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From: Chris M. <cjm...@lb...> - 2021-02-12 02:42:48
|
Important question on scope of NBO https://github.com/obo-behavior/behavior-ontology/issues/109 |
From: Chris M. <cjm...@lb...> - 2020-11-03 08:15:45
|
This paper by Bjoern Brembs argues against the perspective of behavior being an input-output process with stimulus driving behavior. I don't have all the context of a behavior researcher but I found the perspective interesting, and am wondering if there are implications for GO/NBO: https://psyarxiv.com/j37av Aside: do people find this mail list useful? I am not sure who is still on it. Many of us are using slack, we have an obo workspace and could set up a behavior channel, mail me if interested. |
From: Chris M. <cjm...@lb...> - 2013-11-05 02:03:15
|
Nice paper from George, Rob et al on term enrichment using NBO: http://link.springer.com/article/10.1007/s00335-013-9481-z |
From: Paola R. <pa...@eb...> - 2013-09-04 11:56:19
|
Hello, I'm one of the Gene Ontology editors. I'm currently working on GO terms referring to taxis, tropism and kinesis, and Chris Mungall suggested I ask for your feedback please. Details and link in my previous message below. Would you have any concern about the proposal I've outlined in SourceForge? Thanks in advance! Best regards, Paola Roncaglia -------- Original Message -------- Subject: Feedback on GO terms defining taxis, tropism and kinesis Date: Mon, 05 Aug 2013 12:38:28 +0100 From: Paola Roncaglia <pa...@eb...> To: obo...@li... Hello, May I ask for your feedback please, on GO terms referring to taxis, tropism and kinesis. We (GO Editors) recently noticed some possible inconsistencies in the current definitions of such terms, and we'd like to suggest some changes. I've outlined a proposal in a SourceForge ticket (linked below). My fellow editors agree with it, but we'd like to double-check if you'd have any concern. If so, please advice on how you'd rather define those terms. Many thanks in advance for your time. The link is https://sourceforge.net/p/geneontology/ontology-requests/10261/ Best, Paola -- Paola Roncaglia, PhD GO Editorial Office European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Tel: +44 1223 492600 Fax: +44 1223 494468 |
From: Paola R. <pa...@eb...> - 2013-08-05 11:38:31
|
Hello, May I ask for your feedback please, on GO terms referring to taxis, tropism and kinesis. We (GO Editors) recently noticed some possible inconsistencies in the current definitions of such terms, and we'd like to suggest some changes. I've outlined a proposal in a SourceForge ticket (linked below). My fellow editors agree with it, but we'd like to double-check if you'd have any concern. If so, please advice on how you'd rather define those terms. Many thanks in advance for your time. The link is https://sourceforge.net/p/geneontology/ontology-requests/10261/ Best, Paola -- Paola Roncaglia, PhD GO Editorial Office European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Tel: +44 1223 492600 Fax: +44 1223 494468 |
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: Jane L. <ja...@eb...> - 2012-08-15 09:18:07
|
Yes I agree NBO is the best place, but as Melissa says you may want to relate the underlying physiological processes that contribute to the movement from GO. GO also has terms for cellular component movement e.g. flagellum movement which are analogous at a subcellular level. Also some terms for whole organism locomotion e.g. swimming, flight which might be better in NBO. Jane On 15/08/2012 00:16, Melissa Haendel wrote: > Not that I know of, but I think most movements would be represented as > A moving relative to B, where A is some anatomical structure > (including whole organism), and B is either another anatomical > structure, spatial attribute, or some external feature. > > for example, hand waving would be the hand moving left relative to the > body axis, and then to the right. > Probably also need some temporal and/or repetition aspects as well, > probably can't call it waving if you only go left then right once. > > There are also a few relevant GO class that could be made > interoperable here for example ,'musculoskeletal movement' > > Cheers > melissa > > On Aug 14, 2012, at 3:57 PM, Chris Mungall wrote: > >> >> Are there any ontologies that cover >> http://en.wikipedia.org/wiki/Category:Anatomical_terms_of_motion >> >> Perhaps the best place is a under a new class under "body part >> movement" in NBO. This would be under a sort of "primitive" class >> like "motion" from which more complex movements such as chewing, >> licking and headbanging could be composed. Is NBO the best place for >> these? >> >> / NBO:0000000 ! behavior >> is_a NBO:0000313 ! physiological behavior >> is_a NBO:0000338 ! kinesthetic behavior >> is_a NBO:0000403 ! voluntary movement behavior >> is_a NBO:0000001 ! body part movement *** >> is_a NBO:0000007 ! mouth movement >> is_a NBO:0000017 ! biting >> is_a NBO:0000019 ! licking >> is_a NBO:0000073 ! chewing >> is_a NBO:0000074 ! yawning >> is_a NBO:0000020 ! head movement >> is_a NBO:0000023 ! head shaking >> is_a NBO:0000026 ! head rotation >> is_a NBO:0000570 ! head bobbing >> is_a NBO:0000571 ! mutlidirectional head movement >> is_a NBO:0000068 ! shaking >> is_a NBO:0000023 ! head shaking >> is_a NBO:0000444 ! eye movement >> is_a NBO:0000446 ! visual pursuit >> is_a NBO:0000445 ! tail movement >> >> >> ------------------------------------------------------------------------------ >> 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-anatomy mailing list >> Obo...@li... >> <mailto:Obo...@li...> >> https://lists.sourceforge.net/lists/listinfo/obo-anatomy > > *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 > > > > > ------------------------------------------------------------------------------ > 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-behavior mailing list > Obo...@li... > https://lists.sourceforge.net/lists/listinfo/obo-behavior |
From: Chris M. <cjm...@lb...> - 2012-08-15 00:20:21
|
I thought we had arrived at a happy compromise here that didn't involve "BO". I forget what it was. Perhaps the N stood for neuroscience or nervous-system-related...? On Aug 14, 2012, at 4:02 PM, Barry Smith wrote: > I think these are very appropriate for what I hope will be renamed the Behavior Ontology > (Neuro Behavior Ontology has several things wrong with it, above all in that it suggests that it is about the behavior of Neuros) > BS > > On Tue, Aug 14, 2012 at 6:57 PM, Chris Mungall <cjm...@lb...> wrote: > > Are there any ontologies that cover http://en.wikipedia.org/wiki/Category:Anatomical_terms_of_motion > > Perhaps the best place is a under a new class under "body part movement" in NBO. This would be under a sort of "primitive" class like "motion" from which more complex movements such as chewing, licking and headbanging could be composed. Is NBO the best place for these? > > / NBO:0000000 ! behavior > is_a NBO:0000313 ! physiological behavior > is_a NBO:0000338 ! kinesthetic behavior > is_a NBO:0000403 ! voluntary movement behavior > is_a NBO:0000001 ! body part movement *** > is_a NBO:0000007 ! mouth movement > is_a NBO:0000017 ! biting > is_a NBO:0000019 ! licking > is_a NBO:0000073 ! chewing > is_a NBO:0000074 ! yawning > is_a NBO:0000020 ! head movement > is_a NBO:0000023 ! head shaking > is_a NBO:0000026 ! head rotation > is_a NBO:0000570 ! head bobbing > is_a NBO:0000571 ! mutlidirectional head movement > is_a NBO:0000068 ! shaking > is_a NBO:0000023 ! head shaking > is_a NBO:0000444 ! eye movement > is_a NBO:0000446 ! visual pursuit > is_a NBO:0000445 ! tail movement > > > ------------------------------------------------------------------------------ > 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-behavior mailing list > Obo...@li... > https://lists.sourceforge.net/lists/listinfo/obo-behavior > |
From: Chris M. <cjm...@lb...> - 2012-08-15 00:16:21
|
OK, NBO (behavior ontology) it is. I added a tracker item: http://code.google.com/p/behavior-ontology/issues/detail?id=10 On Aug 14, 2012, at 4:25 PM, Peter Midford wrote: > Since I do a fair amount of description at this level, I think this should be in NBO (I don't think there is much of a case for a separate ontology of kinesthetic processes. Agree with Melissa's analysis - most behaviors at this level would be motion relative to other body parts. Other 'primitive' behaviors, such as shape change or surface changes might not fit here, but should be in the same ontology - which I had assumed would be NBO. In theory we may have to draw a line between behavior such as this and the underlying physiology, but that should await a decent physiology ontology. I'm more concerned with issues at the other end of complexity. > > -Peter > > > > On Aug 14, 2012, at 6:57 PM, Chris Mungall wrot >> >> Are there any ontologies that cover http://en.wikipedia.org/wiki/Category:Anatomical_terms_of_motion >> >> Perhaps the best place is a under a new class under "body part movement" in NBO. This would be under a sort of "primitive" class like "motion" from which more complex movements such as chewing, licking and headbanging could be composed. Is NBO the best place for these? >> >> / NBO:0000000 ! behavior >> is_a NBO:0000313 ! physiological behavior >> is_a NBO:0000338 ! kinesthetic behavior >> is_a NBO:0000403 ! voluntary movement behavior >> is_a NBO:0000001 ! body part movement *** >> is_a NBO:0000007 ! mouth movement >> is_a NBO:0000017 ! biting >> is_a NBO:0000019 ! licking >> is_a NBO:0000073 ! chewing >> is_a NBO:0000074 ! yawning >> is_a NBO:0000020 ! head movement >> is_a NBO:0000023 ! head shaking >> is_a NBO:0000026 ! head rotation >> is_a NBO:0000570 ! head bobbing >> is_a NBO:0000571 ! mutlidirectional head movement >> is_a NBO:0000068 ! shaking >> is_a NBO:0000023 ! head shaking >> is_a NBO:0000444 ! eye movement >> is_a NBO:0000446 ! visual pursuit >> is_a NBO:0000445 ! tail movement >> >> >> ------------------------------------------------------------------------------ >> 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-behavior mailing list >> Obo...@li... >> https://lists.sourceforge.net/lists/listinfo/obo-behavior > |
From: Chris M. <cjm...@lb...> - 2012-08-14 23:52:46
|
NBO has a 3 cyclic logical definitions such as 'kinaesthetic movement' EquivalentTo 'kinaesthetic movement' and by_means 'musculoskeletal movement' Note that Oort currently reports these but doesn't penalize you. In future we may have a default setting that prevents a release if these cycles are present. Class NBO:0000130 has a self reference in its logical definition: EquivalentClasses(<http://purl.obolibrary.org/obo/NBO_0000130> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/NBO_0000130> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/nbo#has_participant> <http://purl.obolibrary.org/obo/PATO_0000145>)) ) Class NBO:0001536 has a self reference in its logical definition: EquivalentClasses(<http://purl.obolibrary.org/obo/NBO_0001536> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/NBO_0001536> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/nbo#in_response_to> <http://purl.obolibrary.org/obo/GO_0009314>)) ) Class NBO:0000338 has a self reference in its logical definition: EquivalentClasses(<http://purl.obolibrary.org/obo/NBO_0000338> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/NBO_0000338> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/nbo#by_means> <http://purl.obolibrary.org/obo/GO_0050881>)) ) See Jenkins for full report: http://build.berkeleybop.org/job/build-nbo |
From: Peter M. <pet...@gm...> - 2012-08-14 23:25:36
|
Since I do a fair amount of description at this level, I think this should be in NBO (I don't think there is much of a case for a separate ontology of kinesthetic processes. Agree with Melissa's analysis - most behaviors at this level would be motion relative to other body parts. Other 'primitive' behaviors, such as shape change or surface changes might not fit here, but should be in the same ontology - which I had assumed would be NBO. In theory we may have to draw a line between behavior such as this and the underlying physiology, but that should await a decent physiology ontology. I'm more concerned with issues at the other end of complexity. -Peter On Aug 14, 2012, at 6:57 PM, Chris Mungall wrot > > Are there any ontologies that cover http://en.wikipedia.org/wiki/Category:Anatomical_terms_of_motion > > Perhaps the best place is a under a new class under "body part movement" in NBO. This would be under a sort of "primitive" class like "motion" from which more complex movements such as chewing, licking and headbanging could be composed. Is NBO the best place for these? > > / NBO:0000000 ! behavior > is_a NBO:0000313 ! physiological behavior > is_a NBO:0000338 ! kinesthetic behavior > is_a NBO:0000403 ! voluntary movement behavior > is_a NBO:0000001 ! body part movement *** > is_a NBO:0000007 ! mouth movement > is_a NBO:0000017 ! biting > is_a NBO:0000019 ! licking > is_a NBO:0000073 ! chewing > is_a NBO:0000074 ! yawning > is_a NBO:0000020 ! head movement > is_a NBO:0000023 ! head shaking > is_a NBO:0000026 ! head rotation > is_a NBO:0000570 ! head bobbing > is_a NBO:0000571 ! mutlidirectional head movement > is_a NBO:0000068 ! shaking > is_a NBO:0000023 ! head shaking > is_a NBO:0000444 ! eye movement > is_a NBO:0000446 ! visual pursuit > is_a NBO:0000445 ! tail movement > > > ------------------------------------------------------------------------------ > 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-behavior mailing list > Obo...@li... > https://lists.sourceforge.net/lists/listinfo/obo-behavior |
From: Barry S. <phi...@bu...> - 2012-08-14 23:20:22
|
I think these are very appropriate for what I hope will be renamed the Behavior Ontology (Neuro Behavior Ontology has several things wrong with it, above all in that it suggests that it is about the behavior of Neuros) BS On Tue, Aug 14, 2012 at 6:57 PM, Chris Mungall <cjm...@lb...> wrote: > > Are there any ontologies that cover > http://en.wikipedia.org/wiki/Category:Anatomical_terms_of_motion > > Perhaps the best place is a under a new class under "body part movement" > in NBO. This would be under a sort of "primitive" class like "motion" from > which more complex movements such as chewing, licking and headbanging could > be composed. Is NBO the best place for these? > > / NBO:0000000 ! behavior > is_a NBO:0000313 ! physiological behavior > is_a NBO:0000338 ! kinesthetic behavior > is_a NBO:0000403 ! voluntary movement behavior > is_a NBO:0000001 ! body part movement *** > is_a NBO:0000007 ! mouth movement > is_a NBO:0000017 ! biting > is_a NBO:0000019 ! licking > is_a NBO:0000073 ! chewing > is_a NBO:0000074 ! yawning > is_a NBO:0000020 ! head movement > is_a NBO:0000023 ! head shaking > is_a NBO:0000026 ! head rotation > is_a NBO:0000570 ! head bobbing > is_a NBO:0000571 ! mutlidirectional head movement > is_a NBO:0000068 ! shaking > is_a NBO:0000023 ! head shaking > is_a NBO:0000444 ! eye movement > is_a NBO:0000446 ! visual pursuit > is_a NBO:0000445 ! tail movement > > > > ------------------------------------------------------------------------------ > 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-behavior mailing list > Obo...@li... > https://lists.sourceforge.net/lists/listinfo/obo-behavior > |
From: Melissa H. <ha...@oh...> - 2012-08-14 23:16:13
|
Not that I know of, but I think most movements would be represented as A moving relative to B, where A is some anatomical structure (including whole organism), and B is either another anatomical structure, spatial attribute, or some external feature. for example, hand waving would be the hand moving left relative to the body axis, and then to the right. Probably also need some temporal and/or repetition aspects as well, probably can't call it waving if you only go left then right once. There are also a few relevant GO class that could be made interoperable here for example ,'musculoskeletal movement' Cheers melissa On Aug 14, 2012, at 3:57 PM, Chris Mungall wrote: Are there any ontologies that cover http://en.wikipedia.org/wiki/Category:Anatomical_terms_of_motion Perhaps the best place is a under a new class under "body part movement" in NBO. This would be under a sort of "primitive" class like "motion" from which more complex movements such as chewing, licking and headbanging could be composed. Is NBO the best place for these? / NBO:0000000 ! behavior is_a NBO:0000313 ! physiological behavior is_a NBO:0000338 ! kinesthetic behavior is_a NBO:0000403 ! voluntary movement behavior is_a NBO:0000001 ! body part movement *** is_a NBO:0000007 ! mouth movement is_a NBO:0000017 ! biting is_a NBO:0000019 ! licking is_a NBO:0000073 ! chewing is_a NBO:0000074 ! yawning is_a NBO:0000020 ! head movement is_a NBO:0000023 ! head shaking is_a NBO:0000026 ! head rotation is_a NBO:0000570 ! head bobbing is_a NBO:0000571 ! mutlidirectional head movement is_a NBO:0000068 ! shaking is_a NBO:0000023 ! head shaking is_a NBO:0000444 ! eye movement is_a NBO:0000446 ! visual pursuit is_a NBO:0000445 ! tail movement ------------------------------------------------------------------------------ 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-anatomy mailing list Obo...@li...<mailto:Obo...@li...> https://lists.sourceforge.net/lists/listinfo/obo-anatomy 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...> - 2012-08-14 22:58:07
|
Are there any ontologies that cover http://en.wikipedia.org/wiki/Category:Anatomical_terms_of_motion Perhaps the best place is a under a new class under "body part movement" in NBO. This would be under a sort of "primitive" class like "motion" from which more complex movements such as chewing, licking and headbanging could be composed. Is NBO the best place for these? / NBO:0000000 ! behavior is_a NBO:0000313 ! physiological behavior is_a NBO:0000338 ! kinesthetic behavior is_a NBO:0000403 ! voluntary movement behavior is_a NBO:0000001 ! body part movement *** is_a NBO:0000007 ! mouth movement is_a NBO:0000017 ! biting is_a NBO:0000019 ! licking is_a NBO:0000073 ! chewing is_a NBO:0000074 ! yawning is_a NBO:0000020 ! head movement is_a NBO:0000023 ! head shaking is_a NBO:0000026 ! head rotation is_a NBO:0000570 ! head bobbing is_a NBO:0000571 ! mutlidirectional head movement is_a NBO:0000068 ! shaking is_a NBO:0000023 ! head shaking is_a NBO:0000444 ! eye movement is_a NBO:0000446 ! visual pursuit is_a NBO:0000445 ! tail movement |
From: George G. <g.g...@ge...> - 2012-05-13 22:55:53
|
> > > From: Trish Whetzel <wh...@st...> > Date: 13 May 2012 20:59:20 GMT+01:00 > To: obo...@li... > Subject: Error parsing Neuro Behavior Ontology with OBO-Edit > > Hi Trish, > Hi George, > > I've noticed an error with parsing of the Neuro Behavior Ontology (NBO) in BioPortal. I've tried to load NBO in OBO-Edit, but this results in errors (see attached). yes i am aware of this - Paul Alexander will update the URL so it points to the NBO OWL version. > What editor are you using to develop NBO? Protege. Main file is in OWL then I am using oort for the release. The error was due to the import statements that are pointing to owl versions. behavior-simple.obo works and I have fixed the obo file now which you can get from the project website if you need it (http://code.google.com/p/behavior-ontology/) I am sorry for the trouble and many thanks for letting me know. Best wishes, George > > Trish > > <nbo-error.tiff> > > > > > > From: obo...@li... > Subject: confirm 995f19f95554cd0c2e105248f5f4084eb511f9ca > > > If you reply to this message, keeping the Subject: header intact, > Mailman will discard the held message. Do this if the message is > spam. If you reply to this message and include an Approved: header > with the list password in it, the message will be approved for posting > to the list. The Approved: header can also appear in the first line > of the body of the reply. > |
From: Trish W. <wh...@st...> - 2012-05-13 19:59:28
|
Hi George, I've noticed an error with parsing of the Neuro Behavior Ontology (NBO) in BioPortal. I've tried to load NBO in OBO-Edit, but this results in errors (see attached). What editor are you using to develop NBO? Trish |
From: Mark M. <mu...@st...> - 2012-03-14 15:40:31
|
_______________________________________________ ncbo-survey mailing list ncb...@li... https://mailman.stanford.edu/mailman/listinfo/ncbo-survey |
From: Mark M. <mu...@st...> - 2012-03-07 18:24:46
|
_______________________________________________ ncbo-survey mailing list ncb...@li... https://mailman.stanford.edu/mailman/listinfo/ncbo-survey |
From: Barry S. <phi...@bu...> - 2012-02-10 16:08:39
|
I think the idea of using 'neuro' to distinguish between the sorts of behavior covered by NBO and e.g. cellular behavior is a good one. Problems are: 1. Neuro Behavior Ontology should be grammatically corrected to 'Neuro-Behavior Ontology' 2. It has somehow to be made clear that behavior of neurological cells, etc. is excluded 3. and that we are dealing in NBO with somatic nervous system-caused behavior, i.e. with voluntary behavior (thus not e.g. with the heart's pumping behavior) 4. I hope you agree that NBO is concerned with physical behavior / action. Thus NBO does not cover mental functioning, which we hope to deal with in the Mental Functioning Ontology, of which the Emotion Ontology presented at ICBO was the first part BS On Fri, Feb 10, 2012 at 11:00 AM, George Gkoutos <g.g...@ge...> wrote: > > On 9 Feb 2012, at 02:51, Barry Smith wrote: > >>> >>> >> I believe that we should attempt to define 'behavior' >> I also believe that the title 'Neuro Behavior Ontology' should be >> changed to just 'Behavior Ontology' > > yes I think this would be good - the name was intended to reflect that only behavior as a result of neuroprocesses would be captured as opposed to cellular or bacterial behavior. > > When changing the name we would have to keep the NBO namespace, at least intermediately, since NBO is already being used in annotation. > > George |
From: George G. <g.g...@ge...> - 2012-02-10 16:00:45
|
On 9 Feb 2012, at 02:51, Barry Smith wrote: >> >> > I believe that we should attempt to define 'behavior' > I also believe that the title 'Neuro Behavior Ontology' should be > changed to just 'Behavior Ontology' yes I think this would be good - the name was intended to reflect that only behavior as a result of neuroprocesses would be captured as opposed to cellular or bacterial behavior. When changing the name we would have to keep the NBO namespace, at least intermediately, since NBO is already being used in annotation. George |
From: Richard S. <Richard.Scheuermann@UTSouthwestern.edu> - 2012-02-09 15:12:57
|
In OGMS, we have treated this kind of clinically-relevant increased susceptibility as a disposition to pathological processes. Richard On Feb 9, 2012, at 2:46 AM, Robinson, Peter wrote: >> >>> - Phenotype ontologies avoid labels that sound like processes, and instead use a term that indicates that this is a characteristic of the organism - e.g. "susceptibility to seizures" rather than "seizure" >>> > > Note that in human medicine, what we observe (by medical history) is that a patient, say, has had numerous seizures. We can then infer that this patient has an increased susceptibility to seizures, but we are not able to actually observe susceptibility. Therefore, the HPO has a term called "seizures" (note the "s"). For the MPO, to be specific, for mice, a typical experiment might involve comparison of 100 wt and 100 mutant animals, and let's say 80% of the mutants but 2% of the WT show XYZ. In this case, we observe an increased susceptibility to XYZ as a characteristic of the group (and infer perhaps that also the individual mutant animals have an increased susceptibility to XYZ). > As a general rule, the HPO terms are named and defined according to the way they are used in clinical medicine. Thus, the epilepsy section of the HPO has been revised extensively together with an epilepsy group here in Germany, and the term names reflect standards in that community. The logical (computer readable OWL) definitions might include the concept of susceptibility as an "allowable" inference for this phenotype, but we are currently still considering what the best way is of making ontology design patterns for this. It would be very helpful to have a better behaviour/neurological physiology ontology. Even though several groups ahve now begun to work on this, it is actually a massive task and I think we are still far away from a good solution. > > BW Peter > > > ------------------------------------------------------------------------------ > Virtualization & Cloud Management Using Capacity Planning > Cloud computing makes use of virtualization - but cloud computing > also focuses on allowing computing to be delivered as a service. > http://www.accelacomm.com/jaw/sfnl/114/51521223/ > _______________________________________________ > Obo-phenotype mailing list > Obo...@li... > https://lists.sourceforge.net/lists/listinfo/obo-phenotype ------------------------------------------------------------------------------------------------ Richard H. Scheuermann, Ph.D. Chief, Division of Biomedical Informatics John H. Childers Professorship in Pathology Department of Pathology U.T. Southwestern Medical Center 5323 Harry Hines Blvd. Dallas, TX 75390-9072 phone: 214-648-4115 FAX: 214-648-4070 email: ric...@ut... http://pathcuric1.swmed.edu/Research/scheuermann.html ________________________________ UT Southwestern Medical Center The future of medicine, today. |
From: Robinson, P. <pet...@ch...> - 2012-02-09 10:24:42
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* NBO contains an undefined class "mood disorder", which subclasses like "bipolar disorder". Of course, as expected we find classes with the same label in HPO and DO. => Another comment: I do not think that the various disorders really belong in a behavior ontology. The NBO is currently a sammelsurium of different things, and it will be important to define its mission. I think that it would be of most use to the community to have a behavior ontology that would attempt to describe the components of "normal" behavior. Polydipsia is by definition a deviation from "normal" behavior ("poly-...") and does not really belong in NBO. I think it would be preferable to have deviations in a separate ontology. The HPO is aspiring to provide this for all realms of human medicine, but if there are reasons to have a separate human neuro/behavior-phenotype ontology we would x-link to that also. In any case, it makes little sense to mix "normal" behavior and deviations from normal behavior in the same ontology (NBO), and I would plead for a different focus for NBO. cheers Peter |
From: Robinson, P. <pet...@ch...> - 2012-02-09 08:46:32
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> >> - Phenotype ontologies avoid labels that sound like processes, and instead use a term that indicates that this is a characteristic of the organism - e.g. "susceptibility to seizures" rather than "seizure" >> Note that in human medicine, what we observe (by medical history) is that a patient, say, has had numerous seizures. We can then infer that this patient has an increased susceptibility to seizures, but we are not able to actually observe susceptibility. Therefore, the HPO has a term called "seizures" (note the "s"). For the MPO, to be specific, for mice, a typical experiment might involve comparison of 100 wt and 100 mutant animals, and let's say 80% of the mutants but 2% of the WT show XYZ. In this case, we observe an increased susceptibility to XYZ as a characteristic of the group (and infer perhaps that also the individual mutant animals have an increased susceptibility to XYZ). As a general rule, the HPO terms are named and defined according to the way they are used in clinical medicine. Thus, the epilepsy section of the HPO has been revised extensively together with an epilepsy group here in Germany, and the term names reflect standards in that community. The logical (computer readable OWL) definitions might include the concept of susceptibility as an "allowable" inference for this phenotype, but we are currently still considering what the best way is of making ontology design patterns for this. It would be very helpful to have a better behaviour/neurological physiology ontology. Even though several groups ahve now begun to work on this, it is actually a massive task and I think we are still far away from a good solution. BW Peter |
From: Peter M. <pet...@gm...> - 2012-02-09 03:16:45
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On Feb 8, 2012, at 9:51 PM, Barry Smith wrote: > On Wed, Feb 8, 2012 at 9:29 PM, Chris Mungall <cjm...@lb...> wrote: >> >> Many of the behavioral phenotypes in the phenotype ontologies have labels that are exact matches for classes in NBO. >> >> For example: >> >> * NBO contains an undefined class "mood disorder", which subclasses like "bipolar disorder". Of course, as expected we find classes with the same label in HPO and DO. > > See also OGMS >> >> * The phenotype ontologies also contain classes like "polydipsia" and "seizure", which sound more behavior-like, and we also find these as primary labels in NBO. >> >> This creates a usability problem - when we load the combined ontologies into a single index, database, triplestore or ontology environment we have duplicate labels. Of course this could be solved at the software level, but there are multiple pieces of software to fix here, which is prohibitively costly. >> >> The labeling problem will be easier to fix when we are clear about what the different ontologies are representing (if indeed they're representing different things or the same thing) >> >> Here's one possible solution: >> >> - NBO doesn't use "disorder" in the primary labels, and instead chooses a name that more clearly indicates that we're talking about a process. A good definition can help with a name - ideally a definition of a process class should indicate the start and end of the process. >> > I believe that we should attempt to define 'behavior' > I also believe that the title 'Neuro Behavior Ontology' should be > changed to just 'Behavior Ontology' > > >> - Phenotype ontologies avoid labels that sound like processes, and instead use a term that indicates that this is a characteristic of the organism - e.g. "susceptibility to seizures" rather than "seizure" >> > Excellent > This would be a great step forward > BS > I would also be happy to see an ontology that focuses on the processes, apart from how an organism's participation in a process relates to its phenotype. I want to be able to describe an instance of a seizure without focusing on whether the organism characteristically displays these seizures or is merely susceptible to them. -PEM > ------------------------------------------------------------------------------ > Virtualization & Cloud Management Using Capacity Planning > Cloud computing makes use of virtualization - but cloud computing > also focuses on allowing computing to be delivered as a service. > http://www.accelacomm.com/jaw/sfnl/114/51521223/ > _______________________________________________ > Obo-phenotype mailing list > Obo...@li... > https://lists.sourceforge.net/lists/listinfo/obo-phenotype |
From: Barry S. <phi...@bu...> - 2012-02-09 02:52:43
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On Wed, Feb 8, 2012 at 9:29 PM, Chris Mungall <cjm...@lb...> wrote: > > Many of the behavioral phenotypes in the phenotype ontologies have labels that are exact matches for classes in NBO. > > For example: > > * NBO contains an undefined class "mood disorder", which subclasses like "bipolar disorder". Of course, as expected we find classes with the same label in HPO and DO. See also OGMS > > * The phenotype ontologies also contain classes like "polydipsia" and "seizure", which sound more behavior-like, and we also find these as primary labels in NBO. > > This creates a usability problem - when we load the combined ontologies into a single index, database, triplestore or ontology environment we have duplicate labels. Of course this could be solved at the software level, but there are multiple pieces of software to fix here, which is prohibitively costly. > > The labeling problem will be easier to fix when we are clear about what the different ontologies are representing (if indeed they're representing different things or the same thing) > > Here's one possible solution: > > - NBO doesn't use "disorder" in the primary labels, and instead chooses a name that more clearly indicates that we're talking about a process. A good definition can help with a name - ideally a definition of a process class should indicate the start and end of the process. > I believe that we should attempt to define 'behavior' I also believe that the title 'Neuro Behavior Ontology' should be changed to just 'Behavior Ontology' > - Phenotype ontologies avoid labels that sound like processes, and instead use a term that indicates that this is a characteristic of the organism - e.g. "susceptibility to seizures" rather than "seizure" > Excellent This would be a great step forward BS |