<blockquote>
  <p>I understand that Phenotype is a set of criteria that you apply on your EHR data to select patients of interest from EHR database.</p>
</blockquote>

<p>No, a phenotype is a way of behavior or other observed characteristic of a person, resulting from a combination on its underlying biology and the environment it's in. Think things like, height, running speed, strength, etc.</p>

<p>In the context in which you're interested, this would be more properly, "the clinical presentation of a disease or disorder".</p>

<ol>
<li>Step one of diagnosing a patient is defining exactly how they present (i.e., exactly what their maladies, aberrant electrolyte levels, genetic mutations, etc. are).</li>
<li>An algorithm that only works on the test population is useless. Google "model overfitting".</li>
<li>The point of an algorithm is to take the EHR data and progress to a diagnosis. This isn't real time, you'd just run a batch of algorithms as test results come in.</li>
<li>You need patients in your test/validation sets to have the required inputs for your algorithm.</li>
</ol>

<p>FYI, I don't know of any regulars on this site that deal with EHR data. If there's a community of such people on the web they must be elsewhere.</p>

CC BY-SA 4.0
2019-12-26T00:13:15.827Z
thanks for the response. Upvoted. Can you please help me understand this `The point of an algorithm is to take the EHR data and progress to a diagnosis. `?
The Great
CC BY-SA 4.0
2019-12-26T08:35:32.663Z
What is unclear about that?
Devon Ryan
CC BY-SA 4.0
2020-01-07T13:39:53.707Z
I would suggest looking at the documentation for [phenotips software](https://phenotips.org/) and playing with the online demo.  This would show you some examples of phenotype data and how a database can be implemented to store it.  You may also want to familiarise yourself with HPO terms ([Human Phenotype Ontology](https://hpo.jax.org/app/)), a standardised ontology for recording human phenotypes (physical symptoms and characteristics which may be related to the underlying genotype).
Graeme
CC BY-SA 4.0
2019-12-25T20:29:03.333Z
2019-12-25T20:29:03.333Z
Devon Ryan
<p>May I know what's the use of <code>Electronic Phenotyping using EHR data</code>?</p>

<p>I did refer this <a href="https://currentprotocols.onlinelibrary.wiley.com/doi/full/10.1002/cphg.80" rel="nofollow noreferrer">link</a> but have few questions</p>

<p>I understand that <code>Phenotype</code> is a set of criteria that you apply on your EHR data to select patients of interest from EHR database.</p>

<p>However what I am trying to understand is the difference between ordinary SQL query and electronic Phenotype</p>

<p>If both are same, </p>

<p>1) what I would like to know is the use of <code>electronic phenotyping</code>? How it is used? </p>

<p>2) Why do we have <code>pheKB</code> repository and other repositories? What's the use in validating them in multiple sites?</p>

<p>3) Is it like identifying patients real time? I am not able to get the usefulness of this. I understand that we select patients of our interest (cohort), but i can just write an ordinary SQL and send it to my EHR database to identify patients. but what's special about Electronic Phenotype?</p>

<p>4) I also see that they use multiple conditions (Lab tests, Medications, Diagnosis etc) to identify patients. What am I missing here?</p>

<p>Can someone help me by giving an simple example? I am new to healthcare and trying to learn. Would really be helpful</p>

<phylogenetics><database><genome><r><machine-learning>
Use of Electronic Phenotype in EHR
# Use of Electronic Phenotype in EHR

(Asked by: username_0 on 2019-12-25)

May I know what's the use of `Electronic Phenotyping using EHR data`?

I did refer this [link](https://currentprotocols.onlinelibrary.wiley.com/doi/full/10.1002/cphg.80) but have few questions

I understand that `Phenotype` is a set of criteria that you apply on your EHR data to select patients of interest from EHR database.

However what I am trying to understand is the difference between ordinary SQL query and electronic Phenotype

If both are same,

1) what I would like to know is the use of `electronic phenotyping`? How it is used?

2) Why do we have `pheKB` repository and other repositories? What's the use in validating them in multiple sites?

3) Is it like identifying patients real time? I am not able to get the usefulness of this. I understand that we select patients of our interest (cohort), but i can just write an ordinary SQL and send it to my EHR database to identify patients. but what's special about Electronic Phenotype?

4) I also see that they use multiple conditions (Lab tests, Medications, Diagnosis etc) to identify patients. What am I missing here?

Can someone help me by giving an simple example? I am new to healthcare and trying to learn. Would really be helpful

**Tags:** phylogenetics, database, genome, r, machine-learning

---

## 1 answers

### Answer by username_1 on 2019-12-25. Score: 1 | Accepted answer

> I understand that Phenotype is a set of criteria that you apply on your EHR data to select patients of interest from EHR database.

No, a phenotype is a way of behavior or other observed characteristic of a person, resulting from a combination on its underlying biology and the environment it's in. Think things like, height, running speed, strength, etc.

In the context in which you're interested, this would be more properly, "the clinical presentation of a disease or disorder".

1. Step one of diagnosing a patient is defining exactly how they present (i.e., exactly what their maladies, aberrant electrolyte levels, genetic mutations, etc. are).
2. An algorithm that only works on the test population is useless. Google "model overfitting".
3. The point of an algorithm is to take the EHR data and progress to a diagnosis. This isn't real time, you'd just run a batch of algorithms as test results come in.
4. You need patients in your test/validation sets to have the required inputs for your algorithm.

FYI, I don't know of any regulars on this site that deal with EHR data. If there's a community of such people on the web they must be elsewhere.

> **Comments:**
> **username_0**: thanks for the response. Upvoted. Can you please help me understand this `The point of an algorithm is to take the EHR data and progress to a diagnosis. `?  
> **username_1**: What is unclear about that?  
> **username_2**: I would suggest looking at the documentation for [phenotips software](https://phenotips.org/) and playing with the online demo.  This would show you some examples of phenotype data and how a database can be implemented to store it.  You may also want to familiarise yourself with HPO terms ([Human Phenotype Ontology](https://hpo.jax.org/app/)), a standardised ontology for recording human phenotypes (physical symptoms and characteristics which may be related to the underlying genotype).  

---

