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From: Fostel, J. (NIH/N. [C] <fo...@ni...> - 2009-03-23 14:07:15
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agenda: cover Oliver's immunology terms: 1. 'adjuvant role'; 2. 'vaccine adjuvant role' 3. 'virulence factor' 4. 'vaccine vector role' 5. 'antigen' 6. 'antibody': Note: As I discussed with Jennifer in the OBI Vancouver Workshop, this term may not be a role. Needs confirmation. 7. host 8. parasite 9. pathogen 10. toxin 11. 'vaccine role' Jennifer Fostel, Ph.D. CEBS Scientific Administrator Global Health Sector, SRA International, Inc Laboratory of Respiratory Biology NIEHS, NIH PO Box 12233 Mail Drop F1-05 111 Alexander Drive Research Triangle Park NC 27709-2233 phone 919 541 5055 fax 919 541 1460 |
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From: Alan R. <ala...@gm...> - 2009-03-23 16:39:53
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I can't make it - hoped I could but thought it at 11. Quick comments on these: On Mon, Mar 23, 2009 at 10:06 AM, Fostel, Jennifer (NIH/NIEHS) [C] <fo...@ni...> wrote: > agenda: > cover Oliver's immunology terms: > 1. ‘adjuvant role’; > 2. ‘vaccine adjuvant role’ > 3. ‘virulence factor’ this one requires some explanation - examples would be good. I'm not sure this is a role. > 4. ‘vaccine vector role’ > 5. ‘antigen’ > 6. ‘antibody’: Note: As I discussed with Jennifer in the OBI Vancouver > Workshop, this term may not be a role. Needs confirmation. function, I think. > 7. host > 8. parasite > 9. pathogen > 10. toxin in some cases may be a function. > 11. ‘vaccine role’ > > Jennifer Fostel, Ph.D. > CEBS Scientific Administrator > Global Health Sector, SRA International, Inc > > Laboratory of Respiratory Biology > NIEHS, NIH > PO Box 12233 Mail Drop F1-05 > 111 Alexander Drive > Research Triangle Park NC 27709-2233 > > phone 919 541 5055 > fax 919 541 1460 > > > ------------------------------------------------------------------------------ > Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are > powering Web 2.0 with engaging, cross-platform capabilities. Quickly and > easily build your RIAs with Flex Builder, the Eclipse(TM)based development > software that enables intelligent coding and step-through debugging. > Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com > _______________________________________________ > Obi-role-branch mailing list > Obi...@li... > https://lists.sourceforge.net/lists/listinfo/obi-role-branch > > |
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From: Frank G. <fg...@gm...> - 2009-03-23 16:59:43
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On Mon, Mar 23, 2009 at 4:39 PM, Alan Ruttenberg <ala...@gm...> wrote: > I can't make it - hoped I could but thought it at 11. Quick comments on these: > > On Mon, Mar 23, 2009 at 10:06 AM, Fostel, Jennifer (NIH/NIEHS) [C] > <fo...@ni...> wrote: >> agenda: >> cover Oliver's immunology terms: >> 1. ‘adjuvant role’; >> 2. ‘vaccine adjuvant role’ >> 3. ‘virulence factor’ > this one requires some explanation - examples would be good. I'm not > sure this is a role. >> 4. ‘vaccine vector role’ Please consult the tracker item regarding vector with regards to #4 http://sourceforge.net/tracker/index.php?func=detail&aid=2078795&group_id=177891&atid=886178 Frank >> 5. ‘antigen’ >> 6. ‘antibody’: Note: As I discussed with Jennifer in the OBI Vancouver >> Workshop, this term may not be a role. Needs confirmation. > function, I think. >> 7. host >> 8. parasite >> 9. pathogen >> 10. toxin > in some cases may be a function. >> 11. ‘vaccine role’ >> >> Jennifer Fostel, Ph.D. >> CEBS Scientific Administrator >> Global Health Sector, SRA International, Inc >> >> Laboratory of Respiratory Biology >> NIEHS, NIH >> PO Box 12233 Mail Drop F1-05 >> 111 Alexander Drive >> Research Triangle Park NC 27709-2233 >> >> phone 919 541 5055 >> fax 919 541 1460 >> >> >> ------------------------------------------------------------------------------ >> Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are >> powering Web 2.0 with engaging, cross-platform capabilities. Quickly and >> easily build your RIAs with Flex Builder, the Eclipse(TM)based development >> software that enables intelligent coding and step-through debugging. >> Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com >> _______________________________________________ >> Obi-role-branch mailing list >> Obi...@li... >> https://lists.sourceforge.net/lists/listinfo/obi-role-branch >> >> > > ------------------------------------------------------------------------------ > Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are > powering Web 2.0 with engaging, cross-platform capabilities. Quickly and > easily build your RIAs with Flex Builder, the Eclipse(TM)based development > software that enables intelligent coding and step-through debugging. > Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com > _______________________________________________ > Obi-role-branch mailing list > Obi...@li... > https://lists.sourceforge.net/lists/listinfo/obi-role-branch > -- Frank Gibson, PhD http://peanutbutter.wordpress.com/ |
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From: Fostel, J. (NIH/N. [C] <fo...@ni...> - 2009-03-23 17:13:02
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i am not sure that several of these are roles
Oliver was not able to make the call either
we are postponing until next week
the call was at 11 -- it seems that i am numerically challenged even when using text i'm afraid.
sorry
looking forward to hearing you all next week.
i spent the hour form 11 - 12 working on the current branch.
it would be nice to show more in the logical definitions, so additional agenda will include....
(1) that something was present at the start / end of a process
we probably need start and end under process boundry in OBI
and possibly a relation
(2) how to logically define that something is present, something is causal, something is participating passively
(3)processes for reguatory things; things defined by regulations and processes involved in ensuring compliance with regulations; on agenda for PPA branch
(4)discuss with data transformation - comparison process
(5) discuss with PPA process of
detection in general, not just of substance (need proxy detection?) or label (other ways to detect?)
executing an investigation component
providing nourishment
(6) immune specific questions - do we need epitope role?? is it not part_of an antibody?
process of modifying a biological response; do we need to add immunogen?
(7) need to add to biomaterials: vaccine, virulence factor? antigen in order to define these roles; wikipedia tells me that an antigen must interact with an antibody.
(8) the toxin question will be interesting -- we have had some discussion on this previously!
probably an objective.
-----Original Message-----
From: Alan Ruttenberg [mailto:ala...@gm...]
Sent: Monday, March 23, 2009 12:39 PM
To: Fostel, Jennifer (NIH/NIEHS) [C]
Cc: obi...@li...
Subject: Re: [Obi-role-branch] role call today at noon EDT
I can't make it - hoped I could but thought it at 11. Quick comments on these:
On Mon, Mar 23, 2009 at 10:06 AM, Fostel, Jennifer (NIH/NIEHS) [C] <fo...@ni...> wrote:
> agenda:
> cover Oliver's immunology terms:
> 1. 'adjuvant role';
> 2. 'vaccine adjuvant role'
> 3. 'virulence factor'
this one requires some explanation - examples would be good. I'm not sure this is a role.
> 4. 'vaccine vector role'
> 5. 'antigen'
> 6. 'antibody': Note: As I discussed with Jennifer in the OBI Vancouver
> Workshop, this term may not be a role. Needs confirmation.
function, I think.
> 7. host
> 8. parasite
> 9. pathogen
> 10. toxin
in some cases may be a function.
> 11. 'vaccine role'
>
> Jennifer Fostel, Ph.D.
> CEBS Scientific Administrator
> Global Health Sector, SRA International, Inc
>
> Laboratory of Respiratory Biology
> NIEHS, NIH
> PO Box 12233 Mail Drop F1-05
> 111 Alexander Drive
> Research Triangle Park NC 27709-2233
>
> phone 919 541 5055
> fax 919 541 1460
>
>
> ----------------------------------------------------------------------
> -------- Apps built with the Adobe(R) Flex(R) framework and Flex
> Builder(TM) are powering Web 2.0 with engaging, cross-platform
> capabilities. Quickly and easily build your RIAs with Flex Builder,
> the Eclipse(TM)based development software that enables intelligent
> coding and step-through debugging.
> Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com
> _______________________________________________
> Obi-role-branch mailing list
> Obi...@li...
> https://lists.sourceforge.net/lists/listinfo/obi-role-branch
>
>
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From: Fostel, J. (NIH/N. [C] <fo...@ni...> - 2009-03-23 17:18:15
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we closed the vector tracker items at the end of last year. ..jennifer -----Original Message----- From: Frank Gibson [mailto:fg...@gm...] Sent: Monday, March 23, 2009 1:00 PM To: Alan Ruttenberg Cc: Fostel, Jennifer (NIH/NIEHS) [C]; obi...@li... Subject: Re: [Obi-role-branch] role call today at noon EDT On Mon, Mar 23, 2009 at 4:39 PM, Alan Ruttenberg <ala...@gm...> wrote: > I can't make it - hoped I could but thought it at 11. Quick comments on these: > > On Mon, Mar 23, 2009 at 10:06 AM, Fostel, Jennifer (NIH/NIEHS) [C] > <fo...@ni...> wrote: >> agenda: >> cover Oliver's immunology terms: >> 1. 'adjuvant role'; >> 2. 'vaccine adjuvant role' >> 3. 'virulence factor' > this one requires some explanation - examples would be good. I'm not > sure this is a role. >> 4. 'vaccine vector role' Please consult the tracker item regarding vector with regards to #4 http://sourceforge.net/tracker/index.php?func=detail&aid=2078795&group_id=177891&atid=886178 Frank >> 5. 'antigen' >> 6. 'antibody': Note: As I discussed with Jennifer in the OBI >> Vancouver Workshop, this term may not be a role. Needs confirmation. > function, I think. >> 7. host >> 8. parasite >> 9. pathogen >> 10. toxin > in some cases may be a function. >> 11. 'vaccine role' >> >> Jennifer Fostel, Ph.D. >> CEBS Scientific Administrator >> Global Health Sector, SRA International, Inc >> >> Laboratory of Respiratory Biology >> NIEHS, NIH >> PO Box 12233 Mail Drop F1-05 >> 111 Alexander Drive >> Research Triangle Park NC 27709-2233 >> >> phone 919 541 5055 >> fax 919 541 1460 >> >> >> --------------------------------------------------------------------- >> --------- Apps built with the Adobe(R) Flex(R) framework and Flex >> Builder(TM) are powering Web 2.0 with engaging, cross-platform >> capabilities. Quickly and easily build your RIAs with Flex Builder, >> the Eclipse(TM)based development software that enables intelligent >> coding and step-through debugging. >> Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com >> _______________________________________________ >> Obi-role-branch mailing list >> Obi...@li... >> https://lists.sourceforge.net/lists/listinfo/obi-role-branch >> >> > > ---------------------------------------------------------------------- > -------- Apps built with the Adobe(R) Flex(R) framework and Flex > Builder(TM) are powering Web 2.0 with engaging, cross-platform > capabilities. Quickly and easily build your RIAs with Flex Builder, > the Eclipse(TM)based development software that enables intelligent > coding and step-through debugging. > Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com > _______________________________________________ > Obi-role-branch mailing list > Obi...@li... > https://lists.sourceforge.net/lists/listinfo/obi-role-branch > -- Frank Gibson, PhD http://peanutbutter.wordpress.com/ |
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From: Frank G. <fg...@gm...> - 2009-03-23 17:22:32
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On Mon, Mar 23, 2009 at 5:18 PM, Fostel, Jennifer (NIH/NIEHS) [C] <fo...@ni...> wrote: > we closed the vector tracker items at the end of last year. > ..jennifer Jennifer, you cant close an item without posting a conclusion, there are several people on that thread which appear to be of the same line of thought, which does not correspond to the file Frank > -----Original Message----- > From: Frank Gibson [mailto:fg...@gm...] > Sent: Monday, March 23, 2009 1:00 PM > To: Alan Ruttenberg > Cc: Fostel, Jennifer (NIH/NIEHS) [C]; obi...@li... > Subject: Re: [Obi-role-branch] role call today at noon EDT > > On Mon, Mar 23, 2009 at 4:39 PM, Alan Ruttenberg <ala...@gm...> wrote: >> I can't make it - hoped I could but thought it at 11. Quick comments on these: >> >> On Mon, Mar 23, 2009 at 10:06 AM, Fostel, Jennifer (NIH/NIEHS) [C] >> <fo...@ni...> wrote: >>> agenda: >>> cover Oliver's immunology terms: >>> 1. 'adjuvant role'; >>> 2. 'vaccine adjuvant role' >>> 3. 'virulence factor' >> this one requires some explanation - examples would be good. I'm not >> sure this is a role. >>> 4. 'vaccine vector role' > > Please consult the tracker item regarding vector with regards to #4 > http://sourceforge.net/tracker/index.php?func=detail&aid=2078795&group_id=177891&atid=886178 > > Frank > > > > >>> 5. 'antigen' >>> 6. 'antibody': Note: As I discussed with Jennifer in the OBI >>> Vancouver Workshop, this term may not be a role. Needs confirmation. >> function, I think. >>> 7. host >>> 8. parasite >>> 9. pathogen >>> 10. toxin >> in some cases may be a function. >>> 11. 'vaccine role' >>> >>> Jennifer Fostel, Ph.D. >>> CEBS Scientific Administrator >>> Global Health Sector, SRA International, Inc >>> >>> Laboratory of Respiratory Biology >>> NIEHS, NIH >>> PO Box 12233 Mail Drop F1-05 >>> 111 Alexander Drive >>> Research Triangle Park NC 27709-2233 >>> >>> phone 919 541 5055 >>> fax 919 541 1460 >>> >>> >>> --------------------------------------------------------------------- >>> --------- Apps built with the Adobe(R) Flex(R) framework and Flex >>> Builder(TM) are powering Web 2.0 with engaging, cross-platform >>> capabilities. Quickly and easily build your RIAs with Flex Builder, >>> the Eclipse(TM)based development software that enables intelligent >>> coding and step-through debugging. >>> Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com >>> _______________________________________________ >>> Obi-role-branch mailing list >>> Obi...@li... >>> https://lists.sourceforge.net/lists/listinfo/obi-role-branch >>> >>> >> >> ---------------------------------------------------------------------- >> -------- Apps built with the Adobe(R) Flex(R) framework and Flex >> Builder(TM) are powering Web 2.0 with engaging, cross-platform >> capabilities. Quickly and easily build your RIAs with Flex Builder, >> the Eclipse(TM)based development software that enables intelligent >> coding and step-through debugging. >> Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com >> _______________________________________________ >> Obi-role-branch mailing list >> Obi...@li... >> https://lists.sourceforge.net/lists/listinfo/obi-role-branch >> > > > > -- > Frank Gibson, PhD > http://peanutbutter.wordpress.com/ > -- Frank Gibson, PhD http://peanutbutter.wordpress.com/ |
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From: Alan R. <ala...@gm...> - 2009-03-23 17:56:26
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On Mon, Mar 23, 2009 at 1:12 PM, Fostel, Jennifer (NIH/NIEHS) [C] <fo...@ni...> wrote: > i am not sure that several of these are roles > Oliver was not able to make the call either > we are postponing until next week > > the call was at 11 -- it seems that i am numerically challenged even when using text i'm afraid. > sorry > > looking forward to hearing you all next week. > i spent the hour form 11 - 12 working on the current branch. > > > it would be nice to show more in the logical definitions, so additional agenda will include.... > > (1) that something was present at the start / end of a process > we probably need start and end under process boundry in OBI > and possibly a relation > > (2) how to logically define that something is present, something is causal, something is participating passively Hmm. How to english define it would be a good start :) > (6) immune specific questions - do we need epitope role?? is it not part_of an antibody? > process of modifying a biological response; do we need to add immunogen? I think epitope is a quality. IIRC Bjoern has promised a fight to the death in opposition ;-) > (8) the toxin question will be interesting -- we have had some discussion on this previously! > probably an objective. Not if you're a snake. It's a function in that case. -Alan |
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From: Fostel, J. (NIH/N. [C] <fo...@ni...> - 2009-03-23 18:19:52
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english definitions at the call :-) a snake using toxin is out of scope of obi - that was the resolution that last time this surfaced (as poison) -----Original Message----- From: Alan Ruttenberg [mailto:ala...@gm...] Sent: Monday, March 23, 2009 1:56 PM To: Fostel, Jennifer (NIH/NIEHS) [C] Cc: obi...@li... Subject: Re: [Obi-role-branch] role call today at noon EDT On Mon, Mar 23, 2009 at 1:12 PM, Fostel, Jennifer (NIH/NIEHS) [C] <fo...@ni...> wrote: > i am not sure that several of these are roles Oliver was not able to > make the call either we are postponing until next week > > the call was at 11 -- it seems that i am numerically challenged even when using text i'm afraid. > sorry > > looking forward to hearing you all next week. > i spent the hour form 11 - 12 working on the current branch. > > > it would be nice to show more in the logical definitions, so additional agenda will include.... > > (1) that something was present at the start / end of a process we > probably need start and end under process boundry in OBI and possibly > a relation > > (2) how to logically define that something is present, something is > causal, something is participating passively Hmm. How to english define it would be a good start :) > (6) immune specific questions - do we need epitope role?? is it not part_of an antibody? > process of modifying a biological response; do we need to add immunogen? I think epitope is a quality. IIRC Bjoern has promised a fight to the death in opposition ;-) > (8) the toxin question will be interesting -- we have had some discussion on this previously! > probably an objective. Not if you're a snake. It's a function in that case. -Alan |
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From: Ryan B. <rbr...@bc...> - 2009-03-23 18:03:32
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>> (8) the toxin question will be interesting -- we have had some discussion on this previously! >> probably an objective. >Not if you're a snake. It's a function in that case. I'm all for OBI being extensible, but I don't see a use case for toxin-producing snake overlords performing experiments, so it may be helpful to restrict to the domain of biomedical investigations. Ryan |
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From: Alan R. <ala...@gm...> - 2009-03-23 18:13:06
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If the human overlords are doing experiments on snakes (they have known to do so - retribution in AD 1e6) then we need to be careful about the term "toxin", at least using a preferred term that makes it clear that we are talking about toxins role as reagent, and a definition to suit. -Alan On Mon, Mar 23, 2009 at 2:00 PM, Ryan Brinkman <rbr...@bc...> wrote: > >>> (8) the toxin question will be interesting -- we have had some discussion on this previously! >>> probably an objective. > >>Not if you're a snake. It's a function in that case. > > I'm all for OBI being extensible, but I don't see a use case for toxin-producing snake overlords performing experiments, so it may be helpful to restrict to the domain of biomedical investigations. > > Ryan > > |
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From: Fostel, J. (NIH/N. [C] <fo...@ni...> - 2009-03-23 18:21:39
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right! also rats inadvertantly ingesting an excess of a substance, unless we think they are committing suicide, are also out of scope (committing suicide might permit them the worker role, but in OBI this role is limited to homo sapiens until we get robot in there) -----Original Message----- From: Ryan Brinkman [mailto:rbr...@bc...] Sent: Monday, March 23, 2009 2:01 PM To: Alan Ruttenberg; Fostel, Jennifer (NIH/NIEHS) [C] Cc: obi...@li... Subject: RE: [Obi-role-branch] role call today at noon EDT >> (8) the toxin question will be interesting -- we have had some discussion on this previously! >> probably an objective. >Not if you're a snake. It's a function in that case. I'm all for OBI being extensible, but I don't see a use case for toxin-producing snake overlords performing experiments, so it may be helpful to restrict to the domain of biomedical investigations. Ryan |
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From: Alan R. <ala...@gm...> - 2009-03-23 18:56:15
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I'm unconvinced. Poison is different than toxins, the latter of which can be evolutionarily selected for (see google define of the two terms). In any case, if there is a non function definition that's fine. I'm simply warning that using the name unqualified is likely to lead to confusion in the communities we serve. -Alan On Mon, Mar 23, 2009 at 2:21 PM, Fostel, Jennifer (NIH/NIEHS) [C] <fo...@ni...> wrote: > right! also rats inadvertantly ingesting an excess of a substance, unless we think they are committing suicide, are also out of scope (committing suicide might permit them the worker role, but in OBI this role is limited to homo sapiens until we get robot in there) > > -----Original Message----- > From: Ryan Brinkman [mailto:rbr...@bc...] > Sent: Monday, March 23, 2009 2:01 PM > To: Alan Ruttenberg; Fostel, Jennifer (NIH/NIEHS) [C] > Cc: obi...@li... > Subject: RE: [Obi-role-branch] role call today at noon EDT > > >>> (8) the toxin question will be interesting -- we have had some discussion on this previously! >>> probably an objective. > >>Not if you're a snake. It's a function in that case. > > I'm all for OBI being extensible, but I don't see a use case for toxin-producing snake overlords performing experiments, so it may be helpful to restrict to the domain of biomedical investigations. > > Ryan > > |
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From: Fostel, J. (NIH/N. [C] <fo...@ni...> - 2009-03-23 19:16:55
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i think that toxin as a quality or function or biomaterial or all three is / are good. poison as an objective is good using toxin in the sense of its evolutionary role (eg killing the preditor or lunch-to-be) has a non-human performing the role. -----Original Message----- From: Alan Ruttenberg [mailto:ala...@gm...] Sent: Monday, March 23, 2009 2:56 PM To: Fostel, Jennifer (NIH/NIEHS) [C] Cc: Ryan Brinkman; obi...@li... Subject: Re: [Obi-role-branch] role call today at noon EDT I'm unconvinced. Poison is different than toxins, the latter of which can be evolutionarily selected for (see google define of the two terms). In any case, if there is a non function definition that's fine. I'm simply warning that using the name unqualified is likely to lead to confusion in the communities we serve. -Alan On Mon, Mar 23, 2009 at 2:21 PM, Fostel, Jennifer (NIH/NIEHS) [C] <fo...@ni...> wrote: > right! also rats inadvertantly ingesting an excess of a substance, > unless we think they are committing suicide, are also out of scope > (committing suicide might permit them the worker role, but in OBI this > role is limited to homo sapiens until we get robot in there) > > -----Original Message----- > From: Ryan Brinkman [mailto:rbr...@bc...] > Sent: Monday, March 23, 2009 2:01 PM > To: Alan Ruttenberg; Fostel, Jennifer (NIH/NIEHS) [C] > Cc: obi...@li... > Subject: RE: [Obi-role-branch] role call today at noon EDT > > >>> (8) the toxin question will be interesting -- we have had some discussion on this previously! >>> probably an objective. > >>Not if you're a snake. It's a function in that case. > > I'm all for OBI being extensible, but I don't see a use case for toxin-producing snake overlords performing experiments, so it may be helpful to restrict to the domain of biomedical investigations. > > Ryan > > |
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From: Alan R. <ala...@gm...> - 2009-03-23 19:22:38
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On Mon, Mar 23, 2009 at 3:16 PM, Fostel, Jennifer (NIH/NIEHS) [C] <fo...@ni...> wrote: > i think that toxin as a quality or function or biomaterial or all three is / are good. > poison as an objective is good > > using toxin in the sense of its evolutionary role (eg killing the preditor or lunch-to-be) has a non-human performing the role. Yes. My point was that since the word can be used in two ways (in different parts of something that would be the subject of OBI annotation) we should not use it unadorned. Simple point. -Alan > > -----Original Message----- > From: Alan Ruttenberg [mailto:ala...@gm...] > Sent: Monday, March 23, 2009 2:56 PM > To: Fostel, Jennifer (NIH/NIEHS) [C] > Cc: Ryan Brinkman; obi...@li... > Subject: Re: [Obi-role-branch] role call today at noon EDT > > I'm unconvinced. Poison is different than toxins, the latter of which can be evolutionarily selected for (see google define of the two terms). > In any case, if there is a non function definition that's fine. I'm simply warning that using the name unqualified is likely to lead to confusion in the communities we serve. > -Alan > > On Mon, Mar 23, 2009 at 2:21 PM, Fostel, Jennifer (NIH/NIEHS) [C] <fo...@ni...> wrote: >> right! also rats inadvertantly ingesting an excess of a substance, >> unless we think they are committing suicide, are also out of scope >> (committing suicide might permit them the worker role, but in OBI this >> role is limited to homo sapiens until we get robot in there) >> >> -----Original Message----- >> From: Ryan Brinkman [mailto:rbr...@bc...] >> Sent: Monday, March 23, 2009 2:01 PM >> To: Alan Ruttenberg; Fostel, Jennifer (NIH/NIEHS) [C] >> Cc: obi...@li... >> Subject: RE: [Obi-role-branch] role call today at noon EDT >> >> >>>> (8) the toxin question will be interesting -- we have had some discussion on this previously! >>>> probably an objective. >> >>>Not if you're a snake. It's a function in that case. >> >> I'm all for OBI being extensible, but I don't see a use case for toxin-producing snake overlords performing experiments, so it may be helpful to restrict to the domain of biomedical investigations. >> >> Ryan >> >> > |
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From: Fostel, J. (NIH/N. [C] <fo...@ni...> - 2009-03-23 19:47:43
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totally agree with you re: unadorned. we get some push-back about our adjectives however :-) will leave it for others; i don;t think toxin is a role. -----Original Message----- From: Alan Ruttenberg [mailto:ala...@gm...] Sent: Monday, March 23, 2009 3:22 PM To: Fostel, Jennifer (NIH/NIEHS) [C] Cc: Ryan Brinkman; obi...@li... Subject: Re: [Obi-role-branch] role call today at noon EDT On Mon, Mar 23, 2009 at 3:16 PM, Fostel, Jennifer (NIH/NIEHS) [C] <fo...@ni...> wrote: > i think that toxin as a quality or function or biomaterial or all three is / are good. > poison as an objective is good > > using toxin in the sense of its evolutionary role (eg killing the preditor or lunch-to-be) has a non-human performing the role. Yes. My point was that since the word can be used in two ways (in different parts of something that would be the subject of OBI annotation) we should not use it unadorned. Simple point. -Alan > > -----Original Message----- > From: Alan Ruttenberg [mailto:ala...@gm...] > Sent: Monday, March 23, 2009 2:56 PM > To: Fostel, Jennifer (NIH/NIEHS) [C] > Cc: Ryan Brinkman; obi...@li... > Subject: Re: [Obi-role-branch] role call today at noon EDT > > I'm unconvinced. Poison is different than toxins, the latter of which can be evolutionarily selected for (see google define of the two terms). > In any case, if there is a non function definition that's fine. I'm simply warning that using the name unqualified is likely to lead to confusion in the communities we serve. > -Alan > > On Mon, Mar 23, 2009 at 2:21 PM, Fostel, Jennifer (NIH/NIEHS) [C] <fo...@ni...> wrote: >> right! also rats inadvertantly ingesting an excess of a substance, >> unless we think they are committing suicide, are also out of scope >> (committing suicide might permit them the worker role, but in OBI >> this role is limited to homo sapiens until we get robot in there) >> >> -----Original Message----- >> From: Ryan Brinkman [mailto:rbr...@bc...] >> Sent: Monday, March 23, 2009 2:01 PM >> To: Alan Ruttenberg; Fostel, Jennifer (NIH/NIEHS) [C] >> Cc: obi...@li... >> Subject: RE: [Obi-role-branch] role call today at noon EDT >> >> >>>> (8) the toxin question will be interesting -- we have had some discussion on this previously! >>>> probably an objective. >> >>>Not if you're a snake. It's a function in that case. >> >> I'm all for OBI being extensible, but I don't see a use case for toxin-producing snake overlords performing experiments, so it may be helpful to restrict to the domain of biomedical investigations. >> >> Ryan >> >> > |
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