The core of this process is: first, use multiple queries to perform a reproducible initial screening in PubMed/NCBI E-utilities, then use PMID for deduplication and abstract evidence grading; only a small number of key documents enter the PMC/BioC full-text review; in-text citations must be clickable; complete bibliographic information must be listed at the end of the article; IF can only be conservatively checked through publicly accessible sources, and cannot be assumed to have JCR or local databases, cannot be guessed, and low-confidence matches cannot be treated as definitive results.

1. Preprocessing after a user initiates a search

1.1 First, analyze the user's question.

After receiving a user's question, the natural language question is first broken down into structured elements.

Must be identified:

• Research subjects: genes, proteins, drugs, channels, cell types, tissues, diseases, and models.

• Biological systems: humans, mice, rats, zebrafish, organoids, retina, brain regions, cell lines, etc.

• Relationship types: expression, regulation, function, mechanism, phenotype, death, survival, treatment, toxicity, development, degeneration, etc.

• Evidence requirements: Whether direct evidence, mechanistic evidence, full-text evidence, charts, dosage parameters, and experimental methods are required.

• Time range: unlimited time, the last 5 years, the last 1 year, the latest developments, and classic literature.

• Output types: short answer, representative literature, review summary, experimental design suggestions, evidence table, mechanism diagram.

Example:

User issue:

"Please help me find literature related to retinal organoid death."

Structured decomposition (example):

• Core models: retinal organoid, retina organoid, hPSC-derived retinal organoid, optic cup organoid.

• Phenotype: cell death, apoptosis, degeneration, survival loss, stress, necrosis.

• Related cells: photoreceptor, cone, rod, retinal ganglion cell, Müller glia.

• Potential mechanisms: oxidative stress, ER stress, mitochondrial dysfunction, hypoxia, inflammation, ferroptosis, necroptosis.

• Evidence objectives: Prioritize original studies that directly observe cell death/apoptosis/degeneration in human or animal retinal organoids; then look for literature on indirect mechanisms.

1.2 Keyword Segmentation Principles (Example)

Don't just write one search query. Prepare at least three categories of terms for each concept.

Category 1: Precise words.

• retinal organoid

• retina organoid

• human retinal organoid

• hPSC-derived retinal organoid

• iPSC-derived retinal organoid

The second category: synonyms and hypernyms.

• optic cup organoid

• 3D retinal culture

• stem cell-derived retina

• retinal differentiation

• retinal tissue model

The third category: mechanism and phenotypic terms.

• apoptosis

• cell death

• degeneration

• survival

• stress

• oxidative stress

• ER stress

• mitochondrial dysfunction

• hypoxia

• necroptosis

• ferroptosis

If the user specifies the cell type, add:

• photoreceptor

• cone

• rod

• retinal ganglion cell

• Müller glia

• bipolar cell

• amacrine cell

If the user specifies the species or origin, add:

• human

• mouse

• rat

• zebrafish

• hESC

• iPSC

• pluripotent stem cell

1.3 Generating hierarchical search queries

Generate at least 3–6 queries. Each query corresponds to a search objective.

First layer: Direct evidence retrieval.

Used to find literature that directly matches the target model and target phenotype.

```text

("retinal organoid" OR "retina organoid" OR "human retinal organoid") AND (apoptosis OR "cell death" OR degeneration)

```

Second layer: Extended model retrieval.

Used to capture literature where the author did not use the precise term "retinal organoid" but it is actually relevant.

```text

("optic cup organoid" OR "3D retinal culture" OR "stem cell-derived retina") AND (survival OR apoptosis OR stress)

```

The third layer: mechanism-specific search.

Used to verify specific pathways or mechanisms.

```text

("retinal organoid" OR "retina organoid") AND ("oxidative stress" OR "ER stress" OR hypoxia OR mitochondria)

```

Fourth layer: Cell type specific search.

```text

("retinal organoid" OR "retina organoid") AND (photoreceptor OR cone OR rod OR "retinal ganglion cell") AND (death OR apoptosis OR degeneration)

```

Fifth layer: Disease model retrieval.

```text

("retinal organoid" OR "retina organoid") AND (disease OR degeneration OR dystrophy OR retinitis OR glaucoma)

```

Sixth layer: Review/background search.

```text

("retinal organoid" OR "retina organoid") AND (review OR protocol OR model)

```

2. What methods and websites were used for the search?

2.1 Preferred: PubMed / NCBI E-utilities

PubMed is the preferred tool for searching biomedical literature. Do not default to scraping PubMed pages. Use the NCBI E-utilities API instead.

2.1.1 ESearch: Retrieving PMID using a query

interface:

```text

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi

```

parameter:

```text

db=pubmed

term=

3. How to organize information after retrieval

3.1 Establish a unified record structure

Each document is compiled into a unified record.

Fields:

```text

pmid

doi

pmcid

title

authors

journal

journal_abbrev

issn

eissn

year

abstract

query_source

evidence_level

evidence_tags

paper_type

URL

```

3.2 Deduplication

Priority:

1. PMID deduplication.

2. Use DOI to remove duplicates if PMID is unavailable.

3. If there is no DOI, use lower(title) + year + first_author to remove duplicates.

Retain the query_source that was hit the first time, and record which queries hit the document.

3.3 Evidence Classification

It is necessary to distinguish:

Direct evidence:

The target species, tissue, cell type, model, and treatment conditions are directly matched.

Indirect evidence:

Adjacent systems, similar models, and similar mechanisms are supported, but they are not direct systems for user problems.

No direct evidence found:

Only background, speculation, reviews, or adjacent models can be found; there are no direct experimental results.

3.4 Document Type Labeling

At least the following should be noted:

• original research

• review

• protocol

• preprint

• dataset/resource

• clinical study

• method paper

3.5 Sorting Rules

Recommended sorting:

1. Original research with direct evidence.

2. Research on key mechanisms.

3. Latest important research.

4. Classic foundational studies.

5. High-quality review.

6. Indirect evidence.

Do not sort by IF alone. IF is a journal-level indicator and does not equate to the quality of an individual article.

4. How to organize quotations in a reply

4.1 Text Citation Format

All text citations must be clickable.

Format:

```markdown

[[1. **Journal**, Year]](https://pubmed.ncbi.nlm.nih.gov/PMID/)

```

Example:

```markdown

Previous studies have observed developmental stage-related photoreceptor stress and degeneration in human retinal organoids [[1. **Cell Stem Cell**, 2019]](https://pubmed.ncbi.nlm.nih.gov/xxxxxxx/).

```

Do not write it as:

```text

[1]

(PMID: xxxxx)

See reference 1

```

4.2 Recommended Answer Structure

First paragraph: Direct conclusion.

```text

Conclusion: There have been relevant reports, but the direct evidence mainly focuses on...; direct evidence regarding... is still lacking.

```

Second paragraph: Evidence classification.

```text

Direct evidence:

- Reference A: ...

Indirect evidence:

- Reference B: ...

No direct evidence found:

- Not found in this round...

```

Third paragraph: Mechanism summary.

Group by topic, for example:

• apoptosis/caspase pathway

• oxidative stress

• mitochondrial dysfunction

• ER stress

• hypoxia/metabolic stress

• inflammation

• developmental mismatch

Fourth paragraph: Research gap.

Clearly state which issues lack direct evidence.

Fifth paragraph: Inspiration from the experiment.

If the user needs experimental design, provide the marker, assay, time point, and control.

5. Complete list of references at the end of the article

If a specific reference is cited in the text, a complete list must be attached at the end of the article.

Format:

```markdown

## Complete List of Reference Information

1. Smith J et al., **Journal Name** (2021), [PMID: 12345678](https://pubmed.ncbi.nlm.nih.gov/12345678/). *{IF＝X，Qn}*

2. Wang X et al., **Journal Name** (2022), [DOI: 10.xxxx/xxxxx](https://doi.org/10.xxxx/xxxxx). *{IF=To be verified}*

```

Author format:

• 1–3 authors: List all.

• More than 3 authors: First author et al.

The PMID / DOI / URL must be clickable.

6. IF Verification and Labeling

6.1 First, let's explain the practical limitations of IF checks.

Normally, the official Journal Impact Factor comes from Clarivate Journal Citation Reports (JCR). However, any external agent typically does not have a Clarivate/JCR account or a local JCR table, so do not verify it through this path.

```

6.2 Practical methods for using IF skill

Main route:

1. If the input is PMID, first use NCBI E-utilities to obtain PubMed metadata.

- Retrieve FullJournalName. - Retrieve Source/ISO abbreviation. - Retrieve ISSN/eISSN. - Retrieve auxiliary fields such as title, year, and DOI.

2. Use the publicly available iikx/iscience mobile JSON interface to query journals.

Search API:

```text

https://m.iikx.com/api/restfull/?m=sci&c=index&a=info&keyword=

```

Details API:

```text

https://m.iikx.com/api/restfull/?m=sci/index/detail&id=&classid=

```

3. Perform a conservative match on the search results.

- Prioritizes exact normalized journal title matches. - Second, prioritizes exact abbreviation matches. - Exercises great caution with short and broad terms. - Does not accept obvious substring mismatches, such as mismatching "Nature" as "Nature Reviews" series. - Returns ambiguous/not_found results if the match is unstable, rather than guessing.

4. If PubMed provides an abbreviation, try expanding it to the full name or alternative title using NLM Catalog.

The NLM Catalog search interface remains NCBI E-utilities:

```text

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=nlmcatalog&term=[Title Abbreviation]&retmode=xml&retmax=1

```

Then use ESummary to get the Title / TitleAlternate.

5. Read from the iikx detail results:

- Impact factor. - IF year. - JCR quartile. - CAS/CAS quartile, if applicable. - Source URL. - Match confidence.

6. Do not include the IF year in the main text when annotating; use compact annotations.

The final annotation should only state:

```text

*{IF＝X，Qn}*

```

If it fails:

```text

*{IF=Pending Verification}*

```

or:

```text

*{IF=Not detected}*

```

6.3 Specific Steps

Perform the following procedure for each document.

Step 1: Prepare the journal search name.

Prioritize retrieving from PubMed metadata:

```text

FullJournalName

ISOAbbreviation / Source

ISSN

eISSN

```

If only a DOI is available, first use Crossref or OpenAlex to obtain the journal name.

Crossref:

```text

https://api.crossref.org/works/

```

OpenAlex:

```text

https://api.openalex.org/works/https://doi.org/

```

Step 2: Standardize journal names.

Standardization rules:

• All lowercase.

• HTML unescape.

• Replace & with and.

• Remove punctuation.

• Combine multiple spaces.

• When making comparisons, you can also use the compact form, which removes all spaces.

Example pseudocode:

Python

import re, html

def norm(s):

s = html.unescape(s or '').lower()

s = re.sub(r'&', ' and ', s)

s = re.sub(r'[^a-z0-9]+', ' ', s)

return re.sub(r'\s+', ' ', s).strip()

def compact(s):

return norm(s).replace(' ', '')

```

Step 3: Query the iikx search interface.

```text

https://m.iikx.com/api/restfull/?m=sci&c=index&a=info&keyword=

```

It is recommended to set a User-Agent, for example:

```text

Mozilla/5.0

```

If no exact match is found on the first page, you can flip through a limited number of pages, for example, up to 8 pages.

Page turning parameters are usually:

```text

page=2

page=3

```

Step 4: Select candidates from the search results.

Candidate fields typically include:

```text

id

classid

title

smalltitle

IF or IF2024

zky2020

URL

```

Matching rules:

• If compact(query) == compact(candidate.title), accept.

• If norm(query) == norm(candidate.title), accept.

• If compact(query) == compact(candidate.smalltitle), accept.

• If norm(query) == norm(candidate.smalltitle), accept.

• Do not accept a substring unless the query is long enough and unambiguous.

• Be especially cautious with short words such as Nature, Science, Cell, Brain, Vision, and Retina.

Step 5: If no match is found, use the NLM Catalog extended abbreviation.

For example, in PubMed, the Source is:

```text

Free Radic Biol Med

```

You can check:

```text

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=nlmcatalog&term=Free%20Radic%20Biol%20Med%5BTitle%20Abbreviation%5D&retmode=xml&retmax=1

```

After obtaining the NLM Catalog ID, use it as follows:

```text

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=nlmcatalog&id=&retmode=xml

```

Read:

```text

Title

TitleAlternate

```

Then use these full names to search for iikx.

Step 6: Check the iikx details interface.

If the search results contain:

```text

id=

classid=

```

Call:

```text

https://m.iikx.com/api/restfull/?m=sci/index/detail&id=&classid=

```

Read from detail:

```text

IF2024, IF2023, IF2022 ...

IF

zky2020 or other JCR quartile fields

jcr22 / jcr12 or partition field

issn

eissn

title

smalltitle

category

```

Step 7: Select the latest IF statement.

Search the returned fields for all instances of the form:

```text

IF20xx

```

For example:

```text

IF2024

IF2023

IF2022

```

Choose the year with the largest significant digit.

If IF20xx is not present, attempt to read:

```text

IF

if_value

```

If no valid value is found, it is marked as not detected.

Step 8: Output confidence level and label.

If exact title/abbreviation matches, and detail returns a valid IF:

```text

*{IF＝X，Qn}*

```

If the match is uncertain:

```text

*{IF=Pending Verification}*

```

If the public API returns no results:

```text

*{IF=Not detected}*

```

6.4 IF Annotation Format

Fixed format:

```text

*{IF＝X，Qn}*

```

Example:

```markdown

Smith J et al., **Neuron** (2020), [PMID: 12345678](https://pubmed.ncbi.nlm.nih.gov/12345678/). *{IF＝15.0, Q1}*

```

Notice:

• The JCR year is not written inside the IF annotation.

• Do not write "2024 JCR IF".

• Do not write "JCR 2024".

• Only the year of publication is retained.

• If the IF is 0.0, null, has an unstable source, or an unstable match, the number will not be displayed.

6.5 Standard handling for IF check failures

Don't guess.

Do not use the journal name to fill in the numbers.

Do not use large models to memorize and fill in IF statements.

Only three states are allowed upon failure:

```text

*{IF=Pending Verification}*

```

Used for:

• Search results are vague.

There are several similar journals.

• Only the abbreviation was found, but the full name could not be confirmed.

• The IF returned by publicly available sources is questionable.

```text

*{IF=Not detected}*

```

Used for:

• The public interface returned no results.

• The journal is not covered by SCI/JCR.

• The new issue does not yet have an IF.

```text

*{IF=Not publicly verifiable}*

```

Used for:

• The user requires an official JCR, but the current Agent does not have Clarivate/JCR permissions.

7. Final self-checklist

Must be checked before shipment:

• Should the user's core questions be answered first?

• Whether to distinguish between direct evidence, indirect evidence, and no direct evidence found.

• Are all text citations clickable?

• Is there a complete list of references at the end of the article?

• Does every document include an IF (Input/Output) label or a label indicating pending verification/not detected?

• Whether the PMID/DOI/URL is clickable.

• Does it avoid substituting overall tissue results for conclusions about specific cell types?

• Does it avoid substituting activation/phosphorylation for an increase in total expression?

• Whether to indicate a preprint.

• Does it specify the search boundaries?

• IF whether it was not based on memory or guesswork.

8. Reproducible pseudocode

Python

queries = build_queries(user_question)

all_pmids = []

for query in queries:

pmids = ncbi_esearch(query, retmax=20, sort='relevance')

all_pmids.extend(pmids)

pmids = deduplicate_keep_order(all_pmids)

metadata = ncbi_esummary(pmids)

abstracts = ncbi_efetch_abstract(pmids)

records = merge_metadata_and_abstracts(metadata, abstracts)

records = tag_evidence(records, user_question)

records = rank_records(records)

selected = select_top_records(records)

if need_fulltext:

for record in selected_key_records:

pmcid = idconv_pmid_to_pmcid(record.pmid)

if pmcid:

record.fulltext = fetch_bioc_or_pmc_xml(pmcid)

For record in selected:

journal_query = record.full_journal_name or record.journal_abbrev

if_result = lookup_if_public_iikx(journal_query)

if_result.confident:

record.if_annotation = f'*{IF＝{if_result.if_value}，{if_result.quartile}｝*'

elif if_result.ambiguous:

record.if_annotation = '*{IF＝Pending Verification}*'

else:

record.if_annotation = '*{IF＝Not Detected}*'

answer = compose_answer(

conclusion

evidence_groups,

clickable_body_citations,

full_reference_list_with_if

)

```

9. Recommended final delivery template

```markdown

in conclusion:

...

Level of evidence:

Direct evidence:

- ……[[1. **Journal**, Year]](https://pubmed.ncbi.nlm.nih.gov/PMID/)

Indirect evidence:

- …[[2. **Journal**, Year]](https://pubmed.ncbi.nlm.nih.gov/PMID/)

No direct evidence found:

- ……

Mechanism summary:

1. ……

2. ……

Search boundaries:

This round of searches primarily involved PubMed, PMC, BioC, and bioRxiv; initial screening was based on metadata and abstracts, with only key documents undergoing full-text verification. IF annotations were based on publicly accessible sources; documents that could not be matched with high confidence were marked as pending verification or not detected.

Complete list of literature information:

1. Smith J et al., **Journal Name** (2021), [PMID: 12345678](https://pubmed.ncbi.nlm.nih.gov/12345678/). *{IF＝X，Q1}*

2. Wang X et al., **Journal Name** (2022), [DOI: 10.xxxx/xxxxx](https://doi.org/10.xxxx/xxxxx). *{IF=To be verified}*

```