BP term suggestions from Incyte

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Attached is an excel file containing 21 Biological Process term suggestions, compiled from the Proteome database editors at Incyte, March 2003.

Reported by: reneewhite

Original Ticket: "geneontology/ontology-requests/716":https://sourceforge.net/p/geneontology/ontology-requests/716

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Please could you attach the file? Cheers!

Original comment by: girlwithglasses

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excel file of BP term suggestions from Incyte

Original comment by: reneewhite

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I am attempting again to attach the excel file - thanks!

Original comment by: reneewhite

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Hi Just a couple comments about the term 'biofilm formation'. The book I have suggests that a biofilm forms in an aquatic environment - as a result of the polysaccharride deposition and so forth. It says a biofilm is: A film of microorganisms usually embedded in extracellular polymers, which adheres to surgaces submerged in, or subjected to, aquatic environments. (ISBN:0471940526)

Also, "Formation of a layered culture of microorganisms growing on a surface that they have created themselves..." This sounds funny to me...

Maybe the def could just be: The formation of a film of microorganisms usually embedded in extracellular polymers, which adheres to surgaces submerged in, or subjected to, aquatic environments. (ISBN:0471940526)

I know in the literature there are reports of people growing yeasts to form 'biofilms'. These are a bit dicey...that being said, we still need the term, eh? The parentage sounds good to me - under development.

Chandra

Original comment by: clt4

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All hair cycle terms look fine - I would actually add these as children of 'molting cycle' rather than 'morphogenesis of follicular epithelium' because it's defined as:

'The periodic casting off and regeneration of an outer covering of cuticle, feathers, hair, horns, skin, etc.'

which is perfect and I think we should expand the definition of 'hair cycle' to be:

The cyclical phases of growth (anagen), regression (catagen), quiescence (telogen), and shedding (exogen) in the life of a hair; one of the collection or mass of filaments growing from the skin of an animal, and forming a covering for a part of the head or for any part or the whole of the body.

So it's clear that it applies to organisms other than humans. So it'll look like this:

molting cycle ---%hair cycle ------<regulation of hair cycle ---------%positive regulation of hair cycle ---------%negative regulation of hair cycle ------<categen ------<exogen ------<telogen ------<anagen

For 'response to thirst/water deprivation', we already have a term 'response to drought ; GO:0001494' which is defined as the same thing - unfortunately the word 'drought' makes it sounds rather plant-specific. I think we should change this term name to 'response to water deprivation' and give it the synonyms 'response to thirst' and 'response to drought'. the two instances you suggest for this term sound fine.

'cholesterol homeostasis' also sounds okay, as does 'sperm ejaculation' although I don't think 'spermatogenesis' is the right parent - I guess it should be a part of sexual reproduction (violation of true path? ;) - I think we might need a new child 'sexual intercourse' or something. 'maternal behavior' sounds okay too.

menarche, thelarche and menopause should be okay - but I'm not sure that menstruation is really a secondary sexual characteristic - perhaps we need some new terms here - will think about these some more.

Original comment by: jl242

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Here are all of the suggestions in plain text, alung with some comments.

> term: menarche > parent 1: development of secondary female sexual characteristics > definition: The establishment or beginning of the menstrual function

Change definition wording to 'The beginning of the menstrual cycle; the first menstrual/ cycle in an individual.' Need a definition reference.

> term: thelarche > parent 1: development of secondary female sexual characteristics > definition: The beginning of development of the breasts in the female

> term: menopause > parent 1: development of secondary female sexual characteristics > definition: Cessation of menstruation in the human female, occurring > usually around the age of 50.

Does menstruation occur exclusively in humans? There's a brief snippet in Gilbert's Developmental Biology text that suggests that other primates menstruate. If so, the definitions for menstruation-related terms can't be specific to humans.

> term: hair cycle > parent 1: morphogenesis of follicular epithelium > PMID: 12230507 > definition: The cyclical phases of growth (anagen), regression > (catagen), quiescence (telogen), and shedding (exogen) in the life of > a hair

I agree that this term would fit well under molting cycle.

> term: regulation of hair cycle > parent 1: hair cycle > PMID: 11841365 > definition: Positive or negative regulation of the cyclical phases of > growth (anagen), regression (catagen), quiescence (telogen), and > shedding (exogen) in the life of a hair

> term: positive regulation of hair cycle > parent 1: regulation of hair cycle > definition: Positive regulation of the cyclical phases of growth > (anagen), regression (catagen), quiescence (telogen), and shedding > (exogen) in the life of a hair

> term: negative regulation of hair cycle > parent 1: regulation of hair cycle > definition: Negative regulation of the cyclical phases of growth > (anagen), regression (catagen), quiescence (telogen), and shedding > (exogen) in the life of a hair

GO curators - please use standardized 'regulation' definition wordings.

> term: categen > parent 1: hair cycle > PMID: 12535193 > definition: A regressing phase of the hair growth cycle during which > cell proliferation ceases, the hair follicle shortens, and an anchored > club hair is produced > synonym: regression

The proposed synonym is a very generic word, so I'm reluctant to include it.

> term: exogen > parent 1: hair cycle > PMID: 12230507 > definition: shedding phase of the hair growth cycle > synonym: shedding

Again, the proposed synonym is very generic.

> term: telogen > parent 1: hair cycle > PMID: 12230507 > definition: Resting phase of hair cycle > synonym: resting phase

Again, the proposed synonym is very generic.

> term: anagen > parent 1: hair cycle > PMID: 12230507 > definition: Growth phase of the hair cycle, lasting about 3 to 6 years > in human scalp hair > synonym: hair growth

The definition should not be specific to humans (can include the duration of anagen in humans, as long as the wording makes it clear that it's an example, and the term can be used for other mammals).

> term: response to thirst/water deprivation > parent 1: response to biotic stimulus > sibling: response to starvation > definition: A change in state or activity of an organism or cell (in > terms of movement, secretion, enzyme production.gene expression etc.) > as a result of deprivation of water.

Jane has a good suggestion (also, we try to avoid terms with slashes because it implies that the tems is a compound).

> term: behavioural response to thirst > parent 1: response to thirst/water deprivation > definition: A change in the behaviour of an organism as a result of > deprivation of water.

OK as is-a child of response to water deprivation

> term: cellular response to thirst > parent 1: response to thirst/water deprivation > definition: A change in the state or activity of a cell (in terms of > enzyme production, gene expression etc.) as a result of deprivation of > water

OK as is-a child of response to water deprivation

> term: biofilm formation > parent 1: development > parent 2: response to external stimulus > definition: Formation of a layered culture of microorganisms growing > on a surface that they have created themselves by secreting > polysaccharides and glycoproteins

Chandra's suggestion sounds good.

> term: cholesterol homeostasis > parent 1: homeostasis > PMID: 1015971 > definition: Any of the processes involved in the maintenance of an > internal equilibrium of cholesterol within an organism or cell.

OK

> term: sperm ejaculation > parent 1: spermatogenesis > definition: The sudden expulsion of semen from the prostate gland > through the penis.

This term seems rather more generic than its definition; I also share Jane's concern about the suggested parentage.

> term: maternal behavior > parent 1: reproductive behavior > parent 2: adult behavior > PMID: 1165557 > definition: Female behaviors associated with the care and rearing of > offspring.

OK

> term: dosage compensation complex assembly (sensu nematoda) > parent 1: dosage compensation complex assembly > PMID: 11102361; 10827451; 10364546 > definition:

OK; needs a definition

> term: dosage compensation complex assembly (sensu Drosophila) > parent 1: dosage compensation complex assembly > PMID: 9155031 > definition:

OK; needs a definition

Midori

Original comment by: mah11

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For the generic synonyms, I think we should just prefix with the word hair e.g. hair regression.

Changed the name of 'response to drought ; GO:0001494' -> 'response to water deprivation' with synonyms 'response to drought' and 'response to thirst'.

Added new terms:

behavioural response to water deprivation ; GO:0042630 cellular response to water deprivation ; GO:0042631

both as children of 'response to water deprivation ; GO:0001494' with the second parents 'behaviour' and 'response to extracellular stimulus' respectively. Added synonyms 'behavioural response to thirst', 'behavioural response to drought' and 'cellular response to drought'.

Original comment by: jl242

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• milestone: --> TermGenie

Original comment by: jl242

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Added new term 'cholesterol homeostasis ; GO:0042632' as child of homeostasis.

Original comment by: jl242

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Original comment by: jl242

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Biofilms are formed by cells adhering to each other and to other surfaces (see http://www.wikipedia.org/wiki/Biofilm) so I think the parentage should be is_a 'cell adhesion ; GO:0007155' - development seems a bit broad + it's defined as '...the progression of an organism over time...' which doesn't fit with biofilms.

Original comment by: jl242

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Proposed parenatge for new terms + defintions:

sex differentiation ; GO:0007548 %menarche ; GO:new

aging ; GO:0007568 %menopause ; GO:new

development of secondary sexual characteristics ; GO:0045136 %thelarche

Definitions:

menarche The beginning of the menstrual cycle; the first menstrual cycle in an individual.

menopause Cessation of menstruation, occuring in e.g. the human female usually around the age of 50.

thelarche The beginning of development of the breasts in the female.

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cell adhesion ; GO:007155 %biofilm formation

biofilm formation The formation of a film of microorganisms usually embedded in extracellular polymers, which adheres to surfaces submerged in, or subjected to, aquatic environments. (ISBN:0471940526)

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%copulation ; GO:0007620 <sperm ejaculation ; GO:new

sperm ejaculation The sudden expulsion of semen from the prostate gland through the penis.

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reproductive behavior ; GO:19098 %maternal behavior ; GO:new

maternal behavior Female behaviors associated with the care and rearing of offspring.

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dosage compensation complex assembly ; GO:new %dosage compensation complex assembly (sensu Nematoda) ; GO:new %dosage compensation complex assembly (sensu Drosophila) ; GO:0016457

Definitions:

dosage compensation complex assembly The processes by which the complex that mediates dosage compensation is assembled on one or more X chromosomes in the monogametic sex.

dosage compensation complex assembly (sensu Nematoda) The processes by which the complex that mediates dosage compensation is assembled on both hermaphrodite X chromosomes, ultimately resulting in a two-fold reduction in transcription from these chromosomes.

Original comment by: jl242

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Hello,

We need to revise our initial request regarding the dosage compensation hierarchy. Please consider the following terms, parents, and definitions instead.

The problem is that the definition for 'dosage compensation complex assembly' is specific for hypertranscription (as in Drosophila). This process also occurs in C. elegans (see PMIDs 11102361, 10364546, and 11446112). I can think of at least two ways to correct this:

Keep the current definition of 'dosage compensation complex assembly', but add (sensu Drosophila) or the like. This could be a child of 'dosage compensation, by hyperactivation of X chromosome'. Then add 'dosage compensation complex assembly (sensu Nemotoda) as a child of 'dosage compensation, by hypoactivation of X chromosome'

A possible definition is "dosage compensation complex assembly (sensu Nemotoda) - The process by means of which the dosage compensation complex is assembled on the X chromosomes, as in the C. elegans hermaphodite"

Use a more general definition of 'dosage compensation complex assembly' (e.g. The process by means of which the dosage compensation complex is assembled [on the X chromosome]). Make this a child of 'dosage compensation'.

I don't know of dosage compensation protein complexes in mammals or other organisms, but if these exist or are discovered, perhaps the 2nd option is best.

Thank you,

Karama

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Karama C. Neal, Ph.D. Editor, Human Databases

Incyte Corporation 100 Cummings Center, Suite 420B Beverly, MA 01915 http://www.incyte.com/

Original comment by: karamacneal

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Sorry - I didn't explain myself very well for those dosage compensation assembly terms. What I decided to do (but stupidly not bother explaining!) was change the current term name 'dosage compensation complex assembly ; GO:0016457' to 'dosage compensation complex assembly (sensu Drosophila) ; GO:0016457', because the term's defintion is Drosophila-specific (GO IDs are connected to the defintion not the term name), and then make a new generic parent 'dosage compensation complex assembly ; GO:new' with the defintion:

The processes by which the complex that mediates dosage compensation is assembled on one or more X chromosomes.

(actually, the defintion I did propose was too specific - removed end bit). I'd then make the new child 'dosage compensation complex assembly (sensu Nemotoda)' (C. elegans works by repressing both X chromosomes in the monogametic sex, Drosophila by hyperactivation of the X in the heterogametic sex) with def:

The processes by which the complex that mediates dosage compensation is assembled on both X chromosomes of the monogametic sex, ultimately resulting in a two-fold reduction in transcription from these chromosomes, as described for C. elegans.

(changed that def a bit too). In mammals, one X chromosome is inactivated in females, but no complex has yet been discovered (see PMID: 12672493 for a nice review) so we don't need any other sensu terms for now. So what we'd have is:

dosage compensation complex assembly ; GO:new ---%dosage compensation complex assembly (sensu Drosophila) ; GO:0016457 ---%dosage compensation complex assembly (sensu Nemotoda) ; GO:new

with extra part_of parents 'dosage compensation, by hyperactivation of X chromosome' (for sensu Drosophila term) and
'dosage compensation, by hypoactivation of X chromosome' (for the sensu Nematoda term).

Does that make sense?

Original comment by: jl242

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Expanded tree for menopause etc. terms from David Hill:

development of secondary female sexual characteristics ; GO:0046543 ---%thelarche ; GO:NEW % post-embryonic morphogenesis ; GO:0009886 ---%menarche ; GO:NEW ---%menopause ; GO:NEW % ageing ; GO:0007568

physiological process ---%menstrual cycle ; GO:NEW synonym:estrous cycle % post- embryonic development ; GO:0009791 ------<ovarian follicle development ; GO:0001541 synonym:follicular phase ---------<follicle stimulating hormone signaling pathway ; GO:NEW % G-protein coupled receptor protein signaling pathway ; GO:0007186 ---------<luteinizing hormone signaling pathway ; GO:NEW ------<ovulation : GO:0001542 ------<luteinization ; GO:0001553 synonym:luteal phase ---------<progesterone secretion ; GO:NEW ---------<uterine wall growth ; GO:NEW ------<menstruation ; GO:NEW ---------<luteolysis ; GO:0001554 ---------<uterine wall breakdown ; GO:NEW ------<menarche ; GO:NEW ------<menopause ; GO:NEW % ageing ; GO:0007568

Original comment by: jl242

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Implemented changes in last comment. New ids:

GO:0042695 JL thelarche GO:0042696 JL menarche GO:0042697 JL menopause GO:0042698 JL menstrual cycle GO:0042699 JL follicle stimulating hormone signaling pathway GO:0042700 JL luteinizing hormone signaling pathway GO:0042701 JL progesterone secretion GO:0042702 JL uterine wall growth GO:0042703 JL menstruation GO:0042704 JL uterine wall breakdown

Original comment by: jl242

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Added remaining new terms - new ids marked with *:

cell adhesion ; GO:007155 %biofilm formation ; GO:00042710*

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%copulation ; GO:0007620 <sperm ejaculation ; GO:0042713*

%insemination ; GO:0007320 <sperm ejaculation ; GO:0042713*

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reproductive behavior ; GO:19098 %maternal behavior ; GO:0042711 %paternal behaviour ; GO:0042712

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dosage compensation complex assembly ; GO:0042714 %dosage compensation complex assembly (sensu Nematoda) ; GO:0042715 %dosage compensation complex assembly (sensu Drosophila) ; GO:0016457

Original comment by: jl242

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• status: open --> closed-accepted

Original comment by: jl242