From: Paul S. <ps...@mo...> - 2010-03-12 13:57:14
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Its not increased concentration of alkaline phosphatase that being measured George, its activity. Surely therefore as long as the "intersection_of:towards" works here it should be something like: >> PATO:increased >> GO:alkaline phosphatase activity >> inhering in: FMA serum > intersection_of: towards PRO:000003969 ! alkaline phosphatase, > placental type Syntax not my forte! P. On 12 Mar 2010, at 13:50, George Gkoutos wrote: > > On 12 Mar 2010, at 09:16, Peter Robinson wrote: > >> Dr. med. Sandra Dölken wrote: >>> I added those terms while doing an annotation and have been >>> discussing >>> this with some people from clinical chemistry and with George as >>> well for >>> the decomposition. >>> >>> There are a number of Isozymes of the Alkaline Phosphatase, trying >>> to >>> clarify some of the points from below: >> >> >> >> I think we would need to say in PATO >> >> PATO:increased >> GO:alkaline phosphatase activity >> inhering in: FMA serum >> ???:originating_from FMA placenta >> ???:corresponding to: PRO:Isozyme placental AP >> >> Or something along these lines. > > > Hi Peter, > > Sandra and I have provided definitions for this some time back for > example: > > [Term] > id: HP:0010682 ! Elevated placental alkaline phosphatase > intersection_of: PATO:0001162 ! increased concentration > intersection_of: towards PRO:000003969 ! alkaline phosphatase, > placental type > > > I think that should be sufficient for the observable here but like > Paul points out it does not discriminate between enzyme levels and > activity upregulation. We could possible add something like > results_from ... > > > George > > >> >> -peter >> >>> >>> 1) Elevated placental alkaline phosphatase: PATO:increased_rate of >>> GO:alkaline phosphatase activity and occurs_in placenta: >>> -> That is a bit dodgy. Not the activity in the placenta but the >>> production of AP by the placenta is increased. >>> >>> 2) Tissue non-specific alkaline phosphatase: has a number of >>> differend >>> subset for example "of bone origin", "of hepatic origin"... >>> -> we are talking about the same isozyme which is produced in the >>> liver >>> and in the bone... >>> -> the prefixes "low" or "increased" mean that production of the >>> AP in >>> question is either raised or lowered, which might be due to for >>> example >>> certain liver or bone diseases. >>> >>> -Sandra >>> >>> >>>> I see a few new bulk additions such as >>>> >>>> is_a HP:0000118 ! Organ abnormality >>>> is_a HP:0001939 ! Metabolism abnormality >>>> is_a HP:0004379 ! Abnormality of alkaline phosphatase >>>> metabolism >>>> is_a HP:0003155 ! Elevated alkaline phosphatase >>>> is_a HP:0010682 ! Elevated placental alkaline phosphatase *** >>>> >>>> in Obol I'll treat these as PATO:increased_rate of GO:alkaline >>>> phosphatase activity and occurs_in placenta >>>> >>>> or perhaps not... >>>> >>>> less sure of: >>>> >>>> is_a HP:0004379 ! Abnormality of alkaline phosphatase >>>> metabolism >>>> is_a HP:0003282 ! Low alkaline phosphatase >>>> is_a HP:0010683 ! Low tissue non-specific alkaline >>>> phosphatase >>>> is_a HP:0010684 ! Low alkaline phosphatase of bone origin >>>> *** >>>> >>>> how do we deal with specificity? GO term request? or PRO request >>>> for >>>> ALPL? >>>> >>>> what about bone origin? is this just indicating the specific gene >>>> involved? PRO may be best here. >>>> >>>> Will HPO pre-compose expression terms for a wide variety of genes? >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> Download Intel® Parallel Studio Eval >>>> Try the new software tools for yourself. Speed compiling, find bugs >>>> proactively, and fine-tune applications for parallel performance. >>>> See why Intel Parallel Studio got high marks during beta. >>>> http://p.sf.net/sfu/intel-sw-dev >>>> _______________________________________________ >>>> Obo-human-phenotype mailing list >>>> Obo...@li... >>>> https://lists.sourceforge.net/lists/listinfo/obo-human-phenotype >>>> >>> >>> >>> Dr. med. Sandra Dölken >>> Charité Universitätsmedizin Berlin >>> Campus Virchow Klinikum >>> Institut für Medizinische Genetik >>> Augustenburger Platz 1 >>> 13353 Berlin >>> Germany >>> phone: +49(0)30 450 569 132 >>> fax: +49(0)30 450 569 914 >>> email: san...@ch... >>> http://genetik.charite.de/institut/ >>> >>> >>> ------------------------------------------------------------------------------ >>> Download Intel® Parallel Studio Eval >>> Try the new software tools for yourself. Speed compiling, find bugs >>> proactively, and fine-tune applications for parallel performance. >>> See why Intel Parallel Studio got high marks during beta. >>> http://p.sf.net/sfu/intel-sw-dev >>> _______________________________________________ >>> Obo-human-phenotype mailing list >>> Obo...@li... >>> https://lists.sourceforge.net/lists/listinfo/obo-human-phenotype >>> . >>> >> >> >> -- >> Dr. med. Peter N. Robinson, MSc. >> Institut für Medizinische Genetik >> Charité - Universitätsmedizin Berlin >> Humboldt-Universität >> Augustenburger Platz 1 >> 13353 Berlin >> Germany >> voice: 49-30-450566042 >> fax: 49-30-450569915 >> email: pet...@ch... >> http://compbio.charite.de/ >> http://www.human-phenotype-ontology.org >> >> ------------------------------------------------------------------------------ >> Download Intel® Parallel Studio Eval >> Try the new software tools for yourself. Speed compiling, find bugs >> proactively, and fine-tune applications for parallel performance. >> See why Intel Parallel Studio got high marks during beta. >> http://p.sf.net/sfu/intel-sw-dev >> _______________________________________________ >> Obo-human-phenotype mailing list >> Obo...@li... >> https://lists.sourceforge.net/lists/listinfo/obo-human-phenotype > > --------------------------------------------------- > Dr. G.V.Gkoutos > > University of Cambridge > Department of Genetics > Downing Site, Downing Street > Cambridge, CB2 3EH > > Tel: +44 [0] 1223 333963 > > email: gg...@ca... > url: http://www.gen.cam.ac.uk > > ------------------------------------------------------ > > > > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev_______________________________________________ > Obo-human-phenotype mailing list > Obo...@li... > https://lists.sourceforge.net/lists/listinfo/obo-human-phenotype |