existing semantic models for normal conditions of metabolites in bodily fluids?

Previous Topic Next Topic
 
classic Classic list List threaded Threaded
3 messages Options
Reply | Threaded
Open this post in threaded view
|

existing semantic models for normal conditions of metabolites in bodily fluids?

Egon Willighagen-2
Hi all,

I'm extracting some metabolite-disease relationships and the book I'm
reading also lists normal concentrations metabolites in various bodily
fluids for various age groups.

For example, for Phe 0-1 years in serum it lists <80 micromolar
("newborns" is another age group, but most are like "x-y years").

Has anyone encoded such information in a semantic manner already? What
should I be reading?

Looking forward to hearing from you,

grtz,

Egon

--
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers
ORCID: 0000-0001-7542-0286
ImpactStory: https://impactstory.org/EgonWillighagen

Reply | Threaded
Open this post in threaded view
|

Re: existing semantic models for normal conditions of metabolites in bodily fluids?

Jim McCusker-2
I've been using UBERON for anatomical parts and SIO's attribute/measurement approach for metabolites, using CHEBI to classify the chemical types. The sample (urine, for example,

:X a sio:Sample, UBERON:Urine;
sio:hasPart [
a CHEBI:Creatinine;
sio:hasAttribute [
a sio:Concentration;
sio:hasValue 2.3;
sio:hasUnit uo:ug/mL
];
].

I don't have the right URIs here for UO, UBERON, or CHEBI, of course.

Jim
On Sat, Aug 13, 2016 at 11:19 AM Egon Willighagen <[hidden email]> wrote:
Hi all,

I'm extracting some metabolite-disease relationships and the book I'm
reading also lists normal concentrations metabolites in various bodily
fluids for various age groups.

For example, for Phe 0-1 years in serum it lists <80 micromolar
("newborns" is another age group, but most are like "x-y years").

Has anyone encoded such information in a semantic manner already? What
should I be reading?

Looking forward to hearing from you,

grtz,

Egon

--
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers
ORCID: 0000-0001-7542-0286
ImpactStory: https://impactstory.org/EgonWillighagen

--
James P. McCusker III, Ph.D.
Reply | Threaded
Open this post in threaded view
|

Re: existing semantic models for normal conditions of metabolites in bodily fluids?

Timothy Cook
Seems like you are looking for a modeling approach that support reference ranges.  You might check here http://mlhim.org/documents.html


On Sat, Aug 13, 2016 at 3:50 PM, Jim McCusker <[hidden email]> wrote:
I've been using UBERON for anatomical parts and SIO's attribute/measurement approach for metabolites, using CHEBI to classify the chemical types. The sample (urine, for example,

:X a sio:Sample, UBERON:Urine;
sio:hasPart [
a CHEBI:Creatinine;
sio:hasAttribute [
a sio:Concentration;
sio:hasValue 2.3;
sio:hasUnit uo:ug/mL
];
].

I don't have the right URIs here for UO, UBERON, or CHEBI, of course.

Jim

On Sat, Aug 13, 2016 at 11:19 AM Egon Willighagen <[hidden email]> wrote:
Hi all,

I'm extracting some metabolite-disease relationships and the book I'm
reading also lists normal concentrations metabolites in various bodily
fluids for various age groups.

For example, for Phe 0-1 years in serum it lists <80 micromolar
("newborns" is another age group, but most are like "x-y years").

Has anyone encoded such information in a semantic manner already? What
should I be reading?

Looking forward to hearing from you,

grtz,

Egon

--
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers
ORCID: 0000-0001-7542-0286
ImpactStory: https://impactstory.org/EgonWillighagen

--
James P. McCusker III, Ph.D.



--
Timothy W. Cook, President
Data Insights, Inc.