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Re: [Obi-function-branch] [Obi-instrument-branch] flow cytometer functions
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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 |
