NTRs

[obophenotype-user]

Dear DO developers,

Program for Resistance, Immunology, Surveillance and Modeling of Malaria in Uganda (PRISM) is the dedicated East Africa International Center of Excellence for Malaria Research. We are planning to use DO to annotate over 300 different diagnosis code used in the PRISM project. 139 terms were found in the DO. 236 terms are not available. Some terms might be subclasses of existing DO terms.

I attached the file with a list of terms PRISM need including candidate DO parent classes (generated using BioPortal annotator). Please let me know anything we can help in making terms available in the DO. If any terms are not in the DO scope, we will appreciate it very much if the DO can give some advices on which ontology the terms should go to.

Besides, I have a couple of questions related to use DO in the PRISM project.

1. Since the requested terms are used to annotate diagnosis, some of them are related to the status of a disease realization process, such as, Malnutrition - moderate, Malnutrition - severe (DO has 'malnutrition' DOID_8452). I am wondering whether DO would like to add moderate malnutrition and severe malnutrition. If so, is it ontological correct to specify a disposition with some kinds of quality like moderate, severe which is clearly associated with a specific stage of a disease realization process.
2. I was told that DO will specify symptoms associated with a disease. For a given disease, symptoms may be different at different disease realization stages. How will DO deal with it?

Thanks,

Jie

Reported by: jzheng24

Original Ticket: diseaseontology/feature-requests/69

[obophenotype-user]

We are very excited that you plan on using DO!

1. DOID:8452 is a deprecated term, even so, we don't differentiate between moderate and severe. You can find 'Malnutrition' in HPO (Human Phenotype Ontology).
2. Yes, we plan on specifying the symptoms of a diseases. Since DO doesn't deal with the process of a disease, the plan is to simply state the symptoms that can develop over the whole disease course.

We will look through your list of terms and get back to you with what can be added to DO and what is outside of our scope and where it can be found. As you can imagine, this is a lengthy process and we ask for you patience.

Thank you,

Elvira

Original comment by: emitraka

[obophenotype-user]

• assigned_to: Elvira Mitraka

Original comment by: lschriml

[obophenotype-user]

Any progress and updates on our requested terms?

Thanks!

Jie

Original comment by: jzheng24

[obophenotype-user]

Hello Jie,

working on it. Will be done soon.

Best, Elvira

Original comment by: emitraka

[obophenotype-user]

Thanks, Elvira.

Jie

On Fri, Feb 13, 2015 at 3:58 PM, Elvira Mitraka emitraka@users.sf.net wrote:

Hello Jie,

working on it. Will be done soon.

Best,

Elvira

• [feature-requests:#69] http://sourceforge.net/p/diseaseontology/feature-requests/69 NTRs *

Status: open Group: Next Release (example) Created: Mon Dec 08, 2014 08:49 PM UTC by jzheng Last Updated: Fri Feb 13, 2015 05:43 PM UTC Owner: Elvira Mitraka

Dear DO developers,

Program for Resistance, Immunology, Surveillance and Modeling of Malaria in Uganda (PRISM) is the dedicated East Africa International Center of Excellence for Malaria Research. We are planning to use DO to annotate over 300 different diagnosis code used in the PRISM project. 139 terms were found in the DO. 236 terms are not available. Some terms might be subclasses of existing DO terms.

I attached the file with a list of terms PRISM need including candidate DO parent classes (generated using BioPortal annotator). Please let me know anything we can help in making terms available in the DO. If any terms are not in the DO scope, we will appreciate it very much if the DO can give some advices on which ontology the terms should go to.

Besides, I have a couple of questions related to use DO in the PRISM project.

1.

Since the requested terms are used to annotate diagnosis, some of them are related to the status of a disease realization process, such as, Malnutrition - moderate, Malnutrition - severe (DO has 'malnutrition' DOID_8452). I am wondering whether DO would like to add moderate malnutrition and severe malnutrition. If so, is it ontological correct to specify a disposition with some kinds of quality like moderate, severe which is clearly associated with a specific stage of a disease realization process. 2.

I was told that DO will specify symptoms associated with a disease. For a given disease, symptoms may be different at different disease realization stages. How will DO deal with it?

Thanks,

Jie

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Original comment by: jzheng24