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Re: [Obo-envo] [Obi-relations] habitat relations
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From: Norman M. <mor...@cs...> - 2009-01-20 17:41:25
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The following is a very generic and early definition that we had for environment (...I have to admit that it didn't meet with approval from all parties ;-) Term: environment. Def: The totality of circumstances external to a definable entity The current working definition for habitat in EnvO is: Term: habitat. Def: A spatial region having environmental qualities which may sustain an organism or a community of organisms. It follows that the definable entity, in the case of habitat, is an organism, community or population of organisms. Where confusion lies is that the most commonly held definition of habitat is: 'The natural environment in which an organism lives', where 'natural' in this instance refers to the USUAL or PREFERRED environment in which an organism, community or population of organisms lives. I agree with Barry that EnvO "should supply the resources to state that Zero is currently living in the XYZ compound in the ABC zoo". However, if the body of data surrounding instances of polar bears are most frequently those from zoos (which could easily happen, by virtue of the fact that they are easier to study). Then we have to be careful computationally not to infer a type level relation that asserts the habitat or the 'usual environment' of the type polar bear is a zoo ...even though it is a rather sobering fact that this may soon be true. I like the EnvO definition for habitat. It's just that the term 'habitat' is already heavily overloaded.... anyone good at making up words? Frank Gibson wrote: > Hi Norman > > Would you be able to attempt a definition of between the two? Are you > using it in the sense a habitat or where an organism lives and > environment is where it is found/captured/stuck in a jar from? > > Frank > > On Tue, Jan 20, 2009 at 4:10 PM, Barry Smith <phi...@bu...> wrote: > >> At 08:16 AM 1/20/2009, Norman Morrison wrote: >> >>> Hi Chris / OBI Group, >>> >>> In sending this post, you've actually provided a use case that >>> potentially opens up a (small) can of worms that I've also been thinking >>> about for a while. >>> >>> When including an has_habitat <-> is_habitat_of relation, I think it's >>> worth stepping back for a moment and considering whether or not an >>> has_environment <-> is_environment_of relation might be more appropriate? >>> >>> The reason being is that the definition of habitat amongst >>> biologists/ecologists - more often than not - implies the USUAL or >>> PREFERRED environment of an organism. ie If you were visiting Milwaukee >>> County Zoo, you wouldn't expect to see the habitat of 'Zero' the polar >>> bear described as 'a compound in a zoo' on his plaque, rather you would >>> expect to see something like 'Arctic ice sheets'. As you point out this >>> might make more sense for habitat to be considered as type level relation. >>> >>> I was actually considering a proposal to substitute all instances of the >>> term 'habitat' in EnvO with 'environment', in order to avoid any further >>> confusion. >>> >> Note that we need instances, too -- otherwise >> EnvO won't work with GAZ. That is, EnvO should >> supply the resources to state that Zero is >> currently living in the XYZ compound in the ABC >> zoo. I think that where Zero is living is then an >> instance of the type environment (an organism is >> living in it), even we are not talking here about >> the usual environment for arctic bears >> BS >> >> >> >>> Al the best, >>> Norman >>> >>> >>> Chris Mungall wrote: >>> >>>> The OBI group have proposed a has_habitat relation, connecting an >>>> organism to a material entity (where material entity can be anything >>>> from a patch of skin to a planet; but not a bfo:Site) >>>> >>>> >>>> >>>>> 5/ The inclusion of the habitat relation to determine if a material >>>>> entity is an environment >>>>> >>>>> *has_participant >>>>> **(child) has_habitat <-> is_habitat_of [domain = organism, range = >>>>> material entity] >>>>> >>>>> >>>> Should the domain of this instance-level relation be an organism or a >>>> species? (I'd like the ecologists' answer before delving into thorny >>>> questions about whether a species is an individual or a type. We can >>>> always substitute population). Perhaps this makes more sense as a type- >>>> level relation? >>>> >>>> The relevant portion of ENVO: >>>> >>>> / ENVO:00002297 ! environmental feature [DEF: "A feature that is."] >>>> is_a ENVO:00002036 ! habitat *** [DEF: "A spatial region having >>>> environmental qualities which may sustain an organism or a community >>>> of organisms."] >>>> is_a ENVO:00000144 ! aquatic habitat [DEF: "A habitat that is in >>>> or on water."] >>>> is_a ENVO:00000568 ! aerial habitat [DEF: "A habitat that is >>>> solely in the air."] >>>> is_a ENVO:00000571 ! arboreal habitat [DEF: "A habitat in or on >>>> trees."] >>>> is_a ENVO:00000572 ! subterrestrial habitat [DEF: "A habitat that >>>> is below the surface of the earth."] >>>> is_a ENVO:00002009 ! terrestrial habitat [DEF: "A habitat that is >>>> on or at the boundary of the surface of the Earth."] >>>> is_a ENVO:00002020 ! extreme habitat [DEF: "A habitat having at >>>> least one environmental quality that tends towards either the largest >>>> or smallest element of the set. The physical or geochemical extreme >>>> conditions found in an extreme habitat are often detrimental to the >>>> majority of life on Earth."] >>>> is_a ENVO:00002031 ! anthropogenic habitat [DEF: "A habitat that >>>> is in or on an environmental feature or material derived from human >>>> activity."] >>>> is_a ENVO:00002032 ! organism-associated habitat [DEF: "A habitat >>>> that is in or on a living thing."] >>>> >>>> >>>> On Jan 19, 2009, at 9:02 AM, Melanie Courtot wrote: >>>> >>>> >>>> >>>>> Hi all, >>>>> >>>>> We will have a relations call tomorrow. Frank won't be able to attend >>>>> but he did prepare the agenda at >>>>> >>> http://obi-ontology.org/page/RB_20_01_2009 >>> >>>>> . >>>>> >>>>> Let me know if you can't make it. >>>>> >>>>> Thanks, >>>>> Melanie >>>>> >>>>> --- >>>>> Mélanie Courtot >>>>> TFL- BCCRC >>>>> 675 West 10th Avenue >>>>> Vancouver, BC >>>>> V5Z 1L3, Canada >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>> ------------------------------------------------------------------------------ >>> >>>>> This SF.net email is sponsored by: >>>>> SourcForge Community >>>>> SourceForge wants to tell your story. >>>>> http://p.sf.net/sfu/sf-spreadtheword >>>>> _______________________________________________ >>>>> Obi-relations mailing list >>>>> Obi...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/obi-relations >>>>> >>>>> >>>>> >>>> >>>> >>> ------------------------------------------------------------------------------ >>> >>>> This SF.net email is sponsored by: >>>> SourcForge Community >>>> SourceForge wants to tell your story. >>>> http://p.sf.net/sfu/sf-spreadtheword >>>> _______________________________________________ >>>> Obo-envo mailing list >>>> Obo...@li... >>>> https://lists.sourceforge.net/lists/listinfo/obo-envo >>>> >>>> >>> -- >>> Norman Morrison, PhD >>> NEBC Ontologies & Data Standards Coordinator (http://nebc.nox.ac.uk/) >>> Room LF8, School of Computer Science, Kilburn Building, >>> University of Manchester, Oxford Road, MANCHESTER, UK. M13 9PL. >>> Tel: +44 (0)161 275 0646 Fax: +44 (0)161 275 6236 >>> >>> >>> ------------------------------------------------------------------------------ >>> This SF.net email is sponsored by: >>> SourcForge Community >>> SourceForge wants to tell your story. >>> http://p.sf.net/sfu/sf-spreadtheword >>> _______________________________________________ >>> Obo-envo mailing list >>> Obo...@li... >>> https://lists.sourceforge.net/lists/listinfo/obo-envo >>> >> ------------------------------------------------------------------------------ >> This SF.net email is sponsored by: >> SourcForge Community >> SourceForge wants to tell your story. >> http://p.sf.net/sfu/sf-spreadtheword >> _______________________________________________ >> Obi-relations mailing list >> Obi...@li... >> https://lists.sourceforge.net/lists/listinfo/obi-relations >> >> > > > > -- Norman Morrison, PhD NEBC Ontologies & Data Standards Coordinator (http://nebc.nox.ac.uk/) Room LF8, School of Computer Science, Kilburn Building, University of Manchester, Oxford Road, MANCHESTER, UK. M13 9PL. Tel: +44 (0)161 275 0646 Fax: +44 (0)161 275 6236 |