nations that own them. > > Sent from my iPhone > > On Dec 12, 2012, at 10:11 AM, "Chris Mungall" <cjm...@lb...> wrote: > >> >> Why not just use the relevant subset of ENVO? >> >> Re: namespace although we only require uniqueness of ID space within OBO, I would discourage clashes with commonly used bioinformatics resources >> >> On Dec 12, 2012, at 7:41 AM, Brochhausen, Mathias wrote: >> >>> Hi, >>> >>> To allow representation of geographical entities we have created a BFO-based ontology of geographical entities, GEO. >>> >>> We would like to ask for the OBO namespace GEO for the Geographical Entity Ontology. >>> >>> In addition, we ask for the following PURLs: >>> >>> http://purl.obolibrary.org/obo/geo/ >>> >>> http://purl.obolibrary.org/obo/geo.owl >>> >>> Here is the information about our ontology: >>> >>> Title: Geographical Entity Ontology >>> - Short description: An ontology of geographical entities implemented in Web Ontology Language 2 (OWL2) and based on Basic Formal Ontology (BFO). The developers aim to adhere to the OBO Foundry principles. >>> - Download link: https://ge-ontology.googlecode.com/svn/releases/2012-12-12/geo.owl >>> - Home page: https://code.google.com/p/ge-ontology/ >>> - Contact: Mathias Brochhausen (mbrochhausen) and Bill Hogan (hoganwr) >>> >>> Thanks, >>> Mathias >>> >>> -- >>> Mathias Brochhausen Ph.D. M.A. >>> Assistant Professor >>> Division of Biomedical Informatics >>> University of Arkansas of Medical Sciences >>> 4301 West Markham Slot #782 >>> Little Rock, AR 72205 >>> 501.603.1765 (phone) >>> 501.526.5964 (fax) >>> Confidentiality Notice: This e-mail message, including any attachments, >>> is for the sole use of the intended recipient(s) and may contain >>> confidential and privileged information. Any unauthorized review, >>> use, disclosure or distribution is prohibited. If you are not the >>> intended recipient, please contact the sender by reply >>> e-mail and destroy all copies of the original message. >> > Confidentiality Notice: This e-mail message, including any attachments, > is for the sole use of the intended recipient(s) and may contain > confidential and privileged information. Any unauthorized review, > use, disclosure or distribution is prohibited. If you are not the > intended recipient, please contact the sender by reply > e-mail and destroy all copies of the original message. > |
From: Chris M. <cjm...@lb...> - 2012-12-04 20:58:12
|
sorry for the cross-post. There's still no envo paper - ideally there would be one in a big bioinformatics or even environment journal that focused on the applications - but there aren't many yet. So this seems like a good opportunity Begin forwarded message: > From: Robert Hoehndorf <lee...@le...> > Subject: [Obo-discuss] Invitation to submit to the first annual JBMS Ontology Issue > Date: December 4, 2012 11:46:31 AM PST > To: obo...@li... > Reply-To: obo...@li... > > > ***************************************************** > * Call for papers: First Annual JBMS Ontology Issue * > ***************************************************** > > Dear all, > > The Journal of Biomedical Semantics (JBMS) invites submissions to its > first annual Ontology Issue. > > The purpose of the JBMS Ontology Issue is to provide a single location > at which potential users of ontologies can find ontologies that are > available for their research, and which are free or free for academic > use. Two types of submission will be considered: Ontology Descriptions > and Ontology Updates. > > - Ontology Descriptions can be used to describe an ontology that has not > previously been published in a significant journal. > > - Ontology Updates describes the recent development and changes to an > ontology. > > All ontologies published in the JBMS Ontology Issue must be freely > available (or free for academic use) at the time of submission, and they > must be applicable in biological or biomedical research. > > Before submission, authors must send a short summary of their manuscript > to the organizers at bm...@jb..., outlining the content and > the scope of their ontology and its actual or intended use in biological > or biomedical research. The short summary must be sent by 15 February, > 2013. > > The full submission instructions are attached. If you have any > questions, please do not hesitate to contact Dietrich Rebholz-Schuhmann > or Robert Hoehndorf at bm...@jb.... > > With best regards, > Robert Hoehndorf. > |
From: Chris M. <cjm...@lb...> - 2012-11-14 23:32:36
|
Is anyone aware of any environmental metabolomics datasets or databases? |
From: Chris M. <cjm...@lb...> - 2012-10-30 20:14:08
|
Hi all No activity on this list for a while. I was wondering how the last GSC meeting went - and if there were any implications for future development of ENVO. Cheers Chris |
From: Melissa H. <ha...@oh...> - 2012-10-26 18:05:09
|
Hi all, The OBO Foundry is currently working on some new and improved ontology management strategies. As these strategies and infrastructure mature, we will be making announcements on the OBO-Discuss mailing list and contacting each ontology steward. Because this listserve is currently listed as a contact for an OBO Foundry registered ontology, we would request that someone on this list please suggest a contact person. Please note that we will continue to maintain links to these associated listserves. Each ontology contact/steward (regardless if OBO or OWL) should subscribe to obo-discuss. You can do so here: https://lists.sourceforge.net/lists/listinfo/obo-discuss We would be grateful for your help in accomplishing our goal of having a contact person for each OBO ontology registered with the Foundry. On behalf of the OBO Foundry, Melissa Dr. Melissa Haendel Assistant Professor Ontology Development Group, OHSU Library http://www.ohsu.edu/library/ Department of Medical Informatics and Epidemiology Oregon Health & Science University ha...@oh...<mailto:ha...@oh...> skype: melissa.haendel 503-407-5970 |
From: Chris M. <cjm...@lb...> - 2012-10-03 15:29:55
|
Perhaps of some interest to members of this list Begin forwarded message: > From: "Obrst, Leo J." <lo...@mi...> > Subject: [ontolog-invitation] An Earth Science Ontology Dialog - miniseries session-3 - Co-chairs: Krzysztof Janowicz and Pascal Hitzler - Thu 2012.10.11 > Date: October 3, 2012 8:14:35 AM PDT > To: "Ontolog Invitation (ont...@on...)" <ont...@on...> > > Re: http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2012_10_11. > > Dear Colleagues, > > You are cordially invited to participate at the third "Earth Science Ontology Dialog" mini-series of virtual panel sessions, which is coming up Thursday, 11-October-2012. > > The mini-series (dubbed: "EarthScienceOntolog") is designed to explore the current status and application of multi-level ontologies towards developing a semantically enabled cyberinfrastructure for the Earth Science Community. In addition, one key mission of the mini-series is to bring together members of both communities (Earth Science and Ontology/Semantics) into a meaningful dialog. We anticipate that the sharing of requirements and use cases, geo-science problems and issues, ontological engineering architectures and approaches, and prospective tools, will enable collaborative understanding of the challenges and potential value in the application of ontology and semantics in Earth Science. > > This mini-series of virtual events are co-organized/supported by members of the EarthCube community, Ontolog community, SOCoP community and the IAOA community. > > ****************** Headlines *********************** > > Please join us Thursday (Oct-11) at this "EarthScienceOntolog" mini-series session: > > *Thu 11 Oct 2012* - "Heterogeneity-preserving Data Interoperability: Methods and Challenges” - Co-chairs: Professor Krzysztof Janowicz (UC Santa Barbara) and Professor Pascal Hitzler (Wright State University) - see details on the session page at: http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2012_10_11. > ... *RSVP now*! > > Five virtual panel sessions have been scheduled for the mini-series - see details under: > http://ontolog.cim3.net/cgi-bin/wiki.pl?EarthScienceOntolog#nid3CWE > > Each of these events will be 2-hour virtual panel sessions starting at: 9:30am PDT / 12:30pm EDT / 6:30pm CEST / 16:30 UTC ... please register now and mark your calendars. > > *Register your attendance* by emailing <pet...@ci...> off-line or register yourself directly to the wiki session page (if you are already a part of the Ontolog community). Please include your affiliation and specify the date of the session(s) when you are writing in to register and specify date of the session you plan to attend. > > ********************* Details ************************ > > EarthScienceOntolog: Panel Session-03 - Thu 2012-10-11 > > Mini-Series Theme: An Earth Science Ontology Dialog > > Session Topic: Heterogeneity-preserving Data Interoperability: Methods and Challenges > > Session Co-chairs: Professor Krzysztof Janowicz (UC Santa Barbara) and Professor Pascal Hitzler (Wright State University) > > Panelists / Briefings: > > * Dr. Simon Scheider (University of Muenster, Germany) - "What does it take to interoperate? Semantic interoperability revisited in terms of human digital communication” > > * Dr. Prateek Jain (Knoesis, Wright State University) - "Ontology matching and Data Interoperability using community generate data" > > * Mr. Ben Adams (UC Santa Barbara) - "Semantic Similarity Measurement for Geo-Ontologies" > > * Professor Giancarlo Guizzardi (Federal U of Espírito Santo, Brazil) > > This, and the rest of the mini-series sessions, like all Ontolog virtual events, are open and free of charge. Anyone who is interested, or (better still) who may have something to contribute, is welcome. Please refer to event details on the session pages, to which the hyperlink is given above, where you will find session agenda, conference call dial-in, slides and other pertinent information. Feel free to pass this invitation along to colleagues who may also find these sessions to be of interest. > > *RSVP* by emailing Peter Yim at <pet...@ci...> offline (or add yourself directly to the session page if you are already an Ontolog community member) so that we can prepare enough resources to support everyone. [Please state clearly the date of the session you are registering for in your email.] > > These sessions will be recorded and made available in a publicly accessible archive. Therefore, before participating, please make sure you are cognizant of our IPR policy (ref: http://ontolog.cim3.net/cgi-bin/wiki.pl?WikiHomePage#nid32). > > Regards, > Leo > > For and on behalf of > > the Session-2 co-chairs, > Krzysztof Janowicz and Pascal Hitzler > > and the EarthScienceOntolog mini-series Organizing Committee, > Dalia Varanka > Gary Berg-Cross > Krishna Sinha > Krzysztof Janowicz > Leo Obrst > Mark Schildhauer > Mike Dean > Naicong Li > Nancy Wiegand > Pascal Hitzler > Peter Yim > > http://ontolog.cim3.net/cgi-bin/wiki.pl?EarthScienceOntolog > > p.s. The full proceedings from our kick-off session (including abstracts, slides, audio recording, in-session chat-transcript, etc.) are available online now, for those who have missed the session, or those who desire to revisit the materials and study them in greater detail - please look under the "Archives" section on the session page at: http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2012_08_23 > > > _________________________________________________________________ > Join this list: mailto:ont...@on... > Leave this list: mailto:ont...@on... > Msg Archives: http://ontolog.cim3.net/forum/ontolog-invitation/ > Community Wiki: http://ontolog.cim3.net/wiki/ > Community Portal: http://ontolog.cim3.net/ |
From: Chris M. <cjm...@lb...> - 2012-05-25 23:58:15
|
The source for ENVO is now managed on googlecode using SVN. The project site is: http://code.google.com/p/envo/ Note that in general this should only affect you if you are an editor of the envo source ontology, or if you are keen to track individual commits. As with any OBO library ontology, you can find download information here: http://obofoundry.org/cgi-bin/detail.cgi?id=envo (Note: this will be updated at midnight tonight - until then it points to the cvs repo) The following two URLs are stable regardless of where the repository lives: http://purl.obolibrary.org/obo/envo.owl http://purl.obolibrary.org/obo/envo.obo We are in the process of transitioning GAZ to this repository as well. Regards, Chris |
From: Norman M. <nor...@gm...> - 2012-05-24 19:29:08
|
Hi Maureen, Apologies for not getting back to you sooner, I was on travels last week when I received your request. I will endeavor to have these terms added to the ontology asap. Kind regards, Norman On 18 May 2012, at 18:39, Fallon, Maureen wrote: > Hi, > Will you please consider the addition of 5 new term requests we have > added to the ENVO tracker: > Apiary (requested in fall of 2011) > Confined agricultural feature > Children: > Cage > Drylot > Feedlot > > Thank you! > Maureen > > Maureen Fallon, MS > Veterinary Medical Informatics Lab > Virginia Tech > 1880 Pratt Drive, Ste 1124 > Blacksburg, VA 24060 > Mafallon at vt.edu > (540) 231-4427 > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. > Discussions > will include endpoint security, mobile security and the latest in > malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/_______________________________________________ > Obo-envo mailing list > Obo...@li... > https://lists.sourceforge.net/lists/listinfo/obo-envo |
From: Trish W. <wh...@st...> - 2012-05-21 22:43:57
|
_______________________________________________ bioportal-announce mailing list bio...@li... https://mailman.stanford.edu/mailman/listinfo/bioportal-announce |
From: Fallon, M. <maf...@vt...> - 2012-05-18 17:51:21
|
Hi, Will you please consider the addition of 5 new term requests we have added to the ENVO tracker: Apiary (requested in fall of 2011) Confined agricultural feature Children: Cage Drylot Feedlot Thank you! Maureen Maureen Fallon, MS Veterinary Medical Informatics Lab Virginia Tech 1880 Pratt Drive, Ste 1124 Blacksburg, VA 24060 Mafallon at vt.edu (540) 231-4427 |
From: SourceForge.net <no...@so...> - 2012-05-18 17:10:04
|
Environmental Ontology (EnvO) term requests item #3527965, was opened at 2012-05-18 10:10 Message generated for change (Tracker Item Submitted) made by mafallon You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=934923&aid=3527965&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: New term Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Mo Fallon (mafallon) Assigned to: Norman Morrison (normanmorrison) Summary: Feedlot Initial Comment: A confined agricultural feature that is free of vegetation and is used for the containment, feeding, and fattening of livestock Parent: confined agricultural feature (new term) Superclass: ENVO:00000077 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=934923&aid=3527965&group_id=76834 |
From: SourceForge.net <no...@so...> - 2012-05-18 17:08:55
|
Environmental Ontology (EnvO) term requests item #3527963, was opened at 2012-05-18 10:08 Message generated for change (Tracker Item Submitted) made by mafallon You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=934923&aid=3527963&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: New term Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Mo Fallon (mafallon) Assigned to: Norman Morrison (normanmorrison) Summary: Drylot Initial Comment: A confined agricultural feature that is free of vegetation and is used for the containment and feeding of livestock Parent: confined agricultural feature (new term) Superclass: ENVO:00000077 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=934923&aid=3527963&group_id=76834 |
From: SourceForge.net <no...@so...> - 2012-05-18 17:03:53
|
Environmental Ontology (EnvO) term requests item #3527960, was opened at 2012-05-18 10:03 Message generated for change (Tracker Item Submitted) made by mafallon You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=934923&aid=3527960&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: New term Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Mo Fallon (mafallon) Assigned to: Norman Morrison (normanmorrison) Summary: Cage Initial Comment: A confined agricultural feature where the animal is enclosed in a box-like structure which restricts the movement of an animal to a specific area Parent: confined agricultural feature (new term) Superclass: ENVO:00000077 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=934923&aid=3527960&group_id=76834 |
From: SourceForge.net <no...@so...> - 2012-05-18 16:37:01
|
Environmental Ontology (EnvO) term requests item #3527927, was opened at 2012-05-18 09:37 Message generated for change (Tracker Item Submitted) made by mafallon You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=934923&aid=3527927&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: New term Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Mo Fallon (mafallon) Assigned to: Norman Morrison (normanmorrison) Summary: Confined agricultural feature Initial Comment: An environmental feature for plant or animal organisms that allows for control of the nutrition and conditions in which the organism is living Superclass: agricultural feature ENVO:00000077 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=934923&aid=3527927&group_id=76834 |
From: Chris M. <cjm...@lb...> - 2012-02-18 00:38:49
|
I forgot to send an update to this list - this has been resolved. I have added Gaz to the OBO Jenkins environment: http://ladle.lbl.gov:8080/job/build-gaz/ Every time there is a commit, it triggers a "build" of GAZ, including a conversion to OWL and a run through the ELK reasoner. This is sufficient to catch a good number of syntactic errors (invalid tags) and semantic problems (cycles in the subclass graph). The build takes about 30 mins. I will do my best to keep my eye on this and pre-emptively catch any of the problems that inevitably creep into something the size of Gaz. If other members of the obo-envo community want to keep watch too that would be great - those loading GAZ into their databases may want to do this - it's easy, the ball on the page above should stay blue, it will be red if there's a problem. Blue balls good, red balls bad. You can check on the balls through an RSS feed too. For all the gory details you can read more on the OBO Jenkins environment here: http://douroucouli.wordpress.com/2012/02/16/ontologies-and-continuous-integration/ I will set up this for ENVO too... not much point until we get a few more commits going though... Cheers Chris On Jan 27, 2012, at 10:42 AM, Pankaj Jaiswal (OSU) wrote: > Chris, > > Can you check. Either there is a cycle issue or ~70 children terms with located_in and partial_overlaps relationship. > > Pankaj. > > -------- Original Message -------- > Subject: Bad GAZ term? > Date: Fri, 27 Jan 2012 18:25:22 +0000 > From: Youens-Clark, Ken <kc...@cs...> > To: Pankaj Jaiswal (OSU) <jai...@sc...> > CC: Vindhya Amarasinghe <ama...@sc...>, "van Buren, Peter" <van...@cs...>, Palitha Dharmawardhana <dha...@sc...> > > Pankaj, > > I'm looking into some particularly crippling queries against our servers. Peter forwarded me this one: > > On Jan 11, 2012, at 10:43 AM, Peter Van Buren wrote: > > Here's another one that causes issues: > > 180.76.6.21 www.gramene.org<http://www.gramene.org/> GET /db/ontology/search?id=GAZ:00002564 HTTP/1.1 > > We just had two of these taking up ~ 20GB or ram. > > Looking into it, I suspect there is a circular relationship in the term's parentage. Do you have a way of checking this? This page: > > http://dev.gramene.org/db/ontology/search?id=GAZ:00002564 > > Never loads because of what looks to me like an infinite recursion while querying for the inheritance tree. > > -- > Ken Youens-Clark > kc...@cs...<mailto:kc...@cs...> > Ware Lab/CSHL/USDA-ARS > |
From: Chris M. <cjm...@lb...> - 2012-01-29 15:45:22
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Hi Pankaj Traveling at the moment will do my best I can't test gaz.obo for cycles until I can get it to parse. I'm correcting syntax errors that arose from hand editing at the moment. Can't seem to commit these right now. I had previously intended to get a full automated release cycle going with Oort for gaz so that these don't stack up - will get on this ASAP. OE is way too lenient in parsing unfortunately. The parser Ken is using is also way too lenient it seems, otherwise it would have caught these syntax errors before the cycle error. Note that Oort will check for cycles in the inheritance graph. There is no inheritance cycle in this case GAZ:00002564 "is_a" GAZ:00002561, which has no is_a parent. Maybe Ken means a cycle in the full relational graph? This need not be a problem, it depends on the relation. On Jan 27, 2012, at 10:42 AM, Pankaj Jaiswal (OSU) wrote: > Chris, > > Can you check. Either there is a cycle issue or ~70 children terms with located_in and partial_overlaps relationship. > > Pankaj. > > -------- Original Message -------- > Subject: Bad GAZ term? > Date: Fri, 27 Jan 2012 18:25:22 +0000 > From: Youens-Clark, Ken <kc...@cs...> > To: Pankaj Jaiswal (OSU) <jai...@sc...> > CC: Vindhya Amarasinghe <ama...@sc...>, "van Buren, Peter" <van...@cs...>, Palitha Dharmawardhana <dha...@sc...> > > Pankaj, > > I'm looking into some particularly crippling queries against our servers. Peter forwarded me this one: > > On Jan 11, 2012, at 10:43 AM, Peter Van Buren wrote: > > Here's another one that causes issues: > > 180.76.6.21 www.gramene.org<http://www.gramene.org/> GET /db/ontology/search?id=GAZ:00002564 HTTP/1.1 > > We just had two of these taking up ~ 20GB or ram. > > Looking into it, I suspect there is a circular relationship in the term's parentage. Do you have a way of checking this? This page: > > http://dev.gramene.org/db/ontology/search?id=GAZ:00002564 > > Never loads because of what looks to me like an infinite recursion while querying for the inheritance tree. > > -- > Ken Youens-Clark > kc...@cs...<mailto:kc...@cs...> > Ware Lab/CSHL/USDA-ARS > |
From: Pankaj J. (OSU) <jai...@sc...> - 2012-01-27 18:58:10
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Chris, Can you check. Either there is a cycle issue or ~70 children terms with located_in and partial_overlaps relationship. Pankaj. -------- Original Message -------- Subject: Bad GAZ term? Date: Fri, 27 Jan 2012 18:25:22 +0000 From: Youens-Clark, Ken <kc...@cs...> To: Pankaj Jaiswal (OSU) <jai...@sc...> CC: Vindhya Amarasinghe <ama...@sc...>, "van Buren, Peter" <van...@cs...>, Palitha Dharmawardhana <dha...@sc...> Pankaj, I'm looking into some particularly crippling queries against our servers. Peter forwarded me this one: On Jan 11, 2012, at 10:43 AM, Peter Van Buren wrote: Here's another one that causes issues: 180.76.6.21 www.gramene.org<http://www.gramene.org/> GET /db/ontology/search?id=GAZ:00002564 HTTP/1.1 We just had two of these taking up ~ 20GB or ram. Looking into it, I suspect there is a circular relationship in the term's parentage. Do you have a way of checking this? This page: http://dev.gramene.org/db/ontology/search?id=GAZ:00002564 Never loads because of what looks to me like an infinite recursion while querying for the inheritance tree. -- Ken Youens-Clark kc...@cs...<mailto:kc...@cs...> Ware Lab/CSHL/USDA-ARS |
From: Chris M. <cjm...@lb...> - 2012-01-20 21:43:47
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On Jan 20, 2012, at 7:57 AM, Walls, Ramona wrote: > We have been working on something similar with plants. We have been considering using "found_in", rather than "lives_in", because it does not carry the implication that the organism is necessarily alive. It allows the relation to be used with continuants that are not organisms. Can you give further details? Is this the same as being located in, or is there a more dispositional aspect? E.g. If I'm walking in a spacesuit on the surface of the moon, would you say I was found_in the lunar environment at that time? I'm guessing not as you would just use a more standard locational relation. How about some kind of adaptation-oriented relation? There could be sub-relations for natural and artificial adaptation. The range of this relation would be a high level class in ENVO. But it wouldn't be appropriate to use this for the relationship between a newly captured tiger and the small Manhattan apartment it's living in - but I think this is getting into another category of relation altogether. Maybe raised_in and sub-relations? > I need to describe both class level relations and instance level relations. For class level relations, I need to talk about both classes of organisms in a particular habitats (like what you have below) as well as classes of organisms that live in particular geographic regions, such as "all individuals of the species Dioscorea omiltemensis are found in Guerrero, Mexico". In this case, I think Dioscorea omiltemensis is a class, and Guerrero, Mexico is an instance, since there is only one Guerrero (perhaps instance of the class "Mexican State"). In general relations in RO are object properties (between individuals). You'd just quantify them how you like * some instances of X are found_in instance Y * some instances of X are found_in some instance of Y * all instances of X are found_in instance Y * all instances of X are found_in some instance of Y * all instances of X are found_in only instances of Y * n% of instances of X are found_in an instance of Y The last can't be directly encoded in most ontology languages but that's the idea. These limited forms of quantification may not be sufficient for your use case then there may be reason to add a class relation -- but let's see if we can capture what you require without that > I also want to talk about individual organisms (instances of the class that describes some species) that live in either a specific habitat or in a geographic region or or at a specific locality. For example: "collection #RW107 of Dioscorea omiltemensis was collected in a pine-oak forest" or "collection #RW107 of Dioscorea omiltemensis is from Guerrero, Mexico" or ""collection #RW107 of Dioscorea omiltemensis was collected at W 99 36.147, N 17 38.296". I would like to be able to use "found_in" for all of these (except maybe the last one – not sure about that). It would seem that "found in" implies something a bit different that "collected from". I'm less keen on "found" in that it implies a process of finding. > I also want to talk about, for example, "the plant disease bacterial wilt is found in Iowa, USA". Do you want to say anything stronger than there was an observation of a plant with this disease in the wild in Iowa? If not then simple locational relationships may suffice. > All of the examples I listed are between two continuants, so perhaps something similar to located_in will work, but I am not sure. > > Sorry I don't really have an answer for you, because I just started thinking about this, but I wanted to point out some of the other examples where such a relation could be used. > > Ramona > > From: Suzanne Santamaria <sue...@gm...> > Date: Fri, 20 Jan 2012 10:26:39 -0500 > To: <obo...@li...> > Subject: [Obo-relations] relation for organism living in a site > > Hello, > > We need a relation to associate an organism with the physical location (environment/site) where it lives in the developing ontology of practical animal classes. I see two possible relations in the newest renditions of RO: Located_in and Has_site_of. However, I’m not sure if either are suitable for this situation. Here are some examples of where this relation would be used in our ontology (“Lives_in” is used as placeholder relation for now): > > · Term: Cattle on pasture for beef production > o Text definition: Cattle which produce beef and live on pasture > o Synonym: Pasture beef cattle > o Formal definition: > § isa Cattle for beef production > § Lives_in some pasture (ENVO term) > · Term: Feral pig > o Domesticated species of pig which live in the wild > o Synonym: Feral hog > o Formal definition: > § isa Pig > § Lives_in some terrestrial biome (ENVO) > · Term: Cold-blood aquatic animal > o Text definition: Cold-blooded animal that lives in water. > o Formal definition: > § Isa Cold-blooded animal > § Lives_in some aquatic habitat (ENVO) > > Please advise on whether we should create a new relation “Lives_in” between continuants such as an Object and a Site or use one of the existing RO relations. > > Many thanks, > Suzanne > > -- > Suzanne Santamaria, DVM > Veterinary Terminologist | Veterinary Medical Informatics Laboratory > sls...@vt... | 540-231-4427 | http://informatics.vetmed.vt.edu > > “Information is care” ~ Donald Berwick, M.D. > ------------------------------------------------------------------------------ Keep Your Developer Skills Current with LearnDevNow! 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From: Suzanna L. <su...@be...> - 2011-12-15 08:22:30
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Perhaps of some interest for those interested in describing environments. Begin forwarded message: > Resent-From: pub...@w3... > From: Todd Pehle <tod...@gm...> > Subject: GeoVoCamp - Santa Barbara, CA, USA - February 3rd-5th, 2012 > Date: December 15, 2011 5:30:30 AM GMT+01:00 > To: public-lod <pub...@w3...> > > Quick Note: > > Our friends at UCSB will be hosting a GeoVoCamp in Santa Barbara, California on February 3rd-5th, 2012. > > http://vocamp.org/wiki/GeoVoCampSB2012 > > Hope to see you there! > > -Todd Pehle > |