mgijax / mammalian-phenotype-ontology

Standard terms for annotating mammalian phenotypic data

Source for Mammalian Phenotype Ontology

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Issues

• https://github.com/mgijax/mammalian-phenotype-ontology/issues

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mammalian-phenotype-ontology's Issues

term placement

I notice we have the term abnormal oxygen consumption (MP:0005288)that has the synonym abnormal metabolic rate as a descendant of abnormal homeostasis but not as a descendant of abnormal metabolism. Please consider making this term a child of abnormal metabolism.
Thanks

Reported by: sbello

Original Ticket: obo/mammalian-phenotype-requests/25

location of meiosis vs mitosis

I notice that we have abnormal mitosis under physiology but abnormal meiosis under morphology. Since both of these are processes wouldn’t it be more appropriate to have both under physiology? I think that meiosis is where it is because abnormal gametogenesis is under abnormal reproductive morphology but wouldn’t this also be a better fit under abnormal reproductive system physiology. We would need to split off 2 of the children of gametogenesis ( abnormal germ cell morphology and abnormal sperm number) and keep these under morphology perhaps under an abnormal gamete morphology term.

Reported by: sbello

Original Ticket: obo/mammalian-phenotype-requests/33

ophthalmoplegia is_a ophthalmoparesis?

defs:
“loss of strength in the muscles of the eye”
“paralysis of the ocular muscles”

these are is_a-siblings in MP. The equivalent terms stand in an is_a relationship in HP.

Wikipedia appears to equate partial paralysis with loss of strength, suggesting the relation should be is_a:

http://en.wikipedia.org/wiki/Ophthalmoparesis

In MP-XP we define these using the PATO terms “paralysed” and “decreased strength” respectively (and MA:eye muscle). These terms do NOT stand in an is_a relation in PATO. (which may be correct, as paralysis may not be a loss of strength per se?)

I have no idea what is correct w.r.t medical usage, but I wanted to point out the discrepancy.

From an ontological point of view, 3 terms are best: one grouping term that covers the full spectrum from loss of strength thru complete paralysis; plus two terms for each of the specific types.

Either:

\- ophthalmoparesis/ophthalmoplegia
\ ophthalmoplegia
\ ophthalmoparesis

Or:

\- ophthalmoparesis
\ ophthalmoplegia
\ partial ophthalmoplegia

Reported by: cmungall

Original Ticket: obo/mammalian-phenotype-requests/10

abnormal meiosis- additional terms

Requesting new term under abnormal female meiosis (5168) and abnormal male meiosis (5169)

abnormal chiasmata formation
def: atypical contact between nonsister chromatids of homologous chromosomes during meiosis I, precluding formation of the expected number of cross-shaped configurations representing recombination events

new term under this:
absence of chiasmata formation
def during meiosis I there are no observable cross-over regions where nonsister chromatids of homologous chromosomes recombine with each other

Reported by: llw2

Original Ticket: obo/mammalian-phenotype-requests/31

add abnormal induced cell death terms

We have several terms under cell death for increased or decreased sensitivity to specific classes of inducers. However, I have worked on 2 papers (J:16558 & 136554) today that use agents not in any of the existing classes. I think it would be helpful to add the terms:
abnormal induced cell death
child of abnormal cell death
definition – anomaly in the response to an agent that induces cessation of function at the cellular level

increased sensitivity to induced cell death
child of abnormal induced cell death
definition – decrease in the exposure level to an agent that is required to induce cessation of function at the cellular level

decreased sensitivity to induced cell death
child of abnormal induced cell death
definition – increase in the exposure level to an agent that is required to induce cessation of function at the cellular level

The existing increased and decreased cellular sensitivity terms would then fall under these new terms.

Even with the addition of these terms I’ll end up double annotating the phenotypes in these papers to
decreased sensitivity to induced cell death and decreased sensitivity to xenobiotics. We may want to consider adding the terms increased sensitivity to xenobiotic induced cell death and decreased sensitivity to xenobiotic induced cell death. These terms could be problematic since some of the existing cellular sensitivity terms are defined by the agents mechanism of action (oxidative stress, alkylating) rather than the type of agent. Although others are defined by the type of agent (UV, ionizing radiation). At some point we will run into agents that fall under more than 1 term.

Reported by: sbello

Original Ticket: obo/mammalian-phenotype-requests/14

exocytosis not involving mast cells

I have annotated J:132495 which studies exocytosis in chromaffin cells and the subsequent release of catecholamines. There is no term in the MP currently that covers this topic. For the time being annotations have been placed under “abnormal adrenal gland secretion” [MP:0001739]. This is not entirely satisfactory for two reasons. First, it is not at all descriptive of the biological processes under study. Second, the authors seem to be using chromaffin cells as a model for studying exocytosis release of catecholamines from neural tissues in general. Is a general term for abnormal exocytosis appropriate under “cellular phenotype”?

Reported by: hdene

Original Ticket: obo/mammalian-phenotype-requests/32

hemimelia

From Melissa Berry (GRC):
Would you please create the term hemimelia. I find terms for missing limbs, but not missing parts of limbs.

Thank you,

Melissa

Reported by: cindyJax

Original Ticket: obo/mammalian-phenotype-requests/45

Endotoxin Shock Syn

MP:0008735, “increased susceptibility to endotoxin shock” has the following misleading synonym that is listed twice….
“resistance to endotoxic shock”

Perhaps “decreased resistance to endotoxic shock”

Reported by: tmeehan

Original Ticket: obo/mammalian-phenotype-requests/39

new term

Can a new term for reticulocytopenia be entered? Currently reticulocytosis (increased reticulocyte number MP:0002640) is in the ontology, but decreased reticulocyte number is not. At least, not that I could find.

reticulocytopenia – A decrease in the normal number of circulating reticulocytes, also called “aplastic crisis”

Thanks.

Reported by: rbabiuk

Original Ticket: obo/mammalian-phenotype-requests/15

new MP term

We do not seem to have an MP term for either serum or plasma abnormal osmolality. J:140022 describes mice with increased plasma osmolality.

H Dene

Reported by: hdene

Original Ticket: obo/mammalian-phenotype-requests/50

new term request

From Melissa Berry (GRC):

decreased granule cell number (child of MP:0004098)

Reported by: cindyJax

Original Ticket: obo/mammalian-phenotype-requests/1

MP term request

abnormal cellular/corpuscular hemoglobin content (CH)
decreased cellular/corpuscular hemoglobin content (CH)
increased cellular/corpuscular hemoglobin content (CH)

(This is not the same as mean corpuscular hemoglobin.)

CH is reported in picograms (pg). It is defined as the mean of the red blood cell hemoglobin concentration (RBC CH) histogram. The RBC CH histogram represents the distribution of red blood cells by the amount of hemoglobin present in each individual cell independent of cell volume.

Source: Bayer Advia 120 Hematology System (Siemens Diagnostics) manual

Reported by: nathea

Original Ticket: obo/mammalian-phenotype-requests/19

adipose tissue

Per Randy Babiuk (MGI):

decreased adipose tissue amount is under abnorm. adipose tissue distribution but not under abnormal adipose tissue amount

Reported by: cindyJax

Original Ticket: obo/mammalian-phenotype-requests/7

questionable parent terms

The term “abnormal bone density [MP:0005007]” and its children appears under both “abnormal bone structure [MP:0003795]”, a morphology term, and under “abnormal bone mineralization [MP:0002896]”, a physiology term. Bone density may well be a consequence of the physiological process “mineralization” but it is a morphological consequence. Placement under both morphology and under physiology seems illogical. (All morphology is the result of physiological processes to some extent or other.)

[email protected] org

Reported by: *anonymous

Original Ticket: obo/mammalian-phenotype-requests/9

hair regrowth

In J:139931 the authors describe a phenotype involving more rapid hair regrowth following wounding or depilation. We have a term for delayed hair regrowth but none for rapid hair regrowth. I can’t find any other annotations to this phenotype currently in MGI but I will be adding 2 from this paper. So please consider adding the term advanced hair regrowth (I’m not sure this is the correct word maybe premature?) definition – faster initiation of the hair growth cycle (anagen) after catagen phase
Thanks

Reported by: sbello

Original Ticket: obo/mammalian-phenotype-requests/47

nasolacrimal duct

In J:138854 the phenotype described includes nasolacrimal ducts that are clogged with undefined matter. According to Taber’s the nasolacrimal ducts are part of the lacrimal apparatus and connect the eye (via the lacrimal canals) to the nasal cavity. We currently have 2 alleles with phenotypes that mention nasolacrimal ducts (Aldh1a3<tm1.1Pcn> – absent placed under abnormal nose morphology and Src<tm1Sor> – necrotic debris and inflammatory cells in the ducts under abnormal immune response). Given the location and function of these ducts I’m not sure that the placement of the absent annotation under nose morphology alone is correct. For the phenotype in J:138854 there doesn’t seem to be any good place for this, the best I can come up with is a double annotation under abnormal nose morphology and abnormal eye morphology. In the adult MA the nasolacrimal duct is a descendant of eye surface. The MA also has terms for the lacrimal apparatus and its other parts. We may want to add the terms to cover this apparatus and its substructures. In addition we may want to consult with Terry H. to find out why the MA only has the nasolacrimal ducts associated with the eye.

Reported by: sbello

Original Ticket: obo/mammalian-phenotype-requests/34

new term

Can a generic term, decreased (and increased) neuron number, be created? There are currently only terms for specific neuron subtypes. Thanks.

Reported by: rbabiuk

Original Ticket: obo/mammalian-phenotype-requests/17

IEL synonym

MP:0008349, abnormal gamma-delta intraepithelial T cell morphology, mistakenly has the definition also appear as a synonym.

Reported by: tmeehan

Original Ticket: obo/mammalian-phenotype-requests/42

new pituitary terms

Please add new MP terms:

Add “abnormal pituitary gland size” UNDER “abnormal pituitary gland morphology [MP:0000633]”
def: anomaly in the average size of the compound gland suspended from the base of the hypothalamus, which secretes somatotropins, prolactin, TSH (thyroid-stimulating hormone), gonadotropins, adrenal corticotropin

Then, place “enlarged pituitary gland [MP:0000636]” and “small pituitary gland [MP:0005361]” and children terms thereof UNDER new term “abnormal pituitary gland size”

Add “abnormal pituitary gland weight” UNDER new term “abnormal pituitary gland size”
DEF: anomaly in the average weight of the compound gland suspended from the base of the hypothalamus, which secretes somatotropins, prolactin, TSH (thyroid-stimulating hormone), gonadotropins, adrenal corticotropin

Then add two new terms:

“decreased pituitary gland weight” (synonyms: reduced pituitary gland weight; reduced pituitary weight)
DEF: reduction in the average weight of the compound gland suspended from the base of the hypothalamus, which secretes somatotropins, prolactin, TSH (thyroid-stimulating hormone), gonadotropins, adrenal corticotropin
J:53777

“increased pituitary gland weight” (synonyms: increased pituitary weight)
DEF: greater than average weight of the compound gland suspended from the base of the hypothalamus, which secretes somatotropins, prolactin, TSH (thyroid-stimulating hormone), gonadotropins, adrenal corticotropin
J:33402

These changes are suggested for keeping hierarchical assignment logically consistent (for example, see relevant terms for “abnormal prostate morphology” and “abnormal seminal gland morphology”)

I have indicated the J#s for which annotations need to be revisited and assigned to the new MPs.

Thanks

Anna

Reported by: cindyJax

Original Ticket: obo/mammalian-phenotype-requests/12

location of heterotaxia

I think we may want to move the term heterotaxia and its children. Currently these are under abnormal postnatal growth/weight/body size; however in the paper I am currently working on the authors mention situs reversus (which I think is a synonym for situs inversus) and inconsistent situs in the context of E9.5 – E13.5 embryos. I don’t want to use a postnatal term for prenatal data. Since problems with arrangement of the organs can be seen both prenatally and postnatally maybe we could move this term out to be a direct child of growth/size phenotype. Alternatively since heterotaxia should be the result of abnormalities in development maybe this could move under embryogenesis. The question is should the placement reflect when the observation was made or when the defect originally occurred?
For now I’ve made my annotation to abnormal left-right axis patterning.

Reported by: sbello

Original Ticket: obo/mammalian-phenotype-requests/28

limb flexion and extension

We do not seem to have any MP terms for limb flexion and extension. I am annotating J:128698. The phenotype in this particular case results from an underlying nervous system abnormality but the case could be more variable.

[e-mail]

Reported by: hdene

Original Ticket: obo/mammalian-phenotype-requests/35

location

abnormal pituitary morphology is a child of both nervous system and endocrine/exocrine gland but abnormal pituitary physiology is only a child of endocrine/exocrine gland. Please make the physiology term a child of abnormal nervous system physiology.

Reported by: sbello

Original Ticket: obo/mammalian-phenotype-requests/38

abnormal weight loss

In J:131227 fasted mice lose less weight compared to controls. I can’t but this under increased body weight as the mutants start off weighing less and all I am given is the relative change in body weight for each genotype. Currently I’ve put this under abnormal postnatal growth/weight/body size (MP:0002089) as i can’t see a better term. I tried to search to see if there were any similar phenotypes but there aren’t any under the term I chose and a wider search returns hundreds of results. I checked a few and didn’t find anything but did not check them all. We may want to add a new term abnormal weight loss, although this could be confusing since we already have the term weight loss under decreased body weight. So maybe abnormal change in body weight, although this may be to general. I think the definition would be along the lines of “alteration in the change in body weight in response to a stimulus”. By that definition this term would also have the diet induced obesity terms as children.

Reported by: sbello

Original Ticket: obo/mammalian-phenotype-requests/48

decreased erythroid progenitor cell number

I’m annotating J:81217 in which the mice have lower numbers of erythroid progenitors in the fetal liver. We have increased and absent terms but not a decreased term. Would be useful to have the decreased term.

Thanks,
Monika

Reported by: monikat

Original Ticket: obo/mammalian-phenotype-requests/37

synonym for resistance to fatty liver development

Please add the synonym resistance to hepatic steatosis development to the term resistance to fatty liver development.

Reported by: sbello

Original Ticket: obo/mammalian-phenotype-requests/5

Lymphocyte activation

Abnormal T cell activation (MP:0001828), abnormal B cell activation (MP:0008217) and their “proliferation” children terms are linked to both higher level morphology and physiology terms. Its my understanding that we want to avoid this. This occurs because these terms appear under lymphocyte physiology and development terms (morphology). I don’t think we need these activation terms as children of the differentiation terms. Its true that activation of say a naïve T cell is needed before it differentiates into an effector cell but it’s the function of the cell to do this, and thus in my mind falls under the physiology branch.
A related issue is that the definitions of both these terms are inaccurate in the context of how they are used among immunologists. T cell activation is a cascade of biochemical events initiated by TCR-MHC interactions that lead to physiological responses including growth, proliferation, differentiation, and cytokine secretion. Memory T cells, which are not naïve, can be activated so at the very least “naïve” should be replaced with “resting”.
B cell activation is a cascade of biochemical events initiated by engagement of the BCR with its cognate antigen that, with or without T cell help, leads to formation of memory B cells and antibody-producing cells. B Cell activation is often split into T cell-dependent and T cell-independent activation.

Reported by: tmeehan

Original Ticket: obo/mammalian-phenotype-requests/41

new term

Can a subterm, ventricular tachycardia, be added under increased heart rate?

defn: a rapid heartbeat that starts in the ventricles
(a pulse rate of more than 100 beats per minute, with at least three irregular heartbeats in a row) from MedLine Plus Medical Encyclopedia

synonyms: Wide-complex tachycardia; V tach; Tachycardia – ventricular

Randy

Reported by: rbabiuk

Original Ticket: obo/mammalian-phenotype-requests/20

axon pruning

J:139381 describes a KO mouse with defective pruning of sympathetic axons that project to the eye. The pruning described here is a normal part of development (ie not resulting from a disease or injury state).

My stab at a definition:
defects in the developmental elimination of axons that fail to participate in an active neuronal circuit by retraction, degeneration, shedding or other mechanism

My best guess is that this would be a child term of “abnormal neurogenesis” MP id: MP:0006008.

Reported by: tmeehan

Original Ticket: obo/mammalian-phenotype-requests/29

New vagina terms

Please add:

1. “abnormal vagina size” under “abnormal vagina morphology [MP:0001139]”

DEF: anomaly in the size of the female reproductive canal located between the uterus and the vulva
SYN: abnormal vaginal size

Then add:

2. “abnormal vagina weight” under “abnormal vagina size”
DEF: anomaly in the weight of the female reproductive canal located between the uterus and the vulva
SYN: abnormal vaginal weight

2a. “decreased vagina weight”
DEF: reduction in the weight of the female reproductive canal located between the uterus and the vulva
SYN: reduced vagina weight
From: J:65577

2b. “increased vagina weight”
DEF: increase in the weight of the female reproductive canal located between the uterus and the vulva

3. enlarged vagina under “abnormal vagina size”

Under “enlarged vagina” add:

3a. “increased vagina weight” (see above)

3b. “vagina hyperplasia”
DEF: overdevelopment or increased size of the vagina, usually due an increased number of cells
SYN: vaginal hyperplasia

4. small vagina under “abnormal vagina size”
DEF: reduced size of the female reproductive canal located between the uterus and the vulva

Under “small vagina” add:

4a. “decreased vagina weight” (see above)

4b. “vagina hypoplasia”
DEF: underdevelopment or reduced size of the vagina, usually due to a reduced number of cells
SYN: vaginal hypoplasia

Thanks

Anna

Reported by: anna_anagnos

Original Ticket: obo/mammalian-phenotype-requests/43

embryonic cilia

From Sue Bello:

In the paper I’m working on (J:137163) the authors’ describe a new technique to determine cilia motion on Henson’s node in live embryos. They report a decrease in motile cilia with regular motion and an increase in nonmotile and erratically moving cilia. Currently we have only morphology terms for embryonic cilia and Henson’s node. I can’t find any appropriate term for this phenotype other than abnormal embryogenesis/development. I think we should add the term abnormal embryonic tissue physiology (to parallel abnormal extraembryonic tissue physiology) and maybe also abnormal embryonic ciliary physiology. I don’t know that we really need to add the ciliary term just yet but if the technique is picked up by others we may need to later.

term: abnormal embryonic tissue physiology
def: functional anomaly in any of the tissues of the embryo proper

term abnormal embryonic ciliary physiology
def: functional anomaly of the earliest cilia of the mouse embryo found on the cells of the embryonic node

Reported by: cindyJax

Original Ticket: obo/mammalian-phenotype-requests/6

shivering as synonym

Shivering is a synonym in the MP for Tremors (MP:0000745). However,
shivering can be a thermogenic response to a cold environment and lower
body temperature. I don’t think shivering in this context ought to be
equated with “tremors”. I am annotating J:137664 in which shivering is
described in mice in conjunction with developing hypothermia. In this
case, I am adding a note under “abnormal body temperature regulation”
[MP:0001777].

Howard

\
Howard Dene. PhD
Mouse Genome Informatics
The Jackson Laboratory
Bar Harbor , Maine 04609
[phone]

Reported by: cindyJax

Original Ticket: obo/mammalian-phenotype-requests/3

Synonym for enlarged clitoris

Please add the term “clitorimegaly” as a synonym of enlarged clitoris [MP:0003529]

Thanks

Anna

Reported by: anna_anagnos

Original Ticket: obo/mammalian-phenotype-requests/44

hyperchromic macrocytic anemia

A term is needed for hyperchromic macrocytic anemia. There is a term for hypo..

Defn: increased hemoglobin content per cell

(although the red blood cells are larger than normal and the total amount of hemoglobin per cell is increased, the percentage of hemoglobin per cell is usually in the normochromic range)

synonym macrocytic hyperchromia

Thanks

Reported by: rbabiuk

Original Ticket: obo/mammalian-phenotype-requests/16

new terms

Some new terms may be needed based on a recent annotation. Terms for pancreatic delta cell physiology and somatostatin secretion would be useful and would make the MP more complete, as there is a term for delta cell morphology but no corresponding physiology term as there is for alpha or beta cells.

Randy

Reported by: rbabiuk

Original Ticket: obo/mammalian-phenotype-requests/26

New MP terms

please add:

1. early vaginal opening under "early sexual maturation [MP:0003378]

DEF: the opening of the genital canal in a female occurring at an earlier than expected age
SYN: early onset of vaginal opening
SYN: precocious vaginal opening
From: J:140008, J:92626, J:116663

2. early reproductive senescence under “premature aging [MP:0003786]”
DEF: loss of reproductive capacity occurring at an earlier than expected age
SYN: early onset of reproductive senescence
SYN: precocious reproductive senescence
SYN: premature reproductive aging
SYN: accelerated reproductive aging
From J:65577, J:140008

this can be also a child of abnormal reproductive system physiology [MP:0001919] OR abnormal fertility/fecundity [MP:0002161]

Thanks

Anna

Reported by: anna_anagnos

Original Ticket: obo/mammalian-phenotype-requests/49

polysyndactyly

The paper I’m working on (J:138805) has the phenotype synpolydactyly which I believe should be a synonym for polysyndactyly (MP:0004083). Please add this synonym.
Thanks

Reported by: sbello

Original Ticket: obo/mammalian-phenotype-requests/36

lineage determination

This seems too general for a phenotype term; you might say that the
definition covers all of development? Perhaps this should be limited to
cell types as in the GO (I.e. B cell lineage commitment, etc)\- food for
thought.

Cindy

---

Original Message -——-

Subject: vocab cell lineage/thx
Date: Thu, 04 Sep 2008 13:26:17 -0400
From: Linda Washburn <[email protected]>
To: Cynthia Smith <[email protected]>

under 1672

abnormal lineage determination
*
def . an anomaly in the developmental history of individual blastomeres
from the first cleavage division to their ultimate differentiation into
cells of a specific tissue/ organ.*

Reported by: cindyJax

Original Ticket: obo/mammalian-phenotype-requests/2

increased Cajal-Retzius cell number

The MP currently lists the term decreased Cajal-Retzius cell number (MP:0008031) but lacks the corresponding increased term. Please consider adding it as at least J:139170 describes an increase in Cajal-Retzius cells.

Reported by: michknow

Original Ticket: obo/mammalian-phenotype-requests/21

Red Blood Cell distribution width

Came across this parameter twice in two papers J:139179 and 139213. Wikipedia has a good description.

http://en.wikipedia.org/wiki/Red\blood\cell\distribution\width

the concept is similar for the “abnormal hemoglobulin distribution width” term, MP:0008849.

I placed it under “abnormal erythrocyte morphology”
for both papers.

Reported by: tmeehan

Original Ticket: obo/mammalian-phenotype-requests/22

split dwarf

Melissa Berry (GRB)

Please create two sub-types of dwarf:
proportional dwarf (syn. proportionate dwarf)
disproportionate dwarf
____________________
Melissa Berry
The Jackson Laboratory
600 Main St.
Bar Harbor ME 04609

Reported by: cindyJax

Original Ticket: obo/mammalian-phenotype-requests/4

New MP

Please add:

“long radius” under abnormal radius morphology [MP:0000552]

DEF: increased length of the short bone of the lateral forearm

From J:63006

Thanks

Anna

Reported by: anna_anagnos

Original Ticket: obo/mammalian-phenotype-requests/23

New reproductive system MPs

Please add:

“delayed balanopreputial separation” UNDER delayed sexual maturation [MP:0001938]
synonym: delayed preputial separation

DEF: the separation of the prepuce from the glans penis (balanus), a result of the cornification of the balano-preputial epithelium, occurring at a later than expected age; balanopreputial separation is used as an index for the onset of male puberty and is androgen-sensitive in the rat

From J:105921

---

Other suggestions:

It may be a good idea to split “abnormal sexual maturation [MP:0001937]” into abnormal MALE and FEMALE sexual maturation subterms, as well as “delayed fertility [MP:0002683]” into delayed MALE and FEMALE fertility subterms

Thanks

Anna

[email protected]

Reported by: cindyJax

Original Ticket: obo/mammalian-phenotype-requests/13

placement of extracellular matrix terms

We need to consider where to place terms related to defects in extracellular matrix, when the defect is widespread and not organ or system-specific. GO currently places extracellular matrix as is_a sibling of “cell” and a direct child of “cellular component”. MA only has organ-specific terms that are placed under the appropriate organ system.

Most of these terms in the MP are placed as children of “other phenotype” [MP:0005395]; “other phenotype” is a term that will eventually be rendered obsolete.

Reported by: cindyJax

Original Ticket: obo/mammalian-phenotype-requests/18

new terms for liver vasculature

In J:100427, double transgenic embryos and newborns are analyzed and various problems with the liver vasculature are detected. Some new terms (some may be fairly common, others more rarely used if at all) might be necessary. These include a broad abnormal hepatic vasculature term, and more specific: abnormal space of Disse (perisinusoidal space), abnormal liver or hepatic parenchymal cell morphology, abnormal liver sinusoid/sinusoidal network morphology (ref shows decrease/absence of fenestrations on sinusoidal epithelium surface and accumulation of/congestion with red blood cells), and possibly abnormal liver vascular development incl. microvascular network development.

Reported by: rbabiuk

Original Ticket: obo/mammalian-phenotype-requests/40

decreased mean platelet volume

decreased mean platelet volume

Child of MP:0002586, sibling of MP:0002599

per Melissa Berry (GRC)

Reported by: cindyJax

Original Ticket: obo/mammalian-phenotype-requests/11

new terms

There were several terms used in analysis of the placental phenotype of mutants that are not in the MP.
Can or should terms be added for placental junctional zone, or specific terms including increased/decreased number for specific placental cell types such as spongiotrophoblast cells and glycogen cells, to be consistent with the decreased trophoblast cell number term?

(This is an abstract from Placenta 21(8): 882-888

Among the different trophoblast subtypes of the mouse placenta, the glycogen cells (GC) are one of the trophoblast subtypes that invade the decidua. they directly originate from the central part of the ectoplacental cone at embryonic day (E) 7.5. PCDH12-positive cells start to accumulate glycogen from E10.5 and the first migrating cells could be observed from this age. Unlike other placental and decidual cells, GC do not express P-cadherin, which may explain their migration properties in this organ. In the decidua, GC settle in the vicinity of the maternal vascular sinuses but do not incorporate in the endothelium. By the end of gestation (E17.5), most GC islets of the decidua enter into a lytic phase and form large lacunae. These lacunae, filled with glycogen, may provide a substantial source of energy at the end of gestation or during delivery. Our data suggest that spongiotrophoblasts and GC are two independent lineages and we bring insights into GC migration and fate.)

Randy

Reported by: rbabiuk

Original Ticket: obo/mammalian-phenotype-requests/24

new metabolism related terms

In J:125307 the phenotypes increased CO2 production, increased heat generation and increased muscle ATP production are all reported. Currently we do not have terms for any of these phenotypes so I annotated the first 2 to abnormal metabolism and the last to abnormal muscle physiology. We may want to consider adding terms for these phenotypes.

Reported by: sbello

Original Ticket: obo/mammalian-phenotype-requests/27

proliferation term placements

Hello Pheno people,
Sue just asked me to send a note to look at proliferation terms as some fall under morphology headers while others are under physiology headers. This came up while annotating J:136692 where an increased proliferation in mammary and gut epithelia does not result in a change in morphology due to compensatory apoptosis.

Michelle

\
Michelle Knowlton, PhD
Scientific Curator
Mouse Genome Informatics
The Jackson Laboratory
Bar Harbor, Maine 04609
[phone]

Reported by: cindyJax

Original Ticket: obo/mammalian-phenotype-requests/8

name changes

We have several terms in the MP currently as susceptibility to X (see list below). I think these would be more properly called increased susceptibility to X, since susceptibility on its own can be used to refer to a range of levels of response (i.e. low susceptibility vs. high susceptibility). The majority of these types of terms are currently named as increased or decreased susceptibility to X. Similarly there are several terms that are called resistance to X that I think should be changed to decreased susceptibility to X with the synonym increased resistance to X. Also the increased susceptibility terms should all get the synonym decreased resistance to X.

susceptibility to age related obesity
susceptibility to diet-induced obesity
susceptibility to dystrophic cardiac calcinosis
susceptibility to hepatoma
susceptibility to induced arthritis
susceptibility to induced muscular atrophy
susceptibility to induced pancreatitis
susceptibility to pharmacologically induced seizures

resistance to addictive substance
resistance to age related obesity
resistance to age-related hearing loss
resistance to diet-induced obesity
resistance to dystrophic cardiac calcinosis
resistance to hepatic steatosis
resistance to hepatoma
resistance to hyperlipidemia
resistance to induced arthritis
resistance to induced choroidal neovascularization
resistance to induced joint inflammation
resistance to induced muscular atrophy
resistance to induced pancreatitis
resistance to induced retinal damage
resistance to liver neoplasm
resistance to lung neoplasm
resistance to lymphoma
resistance to mammary neoplasm
resistance to pharmacologically induced seizures
resistance to stomach tumor
resistance to tongue neoplasm
resistance to tumor development
skin irradiation resistance

Reported by: sbello

Original Ticket: obo/mammalian-phenotype-requests/30

new parent term-bilateral symmetry

From Linda Washburn:

RE
(i think 1270 and 4134 , 3385 are misplaced under growth, weight and body size)

“I agree – these are already scheduled to be moved, but I need to find the right place. A new system header (body shape/pattern?) may be needed. "

taking your lead:

bilateral symmetry is expected for any organism our vocab covers
so
abnormal bilateral symmetry def there is an aberration in the expected mirror image appearance of the left and right sides of an organism divided equally along the central axis in one plane
but this is the same as MP 1706 however not as embryological

under either new or under 1706 goes 4133 and all children

1270, 3385, 4134 ( considering def) can stay under abnormal growth as they are the outcome of a variety of possibilities
but emerging ’cause of growth

Reported by: cindyJax

Original Ticket: obo/mammalian-phenotype-requests/46