Las E-Utilities componen una API pública del NCBI que nos permite hacer diversas operaciones como: obtener PubMed ids bajo términos de búsqueda, fetchear la metadata más importante de un PubMed id específico, obtener data relevante sobre algún artículo específico, etc.
En cada llamada a la API, el NCBI incentiva el uso de los parámetros tool e email, donde en el primero se debe especificar el nombre (sin whitespaces) de la aplicación que está
realizando la llamada, mientras que en el segundo se debe especificar el email del usuario realizando la llamada.
Ejemplo
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&id=32945846&retmode=json&tool=i2-covid-site&email=sebastian@hicapps.cl
La utilidad ESearch nos permite obtener los PubMed ids bajo términos de búsqueda.
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi
db
La base de datos donde se buscará el término. Por ejemplo: pubmed, protein, nuccore (por defecto viene pubmed).
Ver todas las bases de datos.
term
El término por el cuál se buscará. Por ejemplo covid, washington+university, school+of+medicine.
Importante: utilizar + en lugar de whitespaces.
retmax
El número de PubMed ids que deseas conseguir.
retmode
El formato en que vendrá la response de la API. Por ejemplo: json o xml.
Si deseo buscar las PubMed ids del término school of medicine, obtenerla en formato JSON y conseguir sólo 10 resultados, la llamada se vería de esta manera:
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&retmode=json&retmax=10&term=school+of+medicine
{
"header": {
"type": "esearch",
"version": "0.3"
},
"esearchresult": {
"count": "2392535",
"retmax": "10",
"retstart": "0",
// las ids que estábamos buscando
"idlist": [
"33036065",
"33036063",
"33036062",
"33036061",
"33036049",
"33036036",
"33036029",
"33036025",
"33036005",
"33035998"
],
...
...
}
}
La utilidad ESummary nos permite obtener la metadata de los artículos a través de los PubMed ids obtenidos previamente con la utilidad ESearch.
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi
id
Lista de PubMed ids por los que se desea obtener la metadata. Si se desea buscar más de un id, se pueden separar por ,.
Si deseo obtener la metadata de las 10 PubMed ids que obtuve anteriormente bajo el término school of medicine, la llamada se vería de la siguiente manera:
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=33036065,33036063,33036062,33036061,33036049,33036036,33036029,33036025,33036005,33035998
{
"header": {
"type": "esummary",
"version": "0.3"
},
"result": {
"33035998": {
"uid": "33035998",
"pubdate": "2020 Oct 9",
"epubdate": "2020 Oct 9",
"source": "J Neurosurg",
"authors": [...],
"lastauthor": "Ramirez-Zamora A",
"title": "Long-term clinical outcomes of bilateral GPi deep brain stimulation in advanced Parkinson's disease: 5 years and beyond.",
"sorttitle": "long term clinical outcomes of bilateral gpi deep brain stimulation in advanced parkinson s disease 5 years and beyond",
"volume": "",
"issue": "",
"pages": "1-10",
"lang": [...],
"nlmuniqueid": "0253357",
"issn": "0022-3085",
"essn": "1933-0693",
"pubtype": [...],
"recordstatus": "PubMed - as supplied by publisher",
"pubstatus": "10",
"articleids": [...],
"history": [...],
"references": [],
"attributes": [...],
"pmcrefcount": "",
"fulljournalname": "Journal of neurosurgery",
"elocationid": "doi: 10.3171/2020.6.JNS20617",
"doctype": "citation",
"srccontriblist": [],
"booktitle": "",
"medium": "",
"edition": "",
"publisherlocation": "",
"publishername": "",
"srcdate": "",
"reportnumber": "",
"availablefromurl": "",
"locationlabel": "",
"doccontriblist": [],
"docdate": "",
"bookname": "",
"chapter": "",
"sortpubdate": "2020/10/09 00:00",
"sortfirstauthor": "Tsuboi T",
"vernaculartitle": ""
},
"33036005": { ... },
"33036025": { ... },
"33036029": { ... },
"33036036": { ... },
"33036049": { ... },
"33036061": { ... },
"33036062": { ... },
"33036063": { ... },
"33036065": { ... },
"uids": [...]
}
}
La utilidad EFetch nos permite obtener información más relevante de uno o más PubMed ids en específico (obtenidos previamente con ESearch), como por ejemplo: Abstract, Publisher, etc.
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi
id
Al igual que en la utilidad ESummary, podemos entregar una lista de PubMed ids para obtener sus datos relevantes. Recordar separar con una , cada PubMed id, en caso de que se busque más de uno.
retmode
El formato en que vendrá la response de la API. Por ejemplo: text o xml.
rettype
Es el tipo de respuesta. Pueden ser medline, abstract o uilist.
Si deseo buscar la data relevante del primer PubMed id que nos retornó la busqueda de school of medicine, la llamada se vería de esta manera:
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&rettype=medline&id=33036065
Nota:
Recomiendo el uso de rettype=medline para este caso. Entrega la data de una manera más ordenada y fácil para encontrar el campo que se necesite.
PMID- 33036065
OWN - NLM
STAT- Publisher
LR - 20201009
IS - 1097-0142 (Electronic)
IS - 0008-543X (Linking)
DP - 2020 Oct 9
TI - Outcomes of Black men with prostate cancer treated with radiation therapy in the
Veterans Health Administration.
LID - 10.1002/cncr.33224 [doi]
AB - BACKGROUND: Population-based studies demonstrate that Black men in the United
States have an increased risk of death from prostate cancer. Determinants of
racial disparities are multifactorial, including socioeconomic and biologic
factors. METHODS: The authors conducted a pooled analysis of patients derived
from 152 centers within the Veterans Health Administration. The cohort included
men who had nonmetastatic prostate diagnosed between 2001 and 2015 and received
definitive radiation therapy. The primary endpoint was prostate cancer-specific
mortality (PCSM). Secondary endpoints included all-cause mortality (ACM) and the
time from a prostate-specific antigen level >/=4 ng/mL to biopsy and radiation
therapy. A Cox regression model was performed to adjust for differences between
clinical parameters. RESULTS: Among the 31,131 patients included in the cohort,
9584 (30.8%) were Black. The 10-year cumulative incidence of death from prostate
cancer was lower in Black men compared with White men (4.0% vs 4.8%; P = .004).
In a competing risk model, Black race was associated with a decreased risk of
PCSM (subdistribution hazard ratio, 0.79; 95% CI, 0.69-0.92; P = .002).
Similarly, the 10-year cumulative incidence of death from any cause was lower in
Black men (27.6% vs 31.8%; P < .001). In multivariable analysis, Black men had a
10% decreased risk of ACM (hazard ratio, 0.90; 95% CI, 0.85-0.95; P < .001).
CONCLUSIONS: The current results indicate relatively lower PCSM and ACM among
Black men who were included in a large Veterans Health Administration cohort and
received radiation therapy as primary treatment for nonmetastatic prostate
cancer. There is an ongoing need to continue to understand and mitigate the
factors associated with disparities in health care outcomes.
CI - (c) 2020 American Cancer Society.
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PubMed APIs
Introduction to the E-Utilities
The E-utilities In-Depth: Parameters, Syntax and More