Cryptococcus NTR: colonization of host and host tissue phenotypes

[dianeoinglis]

Hello,

The ability of fungal cells to survive within a host can be measured but is the exact tissues may not be determined (or the fungal cells disseminate to many tissues). Cryptococcus disseminates to the CNS and brain and causes meningitis. In this case, the route of infection may be intranasal (pulmonary) but the tissue examined for fungal cells is typically the brain or CNS fluid. In rabbits, the route of infection is a direct sub-lethal dose inoculated directly in the CNS. I would like a term for the tissue specific assays used for Cryptococcus.

Is there a reason that OMP:0007252 was formatted as "host colonization phenotype" as opposed to "colonization of a host phenotype?"

Cryptococcus neoformans and C. grubii are opportunistic fungi and require an immunocompromised host for successful infections but C. gattii is considered a primary pathogen and infects immunocompetent hosts.

Compare "immunompromised host colonization phenotype "versus "colonization of immunocompromised host phenotype"

When the immune status of the host is specified, the format "colonization of immunocompromised host phenotype" seems preferable than "immunocompromised host colonization phenotype" but the order verb-noun or noun-verb is more of a minor detail and not a major issue.

These are the new terms I am requesting: Altered, decreased, increased and abolished:

• colonization of host tissue phenotype
• colonization of immunocompromised host tissue phenotype
• colonization of immunocompromised host tissue phenotype
• colonization of mouse tissue phenotype
• colonization of immunocompromised mouse tissue phenotype
• colonization of rabbit tissue phenotype
• colonization of immunocompromised rabbit tissue phenotype

Thank you! Diane

[dsiegele]

Hi Diane,

Thank you! "colonization of a host phenotype" is much better than "host colonization phenotype."

[dsiegele]

Rename existing terms: OMP:0007252 host colonization phenotype change to 'colonization of a host phenotype' OMP:0007254 absence of host colonization change to 'absence of colonization of a host' OMP:0007253 presence of host colonization change to 'presence of colonization of a host' OMP:0007255 altered host colonization change to 'altered colonization of a host' OMP:0007256 Increased host colonization change to 'increased colonization of a host' OMP:0007257 decreased host colonization change to 'decreased colonization of a host' OMP:0007258 abolished host colonization change to 'abolished colonization of a host'

You will need to tweak the definitions to match the new term names.

New terms: Jesus, Here is the pattern for the new terms that Diane requested. Debby

colonization of host tissue phenotype_ (is_a colonization of a host phenotype) .....presence of .....absence of .....altered ..........increased ..........decreased ...............abolished

colonization of immunocompromised host tissue phenotype_ (is_a colonization of host phenotype) .....presence of .....absence of .....altered ..........increased ..........decreased ...............abolished

colonization of immunocompromised host tissue phenotype?? this term name was duplicated. We need to ask Diane if it was supposed to be something else, or if the name just got added twice.

colonization of mouse tissue phenotype_ (is_a colonization of host tissue phenotype) .....presence of .....absence of .....altered ..........increased ..........decreased ...............abolished

colonization of immunocompromised mouse tissue phenotype (is_a colonization of host tissue phenotype) .....presence of .....absence of .....altered ..........increased ..........decreased ...............abolished

colonization of rabbit tissue phenotype (is_a colonization of host tissue phenotype) .....presence of .....absence of .....altered ..........increased ..........decreased ...............abolished

colonization of immunocompromised rabbit tissue phenotype (is_a colonization of host tissue phenotype) .....presence of .....absence of .....altered ..........increased ..........decreased ...............abolished

[dianeoinglis]

Wonderful!!!

[Jguzman210]

Here are the new terms with matching OMP numbers

OMP:0007258 abolished colonization of a host OMP:0005287 abolished colonization of host tissue OMP:0005294 abolished colonization of immunocompromised host tissue OMP:0005301 abolished colonization of mouse tissue OMP:0005315 abolished colonization of rabbit tissue OMP:0005308 abolished colonization of tissue in an immunocompromised mouse OMP:0005322 abolished colonization of tissue in an immunocompromised rabbit OMP:0007254 absence of colonization of a host OMP:0005283 absence of colonization of host tissue OMP:0005290 absence of colonization of immunocompromised host tissue OMP:0005297 absence of colonization of mouse tissue OMP:0005311 absence of colonization of rabbit tissue OMP:0005304 absence of colonization of tissue in an immunocompromised mouse OMP:0005318 absence of colonization of tissue in an immunocompromised rabbit OMP:0007255 altered colonization of a host OMP:0005284 altered colonization of host tissue OMP:0005298 altered colonization of mouse tissue OMP:0005312 altered colonization of rabbit tissue OMP:0005291 altered colonization of tissue in an immunocompromised host OMP:0005305 altered colonization of tissue in an immunocompromised mouse OMP:0005319 altered colonization of tissue in an immunocompromised rabbit OMP:0007252 colonization of a host phenotype OMP:0005281 colonization of host tissue phenotype OMP:0005295 colonization of mouse tissue OMP:0005309 colonization of rabbit tissue phenotype OMP:0005288 colonization of tissue in an immunocompromised host phenotype OMP:0005302 colonization of tissue in an immunocompromised mouse phenotype OMP:0005316 colonization of tissue in an immunocompromised rabbit phenotype OMP:0007257 decreased colonization of a host OMP:0005286 decreased colonization of host tissue OMP:0005293 decreased colonization of immunocompromised host tissue OMP:0005300 decreased colonization of mouse tissue OMP:0005314 decreased colonization of rabbit tissue OMP:0005307 decreased colonization of tissue in an immunocompromised mouse OMP:0005321 decreased colonization of tissue in an immunocompromised rabbit OMP:0007256 increased colonization of a host OMP:0005285 increased colonization of host tissue OMP:0005299 increased colonization of mouse tissue OMP:0005313 increased colonization of rabbit tissue OMP:0005292 increased colonization of tissue in an immunocompromised host OMP:0005306 increased colonization of tissue in an immunocompromised mouse OMP:0005320 increased colonization of tissue in an immunocompromised rabbit OMP:0007253 presence of colonization of a host OMP:0005282 presence of colonization of host tissue OMP:0005296 presence of colonization of mouse tissue OMP:0005310 presence of colonization of rabbit tissue OMP:0005289 presence of colonization of tissue in an immunocompromised host OMP:0005303 presence of colonization of tissue in an immunocompromised mouse OMP:0005317 presence of colonization of tissue in an immunocompromised rabbit

-Thank you for your patience :+1:

[dianeoinglis]

Thank you so much! These are awesome. For just a bit more awesomeness, there are two more host-types to create terms for.. Non-vertebrates (or invertebrates and amoebae) have become popular model hosts for characterizing bacterial and fungal pathogens. The terms for "invertebrate host" will list the exact host in the annotation extension as will the "amoeba host." One question about the extensions. I want the vocabulary of the extensions to be controlled and am wondering if this is something I create outside of the OMP or is there a way to list the allowable terms for the extensions?

presence of lethality in invertebrate host absence of lethality in invertebrate host altered lethality in invertebrate host increased lethality in invertebrate host decreased lethality in invertebrate host abolished lethality in invertebrate host

Extensions for invertebrate hosts: B. mori (silkworm) C. elegans (nematode) D. melanogaster (fruit fly) G. gallonella (wax moth)

presence of lethality in amoeba host absencee of lethality in amoeba host altered lethality in amoeba host increased lethality in amoeba host decreased lethality in amoeba host abolished lethality in amoeba host

Extensions for amoeba hosts: C. castellani (amoeba) D. discoidium (slime-mold)

Thanks!