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From: frank g. <Fra...@nc...> - 2007-07-03 13:20:40
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Hi Ryan As I remember the idea was to collect function of the flow cytometry instruments to help in hierarchy placement. If you have already done this and submitted these to the Function branch then this is excellent. However I had a look at the function branch and at the minute it there seems to no functions. Worryingly it has an Instrument_function class. I know this branch is one of the more recent ones, although, a question for the branch. is it going to be common practice to create a hierarchy based on the object that inheres the function rather that what the function is? Frank On 7/3/07, Ryan Brinkman <rbr...@bc...> wrote: > As I understood it, during the last instrument call I was asked to > provide a list of functions(?) of flow cytometers. I'm a bit stuck. Part of > my confusion relates to the granularity of the requested terms, and how the > requested terms would differ from what we already sent to the function > branch. Many of the properties a flow cytometer can measure are proxies for > biological properties, but they are numerous and I didn't grok how these > other functions help classify a flow cytometer at the moment. > > > > Any help would be very much appreciated. > > > > Cheers, > > Ryan > > ------------------------------------------------------------------------- > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > _______________________________________________ > Obi-instrument-branch mailing list > Obi...@li... > https://lists.sourceforge.net/lists/listinfo/obi-instrument-branch > > -- Frank Gibson Research Associate Room 2.19, Devonshire Building School of Computing Science, University of Newcastle upon Tyne, Newcastle upon Tyne, NE1 7RU United Kingdom Telephone: +44-191-246-4933 Fax: +44-191-246-4905 -- Frank Gibson Research Associate Room 2.19, Devonshire Building School of Computing Science, University of Newcastle upon Tyne, Newcastle upon Tyne, NE1 7RU United Kingdom Telephone: +44-191-246-4933 Fax: +44-191-246-4905 |
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From: frank g. <Fra...@nc...> - 2007-07-03 13:37:33
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> > > I know this branch is one of the more recent ones, although, a question > > for the branch. is it going to be common practice to create a hierarchy > > based on the object that inheres the function rather that what the function > > is? > > > > Yes, that is what we need the *application use case* for. Depending on > > the usage, e.g. for a simple CV/taxonomy RAs we would capture > > Instrument_function classes or for DL RAs moldel these through other RUs, > > e.g. relations... > > Cheers, Daniel. > > > > I was referring to the function heirachy rather than the instrument > hierarchy. I know we need to assign funtions to devices. However, because an > instrument has the function does not mean another object can not have the > same function. Although the current hierarchy in the function branch > enforces this. > > Frank > > > > > > > Frank > > > > On 7/3/07, Ryan Brinkman <rbr...@bc...> wrote: > > > > > > As I understood it, during the last instrument call I was asked to > > > provide a list of functions(?) of flow cytometers. I'm a bit stuck. Part of > > > my confusion relates to the granularity of the requested terms, and how the > > > requested terms would differ from what we already sent to the function > > > branch. Many of the properties a flow cytometer can measure are proxies for > > > biological properties, but they are numerous and I didn't grok how these > > > other functions help classify a flow cytometer at the moment. > > > > > > > > > > > > Any help would be very much appreciated. > > > > > > > > > > > > Cheers, > > > > > > Ryan > > > > > > > > > ------------------------------------------------------------------------- > > > This SF.net email is sponsored by DB2 Express > > > Download DB2 Express C - the FREE version of DB2 express and take > > > control of your XML. No limits. Just data. Click to get it now. > > > http://sourceforge.net/powerbar/db2/ > > > _______________________________________________ > > > Obi-instrument-branch mailing list > > > Obi...@li... > > > https://lists.sourceforge.net/lists/listinfo/obi-instrument-branch > > > > > > > > > > > > -- > > Frank Gibson > > Research Associate > > Room 2.19, Devonshire Building > > School of Computing Science, > > University of Newcastle upon Tyne, > > Newcastle upon Tyne, NE1 7RU > > United Kingdom > > Telephone: +44-191-246-4933 > > Fax: +44-191-246-4905 > > > > ------------------------------ > > > > ------------------------------------------------------------------------- > > This SF.net email is sponsored by DB2 Express > > Download DB2 Express C - the FREE version of DB2 express and take > > control of your XML. No limits. Just data. Click to get it now. > > > > http://sourceforge.net/powerbar/db2/ > > > > ------------------------------ > > > > _______________________________________________ > > Obi-instrument-branch mailing list > > > > Obi...@li...://lists.sourceforge.net/lists/listinfo/obi-instrument-branch > > > > > > -- > > __________________________________________________________________________________________ > > > > Dr. Daniel Schober > > > > NET Project - Ontologist > > > > The European Bioinformatics Institute email: > > sc...@eb... > > EMBL Outstation - Hinxton direct: +44 (0)1223 494410 > > Wellcome Trust Genome Campus fax: +44 (0)1223 494 468 > > Cambridge CB10 1SD, UK Room: A3-141 (extension building) > > > > Project page: www.ebi.ac.uk/net-project > > > > Personal page: http://www.ebi.ac.uk/Information/Staff/person_maint.php?s_person_id=734 > > > > Former home page: http://www.bioinf.mdc-berlin.de/%7Eschober/ > > > > > > > -- > Frank Gibson > Research Associate > Room 2.19, Devonshire Building > School of Computing Science, > University of Newcastle upon Tyne, > Newcastle upon Tyne, NE1 7RU > United Kingdom > Telephone: +44-191-246-4933 > Fax: +44-191-246-4905 > -- Frank Gibson Research Associate Room 2.19, Devonshire Building School of Computing Science, University of Newcastle upon Tyne, Newcastle upon Tyne, NE1 7RU United Kingdom Telephone: +44-191-246-4933 Fax: +44-191-246-4905 |
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From: Daniel S. <sc...@eb...> - 2007-07-03 14:26:42
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Hi, I think the functions should not be sorted according to the instruments that perform them. This should be 'inferable' via a has_function relation. However the inheritance of this has_function relation and its values needs to be discussed. Of cause we will run into problems as long as we have is_a and part_of mixed Hierarchies, e.g. currently we have sample_fluid is_a fluidic_subsystem is_a instrument, which is wrong... and would clearly prevent any function inheritance. Cheers, Daniel. frank gibson wrote: > >> >> I know this branch is one of the more recent ones, although, >> a question for the branch. is it going to be common practice >> to create a hierarchy based on the object that inheres the >> function rather that what the function is? > > Yes, that is what we need the *application use case* for. > Depending on the usage, e.g. for a simple CV/taxonomy RAs we > would capture Instrument_function classes or for DL RAs moldel > these through other RUs, e.g. relations... > Cheers, Daniel. > > > I was referring to the function heirachy rather than the > instrument hierarchy. I know we need to assign funtions to > devices. However, because an instrument has the function does not > mean another object can not have the same function. Although the > current hierarchy in the function branch enforces this. > > > Frank > > > > > > >> Frank >> >> On 7/3/07, *Ryan Brinkman* <rbr...@bc... >> <mailto:rbr...@bc...>> wrote: >> >> As I understood it, during the last instrument call I was >> asked to provide a list of functions(?) of flow >> cytometers. I'm a bit stuck. Part of my confusion relates >> to the granularity of the requested terms, and how the >> requested terms would differ from what we already sent to >> the function branch. Many of the properties a flow >> cytometer can measure are proxies for biological >> properties, but they are numerous and I didn't grok how >> these other functions help classify a flow cytometer at >> the moment. >> >> >> >> Any help would be very much appreciated. >> >> >> >> Cheers, >> >> Ryan >> >> >> ------------------------------------------------------------------------- >> This SF.net email is sponsored by DB2 Express >> Download DB2 Express C - the FREE version of DB2 express >> and take >> control of your XML. No limits. Just data. Click to get >> it now. >> http://sourceforge.net/powerbar/db2/ >> _______________________________________________ >> Obi-instrument-branch mailing list >> Obi...@li... >> <mailto:Obi...@li...> >> https://lists.sourceforge.net/lists/listinfo/obi-instrument-branch >> >> >> >> >> >> -- >> Frank Gibson >> Research Associate >> Room 2.19, Devonshire Building >> School of Computing Science, >> University of Newcastle upon Tyne, >> Newcastle upon Tyne, NE1 7RU >> United Kingdom >> Telephone: +44-191-246-4933 >> Fax: +44-191-246-4905 >> >>------------------------------------------------------------------------ >> >>------------------------------------------------------------------------- >>This SF.net email is sponsored by DB2 Express >>Download DB2 Express C - the FREE version of DB2 express and take >>control of your XML. No limits. Just data. Click to get it now. >> >> >>http://sourceforge.net/powerbar/db2/ >> >>------------------------------------------------------------------------ >> >>_______________________________________________ >>Obi-instrument-branch mailing list >> >> >>Obi...@li... <mailto:Obi...@li...> >>https://lists.sourceforge.net/lists/listinfo/obi-instrument-branch >> >> > >-- >__________________________________________________________________________________________ > >Dr. Daniel Schober > >NET Project - Ontologist > >The European Bioinformatics Institute email: > >sc...@eb... <mailto:sc...@eb...> >EMBL Outstation - Hinxton direct: > > > > > > >+44 (0)1223 494410 > >Wellcome Trust Genome Campus fax: +44 (0)1223 494 468 >Cambridge CB10 1SD, UK Room: A3-141 (extension building) > >Project page: www.ebi.ac.uk/net-project <http://www.ebi.ac.uk/net-project> > >Personal page: http://www.ebi.ac.uk/Information/Staff/person_maint.php?s_person_id=734 > > <http://www.ebi.ac.uk/Information/Staff/person_maint.php?s_person_id=734> >Former home page: http://www.bioinf.mdc-berlin.de/%7Eschober/ > > > > > > > -- > Frank Gibson > Research Associate > Room 2.19, Devonshire Building > School of Computing Science, > University of Newcastle upon Tyne, > Newcastle upon Tyne, NE1 7RU > United Kingdom > Telephone: +44-191-246-4933 > Fax: +44-191-246-4905 > > > > > -- > Frank Gibson > Research Associate > Room 2.19, Devonshire Building > School of Computing Science, > University of Newcastle upon Tyne, > Newcastle upon Tyne, NE1 7RU > United Kingdom > Telephone: +44-191-246-4933 > Fax: +44-191-246-4905 -- __________________________________________________________________________________________ Dr. Daniel Schober NET Project - Ontologist The European Bioinformatics Institute email: sc...@eb... EMBL Outstation - Hinxton direct: +44 (0)1223 494410 Wellcome Trust Genome Campus fax: +44 (0)1223 494 468 Cambridge CB10 1SD, UK Room: A3-141 (extension building) Project page: www.ebi.ac.uk/net-project Personal page: http://www.ebi.ac.uk/Information/Staff/person_maint.php?s_person_id=734 Former home page: http://www.bioinf.mdc-berlin.de/%7Eschober/ |
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From: Allyson L. <a.l...@ne...> - 2007-07-03 14:37:40
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I agree with both Frank and Daniel. On 7/3/07, Daniel Schober <sc...@eb...> wrote: > > Hi, > I think the functions should not be sorted according to the instruments > that perform them. This should be 'inferable' via a has_function relation. > However the inheritance of this has_function relation and its values needs > to be discussed. Of cause we will run into problems as long as we have is_a > and part_of mixed Hierarchies, e.g. currently we have sample_fluid is_a > fluidic_subsystem is_a instrument, which is wrong... and would clearly > prevent any function inheritance. > Cheers, Daniel. > > frank gibson wrote: > > > > > > I know this branch is one of the more recent ones, although, a > > > question for the branch. is it going to be common practice to create a > > > hierarchy based on the object that inheres the function rather that what the > > > function is? > > > > > > Yes, that is what we need the *application use case* for. Depending on > > > the usage, e.g. for a simple CV/taxonomy RAs we would capture > > > Instrument_function classes or for DL RAs moldel these through other RUs, > > > e.g. relations... > > > Cheers, Daniel. > > > > > > > I was referring to the function heirachy rather than the instrument > > hierarchy. I know we need to assign funtions to devices. However, because an > > instrument has the function does not mean another object can not have the > > same function. Although the current hierarchy in the function branch > > enforces this. > > > > > Frank > > > > > > > > > > > > > > Frank > > > > > > On 7/3/07, Ryan Brinkman <rbr...@bc...> wrote: > > > > > > > > As I understood it, during the last instrument call I was asked > > > > to provide a list of functions(?) of flow cytometers. I'm a bit stuck. Part > > > > of my confusion relates to the granularity of the requested terms, and how > > > > the requested terms would differ from what we already sent to the function > > > > branch. Many of the properties a flow cytometer can measure are proxies for > > > > biological properties, but they are numerous and I didn't grok how these > > > > other functions help classify a flow cytometer at the moment. > > > > > > > > > > > > > > > > Any help would be very much appreciated. > > > > > > > > > > > > > > > > Cheers, > > > > > > > > Ryan > > > > > > > > > > > > ------------------------------------------------------------------------- > > > > This SF.net email is sponsored by DB2 Express > > > > Download DB2 Express C - the FREE version of DB2 express and take > > > > control of your XML. No limits. Just data. Click to get it now. > > > > http://sourceforge.net/powerbar/db2/ > > > > _______________________________________________ > > > > Obi-instrument-branch mailing list > > > > Obi...@li... > > > > https://lists.sourceforge.net/lists/listinfo/obi-instrument-branch > > > > > > > > > > > > > > > > > -- > > > Frank Gibson > > > Research Associate > > > Room 2.19, Devonshire Building > > > School of Computing Science, > > > University of Newcastle upon Tyne, > > > Newcastle upon Tyne, NE1 7RU > > > United Kingdom > > > Telephone: +44-191-246-4933 > > > Fax: +44-191-246-4905 > > > > > > ------------------------------ > > > > > > ------------------------------------------------------------------------- > > > This SF.net email is sponsored by DB2 Express > > > Download DB2 Express C - the FREE version of DB2 express and take > > > control of your XML. No limits. Just data. Click to get it now. > > > > > > > > > http://sourceforge.net/powerbar/db2/ > > > > > > ------------------------------ > > > > > > _______________________________________________ > > > Obi-instrument-branch mailing list > > > > > > > > > Obi...@li... > > > https://lists.sourceforge.net/lists/listinfo/obi-instrument-branch > > > > > > > > > -- > > > __________________________________________________________________________________________ > > > > > > Dr. Daniel Schober > > > > > > NET Project - Ontologist > > > > > > The European Bioinformatics Institute email: > > > > > > sc...@eb... > > > EMBL Outstation - Hinxton direct: > > > > > > > > > > > > > > > +44 (0)1223 494410 > > > Wellcome Trust Genome Campus fax: +44 (0)1223 494 468 > > > Cambridge CB10 1SD, UK Room: A3-141 (extension building) > > > > > > Project page: www.ebi.ac.uk/net-project > > > > > > Personal page: http://www.ebi.ac.uk/Information/Staff/person_maint.php?s_person_id=734 > > > > > > > > > Former home page: http://www.bioinf.mdc-berlin.de/%7Eschober/ > > > > > > > > > > > > -- > > Frank Gibson > > Research Associate > > Room 2.19, Devonshire Building > > School of Computing Science, > > University of Newcastle upon Tyne, > > Newcastle upon Tyne, NE1 7RU > > United Kingdom > > Telephone: +44-191-246-4933 > > Fax: +44-191-246-4905 > > > > > > -- > Frank Gibson > Research Associate > Room 2.19, Devonshire Building > School of Computing Science, > University of Newcastle upon Tyne, > Newcastle upon Tyne, NE1 7RU > United Kingdom > Telephone: +44-191-246-4933 > Fax: +44-191-246-4905 > > > -- > __________________________________________________________________________________________ > > Dr. Daniel Schober > > NET Project - Ontologist > > The European Bioinformatics Institute email: sc...@eb... > EMBL Outstation - Hinxton direct: +44 (0)1223 494410 > Wellcome Trust Genome Campus fax: +44 (0)1223 494 468 > Cambridge CB10 1SD, UK Room: A3-141 (extension building) > > Project page: www.ebi.ac.uk/net-project > > Personal page: http://www.ebi.ac.uk/Information/Staff/person_maint.php?s_person_id=734 > Former home page: http://www.bioinf.mdc-berlin.de/%7Eschober/ > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > _______________________________________________ > Obi-instrument-branch mailing list > Obi...@li... > https://lists.sourceforge.net/lists/listinfo/obi-instrument-branch > > -- Thanks, Allyson :) Allyson Lister Research Associate Centre for Integrated Systems Biology for Ageing and Nutrition Newcastle University http://www.cisban.ac.uk School of Computing Science Newcastle University Newcastle upon Tyne, NE1 7RU |
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From: Ryan B. <rbr...@bc...> - 2007-07-03 18:45:31
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=20 What sort of granularity for instrument function hierarchy do you envisage? =20 For example, at the highest level flow cytometers can be used to analyze particles suspended in a fluid (and the subtype of flow cytometer sorters can put them into tubes based on their characteristics). Particles are usually cells, but can be microorganisms. At a more granular level the function of a flow cytometer can be to examine many cellular parameters on live or fixed cells including surface, cytoplasmic and nuclear proteins, DNA, RNA, reactive oxygen species, intracellular pH and calcium flux. Measurement of the expression of cellular activation markers, intracellular cytokines, immunological signaling, cytoplasmic and nuclear cell cycle and transcription factors can also be readily performed. In the tissue-engineering field, FCM can analyze cell proliferation and other critical biological and functional properties of cells. Clinically, FCM is used to analyze a wide array of immunological parameters in disease. Following treatment, FCM can be used to study the humoral and cellular response to vaccines and a variety of other clinically relevant cellular data. Major clinical uses that require multiple samples per patient include the diagnosis and monitoring of leukemia and lymphoma patients, the evaluation of peripheral blood hematopoietic stem cell grafts, and the quantitation of CD4+ vs. CD8+ T lymphocytes in blood to monitor HIV infection and assess the performance of treatment. FCM is also commonly used for measuring the total DNA content per cell in biopsy specimens from tumors for clinical cancer diagnosis and prognosis. Cytometers can also function to determine particle size and shape. =20 =20 Cheers, Ryan =20 =20 =20 =20 From: Daniel Schober [mailto:sc...@eb...]=20 Sent: Tuesday, July 03, 2007 7:26 AM To: frank gibson Cc: Ryan Brinkman; obi...@li...; obi...@li... Subject: Re: [Obi-instrument-branch] flow cytometer functions =20 Hi, I think the functions should not be sorted according to the instruments that perform them. This should be 'inferable' via a has_function relation. However the inheritance of this has_function relation and its values needs to be discussed. Of cause we will run into problems as long as we have is_a and part_of mixed Hierarchies, e.g. currently we have sample_fluid is_a fluidic_subsystem is_a instrument, which is wrong... and would clearly prevent any function inheritance. Cheers, Daniel. frank gibson wrote:=20 =20 =09 I know this branch is one of the more recent ones, although, a question for the branch. is it going to be common practice to create a hierarchy based on the object that inheres the function rather that what the function is?=20 Yes, that is what we need the application use case for. Depending on the usage, e.g. for a simple CV/taxonomy RAs we would capture Instrument_function classes or for DL RAs moldel these through other RUs, e.g. relations... Cheers, Daniel. =09 I was referring to the function heirachy rather than the instrument hierarchy. I know we need to assign funtions to devices. However, because an instrument has the function does not mean another object can not have the same function. Although the current hierarchy in the function branch enforces this.=20 =09 Frank =09 =09 =09 =09 =20 =20 Frank On 7/3/07, Ryan Brinkman <rbr...@bc... <mailto:rbr...@bc...> > wrote:=20 As I understood it, during the last instrument call I was asked to provide a list of functions(?) of flow cytometers. I'm a bit stuck. Part of my confusion relates to the granularity of the requested terms, and how the requested terms would differ from what we already sent to the function branch. Many of the properties a flow cytometer can measure are proxies for biological properties, but they are numerous and I didn't grok how these other functions help classify a flow cytometer at the moment. =20 Any help would be very much appreciated. =20 Cheers, Ryan =09 =09 ------------------------------------------------------------------------ - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now.=20 http://sourceforge.net/powerbar/db2/ <http://sourceforge.net/powerbar/db2/>=20 =09 _______________________________________________ Obi-instrument-branch mailing list=20 =09 Obi...@li... <mailto:Obi...@li...>=20 =09 https://lists.sourceforge.net/lists/listinfo/obi-instrument-branch <https://lists.sourceforge.net/lists/listinfo/obi-instrument-branch> =20 =09 =09 =09 --=20 Frank Gibson Research Associate Room 2.19, Devonshire Building School of Computing Science,=20 University of Newcastle upon Tyne, Newcastle upon Tyne, NE1 7RU United Kingdom Telephone: Error! Filename not specified.Error! Filename not specified.Error! Filename not specified.Error! Filename not specified.Error! Filename not specified.Error! Filename not specified.+44-191-246-4933 Error! Filename not specified. Fax: +44-191-246-4905=20 =09 =09 =09 ________________________________ =20 =09 ------------------------------------------------------------------------ - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. =20 =20 http://sourceforge.net/powerbar/db2/ <http://sourceforge.net/powerbar/db2/>=20 =09 =09 =09 ________________________________ =20 =09 _______________________________________________ Obi-instrument-branch mailing list =09 <mailto:Obi...@li...>=20 =09 <mailto:Obi...@li...>=20 =09 Obi...@li... <mailto:Obi...@li...>=20 =09 https://lists.sourceforge.net/lists/listinfo/obi-instrument-branch <https://lists.sourceforge.net/lists/listinfo/obi-instrument-branch>=20 =20 =09 =09 =09 --=20 =09 ________________________________________________________________________ __________________ =20 Dr. Daniel Schober =20 NET Project - Ontologist =20 The European Bioinformatics Institute email: =20 =20 sc...@eb... <mailto:sc...@eb...>=20 EMBL Outstation - Hinxton direct:=20 =20 Error! Filename not specified. Error! Filename not specified. =20 Error! Filename not specified. Error! Filename not specified.Error! Filename not specified. Error! Filename not specified.+44 (0)1223 494410 Error! Filename not specified. Wellcome Trust Genome Campus fax: +44 (0)1223 494 468 Cambridge CB10 1SD, UK Room: A3-141 (extension building) =20 Project page: www.ebi.ac.uk/net-project <http://www.ebi.ac.uk/net-project>=20 =20 Personal page: http://www.ebi.ac.uk/Information/Staff/person_maint.php?s_person_id=3D734= <http://www.ebi.ac.uk/Information/Staff/person_maint.php?s_person_id=3D73= 4 >=20 =09 <http://www.ebi.ac.uk/Information/Staff/person_maint.php?s_person_id=3D73= 4 >=20 =20 Former home page: http://www.bioinf.mdc-berlin.de/%7Eschober/ <http://www.bioinf.mdc-berlin.de/%7Eschober/>=20 =20 =20 =09 =09 =09 --=20 Frank Gibson Research Associate Room 2.19, Devonshire Building School of Computing Science, University of Newcastle upon Tyne,=20 Newcastle upon Tyne, NE1 7RU=20 United Kingdom Telephone: +44-191-246-4933 Fax: +44-191-246-4905=20 =09 =09 =09 --=20 Frank Gibson Research Associate Room 2.19, Devonshire Building School of Computing Science, University of Newcastle upon Tyne, Newcastle upon Tyne, NE1 7RU=20 United Kingdom Telephone: +44-191-246-4933 Fax: +44-191-246-4905=20 --=20 ________________________________________________________________________ __________________ =20 Dr. Daniel Schober =20 NET Project - Ontologist =20 The European Bioinformatics Institute email: sc...@eb... <mailto:sc...@eb...>=20 EMBL Outstation - Hinxton direct: +44 (0)1223 494410 Wellcome Trust Genome Campus fax: +44 (0)1223 494 468 Cambridge CB10 1SD, UK Room: A3-141 (extension building) =20 Project page: www.ebi.ac.uk/net-project <http://www.ebi.ac.uk/net-project>=20 =20 Personal page: http://www.ebi.ac.uk/Information/Staff/person_maint.php?s_person_id=3D734= <http://www.ebi.ac.uk/Information/Staff/person_maint.php?s_person_id=3D73= 4 >=20 Former home page: http://www.bioinf.mdc-berlin.de/%7Eschober/ <http://www.bioinf.mdc-berlin.de/%7Eschober/>=20 =20 |
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From: Matthew P. <mat...@nc...> - 2007-07-04 08:48:36
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Hi Ryan, Excelent question and example. For my money, you describe what the flow cytometer actually does, not how we use it. They do stuff with particles suspended in a fluid, including sorting and counting. Unless the instrument itself does different things to cells vs other particles, it's probably not that useful to say much more. I think that's the function. Then there are a load of 'typical' processes describing how you use it. E.g. in a cell-counting process, there would be inputs including an instrument flow_cytometer and a sample containing cells in suspension, and the outputs including a count of the cells, or those cells sorted into different fractions by size or whatever. I guess we have a more general class of processes that involve a flow cytometer - it must have an instrument input flow cytometer, and a sample input 'suspension of microscopic particles'. Related question - can we define things like 'suspension of microscopic particles' in the biomaterials branch yet? There's a bunch of great definitions and names for these guys reachable from wikipedia http://en.wikipedia.org/wiki/Suspension_(chemistry) . I'm guessing that materials are linked into these mixtures by roles - since we use words like solvent, slute, and so on. The reason I sudgest modelling this that it gives us loads of extra constraints to validate experimental protocols via. For example, if someone claims to have feed a flow cytometer a solid lump of wood as the sample, and also know that the sample must be a liquid, then we can discover that something is up. Matthew On Tuesday 03 July 2007, Ryan Brinkman wrote: > What sort of granularity for instrument function hierarchy do you > envisage? > > > > For example, at the highest level flow cytometers can be used to analyze > particles suspended in a fluid (and the subtype of flow cytometer > sorters can put them into tubes based on their characteristics). > Particles are usually cells, but can be microorganisms. At a more > granular level the function of a flow cytometer can be to examine many > cellular parameters on live or fixed cells including surface, > cytoplasmic and nuclear proteins, DNA, RNA, reactive oxygen species, > intracellular pH and calcium flux. Measurement of the expression of > cellular activation markers, intracellular cytokines, immunological > signaling, cytoplasmic and nuclear cell cycle and transcription factors > can also be readily performed. In the tissue-engineering field, FCM can > analyze cell proliferation and other critical biological and functional > properties of cells. Clinically, FCM is used to analyze a wide array of > immunological parameters in disease. Following treatment, FCM can be > used to study the humoral and cellular response to vaccines and a > variety of other clinically relevant cellular data. Major clinical uses > that require multiple samples per patient include the diagnosis and > monitoring of leukemia and lymphoma patients, the evaluation of > peripheral blood hematopoietic stem cell grafts, and the quantitation of > CD4+ vs. CD8+ T lymphocytes in blood to monitor HIV infection and assess > the performance of treatment. FCM is also commonly used for measuring > the total DNA content per cell in biopsy specimens from tumors for > clinical cancer diagnosis and prognosis. Cytometers can also function to > determine particle size and shape. > > > > > > Cheers, > > Ryan > > > > > > > > > > From: Daniel Schober [mailto:sc...@eb...] > Sent: Tuesday, July 03, 2007 7:26 AM > To: frank gibson > Cc: Ryan Brinkman; obi...@li...; > obi...@li... > Subject: Re: [Obi-instrument-branch] flow cytometer functions > > > > Hi, > I think the functions should not be sorted according to the instruments > that perform them. This should be 'inferable' via a has_function > relation. However the inheritance of this has_function relation and its > values needs to be discussed. Of cause we will run into problems as long > as we have is_a and part_of mixed Hierarchies, e.g. currently we have > sample_fluid is_a fluidic_subsystem is_a instrument, which is wrong... > and would clearly prevent any function inheritance. > Cheers, Daniel. > > frank gibson wrote: > > > > > I know this branch is one of the more recent > ones, although, a question for the branch. is it going to be common > practice to create a hierarchy based on the object that inheres the > function rather that what the function is? > > Yes, that is what we need the application use case for. > Depending on the usage, e.g. for a simple CV/taxonomy RAs we would > capture Instrument_function classes or for DL RAs moldel these through > other RUs, e.g. relations... > Cheers, Daniel. > > > I was referring to the function heirachy rather than the > instrument hierarchy. I know we need to assign funtions to devices. > However, because an instrument has the function does not mean another > object can not have the same function. Although the current hierarchy in > the function branch enforces this. > > > Frank > > > > > > > > > Frank > > On 7/3/07, Ryan Brinkman > <rbr...@bc... <mailto:rbr...@bc...> > wrote: > > As I understood it, during the last > instrument call I was asked to provide a list of functions(?) of flow > cytometers. I'm a bit stuck. Part of my confusion relates to the > granularity of the requested terms, and how the requested terms would > differ from what we already sent to the function branch. Many of the > properties a flow cytometer can measure are proxies for biological > properties, but they are numerous and I didn't grok how these other > functions help classify a flow cytometer at the moment. > > > > Any help would be very much appreciated. > > > > Cheers, > > Ryan > > > > ------------------------------------------------------------------------ > - > This SF.net email is sponsored by DB2 > Express > Download DB2 Express C - the FREE > version of DB2 express and take > control of your XML. No limits. Just > data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > <http://sourceforge.net/powerbar/db2/> > > _______________________________________________ > Obi-instrument-branch mailing list > > Obi...@li... > <mailto:Obi...@li...> > > https://lists.sourceforge.net/lists/listinfo/obi-instrument-branch > <https://lists.sourceforge.net/lists/listinfo/obi-instrument-branch> > > > > > -- > Frank Gibson > Research Associate > Room 2.19, Devonshire Building > School of Computing Science, > University of Newcastle upon Tyne, > Newcastle upon Tyne, NE1 7RU > United Kingdom > Telephone: Error! Filename not > specified.Error! Filename not specified.Error! Filename not > specified.Error! Filename not specified.Error! Filename not > specified.Error! Filename not specified.+44-191-246-4933 Error! Filename > not specified. > Fax: +44-191-246-4905 > > > > > ________________________________ > > > > > > ------------------------------------------------------------------------ > - > This SF.net email is sponsored by DB2 > Express > Download DB2 Express C - the FREE > version of DB2 express and take > control of your XML. No limits. Just > data. Click to get it now. > > > http://sourceforge.net/powerbar/db2/ > <http://sourceforge.net/powerbar/db2/> > > > > ________________________________ > > > > > > _______________________________________________ > Obi-instrument-branch mailing list > > <mailto:Obi...@li...> > > <mailto:Obi...@li...> > > Obi...@li... > <mailto:Obi...@li...> > > https://lists.sourceforge.net/lists/listinfo/obi-instrument-branch > <https://lists.sourceforge.net/lists/listinfo/obi-instrument-branch> > > > > > > > -- > > ________________________________________________________________________ > __________________ > > Dr. Daniel Schober > > NET Project - Ontologist > > The European Bioinformatics Institute email: > > sc...@eb... <mailto:sc...@eb...> > EMBL Outstation - Hinxton direct: > > Error! Filename not specified. > Error! Filename not specified. > > Error! Filename not specified. > Error! Filename not specified.Error! Filename > not specified. > Error! Filename not specified.+44 (0)1223 494410 > Error! Filename not specified. > Wellcome Trust Genome Campus fax: +44 > (0)1223 494 468 > Cambridge CB10 1SD, UK > Room: A3-141 (extension building) > > Project page: www.ebi.ac.uk/net-project > <http://www.ebi.ac.uk/net-project> > > Personal page: > http://www.ebi.ac.uk/Information/Staff/person_maint.php?s_person_id=734 > <http://www.ebi.ac.uk/Information/Staff/person_maint.php?s_person_id=734 > > > <http://www.ebi.ac.uk/Information/Staff/person_maint.php?s_person_id=734 > > > Former home page: > http://www.bioinf.mdc-berlin.de/%7Eschober/ > <http://www.bioinf.mdc-berlin.de/%7Eschober/> > > > > > > > -- > Frank Gibson > Research Associate > Room 2.19, Devonshire Building > School of Computing Science, > University of Newcastle upon Tyne, > Newcastle upon Tyne, NE1 7RU > United Kingdom > Telephone: +44-191-246-4933 > Fax: +44-191-246-4905 > > > > > -- > Frank Gibson > Research Associate > Room 2.19, Devonshire Building > School of Computing Science, > University of Newcastle upon Tyne, > Newcastle upon Tyne, NE1 7RU > United Kingdom > Telephone: +44-191-246-4933 > Fax: +44-191-246-4905 |
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