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obi-protocol-application-branch — Discussion of terms that are in the Protocol Application branch of OBI.
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From: Fostel, J. (NIH/N. [C] <fo...@ni...> - 2009-01-26 17:22:58
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thanks! i will make that change. -----Original Message----- From: Bjoern Peters [mailto:bp...@li...] Sent: Monday, January 26, 2009 11:00 AM To: Fostel, Jennifer (NIH/NIEHS) [C] Cc: Alan Ruttenberg; obi...@li...; obi...@li... Subject: Re: [Obi-role-branch] Study design execution and performance The question was about the direct relation between study design and the study participant role. I believe what Alan wants is the more complicated version, which by the way I screwed up: study participant role is_realized_in only (realization_of (is_concretization_of some study design)) Which we can now short cut with: study participant role is_realized_in only 'study design execution' Fostel, Jennifer (NIH/NIEHS) [C] wrote: > i agree; but we were seeing a question from Alan > > -----Original Message----- > From: Bjoern Peters [mailto:bp...@li...] > Sent: Monday, January 26, 2009 10:42 AM > To: Fostel, Jennifer (NIH/NIEHS) [C] > Cc: Alan Ruttenberg; obi...@li...; > obi...@li... > Subject: Re: [Obi-role-branch] Study design execution and performance > > I thought what we wanted to have is: > > study participant is_realized_in only (is_concretization_of some study > design) > > - Bjoern > > Fostel, Jennifer (NIH/NIEHS) [C] wrote: > >> we have been working on this for some time. the study participant >> role is defined by the study design. i needed a process for >> realizing-role-defined-in-study-design and we came up with >> is_concretization_of. other suggestions are welcome!! we just do >> not >> > > >> want to have multiple parallel heirarchies in OBI -- a set of roles >> with parallel processes with parallel designs. >> >> -----Original Message----- >> From: Bjoern Peters [mailto:bp...@li...] >> Sent: Sunday, January 25, 2009 6:45 PM >> To: Alan Ruttenberg >> Cc: obi...@li...; >> obi...@li... >> Subject: Re: [Obi-role-branch] Study design execution and performance >> >> Alan Ruttenberg wrote: >> >> >>> For reasons that I don't quite understand yet, dropping the has_part >>> axioms on Study design execution increase Pellet reasoning >>> performance >>> >>> >> >> >>> by a factor of 10. >>> >>> I'd like to drop them for the moment. Perhaps put them in a comment >>> and return to them after we've figured out what the deal is. >>> >>> >>> >> Ok with me. >> >> >>> In reviewing terms nearby I also noticed: >>> >>> 'study participant role' is_concretization_of some 'study design' >>> >>> I don't think that's right, though it's a bit squishy to put my >>> finger >>> >>> >> >> >>> on it. I think it's because the concretization of a gdp is a kind >>> of >>> > > >>> copy of it, and the concretization happens in the entity that has >>> the >>> > > >>> copy. >>> >>> >>> >> Agreed. >> >> >>> -Alan >>> >>> >>> >> --------------------------------------------------------------------- >> - >> -- >> ------ >> This SF.net email is sponsored by: >> SourcForge Community >> SourceForge wants to tell your story. >> http://p.sf.net/sfu/sf-spreadtheword >> _______________________________________________ >> Obi-role-branch mailing list >> Obi...@li... >> https://lists.sourceforge.net/lists/listinfo/obi-role-branch >> >> > > |
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From: Bjoern P. <bp...@li...> - 2009-01-26 16:00:22
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The question was about the direct relation between study design and the study participant role. I believe what Alan wants is the more complicated version, which by the way I screwed up: study participant role is_realized_in only (realization_of (is_concretization_of some study design)) Which we can now short cut with: study participant role is_realized_in only 'study design execution' Fostel, Jennifer (NIH/NIEHS) [C] wrote: > i agree; but we were seeing a question from Alan > > -----Original Message----- > From: Bjoern Peters [mailto:bp...@li...] > Sent: Monday, January 26, 2009 10:42 AM > To: Fostel, Jennifer (NIH/NIEHS) [C] > Cc: Alan Ruttenberg; obi...@li...; > obi...@li... > Subject: Re: [Obi-role-branch] Study design execution and performance > > I thought what we wanted to have is: > > study participant is_realized_in only (is_concretization_of some study > design) > > - Bjoern > > Fostel, Jennifer (NIH/NIEHS) [C] wrote: > >> we have been working on this for some time. the study participant >> role is defined by the study design. i needed a process for >> realizing-role-defined-in-study-design and we came up with >> is_concretization_of. other suggestions are welcome!! we just do not >> > > >> want to have multiple parallel heirarchies in OBI -- a set of roles >> with parallel processes with parallel designs. >> >> -----Original Message----- >> From: Bjoern Peters [mailto:bp...@li...] >> Sent: Sunday, January 25, 2009 6:45 PM >> To: Alan Ruttenberg >> Cc: obi...@li...; >> obi...@li... >> Subject: Re: [Obi-role-branch] Study design execution and performance >> >> Alan Ruttenberg wrote: >> >> >>> For reasons that I don't quite understand yet, dropping the has_part >>> axioms on Study design execution increase Pellet reasoning >>> performance >>> >>> >> >> >>> by a factor of 10. >>> >>> I'd like to drop them for the moment. Perhaps put them in a comment >>> and return to them after we've figured out what the deal is. >>> >>> >>> >> Ok with me. >> >> >>> In reviewing terms nearby I also noticed: >>> >>> 'study participant role' is_concretization_of some 'study design' >>> >>> I don't think that's right, though it's a bit squishy to put my >>> finger >>> >>> >> >> >>> on it. I think it's because the concretization of a gdp is a kind of >>> > > >>> copy of it, and the concretization happens in the entity that has the >>> > > >>> copy. >>> >>> >>> >> Agreed. >> >> >>> -Alan >>> >>> >>> >> ---------------------------------------------------------------------- >> -- >> ------ >> This SF.net email is sponsored by: >> SourcForge Community >> SourceForge wants to tell your story. >> http://p.sf.net/sfu/sf-spreadtheword >> _______________________________________________ >> 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...> - 2009-01-26 15:44:10
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i agree; but we were seeing a question from Alan -----Original Message----- From: Bjoern Peters [mailto:bp...@li...] Sent: Monday, January 26, 2009 10:42 AM To: Fostel, Jennifer (NIH/NIEHS) [C] Cc: Alan Ruttenberg; obi...@li...; obi...@li... Subject: Re: [Obi-role-branch] Study design execution and performance I thought what we wanted to have is: study participant is_realized_in only (is_concretization_of some study design) - Bjoern Fostel, Jennifer (NIH/NIEHS) [C] wrote: > we have been working on this for some time. the study participant > role is defined by the study design. i needed a process for > realizing-role-defined-in-study-design and we came up with > is_concretization_of. other suggestions are welcome!! we just do not > want to have multiple parallel heirarchies in OBI -- a set of roles > with parallel processes with parallel designs. > > -----Original Message----- > From: Bjoern Peters [mailto:bp...@li...] > Sent: Sunday, January 25, 2009 6:45 PM > To: Alan Ruttenberg > Cc: obi...@li...; > obi...@li... > Subject: Re: [Obi-role-branch] Study design execution and performance > > Alan Ruttenberg wrote: > >> For reasons that I don't quite understand yet, dropping the has_part >> axioms on Study design execution increase Pellet reasoning >> performance >> > > >> by a factor of 10. >> >> I'd like to drop them for the moment. Perhaps put them in a comment >> and return to them after we've figured out what the deal is. >> >> > Ok with me. > >> In reviewing terms nearby I also noticed: >> >> 'study participant role' is_concretization_of some 'study design' >> >> I don't think that's right, though it's a bit squishy to put my >> finger >> > > >> on it. I think it's because the concretization of a gdp is a kind of >> copy of it, and the concretization happens in the entity that has the >> copy. >> >> > Agreed. > >> -Alan >> >> > > > ---------------------------------------------------------------------- > -- > ------ > This SF.net email is sponsored by: > SourcForge Community > SourceForge wants to tell your story. > http://p.sf.net/sfu/sf-spreadtheword > _______________________________________________ > Obi-role-branch mailing list > Obi...@li... > https://lists.sourceforge.net/lists/listinfo/obi-role-branch > |
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From: Bjoern P. <bp...@li...> - 2009-01-26 15:42:24
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I thought what we wanted to have is: study participant is_realized_in only (is_concretization_of some study design) - Bjoern Fostel, Jennifer (NIH/NIEHS) [C] wrote: > we have been working on this for some time. the study participant role > is defined by the study design. i needed a process for > realizing-role-defined-in-study-design and we came up with > is_concretization_of. other suggestions are welcome!! we just do not > want to have multiple parallel heirarchies in OBI -- a set of roles with > parallel processes with parallel designs. > > -----Original Message----- > From: Bjoern Peters [mailto:bp...@li...] > Sent: Sunday, January 25, 2009 6:45 PM > To: Alan Ruttenberg > Cc: obi...@li...; > obi...@li... > Subject: Re: [Obi-role-branch] Study design execution and performance > > Alan Ruttenberg wrote: > >> For reasons that I don't quite understand yet, dropping the has_part >> axioms on Study design execution increase Pellet reasoning performance >> > > >> by a factor of 10. >> >> I'd like to drop them for the moment. Perhaps put them in a comment >> and return to them after we've figured out what the deal is. >> >> > Ok with me. > >> In reviewing terms nearby I also noticed: >> >> 'study participant role' is_concretization_of some 'study design' >> >> I don't think that's right, though it's a bit squishy to put my finger >> > > >> on it. I think it's because the concretization of a gdp is a kind of >> copy of it, and the concretization happens in the entity that has the >> copy. >> >> > Agreed. > >> -Alan >> >> > > > ------------------------------------------------------------------------ > ------ > This SF.net email is sponsored by: > SourcForge Community > SourceForge wants to tell your story. > http://p.sf.net/sfu/sf-spreadtheword > _______________________________________________ > 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...> - 2009-01-26 13:59:29
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we have been working on this for some time. the study participant role is defined by the study design. i needed a process for realizing-role-defined-in-study-design and we came up with is_concretization_of. other suggestions are welcome!! we just do not want to have multiple parallel heirarchies in OBI -- a set of roles with parallel processes with parallel designs. -----Original Message----- From: Bjoern Peters [mailto:bp...@li...] Sent: Sunday, January 25, 2009 6:45 PM To: Alan Ruttenberg Cc: obi...@li...; obi...@li... Subject: Re: [Obi-role-branch] Study design execution and performance Alan Ruttenberg wrote: > For reasons that I don't quite understand yet, dropping the has_part > axioms on Study design execution increase Pellet reasoning performance > by a factor of 10. > > I'd like to drop them for the moment. Perhaps put them in a comment > and return to them after we've figured out what the deal is. > Ok with me. > In reviewing terms nearby I also noticed: > > 'study participant role' is_concretization_of some 'study design' > > I don't think that's right, though it's a bit squishy to put my finger > on it. I think it's because the concretization of a gdp is a kind of > copy of it, and the concretization happens in the entity that has the > copy. > Agreed. > -Alan > ------------------------------------------------------------------------ ------ This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword _______________________________________________ Obi-role-branch mailing list Obi...@li... https://lists.sourceforge.net/lists/listinfo/obi-role-branch |
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From: Bjoern P. <bp...@li...> - 2009-01-25 23:44:47
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Alan Ruttenberg wrote: > For reasons that I don't quite understand yet, dropping the has_part > axioms on Study design execution increase Pellet reasoning performance > by a factor of 10. > > I'd like to drop them for the moment. Perhaps put them in a comment > and return to them after we've figured out what the deal is. > Ok with me. > In reviewing terms nearby I also noticed: > > 'study participant role' is_concretization_of some 'study design' > > I don't think that's right, though it's a bit squishy to put my finger > on it. I think it's because the concretization of a gdp is a kind of > copy of it, and the concretization happens in the entity that has the > copy. > Agreed. > -Alan > |
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From: Alan R. <ala...@gm...> - 2009-01-25 05:51:47
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For reasons that I don't quite understand yet, dropping the has_part axioms on Study design execution increase Pellet reasoning performance by a factor of 10. I'd like to drop them for the moment. Perhaps put them in a comment and return to them after we've figured out what the deal is. In reviewing terms nearby I also noticed: 'study participant role' is_concretization_of some 'study design' I don't think that's right, though it's a bit squishy to put my finger on it. I think it's because the concretization of a gdp is a kind of copy of it, and the concretization happens in the entity that has the copy. -Alan |
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From: Bjoern P. <bp...@li...> - 2009-01-23 04:10:41
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In todays call, we worked on plan specification, objective specification, (concretized) plan and planned process. - It was decided to merge objective driven process, planned process and protocol applications into one (planned process), as the difference is hard to maintain on the process level. AI for MC to report about usage of each term in the ontology to assess impact of obsoletion. AI for BP to do the obsoletion. - Alan had a number of additions to the proposal below, specifically that he wants the possibility for objectives to be realized, and the possibility for plans that are not concretizations of plan specifications. However, we all agree that for OBI we are fine to deal only with planned processes that are realizations of conretized plan specifications which have objective specifications as their parts. - updates were committed to svn apart from those that go to IAO. - the slides on the google docs have been udpated. please take a look, or let me know if you need access. - Bjoern Bjoern Peters wrote: > The call tomorrow is on. We have as a major remaining action item core > terms #7 and #8. The following is a proposal summarizing several > previous discussions and incorporating feedback from Alan. If possible, > please review before the call tomorrow. > > 7. objective driven process, planned process, and protocol application > status: not done. suggestion to merge two or more > 8. objective specification, plan specification status: not done. > includes the concretization and realization relationships > > > The reason for the desired merge of objective driven process, planned > process and protocol application is that they are hard to keep apart by > both reasoners and humans. Here are the classes, including updated > definitions: > > planned process > > A planned process is the realization of a concretized plan borne by an > agent that initiates this process in order to bring about the > objective(s) specified as part of the plan specification. > > editor note:We are only considering successfully completed planned > processes. A plan may be modified, and details added during execution. > For a given planned process,the associated realized plan specification > is the one encompassing all changes made during execution. This means > that all processes in which an agent acts towards achieving some > objectives is a planned process. > > concretized plan > A concretized plan is a realizable entity that is the concretization of a > plan specification. It inheres in a bearer who is committed to realizing it. > > editor note: This class is included to make clear what the difference > between the plan specification and the concretized plan specification > is. OBI will however only subclass and work under the 'plan > specification' class, as we want to avoid to get deep into discussions > of 'intend' etc. > > plan specification > A plan specification is an information entity about a realizable > entity. The specification includes parts such as objective > specification, action specifications and conditional specifications. > When concretized it is realized in a process in which the bearer tries > to achieve the objectives, in part by taking the actions specified. > > objective specification > An objective specification is an information entity about a part of a realizable > entity. Objective specifications describe a intended process endpoint. > When concretized as part of a plan specification, it is realized in a process in which the bearer tries > to effect the world so that the process endpoint is achieved. > > > Hierarchy: > > information content entity > 'information entity about a realizable and its parts' > plan specification > objective specification > conditional specification > action specification (currently: all utilizes device relations) > realizable entity > concretized plan > process > planned process > > > > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by: > SourcForge Community > SourceForge wants to tell your story. > http://p.sf.net/sfu/sf-spreadtheword > _______________________________________________ > Obi-protocol-application-branch mailing list > Obi...@li... > https://lists.sourceforge.net/lists/listinfo/obi-protocol-application-branch > |
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From: <bjo...@gm...> - 2009-01-23 04:08:58
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I've shared a document with you called "Plans and Planned Processes": http://docs.google.com/Presentation?id=dfn5pq8x_15gjkbdrhf&invite=sq7pq8 It's not an attachment -- it's stored online at Google Docs. To open this document, just click the link above. --- Slides for the obi workshop presentation of the plan and planned process branch |
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From: Clancy, K. <Kev...@in...> - 2009-01-22 04:38:30
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Bjoern - will this be on Skype or Centra? Has a summary of the workshop been posted to the web site from the meeting? Thanks kevin Kevin Clancy, PhD Senior Scientist Invitrogen Corp 5791 Van Allen Way Carlsbad CA 92008 phone: 760 268 8356 cell: 240 417 8604 email: kev...@in... -----Original Message----- From: Bjoern Peters [mailto:bp...@li...] Sent: Wed 1/21/2009 6:42 PM To: obi...@li... Subject: Re: [Obi-protocol-application-branch] Call tomorrow - merge of objective driven process and protocol application with planned process Addendum to this: Currently the data transformation branch uses the 'has objective' relation, which is not linked to the below. I propose to modify the label for 'has objective' to 'achieves objective specification'. Domain: 'planned process', range 'objective specification'. It is then a shorthand relation for process achieves_objective_specification' some X => process realizes some (is_concretization_of some (plan_specification has_part some X)) - Bjoern Bjoern Peters wrote: > The call tomorrow is on. We have as a major remaining action item core > terms #7 and #8. The following is a proposal summarizing several > previous discussions and incorporating feedback from Alan. If possible, > please review before the call tomorrow. > > 7. objective driven process, planned process, and protocol application > status: not done. suggestion to merge two or more > 8. objective specification, plan specification status: not done. > includes the concretization and realization relationships > > > The reason for the desired merge of objective driven process, planned > process and protocol application is that they are hard to keep apart by > both reasoners and humans. Here are the classes, including updated > definitions: > > planned process > > A planned process is the realization of a concretized plan borne by an > agent that initiates this process in order to bring about the > objective(s) specified as part of the plan specification. > > editor note:We are only considering successfully completed planned > processes. A plan may be modified, and details added during execution. > For a given planned process,the associated realized plan specification > is the one encompassing all changes made during execution. This means > that all processes in which an agent acts towards achieving some > objectives is a planned process. > > concretized plan > A concretized plan is a realizable entity that is the concretization of a > plan specification. It inheres in a bearer who is committed to realizing it. > > editor note: This class is included to make clear what the difference > between the plan specification and the concretized plan specification > is. OBI will however only subclass and work under the 'plan > specification' class, as we want to avoid to get deep into discussions > of 'intend' etc. > > plan specification > A plan specification is an information entity about a realizable > entity. The specification includes parts such as objective > specification, action specifications and conditional specifications. > When concretized it is realized in a process in which the bearer tries > to achieve the objectives, in part by taking the actions specified. > > objective specification > An objective specification is an information entity about a part of a realizable > entity. Objective specifications describe a intended process endpoint. > When concretized as part of a plan specification, it is realized in a process in which the bearer tries > to effect the world so that the process endpoint is achieved. > > > Hierarchy: > > information content entity > 'information entity about a realizable and its parts' > plan specification > objective specification > conditional specification > action specification (currently: all utilizes device relations) > realizable entity > concretized plan > process > planned process > > > > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by: > SourcForge Community > SourceForge wants to tell your story. > http://p.sf.net/sfu/sf-spreadtheword > _______________________________________________ > Obi-protocol-application-branch mailing list > Obi...@li... > https://lists.sourceforge.net/lists/listinfo/obi-protocol-application-branch > ------------------------------------------------------------------------------ This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword _______________________________________________ Obi-protocol-application-branch mailing list Obi...@li... https://lists.sourceforge.net/lists/listinfo/obi-protocol-application-branch |
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From: Bjoern P. <bp...@li...> - 2009-01-22 02:43:06
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Addendum to this: Currently the data transformation branch uses the 'has objective' relation, which is not linked to the below. I propose to modify the label for 'has objective' to 'achieves objective specification'. Domain: 'planned process', range 'objective specification'. It is then a shorthand relation for process achieves_objective_specification' some X => process realizes some (is_concretization_of some (plan_specification has_part some X)) - Bjoern Bjoern Peters wrote: > The call tomorrow is on. We have as a major remaining action item core > terms #7 and #8. The following is a proposal summarizing several > previous discussions and incorporating feedback from Alan. If possible, > please review before the call tomorrow. > > 7. objective driven process, planned process, and protocol application > status: not done. suggestion to merge two or more > 8. objective specification, plan specification status: not done. > includes the concretization and realization relationships > > > The reason for the desired merge of objective driven process, planned > process and protocol application is that they are hard to keep apart by > both reasoners and humans. Here are the classes, including updated > definitions: > > planned process > > A planned process is the realization of a concretized plan borne by an > agent that initiates this process in order to bring about the > objective(s) specified as part of the plan specification. > > editor note:We are only considering successfully completed planned > processes. A plan may be modified, and details added during execution. > For a given planned process,the associated realized plan specification > is the one encompassing all changes made during execution. This means > that all processes in which an agent acts towards achieving some > objectives is a planned process. > > concretized plan > A concretized plan is a realizable entity that is the concretization of a > plan specification. It inheres in a bearer who is committed to realizing it. > > editor note: This class is included to make clear what the difference > between the plan specification and the concretized plan specification > is. OBI will however only subclass and work under the 'plan > specification' class, as we want to avoid to get deep into discussions > of 'intend' etc. > > plan specification > A plan specification is an information entity about a realizable > entity. The specification includes parts such as objective > specification, action specifications and conditional specifications. > When concretized it is realized in a process in which the bearer tries > to achieve the objectives, in part by taking the actions specified. > > objective specification > An objective specification is an information entity about a part of a realizable > entity. Objective specifications describe a intended process endpoint. > When concretized as part of a plan specification, it is realized in a process in which the bearer tries > to effect the world so that the process endpoint is achieved. > > > Hierarchy: > > information content entity > 'information entity about a realizable and its parts' > plan specification > objective specification > conditional specification > action specification (currently: all utilizes device relations) > realizable entity > concretized plan > process > planned process > > > > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by: > SourcForge Community > SourceForge wants to tell your story. > http://p.sf.net/sfu/sf-spreadtheword > _______________________________________________ > Obi-protocol-application-branch mailing list > Obi...@li... > https://lists.sourceforge.net/lists/listinfo/obi-protocol-application-branch > |
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From: Bjoern P. <bp...@li...> - 2009-01-22 02:13:20
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The call tomorrow is on. We have as a major remaining action item core terms #7 and #8. The following is a proposal summarizing several previous discussions and incorporating feedback from Alan. If possible, please review before the call tomorrow. 7. objective driven process, planned process, and protocol application status: not done. suggestion to merge two or more 8. objective specification, plan specification status: not done. includes the concretization and realization relationships The reason for the desired merge of objective driven process, planned process and protocol application is that they are hard to keep apart by both reasoners and humans. Here are the classes, including updated definitions: planned process A planned process is the realization of a concretized plan borne by an agent that initiates this process in order to bring about the objective(s) specified as part of the plan specification. editor note:We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process,the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process. concretized plan A concretized plan is a realizable entity that is the concretization of a plan specification. It inheres in a bearer who is committed to realizing it. editor note: This class is included to make clear what the difference between the plan specification and the concretized plan specification is. OBI will however only subclass and work under the 'plan specification' class, as we want to avoid to get deep into discussions of 'intend' etc. plan specification A plan specification is an information entity about a realizable entity. The specification includes parts such as objective specification, action specifications and conditional specifications. When concretized it is realized in a process in which the bearer tries to achieve the objectives, in part by taking the actions specified. objective specification An objective specification is an information entity about a part of a realizable entity. Objective specifications describe a intended process endpoint. When concretized as part of a plan specification, it is realized in a process in which the bearer tries to effect the world so that the process endpoint is achieved. Hierarchy: information content entity 'information entity about a realizable and its parts' plan specification objective specification conditional specification action specification (currently: all utilizes device relations) realizable entity concretized plan process planned process |
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From: Melanie C. <mco...@gm...> - 2009-01-15 23:24:35
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That restriction is in the Role.owl file http://obi.svn.sourceforge.net/viewvc/obi/trunk/src/ontology/branches/Role.owl?revision=1353&view=markup , at the end (very last lines) I know that Jennifer is currently editing the Role file so I don't want to create conflict. Jennifer - if you can send me an email when you are done editing for today, I'll make the following modifications: <rdf:Description rdf:about="http://purl.obofoundry.org/obo/OBI_0000094 "> <IAO_0000115 xml:lang="en">a material_application is protocol_application which has the objective to produce output material(s) from input material(s)</IAO_0000115> </rdf:Description> => extra definition for artifact material creation: I will remove it <rdf:Description rdf:about="http://purl.obofoundry.org/obo/OBI_0200000 "> <IAO_0000115 xml:lang="en">a protocol application which has the objective to produce output data from input data</IAO_0000115> </rdf:Description> => extra definition for data transformation: I will remove it <rdf:Description rdf:about="http://purl.obofoundry.org/obo/OBI_0000011 "> <rdfs:subClassOf rdf:resource="http://www.ifomis.org/bfo/1.1/span#Process "/> </rdf:Description> => assertion of ODP under Process: I will remove it Bjoern, can you confirm the above changes are ok? Thanks, Melanie On 15-Jan-09, at 2:44 PM, Bjoern Peters wrote: > We worked on the 'adminstering substance' and children terms, > resulting > in the following (some of it done by myself after the call, but > hopefully in the spirit of what was discussed): > > - As 'administering' seems to be commonly associated only with > organisms, it will only be used for 'administering in vivo'. The more > general class will be called 'adding material entity into target'. It > will encompass any process in which one material is added into another > one. This includes processes like 'injecting label into organ > section', > or 'adding nutrient to cell culture', or 'adding drug into buffer'. > - the corresponding roles for the 'added material' and 'target > material' > will be updated by Jennifer. > - metadata for the terms was increased (examples, missing definitions, > editor notes), and definitions updated > > In the process, I further cleaned up the file to move all defined > classes under '_defined protocol applications', and removed > additional > asserted classes. The one term I could not do that is 'objective > driven > process', where the asserted 'process' class seems to have been > added in > a different file. Melanie, could you find out where? > > - Bjoern > > > -- > Bjoern Peters > Assistant Member > La Jolla Institute for Allergy and Immunology > 9420 Athena Circle > La Jolla, CA 92037, USA > Tel: 858/752-6914 > Fax: 858/752-6987 > http://www.liai.org/pages/faculty-peters > > > > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by: > SourcForge Community > SourceForge wants to tell your story. > http://p.sf.net/sfu/sf-spreadtheword > _______________________________________________ > Obi-protocol-application-branch mailing list > Obi...@li... > https://lists.sourceforge.net/lists/listinfo/obi-protocol-application-branch --- Mélanie Courtot TFL- BCCRC 675 West 10th Avenue Vancouver, BC V5Z 1L3, Canada |
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From: Bjoern P. <bp...@li...> - 2009-01-15 23:08:25
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We worked on the 'adminstering substance' and children terms, resulting in the following (some of it done by myself after the call, but hopefully in the spirit of what was discussed): - As 'administering' seems to be commonly associated only with organisms, it will only be used for 'administering in vivo'. The more general class will be called 'adding material entity into target'. It will encompass any process in which one material is added into another one. This includes processes like 'injecting label into organ section', or 'adding nutrient to cell culture', or 'adding drug into buffer'. - the corresponding roles for the 'added material' and 'target material' will be updated by Jennifer. - metadata for the terms was increased (examples, missing definitions, editor notes), and definitions updated In the process, I further cleaned up the file to move all defined classes under '_defined protocol applications', and removed additional asserted classes. The one term I could not do that is 'objective driven process', where the asserted 'process' class seems to have been added in a different file. Melanie, could you find out where? - Bjoern -- Bjoern Peters Assistant Member La Jolla Institute for Allergy and Immunology 9420 Athena Circle La Jolla, CA 92037, USA Tel: 858/752-6914 Fax: 858/752-6987 http://www.liai.org/pages/faculty-peters |
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From: Frank G. <fg...@gm...> - 2009-01-15 19:20:53
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On Thu, Jan 15, 2009 at 6:36 PM, Richard H. Scheuermann, Ph.D. <ric...@ut...> wrote: > I guess I would like to hear the argument for why humans should be > considered as a special case. Agreed, I don't believe it is a special case. I still think the use of the prefix study_ is confusion the issue. The Ontology of Biomedical Investigation deals with investigations. Investigations can have subjects and specimens, they are not a special case for the process of study (or realisation of study design). We use the words subject and specimen with no reference to a "study". I would suggest that subjects are only roles played by whole organisms and specimens are only roles played by entites_of_organism_origin. However, the definition of what a specimen is still conflated with sample, which is an outstanding issue that still has not been addressed. Frank If the argument is based on the special > recording requirements associated with human studies research, the same > argument could be made for research involving vertebrate animals, which also > have a whole series of special approval and reporting requirements. > Apparently no one cares about microbes or plants; we can do as we like to > them. > But the point is, why should humans be treated differently from a > theoretical perspective? > Richard > On Jan 15, 2009, at 10:31 AM, Bjoern Peters wrote: > > - I don't understand what the terms on the top of the email have to do > with the question at the end. > - For the question: You need to create a defined organism class: > 'organism and not homo sapiens'. For that to infer correctly, disjoints > would have to be set througout the entire organism hierarchy. > - I understand that you want to keep the separation between study > subject and specimen, but this will be difficult to maintain. I still > think we need a parent role 'study object(?)' with children 'human study > subject' and 'study specimen'. > Bjoern > Fostel, Jennifer (NIH/NIEHS) [C] wrote: > > biomaterials: > transgenic organism > cell lysate > processes: > electrocuted > enrolled > cervical dislocation > killing > genetic trasnformation > decapitation > DNA transformation > cell lysis > electroporation > asphyxiation > intentional overdosing > DNA transduction > i need to allow all organisms with the exception of humans to play the > role of a study specimen > what should i do? > > 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 > > --~--~---------~--~----~------------~-------~--~----~ > You received this message because you are subscribed to the Google > Groups "obi-biomaterial" group. > To post to this group, send email to obi...@go... > To unsubscribe from this group, send email to > obi...@go... > For more options, visit this group at > http://groups.google.com/group/obi-biomaterial?hl=en > -~----------~----~----~----~------~----~------~--~--- > > > -- > Bjoern Peters > Assistant Member > La Jolla Institute for Allergy and Immunology > 9420 Athena Circle > La Jolla, CA 92037, USA > Tel: 858/752-6914 > Fax: 858/752-6987 > http://www.liai.org/pages/faculty-peters > > > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by: > SourcForge Community > SourceForge wants to tell your story. > http://p.sf.net/sfu/sf-spreadtheword > _______________________________________________ > Obi-role-branch mailing list > Obi...@li... > https://lists.sourceforge.net/lists/listinfo/obi-role-branch > > ------------------------------------------------------------------------------------------------ > Richard H. Scheuermann, Ph.D. > Chief, Division of Biomedical Informatics > Director, Division of Translational Pathology > 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 > > > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by: > SourcForge Community > SourceForge wants to tell your story. > http://p.sf.net/sfu/sf-spreadtheword > _______________________________________________ > 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...> - 2009-01-15 19:10:32
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i cannot think of a case where an entire human is dropped into a blender or put into a freezer for long-term storage for later assay. these are what we do with specimens. we can observe humans, as you have exemplified, but these humans do not bear the specimen role. they do bear specified_input_role ________________________________ From: Richard H. Scheuermann, Ph.D. [mailto:ric...@ut...] Sent: Thursday, January 15, 2009 1:37 PM To: Bjoern Peters Cc: obi...@li...; obi...@li...; obi...@go... Subject: Re: [Obi-protocol-application-branch] [Obi-role-branch][obi-biomaterial] inconsistency when adding organism to studyspecinem role I guess I would like to hear the argument for why humans should be considered as a special case. If the argument is based on the special recording requirements associated with human studies research, the same argument could be made for research involving vertebrate animals, which also have a whole series of special approval and reporting requirements. Apparently no one cares about microbes or plants; we can do as we like to them. But the point is, why should humans be treated differently from a theoretical perspective? Richard On Jan 15, 2009, at 10:31 AM, Bjoern Peters wrote: - I don't understand what the terms on the top of the email have to do with the question at the end. - For the question: You need to create a defined organism class: 'organism and not homo sapiens'. For that to infer correctly, disjoints would have to be set througout the entire organism hierarchy. - I understand that you want to keep the separation between study subject and specimen, but this will be difficult to maintain. I still think we need a parent role 'study object(?)' with children 'human study subject' and 'study specimen'. Bjoern Fostel, Jennifer (NIH/NIEHS) [C] wrote: biomaterials: transgenic organism cell lysate processes: electrocuted enrolled cervical dislocation killing genetic trasnformation decapitation DNA transformation cell lysis electroporation asphyxiation intentional overdosing DNA transduction i need to allow all organisms with the exception of humans to play the role of a study specimen what should i do? 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 --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "obi-biomaterial" group. To post to this group, send email to obi...@go... To unsubscribe from this group, send email to obi...@go... For more options, visit this group at http://groups.google.com/group/obi-biomaterial?hl=en -~----------~----~----~----~------~----~------~--~--- -- Bjoern Peters Assistant Member La Jolla Institute for Allergy and Immunology 9420 Athena Circle La Jolla, CA 92037, USA Tel: 858/752-6914 Fax: 858/752-6987 http://www.liai.org/pages/faculty-peters ------------------------------------------------------------------------ ------ This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword _______________________________________________ Obi-role-branch mailing list Obi...@li... https://lists.sourceforge.net/lists/listinfo/obi-role-branch ------------------------------------------------------------------------ ------------------------ Richard H. Scheuermann, Ph.D. Chief, Division of Biomedical Informatics Director, Division of Translational Pathology 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 |
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From: Fostel, J. (NIH/N. [C] <fo...@ni...> - 2009-01-15 19:09:01
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these are not specimens..... ________________________________ From: Richard H. Scheuermann, Ph.D. [mailto:ric...@ut...] Sent: Thursday, January 15, 2009 1:27 PM To: Fostel, Jennifer (NIH/NIEHS) [C] Cc: obi...@li...; obi...@li...; obi...@go... Subject: Re: [Obi-role-branch] inconsistency when adding organism to study specinem role behavioral research, imaging analysis, height measurement On Jan 15, 2009, at 10:12 AM, Fostel, Jennifer (NIH/NIEHS) [C] wrote: a human can be a study subject, and tissue from a human can be a specimen but i cannot imagine a study in which a human is entirely converted into a specimen ________________________________ From: Richard H. Scheuermann, Ph.D. [mailto:ric...@ut...] Sent: Thursday, January 15, 2009 11:08 AM To: Fostel, Jennifer (NIH/NIEHS) [C] Cc: obi...@li...; obi...@go...; obi...@li... Subject: Re: [Obi-role-branch] inconsistency when adding organism to study specinem role Why is it that a human participant can't be a study specimen? Richard On Jan 15, 2009, at 9:54 AM, Fostel, Jennifer (NIH/NIEHS) [C] wrote: biomaterials: transgenic organism cell lysate processes: electrocuted enrolled cervical dislocation killing genetic trasnformation decapitation DNA transformation cell lysis electroporation asphyxiation intentional overdosing DNA transduction i need to allow all organisms with the exception of humans to play the role of a study specimen what should i do? 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 ------------------------------------------------------------------------ ------ This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword____________________________________ ___________ Obi-role-branch mailing list Obi...@li... https://lists.sourceforge.net/lists/listinfo/obi-role-branch ------------------------------------------------------------------------ ------------------------ Richard H. Scheuermann, Ph.D. Chief, Division of Biomedical Informatics Director, Division of Translational Pathology 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 ------------------------------------------------------------------------ ------ This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword____________________________________ ___________ Obi-role-branch mailing list Obi...@li... https://lists.sourceforge.net/lists/listinfo/obi-role-branch ------------------------------------------------------------------------ ------------------------ Richard H. Scheuermann, Ph.D. Chief, Division of Biomedical Informatics Director, Division of Translational Pathology 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 |
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From: Richard H. S. Ph.D. <ric...@ut...> - 2009-01-15 18:36:57
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I guess I would like to hear the argument for why humans should be considered as a special case. If the argument is based on the special recording requirements associated with human studies research, the same argument could be made for research involving vertebrate animals, which also have a whole series of special approval and reporting requirements. Apparently no one cares about microbes or plants; we can do as we like to them. But the point is, why should humans be treated differently from a theoretical perspective? Richard On Jan 15, 2009, at 10:31 AM, Bjoern Peters wrote: > - I don't understand what the terms on the top of the email have to do > with the question at the end. > > - For the question: You need to create a defined organism class: > 'organism and not homo sapiens'. For that to infer correctly, > disjoints > would have to be set througout the entire organism hierarchy. > > - I understand that you want to keep the separation between study > subject and specimen, but this will be difficult to maintain. I still > think we need a parent role 'study object(?)' with children 'human > study > subject' and 'study specimen'. > > Bjoern > > Fostel, Jennifer (NIH/NIEHS) [C] wrote: >> >> biomaterials: >> transgenic organism >> cell lysate >> >> processes: >> electrocuted >> enrolled >> cervical dislocation >> killing >> genetic trasnformation >> decapitation >> DNA transformation >> cell lysis >> electroporation >> asphyxiation >> intentional overdosing >> DNA transduction >> >> i need to allow all organisms with the exception of humans to play >> the >> role of a study specimen >> what should i do? >> >> >> 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 >> >> >> --~--~---------~--~----~------------~-------~--~----~ >> You received this message because you are subscribed to the Google >> Groups "obi-biomaterial" group. >> To post to this group, send email to obi...@go... >> To unsubscribe from this group, send email to >> obi...@go... >> For more options, visit this group at >> http://groups.google.com/group/obi-biomaterial?hl=en >> -~----------~----~----~----~------~----~------~--~--- >> > > > -- > Bjoern Peters > Assistant Member > La Jolla Institute for Allergy and Immunology > 9420 Athena Circle > La Jolla, CA 92037, USA > Tel: 858/752-6914 > Fax: 858/752-6987 > http://www.liai.org/pages/faculty-peters > > > > > ---------------------------------------------------------------------- > -------- > This SF.net email is sponsored by: > SourcForge Community > SourceForge wants to tell your story. > http://p.sf.net/sfu/sf-spreadtheword > _______________________________________________ > Obi-role-branch mailing list > Obi...@li... > https://lists.sourceforge.net/lists/listinfo/obi-role-branch ------------------------------------------------------------------------ ------------------------ Richard H. Scheuermann, Ph.D. Chief, Division of Biomedical Informatics Director, Division of Translational Pathology 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 |
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From: Richard H. S. Ph.D. <ric...@ut...> - 2009-01-15 18:27:35
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behavioral research, imaging analysis, height measurement On Jan 15, 2009, at 10:12 AM, Fostel, Jennifer (NIH/NIEHS) [C] wrote: > a human can be a study subject, and tissue from a human can be a > specimen but i cannot imagine a study in which a human is entirely > converted into a specimen > > From: Richard H. Scheuermann, Ph.D. > [mailto:ric...@ut...] > Sent: Thursday, January 15, 2009 11:08 AM > To: Fostel, Jennifer (NIH/NIEHS) [C] > Cc: obi...@li...; obi- > bio...@go...; obi-protocol-application- > br...@li... > Subject: Re: [Obi-role-branch] inconsistency when adding organism > to study specinem role > > Why is it that a human participant can't be a study specimen? > > Richard > > On Jan 15, 2009, at 9:54 AM, Fostel, Jennifer (NIH/NIEHS) [C] wrote: > >> biomaterials: >> transgenic organism >> cell lysate >> >> processes: >> electrocuted >> enrolled >> cervical dislocation >> killing >> genetic trasnformation >> decapitation >> DNA transformation >> cell lysis >> electroporation >> asphyxiation >> intentional overdosing >> DNA transduction >> >> i need to allow all organisms with the exception of humans to play >> the role of a study specimen >> what should i do? >> >> >> 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 >> >> --------------------------------------------------------------------- >> --------- >> This SF.net email is sponsored by: >> SourcForge Community >> SourceForge wants to tell your story. >> http://p.sf.net/sfu/sf- >> spreadtheword_______________________________________________ >> Obi-role-branch mailing list >> Obi...@li... >> https://lists.sourceforge.net/lists/listinfo/obi-role-branch > > ---------------------------------------------------------------------- > -------------------------- > > Richard H. Scheuermann, Ph.D. > Chief, Division of Biomedical Informatics > Director, Division of Translational Pathology > 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 > > > > ---------------------------------------------------------------------- > -------- > This SF.net email is sponsored by: > SourcForge Community > SourceForge wants to tell your story. > http://p.sf.net/sfu/sf- > spreadtheword_______________________________________________ > Obi-role-branch mailing list > Obi...@li... > https://lists.sourceforge.net/lists/listinfo/obi-role-branch ------------------------------------------------------------------------ ------------------------ Richard H. Scheuermann, Ph.D. Chief, Division of Biomedical Informatics Director, Division of Translational Pathology 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 |
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From: Bjoern P. <bp...@li...> - 2009-01-15 16:31:55
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- I don't understand what the terms on the top of the email have to do with the question at the end. - For the question: You need to create a defined organism class: 'organism and not homo sapiens'. For that to infer correctly, disjoints would have to be set througout the entire organism hierarchy. - I understand that you want to keep the separation between study subject and specimen, but this will be difficult to maintain. I still think we need a parent role 'study object(?)' with children 'human study subject' and 'study specimen'. Bjoern Fostel, Jennifer (NIH/NIEHS) [C] wrote: > > biomaterials: > transgenic organism > cell lysate > > processes: > electrocuted > enrolled > cervical dislocation > killing > genetic trasnformation > decapitation > DNA transformation > cell lysis > electroporation > asphyxiation > intentional overdosing > DNA transduction > > i need to allow all organisms with the exception of humans to play the > role of a study specimen > what should i do? > > > 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 > > > --~--~---------~--~----~------------~-------~--~----~ > You received this message because you are subscribed to the Google > Groups "obi-biomaterial" group. > To post to this group, send email to obi...@go... > To unsubscribe from this group, send email to > obi...@go... > For more options, visit this group at > http://groups.google.com/group/obi-biomaterial?hl=en > -~----------~----~----~----~------~----~------~--~--- > -- Bjoern Peters Assistant Member La Jolla Institute for Allergy and Immunology 9420 Athena Circle La Jolla, CA 92037, USA Tel: 858/752-6914 Fax: 858/752-6987 http://www.liai.org/pages/faculty-peters |
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From: Fostel, J. (NIH/N. [C] <fo...@ni...> - 2009-01-15 16:13:02
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a human can be a study subject, and tissue from a human can be a specimen but i cannot imagine a study in which a human is entirely converted into a specimen ________________________________ From: Richard H. Scheuermann, Ph.D. [mailto:ric...@ut...] Sent: Thursday, January 15, 2009 11:08 AM To: Fostel, Jennifer (NIH/NIEHS) [C] Cc: obi...@li...; obi...@go...; obi...@li... Subject: Re: [Obi-role-branch] inconsistency when adding organism to study specinem role Why is it that a human participant can't be a study specimen? Richard On Jan 15, 2009, at 9:54 AM, Fostel, Jennifer (NIH/NIEHS) [C] wrote: biomaterials: transgenic organism cell lysate processes: electrocuted enrolled cervical dislocation killing genetic trasnformation decapitation DNA transformation cell lysis electroporation asphyxiation intentional overdosing DNA transduction i need to allow all organisms with the exception of humans to play the role of a study specimen what should i do? 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 ------------------------------------------------------------------------ ------ This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword____________________________________ ___________ Obi-role-branch mailing list Obi...@li... https://lists.sourceforge.net/lists/listinfo/obi-role-branch ------------------------------------------------------------------------ ------------------------ Richard H. Scheuermann, Ph.D. Chief, Division of Biomedical Informatics Director, Division of Translational Pathology 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 |
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From: Richard H. S. Ph.D. <ric...@ut...> - 2009-01-15 16:07:58
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Why is it that a human participant can't be a study specimen? Richard On Jan 15, 2009, at 9:54 AM, Fostel, Jennifer (NIH/NIEHS) [C] wrote: > biomaterials: > transgenic organism > cell lysate > > processes: > electrocuted > enrolled > cervical dislocation > killing > genetic trasnformation > decapitation > DNA transformation > cell lysis > electroporation > asphyxiation > intentional overdosing > DNA transduction > > i need to allow all organisms with the exception of humans to play > the role of a study specimen > what should i do? > > > 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 > > ---------------------------------------------------------------------- > -------- > This SF.net email is sponsored by: > SourcForge Community > SourceForge wants to tell your story. > http://p.sf.net/sfu/sf- > spreadtheword_______________________________________________ > Obi-role-branch mailing list > Obi...@li... > https://lists.sourceforge.net/lists/listinfo/obi-role-branch ------------------------------------------------------------------------ ------------------------ Richard H. Scheuermann, Ph.D. Chief, Division of Biomedical Informatics Director, Division of Translational Pathology 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 |
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From: Fostel, J. (NIH/N. [C] <fo...@ni...> - 2009-01-15 15:54:36
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biomaterials: transgenic organism cell lysate processes: electrocuted enrolled cervical dislocation killing genetic trasnformation decapitation DNA transformation cell lysis electroporation asphyxiation intentional overdosing DNA transduction i need to allow all organisms with the exception of humans to play the role of a study specimen what should i do? 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: Bjoern P. <bp...@li...> - 2009-01-15 15:54:03
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Just a reminder that calls will resume today. Agenda: finish up on core terms. Bjoern Peters wrote: > I will be traveling starting next week, and won't be able to attend the > Thursday calls. Let's resume next year, and maybe get a bit more done by > email before that. > > -- Bjoern Peters Assistant Member La Jolla Institute for Allergy and Immunology 9420 Athena Circle La Jolla, CA 92037, USA Tel: 858/752-6914 Fax: 858/752-6987 http://www.liai.org/pages/faculty-peters |
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From: Bjoern P. <bp...@li...> - 2008-12-12 22:35:46
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I will be traveling starting next week, and won't be able to attend the Thursday calls. Let's resume next year, and maybe get a bit more done by email before that. -- Bjoern Peters Assistant Member La Jolla Institute for Allergy and Immunology 9420 Athena Circle La Jolla, CA 92037, USA Tel: 858/752-6914 Fax: 858/752-6987 http://www.liai.org/pages/faculty-peters |
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