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Re: [Obo-human-phenotype] Elevated alkaline phosphatase
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From: Paul S. <ps...@mo...> - 2010-03-11 09:08:11
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Just a quick intervention - I'll get back later. The term alkaline phospatase metabolism doesnt really mean anything. This is an enzyme activity which is a property of several distinct isoforms of alkaline phosphatase so to specify its metabolism is a very odd way of phrasing it. Uniprot lists four genes and within those there are different isoforms. What is being measured here is AP activity, which depending on the assay, is attributable to different forms or isoforms. I think this should therefore be abnormality of alkaline phosphatase *activity* which is consistent with the parent term. The children could be elevated activity due to APL, ALPP, ALPPL2 maybe? As a *phenotype* assay this is an enzyme assay and the elevation of activity can suggest an increased level of enzyme but doesnt discriminate between enzyme levels and activity upregulation. P. On 11 Mar 2010, at 08:52, 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: > > 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 |