From: Fostel, J. (NIH/N. [C] <fo...@ni...> - 2008-10-02 19:08:38
Attachments:
bloodAssayUseCase.txt
|
Obtain urine from a rat which is participating in a study. urine is collected at a particular time in the study timeline rat has_role study subject urine has_role biological specimen needa relation to link the specimen to the former "owner" Assay 1 = urine color Place a drop of urine on a microscope slide Record the color, based on visual inspection urine has_role "thing which is assayed" assay_output = paper with color name written next to specimen ID i no longer think color is an evaluant, but a quality Assay 2 = urine albumin concentration (Centrifuge urine to remove debris) Place urine into assay tube Add antibody to albumin Incubate room temperature, 1 hour Wash Add chromogen solution incubate 10 minutes add stop solution read Absorbance at 492 nm using spectrophotometer (Model 550, Microplate Reader, BIORAD, California, USA) urine (or resulting supernatant) has_role "thing being assayed" albumin has role evaluant assay_output = absorbance at 492 nm written on a piece of paper spectrophotometer has_function measuring device antibody, chromagen, stop solution and buffer have_role reagent(s) data transformation: standard curve with albumin at 0, 16, 31, 63, 125, 500, and 1000 ng/ml used to interpolate to concentration of albumin in the urine. Y. L. Qie, K. Kaizu, K. Uriu, I. Takagi, Y. Inada and S. Eto Measurement of urinary albumin using newly developed enzyme immunoassay in the rat Clinical and Experimental Nephrology 2000, vol 4, p99-104 |
From: <ro...@eb...> - 2008-10-02 22:31:24
|
Dear All, Following our (long) discussions during today's PA call, I have put tried to go over the following mini use case Assay: measuring mouse body weight, trying to summerize all our pb/questions. i. the first pass was to identify all things that would the present at the begining of the assay and result from it. We therefore identified: -a mouse -a scale -data all of which are called 'participant' but each of which has a different roles, realized over the course of an assay. the main point of discussion is determining how we call: the 'thing being assayed': -> should be an independent continuant/material entity/ mouse in our example the 'thing being measured': ->thing should be an dependent continuant/quality/weight in our example BP:'thing being measured' = range of 'is measurement of' in assay the thing being measured has been called 'evaluant' (Richard), which would realize its evaluant_role. so this becomes: assay "measuring weight" utilizes_device = scale (this implies realization of the function of scale) scale has_function = weight_measuring_function has_input = mouse (independent continuant ) in this case, has_input range would always be 'thing being assayed' has_evaluant = weight (dependent continuant), in this case, has_evaluant range would always be 'thing being measured' has_output = datum possibly qualified by a unit the problem that then arises is the following: weight would play the role of evaluant , but bfo does not allow dependent continuant to bear roles. but is that really so ? should 'weight' bear the evaluant role or should it be 'weight of whole_body' ? And it seems that I've lost the path to relate to objective... Cheers Philippe (Then a side note about assay labels in OBI: assay name should probably sound like occurent: "body weight" should probably not be used as a label for an assay, since body weight <=> quality/weight about_of independent_continuant/body so "measuring body weight" would probably be a label to choose (so ALT is not an assay, measuring ALT activity sounds like one) |
From: Melanie C. <mco...@gm...> - 2008-10-02 22:55:24
Attachments:
Concentration.pdf
|
Hi all, Thanks for putting the use case together Philippe. I had a look at the "analyte" discussion that happened a while ago, and I agree with Jennifer, evaluant is a independent continuant. Remembering that we chose to rename analyte to evaluant, the analyte discussion was referring to measuring the level of glucose, and in that case the glucose was the analyte/evaluant. So what we called the "thing being assayed" is indeed the evaluant. So I think we have: - weight assessment (OBI_0600026) has_participants mouse, scale, weight datum - mouse (material entity to be added to OBI) has_role evaluant and has_role input_role (I don't think evaluant and input role overlap, we might be measuring the formation of a substance for example) - mouse is_input_of weight assessment (<=> weight assessment has_input mouse) - weight assessment utilizes_device scale (to be added under device) (note: cf discussion at http://groups.google.com/group/obi-owl/browse_thread/thread/5bf2906bec8da16b?hl=en for utilizes_device - The scale bears a role "measurer role" (or other name) and realizes its function "measuring". (the same scale used as a door stopper still bears the role "measurer" but doesn't realize its function)) - weight datum is_output of weight assessment (<=> weight assessment has output datum) - weight datum is a datum (under information content entity) (analogy with concentration example made by Alan and attached) Regarding objective, I think we might want to have a global "measuring" objective, without having details like "weight measuring" etc. Any "assessment" kind of protocol would probably have an objective of measuring something, is it useful to have? Regarding is_input_of and has_role input role I think this is redundant, and I think that's why we decided to not keep the input role a while ago. We might want to work on the definition of is_input, to make it clear that in this case the scale for example is not input of the assay. Of course, don't hesitate to prove me wrong :) Thanks, Melanie |
From: Richard H. S. , Ph.D. <ric...@ut...> - 2008-10-02 22:41:37
|
My proposal was that 'evaluant' was the 'thing being assayed', i.e. the independent continuant; the mouse in this case. The thing being measured would be the quality (weight). In some cases the thing being measured would be the concentration of an analyte. Although the analyte itself is an independent continuant, its concentration within another IC is a quality of that IC. Richard On Oct 2, 2008, at 5:26 PM, ro...@eb... wrote: > Dear All, > > Following our (long) discussions during today's PA call, I have put > tried > to go over the following mini use case > > Assay: measuring mouse body weight, trying to summerize all our pb/ > questions. > > i. the first pass was to identify all things that would the present > at the > begining of the assay and result from it. We therefore identified: > -a mouse > -a scale > -data > > all of which are called 'participant' but each of which has a > different > roles, realized over the course of an assay. the main point of > discussion > is determining how we call: > > the 'thing being assayed': -> should be an independent continuant/ > material > entity/ mouse in our example > > the 'thing being measured': ->thing should be an dependent > continuant/quality/weight in our example > > BP:'thing being measured' = range of 'is measurement of' in assay > > the thing being measured has been called 'evaluant' (Richard), > which would > realize its evaluant_role. > > so this becomes: > > assay "measuring weight" > utilizes_device = scale (this implies realization of the function > of scale) > scale has_function = weight_measuring_function > has_input = mouse (independent continuant ) in this case, > has_input range > would always be 'thing being assayed' > has_evaluant = weight (dependent continuant), in this case, > has_evaluant > range would always be 'thing being measured' > has_output = datum possibly qualified by a unit > > the problem that then arises is the following: > weight would play the role of evaluant , but bfo does not allow > dependent > continuant to bear roles. but is that really so ? > should 'weight' bear the evaluant role or should it be 'weight of > whole_body' ? > > And it seems that I've lost the path to relate to objective... > > Cheers > > Philippe > > > (Then a side note about assay labels in OBI: assay name should > probably > sound like occurent: > "body weight" should probably not be used as a label for an assay, > since > body weight <=> quality/weight about_of independent_continuant/body > so "measuring body weight" would probably be a label to choose > (so ALT is not an assay, measuring ALT activity sounds like one) > > > > > > ---------------------------------------------------------------------- > --- > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win > great prizes > Grand prize is a trip for two to an Open Source event anywhere in > the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > 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 |
From: Bjoern P. <bp...@li...> - 2008-10-03 02:22:44
|
That's how I recalled your definition of 'evaluant' in todays call as well, but the role branch had a different understanding , thinking it was a less controversial but similar concept to 'analyte'. The terms 'thing being assayed' and 'thing being measured' where introduced as placeholders during the call to not argue what the true meaning of 'evaluant' is. Richard H. Scheuermann , Ph.D. wrote: > My proposal was that 'evaluant' was the 'thing being assayed', i.e. > the independent continuant; the mouse in this case. The thing being > measured would be the quality (weight). In some cases the thing being > measured would be the concentration of an analyte. Although the > analyte itself is an independent continuant, its concentration within > another IC is a quality of that IC. > > Richard > > > On Oct 2, 2008, at 5:26 PM, ro...@eb... <mailto:ro...@eb...> > wrote: > >> Dear All, >> >> Following our (long) discussions during today's PA call, I have put tried >> to go over the following mini use case >> >> Assay: measuring mouse body weight, trying to summerize all our >> pb/questions. >> >> i. the first pass was to identify all things that would the present >> at the >> begining of the assay and result from it. We therefore identified: >> -a mouse >> -a scale >> -data >> >> all of which are called 'participant' but each of which has a different >> roles, realized over the course of an assay. the main point of discussion >> is determining how we call: >> >> the 'thing being assayed': -> should be an independent >> continuant/material >> entity/ mouse in our example >> >> the 'thing being measured': ->thing should be an dependent >> continuant/quality/weight in our example >> >> BP:'thing being measured' = range of 'is measurement of' in assay >> >> the thing being measured has been called 'evaluant' (Richard), which >> would >> realize its evaluant_role. >> >> so this becomes: >> >> assay "measuring weight" >> utilizes_device = scale (this implies realization of the function of >> scale) >> scale has_function = weight_measuring_function >> has_input = mouse (independent continuant ) in this case, has_input range >> would always be 'thing being assayed' >> has_evaluant = weight (dependent continuant), in this case, has_evaluant >> range would always be 'thing being measured' >> has_output = datum possibly qualified by a unit >> >> the problem that then arises is the following: >> weight would play the role of evaluant , but bfo does not allow dependent >> continuant to bear roles. but is that really so ? >> should 'weight' bear the evaluant role or should it be 'weight of >> whole_body' ? >> >> And it seems that I've lost the path to relate to objective... >> >> Cheers >> >> Philippe >> >> >> (Then a side note about assay labels in OBI: assay name should probably >> sound like occurent: >> "body weight" should probably not be used as a label for an assay, since >> body weight <=> quality/weight about_of independent_continuant/body >> so "measuring body weight" would probably be a label to choose >> (so ALT is not an assay, measuring ALT activity sounds like one) >> >> >> >> >> >> ------------------------------------------------------------------------- >> This SF.Net email is sponsored by the Moblin Your Move Developer's >> challenge >> Build the coolest Linux based applications with Moblin SDK & win >> great prizes >> Grand prize is a trip for two to an Open Source event anywhere in the >> world >> http://moblin-contest.org/redirect.php?banner_id=100&url=/ >> <http://moblin-contest.org/redirect.php?banner_id=100&url=/> >> _______________________________________________ >> Obi-role-branch mailing list >> Obi...@li... >> <mailto: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... > <mailto:ric...@ut...> > http://pathcuric1.swmed.edu/Research/scheuermann.html > > > -- 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 |
From: Richard H. S. , Ph.D. <ric...@ut...> - 2008-10-03 13:21:13
|
And I should say that I am certainly not wedded to the term. My only goal was to make the following distinctions - that a material sample removed from a subject during a partitioning type of material transformation would play the role of 'specimen'; when the same material sample was used as an input to an assay it would change its role to 'evaluant'; which would be distinct from the thing being measured, which if it were an IC it would be playing the role of 'analyte'. I didn't think that 'analyte' was controversial. It is pretty well established in the clinical chemistry community. On Oct 2, 2008, at 9:22 PM, Bjoern Peters wrote: > That's how I recalled your definition of 'evaluant' in todays call > as well, but the role branch had a different understanding , > thinking it was a less controversial but similar concept to > 'analyte'. The terms 'thing being assayed' and 'thing being > measured' where introduced as placeholders during the call to not > argue what the true meaning of 'evaluant' is. > > Richard H. Scheuermann , Ph.D. wrote: >> My proposal was that 'evaluant' was the 'thing being assayed', >> i.e. the independent continuant; the mouse in this case. The >> thing being measured would be the quality (weight). In some cases >> the thing being measured would be the concentration of an >> analyte. Although the analyte itself is an independent >> continuant, its concentration within another IC is a quality of >> that IC. >> >> Richard >> >> >> On Oct 2, 2008, at 5:26 PM, ro...@eb... >> <mailto:ro...@eb...> wrote: >> >>> Dear All, >>> >>> Following our (long) discussions during today's PA call, I have >>> put tried >>> to go over the following mini use case >>> >>> Assay: measuring mouse body weight, trying to summerize all our >>> pb/questions. >>> >>> i. the first pass was to identify all things that would the >>> present at the >>> begining of the assay and result from it. We therefore identified: >>> -a mouse >>> -a scale >>> -data >>> >>> all of which are called 'participant' but each of which has a >>> different >>> roles, realized over the course of an assay. the main point of >>> discussion >>> is determining how we call: >>> >>> the 'thing being assayed': -> should be an independent continuant/ >>> material >>> entity/ mouse in our example >>> >>> the 'thing being measured': ->thing should be an dependent >>> continuant/quality/weight in our example >>> >>> BP:'thing being measured' = range of 'is measurement of' in assay >>> >>> the thing being measured has been called 'evaluant' (Richard), >>> which would >>> realize its evaluant_role. >>> >>> so this becomes: >>> >>> assay "measuring weight" >>> utilizes_device = scale (this implies realization of the function >>> of scale) >>> scale has_function = weight_measuring_function >>> has_input = mouse (independent continuant ) in this case, >>> has_input range >>> would always be 'thing being assayed' >>> has_evaluant = weight (dependent continuant), in this case, >>> has_evaluant >>> range would always be 'thing being measured' >>> has_output = datum possibly qualified by a unit >>> >>> the problem that then arises is the following: >>> weight would play the role of evaluant , but bfo does not allow >>> dependent >>> continuant to bear roles. but is that really so ? >>> should 'weight' bear the evaluant role or should it be 'weight of >>> whole_body' ? >>> >>> And it seems that I've lost the path to relate to objective... >>> >>> Cheers >>> >>> Philippe >>> >>> >>> (Then a side note about assay labels in OBI: assay name should >>> probably >>> sound like occurent: >>> "body weight" should probably not be used as a label for an >>> assay, since >>> body weight <=> quality/weight about_of independent_continuant/body >>> so "measuring body weight" would probably be a label to choose >>> (so ALT is not an assay, measuring ALT activity sounds like one) >>> >>> >>> >>> >>> >>> -------------------------------------------------------------------- >>> ----- >>> This SF.Net email is sponsored by the Moblin Your Move >>> Developer's challenge >>> Build the coolest Linux based applications with Moblin SDK & win >>> great prizes >>> Grand prize is a trip for two to an Open Source event anywhere in >>> the world >>> http://moblin-contest.org/redirect.php?banner_id=100&url=/ >>> <http://moblin-contest.org/redirect.php?banner_id=100&url=/> >>> _______________________________________________ >>> Obi-role-branch mailing list >>> Obi...@li... <mailto:Obi-role- >>> br...@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... >> <mailto:ric...@ut...> >> http://pathcuric1.swmed.edu/Research/scheuermann.html >> >> >> > > > -- > 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 > > > ------------------------------------------------------------------------ ------------------------ 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 |
From: Richard H. S. , Ph.D. <ric...@ut...> - 2008-10-02 22:43:41
|
Isn't the 'evaluator' also a participant? On Oct 2, 2008, at 5:26 PM, ro...@eb... wrote: > Dear All, > > Following our (long) discussions during today's PA call, I have put > tried > to go over the following mini use case > > Assay: measuring mouse body weight, trying to summerize all our pb/ > questions. > > i. the first pass was to identify all things that would the present > at the > begining of the assay and result from it. We therefore identified: > -a mouse > -a scale > -data > > all of which are called 'participant' but each of which has a > different > roles, realized over the course of an assay. the main point of > discussion > is determining how we call: > > the 'thing being assayed': -> should be an independent continuant/ > material > entity/ mouse in our example > > the 'thing being measured': ->thing should be an dependent > continuant/quality/weight in our example > > BP:'thing being measured' = range of 'is measurement of' in assay > > the thing being measured has been called 'evaluant' (Richard), > which would > realize its evaluant_role. > > so this becomes: > > assay "measuring weight" > utilizes_device = scale (this implies realization of the function > of scale) > scale has_function = weight_measuring_function > has_input = mouse (independent continuant ) in this case, > has_input range > would always be 'thing being assayed' > has_evaluant = weight (dependent continuant), in this case, > has_evaluant > range would always be 'thing being measured' > has_output = datum possibly qualified by a unit > > the problem that then arises is the following: > weight would play the role of evaluant , but bfo does not allow > dependent > continuant to bear roles. but is that really so ? > should 'weight' bear the evaluant role or should it be 'weight of > whole_body' ? > > And it seems that I've lost the path to relate to objective... > > Cheers > > Philippe > > > (Then a side note about assay labels in OBI: assay name should > probably > sound like occurent: > "body weight" should probably not be used as a label for an assay, > since > body weight <=> quality/weight about_of independent_continuant/body > so "measuring body weight" would probably be a label to choose > (so ALT is not an assay, measuring ALT activity sounds like one) > > > > > > ---------------------------------------------------------------------- > --- > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win > great prizes > Grand prize is a trip for two to an Open Source event anywhere in > the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > 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 |
From: Bjoern P. <bp...@li...> - 2008-10-03 02:23:34
|
Yes, every objective driven process has an 'objective realizing agent' as a participant as well. Richard H. Scheuermann , Ph.D. wrote: > Isn't the 'evaluator' also a participant? > > > On Oct 2, 2008, at 5:26 PM, ro...@eb... <mailto:ro...@eb...> > wrote: > >> Dear All, >> >> Following our (long) discussions during today's PA call, I have put tried >> to go over the following mini use case >> >> Assay: measuring mouse body weight, trying to summerize all our >> pb/questions. >> >> i. the first pass was to identify all things that would the present >> at the >> begining of the assay and result from it. We therefore identified: >> -a mouse >> -a scale >> -data >> >> all of which are called 'participant' but each of which has a different >> roles, realized over the course of an assay. the main point of discussion >> is determining how we call: >> >> the 'thing being assayed': -> should be an independent >> continuant/material >> entity/ mouse in our example >> >> the 'thing being measured': ->thing should be an dependent >> continuant/quality/weight in our example >> >> BP:'thing being measured' = range of 'is measurement of' in assay >> >> the thing being measured has been called 'evaluant' (Richard), which >> would >> realize its evaluant_role. >> >> so this becomes: >> >> assay "measuring weight" >> utilizes_device = scale (this implies realization of the function of >> scale) >> scale has_function = weight_measuring_function >> has_input = mouse (independent continuant ) in this case, has_input range >> would always be 'thing being assayed' >> has_evaluant = weight (dependent continuant), in this case, has_evaluant >> range would always be 'thing being measured' >> has_output = datum possibly qualified by a unit >> >> the problem that then arises is the following: >> weight would play the role of evaluant , but bfo does not allow dependent >> continuant to bear roles. but is that really so ? >> should 'weight' bear the evaluant role or should it be 'weight of >> whole_body' ? >> >> And it seems that I've lost the path to relate to objective... >> >> Cheers >> >> Philippe >> >> >> (Then a side note about assay labels in OBI: assay name should probably >> sound like occurent: >> "body weight" should probably not be used as a label for an assay, since >> body weight <=> quality/weight about_of independent_continuant/body >> so "measuring body weight" would probably be a label to choose >> (so ALT is not an assay, measuring ALT activity sounds like one) >> >> >> >> >> >> ------------------------------------------------------------------------- >> This SF.Net email is sponsored by the Moblin Your Move Developer's >> challenge >> Build the coolest Linux based applications with Moblin SDK & win >> great prizes >> Grand prize is a trip for two to an Open Source event anywhere in the >> world >> http://moblin-contest.org/redirect.php?banner_id=100&url=/ >> <http://moblin-contest.org/redirect.php?banner_id=100&url=/> >> _______________________________________________ >> Obi-role-branch mailing list >> Obi...@li... >> <mailto: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... > <mailto:ric...@ut...> > http://pathcuric1.swmed.edu/Research/scheuermann.html > > > -- 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 |
From: Fostel, J. (NIH/N. [C] <fo...@ni...> - 2008-10-03 12:39:18
|
given that we are not looking at evaluant and analyte as sysmonyms, let's call the "thing being assayed" as bearing the evaluant role, and the "thing being measured, when it is an IC," as bearing the analyte role. -----Original Message----- From: Bjoern Peters [mailto:bp...@li...] Sent: Thursday, October 02, 2008 10:23 PM To: Richard H. Scheuermann , Ph.D. Cc: ro...@eb...; Fostel, Jennifer (NIH/NIEHS) [C]; obi...@li...; Melanie Courtot; obi...@li... Subject: Re: [Obi-role-branch] [Obi-protocol-application-branch] Mini-use case: measuring body weight Yes, every objective driven process has an 'objective realizing agent' as a participant as well. Richard H. Scheuermann , Ph.D. wrote: > Isn't the 'evaluator' also a participant? > > > On Oct 2, 2008, at 5:26 PM, ro...@eb... <mailto:ro...@eb...> > wrote: > >> Dear All, >> >> Following our (long) discussions during today's PA call, I have put >> tried to go over the following mini use case >> >> Assay: measuring mouse body weight, trying to summerize all our >> pb/questions. >> >> i. the first pass was to identify all things that would the present >> at the begining of the assay and result from it. We therefore >> identified: >> -a mouse >> -a scale >> -data >> >> all of which are called 'participant' but each of which has a >> different roles, realized over the course of an assay. the main point >> of discussion is determining how we call: >> >> the 'thing being assayed': -> should be an independent >> continuant/material entity/ mouse in our example >> >> the 'thing being measured': ->thing should be an dependent >> continuant/quality/weight in our example >> >> BP:'thing being measured' = range of 'is measurement of' in assay >> >> the thing being measured has been called 'evaluant' (Richard), which >> would realize its evaluant_role. >> >> so this becomes: >> >> assay "measuring weight" >> utilizes_device = scale (this implies realization of the function of >> scale) >> scale has_function = weight_measuring_function has_input = mouse >> (independent continuant ) in this case, has_input range would always >> be 'thing being assayed' >> has_evaluant = weight (dependent continuant), in this case, >> has_evaluant range would always be 'thing being measured' >> has_output = datum possibly qualified by a unit >> >> the problem that then arises is the following: >> weight would play the role of evaluant , but bfo does not allow >> dependent continuant to bear roles. but is that really so ? >> should 'weight' bear the evaluant role or should it be 'weight of >> whole_body' ? >> >> And it seems that I've lost the path to relate to objective... >> >> Cheers >> >> Philippe >> >> >> (Then a side note about assay labels in OBI: assay name should >> probably sound like occurent: >> "body weight" should probably not be used as a label for an assay, >> since body weight <=> quality/weight about_of >> independent_continuant/body so "measuring body weight" would probably >> be a label to choose (so ALT is not an assay, measuring ALT activity >> sounds like one) >> >> >> >> >> >> --------------------------------------------------------------------- >> ---- This SF.Net email is sponsored by the Moblin Your Move >> Developer's challenge Build the coolest Linux based applications with >> Moblin SDK & win great prizes Grand prize is a trip for two to an >> Open Source event anywhere in the world >> http://moblin-contest.org/redirect.php?banner_id=100&url=/ >> <http://moblin-contest.org/redirect.php?banner_id=100&url=/> >> _______________________________________________ >> Obi-role-branch mailing list >> Obi...@li... >> <mailto: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... > <mailto:ric...@ut...> > http://pathcuric1.swmed.edu/Research/scheuermann.html > > > -- 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 |
From: Philippe Rocca-S. <ro...@eb...> - 2008-10-03 13:07:10
|
could you give an example of "thing being measured"that is an IC ? so far, in the example that we have discussed, weight of body, count of cells, concentration of glucose (which are actually dependent continuant /about_of/ independent continuant). This is where for me thing become blurry as to what we mean exactly by 'thing being measured'. The difference between 'weight measurement' and 'glucose concentration measurement' is that in the case of glucose concentration measurement, we need to specify "where" we are looking for glucose located_in another entity (urine, blood). Can we really say, we are 'measuring glucose' ? It seems to me we should only be saying 'measuring some quality about glucose' 2 comments: i. I will leave side additional information we would need to capture related to the 'when' the assay was performed (measuring glucose concentration at 10 minutes post drug injection) But this would relate to describing how the 'thing being assayed' has been collected and we would need to relate a part_protocolapplication and introduce the ability to specify a collection time. ii. I am a bit worried by all this complexity to describe an assay and how we can expect OBI users to deal with this. People doing phenotyping have a number of very fancy assays and we are dealing with fairly simple cases. Philippe Fostel, Jennifer (NIH/NIEHS) [C] wrote: > given that we are not looking at evaluant and analyte as sysmonyms, > let's call the "thing being assayed" as bearing the evaluant role, and > the "thing being measured, when it is an IC," as bearing the analyte > role. > > -----Original Message----- > From: Bjoern Peters [mailto:bp...@li...] > Sent: Thursday, October 02, 2008 10:23 PM > To: Richard H. Scheuermann , Ph.D. > Cc: ro...@eb...; Fostel, Jennifer (NIH/NIEHS) [C]; > obi...@li...; Melanie Courtot; > obi...@li... > Subject: Re: [Obi-role-branch] [Obi-protocol-application-branch] > Mini-use case: measuring body weight > > Yes, every objective driven process has an 'objective realizing agent' > as a participant as well. > > Richard H. Scheuermann , Ph.D. wrote: > >> Isn't the 'evaluator' also a participant? >> >> >> On Oct 2, 2008, at 5:26 PM, ro...@eb... <mailto:ro...@eb...> >> wrote: >> >> >>> Dear All, >>> >>> Following our (long) discussions during today's PA call, I have put >>> tried to go over the following mini use case >>> >>> Assay: measuring mouse body weight, trying to summerize all our >>> pb/questions. >>> >>> i. the first pass was to identify all things that would the present >>> at the begining of the assay and result from it. We therefore >>> identified: >>> -a mouse >>> -a scale >>> -data >>> >>> all of which are called 'participant' but each of which has a >>> different roles, realized over the course of an assay. the main point >>> > > >>> of discussion is determining how we call: >>> >>> the 'thing being assayed': -> should be an independent >>> continuant/material entity/ mouse in our example >>> >>> the 'thing being measured': ->thing should be an dependent >>> continuant/quality/weight in our example >>> >>> BP:'thing being measured' = range of 'is measurement of' in assay >>> >>> the thing being measured has been called 'evaluant' (Richard), which >>> would realize its evaluant_role. >>> >>> so this becomes: >>> >>> assay "measuring weight" >>> utilizes_device = scale (this implies realization of the function of >>> scale) >>> scale has_function = weight_measuring_function has_input = mouse >>> (independent continuant ) in this case, has_input range would always >>> be 'thing being assayed' >>> has_evaluant = weight (dependent continuant), in this case, >>> has_evaluant range would always be 'thing being measured' >>> has_output = datum possibly qualified by a unit >>> >>> the problem that then arises is the following: >>> weight would play the role of evaluant , but bfo does not allow >>> dependent continuant to bear roles. but is that really so ? >>> should 'weight' bear the evaluant role or should it be 'weight of >>> whole_body' ? >>> >>> And it seems that I've lost the path to relate to objective... >>> >>> Cheers >>> >>> Philippe >>> >>> >>> (Then a side note about assay labels in OBI: assay name should >>> probably sound like occurent: >>> "body weight" should probably not be used as a label for an assay, >>> since body weight <=> quality/weight about_of >>> independent_continuant/body so "measuring body weight" would probably >>> > > >>> be a label to choose (so ALT is not an assay, measuring ALT activity >>> sounds like one) >>> >>> >>> >>> >>> >>> --------------------------------------------------------------------- >>> ---- This SF.Net email is sponsored by the Moblin Your Move >>> Developer's challenge Build the coolest Linux based applications with >>> > > >>> Moblin SDK & win great prizes Grand prize is a trip for two to an >>> Open Source event anywhere in the world >>> http://moblin-contest.org/redirect.php?banner_id=100&url=/ >>> <http://moblin-contest.org/redirect.php?banner_id=100&url=/> >>> _______________________________________________ >>> Obi-role-branch mailing list >>> Obi...@li... >>> <mailto: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... >> <mailto:ric...@ut...> >> http://pathcuric1.swmed.edu/Research/scheuermann.html >> >> >> >> > > > -- > 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 > > > > |
From: Bjoern P. <bp...@li...> - 2008-10-03 22:37:07
|
I agree with this perfectly. In addition, 'thing being measured' is something that every assay will have, while not every assay will have an analyte. In Jennifer's example, measuring 'concentration of glucose' implies analyte = glucose. In the mouse weight example, 'weight of mouse' is the thing being measured, without there being an analyte. This ties into assay objectives: There is a shared objective for assays that have analytes, namely to determine the presence or quantity of the analyte in the evaluant. - Bjoern Fostel, Jennifer (NIH/NIEHS) [C] wrote: > mouse -> urine -> measure [glucose] > > wrt study timeline > mouse has_role subject > urine has_role specimen > > wrt assay > urine has_role evaluant > glucose_in_urine has_role analyte > assay_output = paper containing information reporting measured > concentration of glucose > > assay_participants include urine, reagents used to measure, device > used to measure, tubes used to collect, prepare and assay the urine, > the standard curve reagents, assay_output > > we need to capture the relationship between the output report, the > "real" concentration of glucose and the subject > > > ------------------------------------------------------------------------ > *From:* Richard H. Scheuermann , Ph.D. > [mailto:ric...@ut...] > *Sent:* Friday, October 03, 2008 9:25 AM > *To:* Philippe Rocca-Serra > *Cc:* Fostel, Jennifer (NIH/NIEHS) [C]; Melanie Courtot; > obi...@li...; Bjoern Peters; > obi...@li... > *Subject:* Re: [Obi-role-branch] [Obi-protocol-application-branch] > Mini-use case: measuring body weight > > I think we are on the same page. While glucose is an IC, glucose > concentration is a DC. This is really an important concept that we > need to be consistent in treating, since it can be a little confusing. > > Richard > > > On Oct 3, 2008, at 8:06 AM, Philippe Rocca-Serra wrote: > >> could you give an example of "thing being measured"that is an IC ? >> >> so far, in the example that we have discussed, weight of body, count of >> cells, concentration of glucose (which are actually dependent continuant >> /about_of/ independent continuant). >> >> This is where for me thing become blurry as to what we mean exactly by >> 'thing being measured'. >> >> The difference between 'weight measurement' and 'glucose concentration >> measurement' is that in the case of glucose concentration measurement, >> we need to specify "where" we are looking for glucose located_in another >> entity (urine, blood). >> >> Can we really say, we are 'measuring glucose' ? It seems to me we should >> only be saying 'measuring some quality about glucose' >> >> 2 comments: >> >> i. I will leave side additional information we would need to capture >> related to the 'when' the assay was performed (measuring glucose >> concentration at 10 minutes post drug injection) >> But this would relate to describing how the 'thing being assayed' has >> been collected and we would need to relate a part_protocolapplication >> and introduce the ability to specify a collection time. >> >> ii. I am a bit worried by all this complexity to describe an assay and >> how we can expect OBI users to deal with this. People doing phenotyping >> have a number of very fancy assays and we are dealing with fairly >> simple cases. >> >> >> >> Philippe >> >> >> >> >> >> Fostel, Jennifer (NIH/NIEHS) [C] wrote: >>> given that we are not looking at evaluant and analyte as sysmonyms, >>> let's call the "thing being assayed" as bearing the evaluant role, and >>> the "thing being measured, when it is an IC," as bearing the analyte >>> role. >>> >>> -----Original Message----- >>> From: Bjoern Peters [mailto:bp...@li...] >>> Sent: Thursday, October 02, 2008 10:23 PM >>> To: Richard H. Scheuermann , Ph.D. >>> Cc: ro...@eb... <mailto:ro...@eb...>; Fostel, Jennifer >>> (NIH/NIEHS) [C]; >>> obi...@li... >>> <mailto:obi...@li...>; >>> Melanie Courtot; >>> obi...@li... >>> <mailto:obi...@li...> >>> Subject: Re: [Obi-role-branch] [Obi-protocol-application-branch] >>> Mini-use case: measuring body weight >>> >>> Yes, every objective driven process has an 'objective realizing agent' >>> as a participant as well. >>> >>> Richard H. Scheuermann , Ph.D. wrote: >>> >>>> Isn't the 'evaluator' also a participant? >>>> >>>> >>>> On Oct 2, 2008, at 5:26 PM, ro...@eb... <mailto:ro...@eb...> >>>> wrote: >>>> >>>> >>>>> Dear All, >>>>> >>>>> Following our (long) discussions during today's PA call, I have put >>>>> tried to go over the following mini use case >>>>> >>>>> Assay: measuring mouse body weight, trying to summerize all our >>>>> pb/questions. >>>>> >>>>> i. the first pass was to identify all things that would the present >>>>> at the begining of the assay and result from it. We therefore >>>>> identified: >>>>> -a mouse >>>>> -a scale >>>>> -data >>>>> >>>>> all of which are called 'participant' but each of which has a >>>>> different roles, realized over the course of an assay. the main point >>>>> >>> >>> >>>>> of discussion is determining how we call: >>>>> >>>>> the 'thing being assayed': -> should be an independent >>>>> continuant/material entity/ mouse in our example >>>>> >>>>> the 'thing being measured': ->thing should be an dependent >>>>> continuant/quality/weight in our example >>>>> >>>>> BP:'thing being measured' = range of 'is measurement of' in assay >>>>> >>>>> the thing being measured has been called 'evaluant' (Richard), which >>>>> would realize its evaluant_role. >>>>> >>>>> so this becomes: >>>>> >>>>> assay "measuring weight" >>>>> utilizes_device = scale (this implies realization of the function of >>>>> scale) >>>>> scale has_function = weight_measuring_function has_input = mouse >>>>> (independent continuant ) in this case, has_input range would always >>>>> be 'thing being assayed' >>>>> has_evaluant = weight (dependent continuant), in this case, >>>>> has_evaluant range would always be 'thing being measured' >>>>> has_output = datum possibly qualified by a unit >>>>> >>>>> the problem that then arises is the following: >>>>> weight would play the role of evaluant , but bfo does not allow >>>>> dependent continuant to bear roles. but is that really so ? >>>>> should 'weight' bear the evaluant role or should it be 'weight of >>>>> whole_body' ? >>>>> >>>>> And it seems that I've lost the path to relate to objective... >>>>> >>>>> Cheers >>>>> >>>>> Philippe >>>>> >>>>> >>>>> (Then a side note about assay labels in OBI: assay name should >>>>> probably sound like occurent: >>>>> "body weight" should probably not be used as a label for an assay, >>>>> since body weight <=> quality/weight about_of >>>>> independent_continuant/body so "measuring body weight" would probably >>>>> >>> >>> >>>>> be a label to choose (so ALT is not an assay, measuring ALT activity >>>>> sounds like one) >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> --------------------------------------------------------------------- >>>>> ---- This SF.Net email is sponsored by the Moblin Your Move >>>>> Developer's challenge Build the coolest Linux based applications with >>>>> >>> >>> >>>>> Moblin SDK & win great prizes Grand prize is a trip for two to an >>>>> Open Source event anywhere in the world >>>>> http://moblin-contest.org/redirect.php?banner_id=100&url=/ >>>>> <http://moblin-contest.org/redirect.php?banner_id=100&url=/> >>>>> <http://moblin-contest.org/redirect.php?banner_id=100&url=/ >>>>> <http://moblin-contest.org/redirect.php?banner_id=100&url=/>> >>>>> _______________________________________________ >>>>> Obi-role-branch mailing list >>>>> Obi...@li... >>>>> <mailto:Obi...@li...> >>>>> <mailto: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... >>>> <mailto:ric...@ut...> >>>> <mailto:ric...@ut...> >>>> http://pathcuric1.swmed.edu/Research/scheuermann.html >>>> >>>> >>>> >>>> >>> >>> >>> -- >>> 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 the Moblin Your Move Developer's >> challenge >> Build the coolest Linux based applications with Moblin SDK & win >> great prizes >> Grand prize is a trip for two to an Open Source event anywhere in the >> world >> http://moblin-contest.org/redirect.php?banner_id=100&url=/ >> <http://moblin-contest.org/redirect.php?banner_id=100&url=/> >> _______________________________________________ >> Obi-role-branch mailing list >> Obi...@li... >> <mailto: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... > <mailto:ric...@ut...> > http://pathcuric1.swmed.edu/Research/scheuermann.html > > > -- 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 |
From: Richard H. S. , Ph.D. <ric...@ut...> - 2008-10-04 02:38:04
|
Me too. Richard On Oct 3, 2008, at 5:36 PM, Bjoern Peters wrote: > I agree with this perfectly. > > In addition, 'thing being measured' is something that every assay > will have, while not every assay will have an analyte. In > Jennifer's example, measuring 'concentration of glucose' implies > analyte = glucose. In the mouse weight example, 'weight of mouse' > is the thing being measured, without there being an analyte. > > This ties into assay objectives: There is a shared objective for > assays that have analytes, namely to determine the presence or > quantity of the analyte in the evaluant. > > - Bjoern > > > Fostel, Jennifer (NIH/NIEHS) [C] wrote: >> mouse -> urine -> measure [glucose] >> wrt study timeline >> mouse has_role subject >> urine has_role specimen >> wrt assay >> urine has_role evaluant >> glucose_in_urine has_role analyte >> assay_output = paper containing information reporting measured >> concentration of glucose >> assay_participants include urine, reagents used to measure, >> device used to measure, tubes used to collect, prepare and assay >> the urine, the standard curve reagents, assay_output >> we need to capture the relationship between the output report, >> the "real" concentration of glucose and the subject >> >> --------------------------------------------------------------------- >> --- >> *From:* Richard H. Scheuermann , Ph.D. >> [mailto:ric...@ut...] >> *Sent:* Friday, October 03, 2008 9:25 AM >> *To:* Philippe Rocca-Serra >> *Cc:* Fostel, Jennifer (NIH/NIEHS) [C]; Melanie Courtot; obi- >> pro...@li...; Bjoern Peters; >> obi...@li... >> *Subject:* Re: [Obi-role-branch] [Obi-protocol-application-branch] >> Mini-use case: measuring body weight >> >> I think we are on the same page. While glucose is an IC, glucose >> concentration is a DC. This is really an important concept that >> we need to be consistent in treating, since it can be a little >> confusing. >> >> Richard >> >> >> On Oct 3, 2008, at 8:06 AM, Philippe Rocca-Serra wrote: >> >>> could you give an example of "thing being measured"that is an IC ? >>> >>> so far, in the example that we have discussed, weight of body, >>> count of cells, concentration of glucose (which are actually >>> dependent continuant /about_of/ independent continuant). >>> >>> This is where for me thing become blurry as to what we mean >>> exactly by 'thing being measured'. >>> >>> The difference between 'weight measurement' and 'glucose >>> concentration measurement' is that in the case of glucose >>> concentration measurement, we need to specify "where" we are >>> looking for glucose located_in another entity (urine, blood). >>> >>> Can we really say, we are 'measuring glucose' ? It seems to me we >>> should only be saying 'measuring some quality about glucose' >>> >>> 2 comments: >>> >>> i. I will leave side additional information we would need to >>> capture related to the 'when' the assay was performed (measuring >>> glucose concentration at 10 minutes post drug injection) >>> But this would relate to describing how the 'thing being assayed' >>> has been collected and we would need to relate a >>> part_protocolapplication and introduce the ability to specify a >>> collection time. >>> >>> ii. I am a bit worried by all this complexity to describe an >>> assay and how we can expect OBI users to deal with this. People >>> doing phenotyping have a number of very fancy assays and we are >>> dealing with fairly simple cases. >>> >>> >>> >>> Philippe >>> >>> >>> >>> >>> >>> Fostel, Jennifer (NIH/NIEHS) [C] wrote: >>>> given that we are not looking at evaluant and analyte as sysmonyms, >>>> let's call the "thing being assayed" as bearing the evaluant >>>> role, and >>>> the "thing being measured, when it is an IC," as bearing the >>>> analyte >>>> role. >>>> -----Original Message----- >>>> From: Bjoern Peters [mailto:bp...@li...] Sent: Thursday, >>>> October 02, 2008 10:23 PM >>>> To: Richard H. Scheuermann , Ph.D. >>>> Cc: ro...@eb... <mailto:ro...@eb...>; Fostel, Jennifer >>>> (NIH/NIEHS) [C]; >>>> obi...@li... >>>> <mailto:obi...@li...>; >>>> Melanie Courtot; >>>> obi...@li... <mailto:obi-role- >>>> br...@li...> >>>> Subject: Re: [Obi-role-branch] [Obi-protocol-application-branch] >>>> Mini-use case: measuring body weight >>>> >>>> Yes, every objective driven process has an 'objective realizing >>>> agent' as a participant as well. >>>> >>>> Richard H. Scheuermann , Ph.D. wrote: >>>> >>>>> Isn't the 'evaluator' also a participant? >>>>> >>>>> >>>>> On Oct 2, 2008, at 5:26 PM, ro...@eb... >>>>> <mailto:ro...@eb...> >>>>> wrote: >>>>> >>>>> >>>>>> Dear All, >>>>>> >>>>>> Following our (long) discussions during today's PA call, I >>>>>> have put tried to go over the following mini use case >>>>>> >>>>>> Assay: measuring mouse body weight, trying to summerize all >>>>>> our pb/questions. >>>>>> >>>>>> i. the first pass was to identify all things that would the >>>>>> present at the begining of the assay and result from it. We >>>>>> therefore identified: >>>>>> -a mouse >>>>>> -a scale >>>>>> -data >>>>>> >>>>>> all of which are called 'participant' but each of which has a >>>>>> different roles, realized over the course of an assay. the >>>>>> main point >>>>>> >>>> >>>> >>>>>> of discussion is determining how we call: >>>>>> >>>>>> the 'thing being assayed': -> should be an independent >>>>>> continuant/material entity/ mouse in our example >>>>>> >>>>>> the 'thing being measured': ->thing should be an dependent >>>>>> continuant/quality/weight in our example >>>>>> >>>>>> BP:'thing being measured' = range of 'is measurement of' in assay >>>>>> >>>>>> the thing being measured has been called 'evaluant' (Richard), >>>>>> which would realize its evaluant_role. >>>>>> >>>>>> so this becomes: >>>>>> >>>>>> assay "measuring weight" >>>>>> utilizes_device = scale (this implies realization of the >>>>>> function of >>>>>> scale) >>>>>> scale has_function = weight_measuring_function has_input = >>>>>> mouse (independent continuant ) in this case, has_input range >>>>>> would always be 'thing being assayed' >>>>>> has_evaluant = weight (dependent continuant), in this case, >>>>>> has_evaluant range would always be 'thing being measured' >>>>>> has_output = datum possibly qualified by a unit >>>>>> >>>>>> the problem that then arises is the following: >>>>>> weight would play the role of evaluant , but bfo does not >>>>>> allow dependent continuant to bear roles. but is that really so ? >>>>>> should 'weight' bear the evaluant role or should it be 'weight >>>>>> of whole_body' ? >>>>>> >>>>>> And it seems that I've lost the path to relate to objective... >>>>>> >>>>>> Cheers >>>>>> >>>>>> Philippe >>>>>> >>>>>> >>>>>> (Then a side note about assay labels in OBI: assay name should >>>>>> probably sound like occurent: >>>>>> "body weight" should probably not be used as a label for an >>>>>> assay, since body weight <=> quality/weight about_of >>>>>> independent_continuant/body so "measuring body weight" would >>>>>> probably >>>>>> >>>> >>>> >>>>>> be a label to choose (so ALT is not an assay, measuring ALT >>>>>> activity sounds like one) >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> ----------------------------------------------------------------- >>>>>> ---- >>>>>> ---- This SF.Net email is sponsored by the Moblin Your Move >>>>>> Developer's challenge Build the coolest Linux based >>>>>> applications with >>>>>> >>>> >>>> >>>>>> Moblin SDK & win great prizes Grand prize is a trip for two to >>>>>> an Open Source event anywhere in the world http://moblin- >>>>>> contest.org/redirect.php?banner_id=100&url=/ <http://moblin- >>>>>> contest.org/redirect.php?banner_id=100&url=/> >>>>>> <http://moblin-contest.org/redirect.php?banner_id=100&url=/ >>>>>> <http://moblin-contest.org/redirect.php?banner_id=100&url=/>> >>>>>> _______________________________________________ >>>>>> Obi-role-branch mailing list >>>>>> Obi...@li... <mailto:Obi-role- >>>>>> br...@li...> >>>>>> <mailto: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... >>>>> <mailto:ric...@ut...> >>>>> <mailto:ric...@ut...> >>>>> http://pathcuric1.swmed.edu/Research/scheuermann.html >>>>> >>>>> >>>>> >>>>> >>>> >>>> >>>> -- >>>> 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 the Moblin Your Move >>> Developer's challenge >>> Build the coolest Linux based applications with Moblin SDK & win >>> great prizes >>> Grand prize is a trip for two to an Open Source event anywhere in >>> the world >>> http://moblin-contest.org/redirect.php?banner_id=100&url=/ >>> <http://moblin-contest.org/redirect.php?banner_id=100&url=/> >>> _______________________________________________ >>> Obi-role-branch mailing list >>> Obi...@li... <mailto:Obi-role- >>> br...@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... >> <mailto:ric...@ut...> >> http://pathcuric1.swmed.edu/Research/scheuermann.html >> >> >> > > > -- > 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 > > > ------------------------------------------------------------------------ ------------------------ 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 |
From: Richard H. S. , Ph.D. <ric...@ut...> - 2008-10-03 13:25:17
|
I think we are on the same page. While glucose is an IC, glucose concentration is a DC. This is really an important concept that we need to be consistent in treating, since it can be a little confusing. Richard On Oct 3, 2008, at 8:06 AM, Philippe Rocca-Serra wrote: > could you give an example of "thing being measured"that is an IC ? > > so far, in the example that we have discussed, weight of body, > count of > cells, concentration of glucose (which are actually dependent > continuant > /about_of/ independent continuant). > > This is where for me thing become blurry as to what we mean exactly by > 'thing being measured'. > > The difference between 'weight measurement' and 'glucose concentration > measurement' is that in the case of glucose concentration measurement, > we need to specify "where" we are looking for glucose located_in > another > entity (urine, blood). > > Can we really say, we are 'measuring glucose' ? It seems to me we > should > only be saying 'measuring some quality about glucose' > > 2 comments: > > i. I will leave side additional information we would need to capture > related to the 'when' the assay was performed (measuring glucose > concentration at 10 minutes post drug injection) > But this would relate to describing how the 'thing being assayed' has > been collected and we would need to relate a part_protocolapplication > and introduce the ability to specify a collection time. > > ii. I am a bit worried by all this complexity to describe an assay and > how we can expect OBI users to deal with this. People doing > phenotyping > have a number of very fancy assays and we are dealing with fairly > simple cases. > > > > Philippe > > > > > > Fostel, Jennifer (NIH/NIEHS) [C] wrote: >> given that we are not looking at evaluant and analyte as sysmonyms, >> let's call the "thing being assayed" as bearing the evaluant role, >> and >> the "thing being measured, when it is an IC," as bearing the analyte >> role. >> >> -----Original Message----- >> From: Bjoern Peters [mailto:bp...@li...] >> Sent: Thursday, October 02, 2008 10:23 PM >> To: Richard H. Scheuermann , Ph.D. >> Cc: ro...@eb...; Fostel, Jennifer (NIH/NIEHS) [C]; >> obi...@li...; Melanie >> Courtot; >> obi...@li... >> Subject: Re: [Obi-role-branch] [Obi-protocol-application-branch] >> Mini-use case: measuring body weight >> >> Yes, every objective driven process has an 'objective realizing >> agent' >> as a participant as well. >> >> Richard H. Scheuermann , Ph.D. wrote: >> >>> Isn't the 'evaluator' also a participant? >>> >>> >>> On Oct 2, 2008, at 5:26 PM, ro...@eb... <mailto:ro...@eb...> >>> wrote: >>> >>> >>>> Dear All, >>>> >>>> Following our (long) discussions during today's PA call, I have put >>>> tried to go over the following mini use case >>>> >>>> Assay: measuring mouse body weight, trying to summerize all our >>>> pb/questions. >>>> >>>> i. the first pass was to identify all things that would the present >>>> at the begining of the assay and result from it. We therefore >>>> identified: >>>> -a mouse >>>> -a scale >>>> -data >>>> >>>> all of which are called 'participant' but each of which has a >>>> different roles, realized over the course of an assay. the main >>>> point >>>> >> >> >>>> of discussion is determining how we call: >>>> >>>> the 'thing being assayed': -> should be an independent >>>> continuant/material entity/ mouse in our example >>>> >>>> the 'thing being measured': ->thing should be an dependent >>>> continuant/quality/weight in our example >>>> >>>> BP:'thing being measured' = range of 'is measurement of' in assay >>>> >>>> the thing being measured has been called 'evaluant' (Richard), >>>> which >>>> would realize its evaluant_role. >>>> >>>> so this becomes: >>>> >>>> assay "measuring weight" >>>> utilizes_device = scale (this implies realization of the >>>> function of >>>> scale) >>>> scale has_function = weight_measuring_function has_input = mouse >>>> (independent continuant ) in this case, has_input range would >>>> always >>>> be 'thing being assayed' >>>> has_evaluant = weight (dependent continuant), in this case, >>>> has_evaluant range would always be 'thing being measured' >>>> has_output = datum possibly qualified by a unit >>>> >>>> the problem that then arises is the following: >>>> weight would play the role of evaluant , but bfo does not allow >>>> dependent continuant to bear roles. but is that really so ? >>>> should 'weight' bear the evaluant role or should it be 'weight of >>>> whole_body' ? >>>> >>>> And it seems that I've lost the path to relate to objective... >>>> >>>> Cheers >>>> >>>> Philippe >>>> >>>> >>>> (Then a side note about assay labels in OBI: assay name should >>>> probably sound like occurent: >>>> "body weight" should probably not be used as a label for an assay, >>>> since body weight <=> quality/weight about_of >>>> independent_continuant/body so "measuring body weight" would >>>> probably >>>> >> >> >>>> be a label to choose (so ALT is not an assay, measuring ALT >>>> activity >>>> sounds like one) >>>> >>>> >>>> >>>> >>>> >>>> ------------------------------------------------------------------- >>>> -- >>>> ---- This SF.Net email is sponsored by the Moblin Your Move >>>> Developer's challenge Build the coolest Linux based applications >>>> with >>>> >> >> >>>> Moblin SDK & win great prizes Grand prize is a trip for two to an >>>> Open Source event anywhere in the world >>>> http://moblin-contest.org/redirect.php?banner_id=100&url=/ >>>> <http://moblin-contest.org/redirect.php?banner_id=100&url=/> >>>> _______________________________________________ >>>> Obi-role-branch mailing list >>>> Obi...@li... >>>> <mailto: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... >>> <mailto:ric...@ut...> >>> http://pathcuric1.swmed.edu/Research/scheuermann.html >>> >>> >>> >>> >> >> >> -- >> 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 the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win > great prizes > Grand prize is a trip for two to an Open Source event anywhere in > the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > 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 |
From: Fostel, J. (NIH/N. [C] <fo...@ni...> - 2008-10-03 14:44:28
|
mouse -> urine -> measure [glucose] wrt study timeline mouse has_role subject urine has_role specimen wrt assay urine has_role evaluant glucose_in_urine has_role analyte assay_output = paper containing information reporting measured concentration of glucose assay_participants include urine, reagents used to measure, device used to measure, tubes used to collect, prepare and assay the urine, the standard curve reagents, assay_output we need to capture the relationship between the output report, the "real" concentration of glucose and the subject ________________________________ From: Richard H. Scheuermann , Ph.D. [mailto:ric...@ut...] Sent: Friday, October 03, 2008 9:25 AM To: Philippe Rocca-Serra Cc: Fostel, Jennifer (NIH/NIEHS) [C]; Melanie Courtot; obi...@li...; Bjoern Peters; obi...@li... Subject: Re: [Obi-role-branch] [Obi-protocol-application-branch] Mini-use case: measuring body weight I think we are on the same page. While glucose is an IC, glucose concentration is a DC. This is really an important concept that we need to be consistent in treating, since it can be a little confusing. Richard On Oct 3, 2008, at 8:06 AM, Philippe Rocca-Serra wrote: could you give an example of "thing being measured"that is an IC ? so far, in the example that we have discussed, weight of body, count of cells, concentration of glucose (which are actually dependent continuant /about_of/ independent continuant). This is where for me thing become blurry as to what we mean exactly by 'thing being measured'. The difference between 'weight measurement' and 'glucose concentration measurement' is that in the case of glucose concentration measurement, we need to specify "where" we are looking for glucose located_in another entity (urine, blood). Can we really say, we are 'measuring glucose' ? It seems to me we should only be saying 'measuring some quality about glucose' 2 comments: i. I will leave side additional information we would need to capture related to the 'when' the assay was performed (measuring glucose concentration at 10 minutes post drug injection) But this would relate to describing how the 'thing being assayed' has been collected and we would need to relate a part_protocolapplication and introduce the ability to specify a collection time. ii. I am a bit worried by all this complexity to describe an assay and how we can expect OBI users to deal with this. People doing phenotyping have a number of very fancy assays and we are dealing with fairly simple cases. Philippe Fostel, Jennifer (NIH/NIEHS) [C] wrote: given that we are not looking at evaluant and analyte as sysmonyms, let's call the "thing being assayed" as bearing the evaluant role, and the "thing being measured, when it is an IC," as bearing the analyte role. -----Original Message----- From: Bjoern Peters [mailto:bp...@li...] Sent: Thursday, October 02, 2008 10:23 PM To: Richard H. Scheuermann , Ph.D. Cc: ro...@eb...; Fostel, Jennifer (NIH/NIEHS) [C]; obi...@li...; Melanie Courtot; obi...@li... Subject: Re: [Obi-role-branch] [Obi-protocol-application-branch] Mini-use case: measuring body weight Yes, every objective driven process has an 'objective realizing agent' as a participant as well. Richard H. Scheuermann , Ph.D. wrote: Isn't the 'evaluator' also a participant? On Oct 2, 2008, at 5:26 PM, ro...@eb... <mailto:ro...@eb...> wrote: Dear All, Following our (long) discussions during today's PA call, I have put tried to go over the following mini use case Assay: measuring mouse body weight, trying to summerize all our pb/questions. i. the first pass was to identify all things that would the present at the begining of the assay and result from it. We therefore identified: -a mouse -a scale -data all of which are called 'participant' but each of which has a different roles, realized over the course of an assay. the main point of discussion is determining how we call: the 'thing being assayed': -> should be an independent continuant/material entity/ mouse in our example the 'thing being measured': ->thing should be an dependent continuant/quality/weight in our example BP:'thing being measured' = range of 'is measurement of' in assay the thing being measured has been called 'evaluant' (Richard), which would realize its evaluant_role. so this becomes: assay "measuring weight" utilizes_device = scale (this implies realization of the function of scale) scale has_function = weight_measuring_function has_input = mouse (independent continuant ) in this case, has_input range would always be 'thing being assayed' has_evaluant = weight (dependent continuant), in this case, has_evaluant range would always be 'thing being measured' has_output = datum possibly qualified by a unit the problem that then arises is the following: weight would play the role of evaluant , but bfo does not allow dependent continuant to bear roles. but is that really so ? should 'weight' bear the evaluant role or should it be 'weight of whole_body' ? And it seems that I've lost the path to relate to objective... Cheers Philippe (Then a side note about assay labels in OBI: assay name should probably sound like occurent: "body weight" should probably not be used as a label for an assay, since body weight <=> quality/weight about_of independent_continuant/body so "measuring body weight" would probably be a label to choose (so ALT is not an assay, measuring ALT activity sounds like one) --------------------------------------------------------------------- ---- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ <http://moblin-contest.org/redirect.php?banner_id=100&url=/> _______________________________________________ Obi-role-branch mailing list Obi...@li... <mailto: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... <mailto:ric...@ut...> http://pathcuric1.swmed.edu/Research/scheuermann.html -- 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 the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ 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 |