As far as I can see, the only entities in MPD that have been ontologized so far are the measurement informations, which are project-, method- and age-specific (there are about 18,000 in total). Measurement informations do not include any measured values, but only information about values that were measured within a project using a specific method for one or more mice of the same age. Via the key measnum, one or more terms from the mammalian phenotype (MP), adult mouse anatomy (MA) or vertebrate trait (VT) ontology are assigned to a measurement information.
For example, the measurement information with the ID measum=114532 corresponds to the weight measurements of 80 animals aged 8 weeks fed a high-fat diet (HFD) in the course of the Auwerx2 project. This measurement information is assigned 2 terms, one of which is abnormal body weight.
The same project includes another measurement information with ID measnum=114531 for the weight measurements of 74 animals at 8 weeks of age fed a standard rodent chow diet (CD). This measurement information was assigned the same ontology terms, one of which is abnormal body weight.
I don't understand this mapping of ontology terms to measurement informations. Here are some questions:
Why are the ontology terms assigned to the measurement informations and not to the individual measured values?
How is a term assigned to a measurement information?
When is a measurement information considered abnormal? Do all measured values have to be outside a normal range? Or does the mean or maximum value have to be outside a normal range?
Are there corresponding reference ranges in MPD that can be used to decide that a measurement information is abnormal?
Specifically regarding the example above: Why was the term abnormal body weight assigned to the measurement information measnum=114531?
As far as I can see, the only entities in MPD that have been ontologized so far are the measurement informations, which are project-, method- and age-specific (there are about 18,000 in total). Measurement informations do not include any measured values, but only information about values that were measured within a project using a specific method for one or more mice of the same age. Via the key
measnum, one or more terms from the mammalian phenotype (MP), adult mouse anatomy (MA) or vertebrate trait (VT) ontology are assigned to a measurement information.For example, the measurement information with the ID
measum=114532corresponds to the weight measurements of 80 animals aged 8 weeks fed a high-fat diet (HFD) in the course of theAuwerx2project. This measurement information is assigned 2 terms, one of which isabnormal body weight.The same project includes another measurement information with ID
measnum=114531for the weight measurements of 74 animals at 8 weeks of age fed a standard rodent chow diet (CD). This measurement information was assigned the same ontology terms, one of which isabnormal body weight.I don't understand this mapping of ontology terms to measurement informations. Here are some questions:
Why are the ontology terms assigned to the measurement informations and not to the individual measured values?
How is a term assigned to a measurement information?
When is a measurement information considered abnormal? Do all measured values have to be outside a normal range? Or does the mean or maximum value have to be outside a normal range?
Are there corresponding reference ranges in MPD that can be used to decide that a measurement information is abnormal?
Specifically regarding the example above: Why was the term
abnormal body weightassigned to the measurement informationmeasnum=114531?What are the ontology mappings in MPD used for?