CALOHA - UBERON mapping problems

[lydiecalipho]

Among the mappings to CALOHA that you are providing, could you please check the three following ones :

1) late embryo UBERON:0000323 fetus TS-0360 -> there is no def for the UBERON term so we do not know if both terms are equivalent

2) Egg UBERON:0007379 Ovum TS-2191 This is not correct according to UBERON definition for Egg: The hard-shelled reproductive body produced by a bird and especially by the common domestic chicken; also: its contents used as food.

3) synovial membrane of synovial joint UBERON:0002018 Synovium TS-0998 It seems that layer of synovial tissue UBERON:0007616 would be more appropriate

Thanks!

Lydie and Paula (CALIPHO)

[cmungall]

There is some discussion of fetus vs late embryo here: https://docs.google.com/document/d/11y-8bFnsGaT8phrAvSl9szR_LXAANm43N-0Faq5sjrI/edit#heading=h.tj7d3b26x957

A multi-species definition is hard but we could include a statement that in humans this is synonymous with fetus (week 9 pf?)

[lydiecalipho]

Thanks for the comment. The problem here is exactly the one that was discussed in your document! You consider that a fetus ("late embryo") IS an embryo , and we do not. According to our definition for fetus : "The unborn young of a viviparous mammal, in the postembryonic period, after the major structures have been outlined."

I suggest that we do not map both terms for now, since it may be confusing for users.

we will review all the embryo/fetal part of CALOHA and come back to you later.

[cmungall]

I noticed in Caloha there are 38 or so "Fetal X" terms, and 20 or so "embryonic X" terms. In general we prefer to create subclasses where there is some biological characteristic that differentiates the class from a parent class, and suggest that annotations incorporate stage separately (allowing more precise specification, in terms of Carnegie Stages, or weeks pf, etc). But if these are useful for annotation we can add them, but we do have to be careful we mean the same thing by fetus.

On Mar 27, 2013, at 3:47 AM, lydiecalipho wrote:

Thanks for the comment. The problem here is exactly the one that was discussed in your document! You consider that a fetus ("late embryo") IS an embryo , and we do not. According to our definition for fetus : "The unborn young of a viviparous mammal, in the postembryonic period, after the major structures have been outlined."

I suggest that we do not map both terms for now, since it may be confusing for users.

we will review all the embryo/fetal part of CALOHA and come back to you later.

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[paulacalipho]

Hello,

We have been revising our gestational structure part of the ontology that includes embryonic and fetal tissues, organs and structures with the aim to map to UBERON.

Because of the usage we would like to give to our ontology in neXtProt, we try to give functional definitions to the terms in Caloha. That is why we map, for example, data obtained from a fetal kidney (or from a kidney from an embryo) to the term “fetal kidney” (or “embryonic kidney”). Mapping the data to “kidney” at developmental stage “fetal stage” (or “embryonic stage”) brings us the problem on how we define “kidney”, because it is defined with the function that the kidney has in adults.

To manage this discrepancy we envisaged two possible solutions: 1- First option (the one we took)

[Term] id: TS-0510 name: Kidney def: "Body organ that filters blood for the secretion of urine and that regulates ion concentrations." [MeSH:Kidney] synonym: "Renal" RELATED [] xref: BTO:0000671 xref: EV:0100096 xref: FMA:7203 xref: MESH:D007668 xref: UBERON:0002113 xref: URL:http://www.proteinatlas.org/dictionary/normal/kidney relationship: part_of TS-1323 ! Urinary system

[Term] id: TS-0342 name: Fetal kidney def: "Fetal structure that gives rise to adult kidney." [NPX:PDR] relationship: part_of TS-0360 ! Fetus

In the future we are planning to complete the ontology with the relationship “develop_from” to be able to connect both terms (useful for users searching for example data in kidney adult and not in fetal kidney, for example).

2- Second option (rejected) Define each term with the adult function and a description of fetal (and embryonic) development and function. This brings us the problem of mapping to other ontologies and more philosophical issues also.

We know that this is an issue of discussion in different ontologies (one can even argue that some organs continue to develop after birth!). This is - at least for the moment- the solution we found. So we propose you not to create those terms in UBERON (we make a step back) and see how the ontology evolves. In that way each ontology (UBERON and Caloha) maintain the internal coherence.

Here I give you some examples that show that some organs are not fully developed and functional at fetal stage, or have a different function in fetus.

• The fetal kidneys do not have to maintain the water and electrolyte households in the organism nor do they have to clean the blood from substances (mainly end products of cellular metabolism in the form of urea, uric acid and creatinine ) that are usually eliminated with the urine. These functions are performed by the placenta. The kidneys are, however, involved in the production of amniotic fluid. Naturally, besides their excretory function, the kidneys also have an endocrine one in that they secrete hormones (renin, erythropoetin, prostaglandin and kallikrein). Even though some of the endocrine functions only begin at birth, the embryonic kidneys nevertheless have an important task to fulfill, namely the production of erythropoetin. In addition, renin-positive cells can already be found in the mesonephros of 5-6 week old embryos (source: http://www.embryology.ch/anglais/turinary/urinhaute03.html )
• Lungs: At birth, the respiratory system becomes fully functional upon exposure to air, although some lung development and growth continues throughout childhood
• Pancreas: Insulin and glucagon can be detected in the human fetal circulation by the fourth or fifth month of fetal development (http://en.wikipedia.org/wiki/Development_of_pancreas#Embryological_development)
• Spleen: Reticular framework of white pulp and marginal zone in human fetal spleens from the 17th to 40th week of gestation. (http://php.med.unsw.edu.au/embryology/index.php?title=Cardiovascular_System_-_Spleen_Development#Fetal_Spleen)
• Adrenal gland: in a human fetus at 10 week one can observe the developing adrenal gland containing the degenerating fetal cortex and the developing adult cortex (http://php.med.unsw.edu.au/embryology/index.php?title=Endocrine_-_Adrenal_Development)
• Heart: In human embryos the heart begins to beat at about 22-23 days, with blood flow beginning in the 4th week. The heart is therefore one of the earliest differentiating and functioning organs. Week 40 At birth pressure difference closes foramen ovale leaving a fossa ovalis (http://php.med.unsw.edu.au/embryology/index.php?title=Cardiovascular_System_-_Heart_Development#Human_Development_Timecourse)
• Hippocampus: 18 to 20 weeks - fetal hippocampus begins to resemble the adult hippocampus. The dentate gyrus and cornu ammonis have folded into the temporal lobe. The hippocampus and subiculum approximate each other across a narrow hippocampal sulcus. The CA1-3 fields form an arc and the CA4 field has increased in size within the widened arch of the dentate gyrus. (http://php.med.unsw.edu.au/embryology/index.php?title=Neural_-_Hippocampus_Development)
• Pituitary gland: Week 16 - adenohypophysis fully differentiated (http://php.med.unsw.edu.au/embryology/index.php?title=Endocrine_-_Pituitary_Development)
• Liver: In the fetus, the liver develops throughout normal gestation, and does not perform the normal filtration of the infant liver. The liver does not perform digestive processes because the fetus does not consume meals directly, but receives nourishment from the mother via the placenta. The fetal liver releases some blood stem cells that migrate to the fetal thymus, so initially the lymphocytes, called T-cells, are created from fetal liver stem cells. Once the fetus is delivered, the formation of blood stem cells in infants shifts to the red bone marrow.(http://en.wikipedia.org/wiki/Liver#Other_functions)

Many thanks Paula from Calipho group

[gouttegd]

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