Increased tumor incidence terms

[obophenotype-user]

1. What's the difference between our terms hepatoma and increased susceptibility to hepatoma? These terms seem to reflect the same thing (i.e. an increased incidence of hepatoma).

2. We have many specific tumor types that are not listed as children of more general tumor types: -adrenal gland adenoma [MP:0009044] is not a child of adrenal tumor -skin hamartoma [MP:0009469] is not a child of skin tumor -hepatic hemangioma [MP:0002047] is not a child of liver tumor while retinal hemangioma is a child of retinal tumor -medulloblastoma [MP:0006283] is not a child of brain tumor

3. We have specific organ tumors without parents for the general tumor type: -no renal tumor even though we have several types or renal tumors

4. Some tumor types we do not list: -mesothelioma (3 associated alleles I will be adding 10 more using various combinations of 3 alleles not already associated with this tumor type) -schwannoma (2 plus 5 more genotypes entered earlier today and more to come) -meningioma (4 plus) -osteomas (10 plus) -lymphosarcoma (4 plus) -neurofibroma (18 plus) -cholangiocarcinoma (2 plus) -odontosarcoma (just added alleles with this term in the genotype) -odontoma (just added alleles with this term in the genotype)

This terms might not all be needed but are suggestions. Michelle

Reported by: michknow

Original Ticket: obo/mammalian-phenotype-requests/363

[obophenotype-user]

The whole tumor section is rather badly in need of revision. There is a previous ticket ( ID: 2597179 ) that suggests this in a more general way, but had not yet been addressed. It's time to make this a priority. I'll start with adding the terms that you describe above; I'll look for more types to add during the updates and then reconsider the organization.

Original comment by: cindyJax

[obophenotype-user]

Struggling with term names for new primary subdivisions of MP:0002020 [increased tumor incidence]. We want something like:

increased organ/body region tumor incidence increased tumor type incidence

More granular terms would then fall under one or both subdivisions.

A survey of existing terms in the tumor incidence subdivision has suggested quite a few additional terms in addition to the ones listed in the primary request above are needed. After this reorganization is done, I'll start adding the new terms. I'd like to consult with Debbie Krupke first.

Original comment by: cindyJax

[obophenotype-user]

Merging Tracker ID: 2597179 into this record:

A. Terms under "increased tumor incidence" should be more clearly organized by 1) tumor type (sarcoma, carcinoma, etc) and 2) by location (liver, mammary gland, prostate, etc).

B. The >350 annotations to this term should be studied for possible new terms to be added

Original comment by: cindyJax

[obophenotype-user]

tumor types/organs affected in MTB

Original comment by: cindyJax

[obophenotype-user]

I've attached a file from MTB that lists tumor types and organ systems affected. Also included is the number of records that are attached to various combinations of these. This will help with general organization and may suggest additional terms for consideration other than those listed above and from the general survey.

Original comment by: cindyJax

[obophenotype-user]

Another point on this, currently all the tumor type terms are just the name of the tumor type. I think this terms should be increased incidence of (tumor type) in keeping with the parent term.

Original comment by: sbello

[obophenotype-user]

just another vote for cholangiocarcinoma J:156531

Original comment by: jbubier

[obophenotype-user]

This is indeed the plan; see comments below.

"Date: 2010-03-02 13:51:11 EST Sender: suebello Hide

Another point on this, currently all the tumor type terms are just the name of the tumor type. I think this terms should be increased incidence of (tumor type) in keeping with the parent term."

Original comment by: cindyJax

[cindyJax]

Section was previously reorganized.