PubMed + My NCBI
Saved searches act as a continuous surveillance engine. Each query watches a specific domain and sends new results automatically.
How-to • PubMed • My NCBI • Outlook • Zotero
Build a literature surveillance system you can actually run every week.
This guide shows exactly how to create a repeatable evidence pipeline: build saved PubMed searches, turn them into My NCBI alerts, route the alerts automatically in Outlook, curate high-value studies into My NCBI collections, and maintain a shared Zotero library.
Purpose
Three connected layers create one reproducible system.
Email + Outlook rules
Each alert is routed to a matching folder using the saved-search name in the email subject line, keeping streams separate and reviewable.
Collections + Zotero
Saved searches capture incoming evidence. Collections and Zotero organize the studies that actually matter into a reusable evidence base.
System flow: PubMed → My NCBI alert → email → Outlook rule → review folder → human screening → My NCBI collection → shared Zotero library → annotated bibliography, executive synthesis, and toolkit updates.
Step 1
Create the PubMed search.
Start with one broad master query that captures the core topic. The example below is the APE master search. Other teams can reuse the structure by replacing the topic terms with language relevant to their own question.
Sample master query
(
"Patient Participation"[Mesh]
OR "Patient-Centered Care"[Mesh]
OR "Community Participation"[Mesh]
OR PFAC[tiab]
OR PFACs[tiab]
OR "patient and family advisory council"[tiab]
OR "patient and family advisory councils"[tiab]
OR "patient engagement"[tiab]
OR "patient voice"[tiab]
OR "patient partnership"[tiab]
OR "patient partnerships"[tiab]
OR codesign[tiab]
OR "co-design"[tiab]
)
AND
(
"Hospitals"[Mesh]
OR "Inpatients"[Mesh]
OR hospital*[tiab]
OR inpatient*[tiab]
OR "acute care"[tiab]
)
AND
(
"Patient Safety"[Mesh]
OR "Quality Improvement"[Mesh]
OR "patient experience"[tiab]
OR "inpatient experience"[tiab]
OR "patient reported experience"[tiab]
OR "patient reported experiences"[tiab]
OR PREM[tiab]
OR PREMs[tiab]
OR "patient safety"[tiab]
OR "safety culture"[tiab]
OR "access to care"[tiab]
)Run the query in PubMed.
Check that the results are broadly on-topic. If the search is too narrow, remove unnecessary restrictions. If it is too broad, refine the topic terms before saving it.
Keep capture broad.
The saved search is the surveillance layer. Human screening and collections decide what is actually retained, so the capture step should not be over-filtered.
Step 2
Save the searches in My NCBI and turn on alerts.
Sign in to My NCBI.
Run the PubMed search while signed in.
Save the search.
Use the saved-search function in PubMed/My NCBI and give the search a clear, stable name.
Enable email alerts.
Choose email delivery, use Abstract format, and request approximately 25 to 100 items so enough context is available for screening.
Set the cadence.
High-volume master and experience streams are reviewed weekly. More targeted streams are reviewed monthly.
| Saved search example | Purpose | Cadence |
|---|---|---|
| APE_MASTER_PFAC_Inpatient_Experience_Safety | Broad master surveillance stream | Weekly |
| APE_PFAC_Core | PFAC-specific evidence | Monthly |
| APE_Experience_Access | Patient experience and access | Weekly |
| APE_PSSM_Structural | PSSM and structural policy evidence | Monthly |
| APE_Implementation_Frameworks | Implementation and toolkit evidence | Monthly |
| APE_Learning_System | Learning-system and improvement evidence | Monthly |
| APE_High_Evidence | Systematic reviews and higher-level evidence | Monthly |
Step 3
Create the Outlook folders before creating the rules.
Create one folder for each evidence stream so alerts never arrive as one mixed inbox.
APE_ALERTS_MASTER
Master PFAC, inpatient experience, and safety stream.
APE_ALERTS_PFAC
PFAC-specific stream.
APE_ALERTS_EXP
Experience and access stream.
APE_ALERTS_PSSM
PSSM structural stream.
APE_ALERTS_IMPL
Implementation-framework stream.
APE_ALERTS_LHS
Learning-system stream.
APE_ALERTS_SR
Systematic reviews and higher-level evidence for periodic cross-checking.
Step 4
Create one Outlook rule per saved search.
The logic is intentionally simple so it is reproducible.
Subject contains saved-search name.
Use the exact My NCBI saved-search name as the subject-match condition.
Move to matching folder.
Route the alert into the folder assigned to that search stream.
Stop processing more rules.
This prevents one message from being moved again by a later rule.
Example rule
Rule name:
RULE_APE_MASTER_PFAC_Inpatient_Experience_Safety
Condition:
Subject contains APE_MASTER_PFAC_Inpatient_Experience_Safety
Action:
Move to APE_ALERTS_MASTER
Option:
Stop processing more rulesResult: PubMed → My NCBI alert → email → Outlook rule → matching review folder.
Step 5
Create My NCBI collections for what you decide to keep.
Saved searches capture incoming evidence. Collections are different: they are the curated knowledge buckets containing studies that passed human review.
Open PubMed.
Collections are created from PubMed, not from the My NCBI dashboard alone.
Run a search and select an article.
Choose at least one record you want to retain.
Select Send to → Collections.
Create a new collection or add the article to an existing one.
APE_HIGH_VALUE
Systematic reviews, umbrella reviews, and especially useful implementation evidence.
APE_PFAC
PFAC-specific research.
APE_EXPERIENCE_ACCESS
Patient experience, communication, and access evidence.
APE_PSSM_POLICY
Policy, governance, and structural-measure material.
APE_IMPLEMENTATION
Toolkits, interventions, and implementation evidence.
Step 6
Use a simple curation decision engine.
Keep studies that fit the practice question.
Hospital or inpatient studies; interventions and toolkits; system-level research; PFAC or engagement studies; and work linking experience, safety, access, or implementation.
Remove clearly off-scope material.
Out-of-hospital settings, irrelevant populations, and material that does not inform the defined practice question or evidence map.
Do not use filters as the methodology.
Humans-only, systematic-review/meta-analysis, and free-full-text filters are temporary tools for curation, validation, or reading. They are not part of the core search methodology.
| Study type | Route to |
|---|---|
| Toolkit / intervention | APE_IMPLEMENTATION + APE_HIGH_VALUE |
| Systematic / umbrella review | APE_HIGH_VALUE |
| PFAC-specific | APE_PFAC |
| Experience / communication | APE_EXPERIENCE_ACCESS |
| Policy / governance | APE_PSSM_POLICY |
Step 7
Run the system on a small, predictable cadence.
Weekly, about 10–15 minutes: open Outlook, review APE_ALERTS_MASTER and the high-volume experience stream, scan titles and abstracts, identify high-signal records, open them in PubMed, and route accepted studies into the appropriate collections.
Monthly validation: review APE_ALERTS_SR and the other targeted streams, then confirm that systematic reviews or higher-level evidence still align with the working evidence base.
Is this study relevant to the defined practice question?
Does it change, strengthen, or challenge the current evidence base?
Which collection should receive it?
Should it update the bibliography, executive summary, matrix, or toolkit?
Step 8
Use Zotero as the shared working library.
My NCBI collections organize evidence inside PubMed. Zotero adds collaboration, tagging, annotations, citation management, and a shared source trail.
Send accepted articles to Zotero.
Add records directly from PubMed using the Zotero browser connector or citation export.
Use topic tags.
Tag sources with terms such as PFAC, experience, PSSM, implementation, safety, access, or other project-specific domains.
Create a group library.
The APE used the shared group library “Bolton TDI APE 27” with the preceptor. Another researcher can reproduce the same approach with a project-specific shared group library.
Annotate and update.
Use the shared library as the working evidence base for annotations, bibliography development, cross-topic filtering, and review with collaborators.
What this produces
A surveillance system is useful only if it feeds the work.
Curated annotated bibliography
Accepted sources remain organized and traceable for annotation and synthesis.
Executive evidence base
New evidence can be incorporated into the executive summary when it materially changes the findings.
PSSM / PFAC roadmap inputs
Implementation, governance, experience, and policy evidence can be routed directly into leadership tools and roadmap decisions.
Reproducible research pipeline
The same skeleton can be reused for another APE, ILE, public-health question, or health-system improvement topic by changing queries, folders, collections, and tags.
Adapt it
Keep the architecture. Change the topic.
Replace the topic terms in the PubMed query.
Keep the Boolean structure and database-specific field logic, but use terms relevant to the new research question.
Rename the saved searches and Outlook folders.
Use a consistent naming convention so each alert can be matched reliably to one folder.
Create collections that reflect the new evidence domains.
Collections should represent the decisions the researcher needs to make, not just broad subject labels.
Keep human curation in the loop.
Automation captures and routes evidence; the researcher still decides what is relevant, how strong it is, and where it belongs.