Closed 8hk closed 4 years ago
Quick Start Sample Code E-Utilities: 1 2
Example
Search abstracts with the "cancer" keyword in PubMed and retrieve the IDs of 60 of them: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=cancer&retmax=60
Fetch 2 of these abstracts with the given IDs in the text format: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=33147463,33147101&retmode=text&rettype=abstract
sample postman collection for simple Entrez api call for pubmed
{
"info": {
"_postman_id": "c05d2c34-b3e6-409a-b9f4-eb5c3b9e29db",
"name": "entrez",
"schema": "https://schema.getpostman.com/json/collection/v2.1.0/collection.json"
},
"item": [
{
"name": "simplerequest",
"event": [
{
"listen": "test",
"script": {
"id": "c80db599-76fd-4814-a549-73725ba35d5c",
"exec": [
"pm.environment.set(\"api_key_var\", \"\");"
],
"type": "text/javascript"
}
}
],
"request": {
"method": "GET",
"header": [],
"url": {
"raw": "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&id=123456&api_key={{api_key_var}}",
"protocol": "https",
"host": [
"eutils",
"ncbi",
"nlm",
"nih",
"gov"
],
"path": [
"entrez",
"eutils",
"esummary.fcgi"
],
"query": [
{
"key": "db",
"value": "pubmed"
},
{
"key": "id",
"value": "123456"
},
{
"key": "api_key",
"value": "{{api_key_var}}"
}
]
}
},
"response": []
}
],
"protocolProfileBehavior": {}
}
we can use the following features of Entrez
We mostly will use 1,3,4,5,7. They can be found in here briefly. And Esma shared the Quick Start link at her comment below.
Quick Start Sample Code E-Utilities: 1 2
Example
Search abstracts with the "cancer" keyword in PubMed and retrieve the IDs of 60 of them: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=cancer&retmax=60
Fetch 2 of these abstracts with the given IDs in the text format: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=33147463,33147101&retmode=text&rettype=abstract
In addition to the ones above mentioned EFetch will also be useful in retrieving abstracts.
Do we want to use the Entrez History server / Web Environment functionality and how can we make use of it.... Something to think about.
Basic Searching
esearch.fcgi?db=
Example: Get the PubMed IDs (PMIDs) for articles about breast cancer published in Science in 2008 https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi db=pubmed&term=science[journal]+AND+breast+cancer+AND+2008[pdat]
Summary of the comments is added to the Entrez wiki page
The Entrez has very powerful API for query the medical publications. Its API should be tested in the basic level and the notes should be taken from these tests. The Entrez will be implemented into project. That's why it has very significant role on this project. The test results will be discussed during 3th Group Meeting.