bio-research-lookup

---
name: bio-research-lookup
description: Search scientific papers on biology, medicine, health, weight loss, psychology, nutrition, neuroscience, fitness, aging, sleep, gut microbiome, mental health, psychiatry, pharmacology. Use when user asks health/medical/biology questions, wants scientific evidence for a claim, or provides a PMID/DOI/bioRxiv link. Also triggers on "clinical trials", "испытания", "фаза 3". Triggers on questions like "does X help with Y?", "what does science say about...", "find studies on...", "is there evidence for...", "PMID:", "doi:", medrxiv/biorxiv URLs.
---

# Bio Research Lookup

Search scientific literature across PubMed, Semantic Scholar, bioRxiv/medRxiv, ClinicalTrials.gov, and OpenAlex.

---

## Step 0 — Pre-flight: interpret and clarify the query

Before any API calls, parse the user's intent and reformulate it as a scientific search query.

**Always show this block first:**

```
🔍 Понял как: **[научная формулировка на русском]**
Термины для поиска: `term1 term2 term3`
```

**Then decide:**

| Condition | Action |
|---|---|
| Direct PMID / DOI / URL provided | Skip Step 0 entirely — go straight to Step 2 |
| Query already uses scientific terms | Show interpretation block, proceed immediately |
| Query is clear and unambiguous | Show interpretation block, proceed immediately |
| Query is vague, multi-topic, or ambiguous | Show interpretation block + ask clarifying question, wait for user reply |

**When to ask a clarifying question (append after the interpretation block):**
- Query contains multiple unrelated topics (`"кофе, алкоголь и сон"` → ask: "Это три отдельных поиска или вас интересует их совместное влияние?")
- Term is polysemous (`"стресс"` → ask: "Психологический стресс, физиологический (кортизол, HPA), или оба?")
- Scope unclear (`"витамин D"` → ask: "Вас интересует дефицит, дозировка, конкретное заболевание?")
- Mechanism vs. clinical evidence unclear → ask which is needed

**When NOT to ask — just proceed:**
- PMID / DOI / link
- Already contains MeSH or scientific terms
- Clear causal question (`"интервальное голодание и инсулинорезистентность"`)
- User already specified study type (`"найди мета-анализы про..."`)

**Reformulation examples:**

| User query | Scientific formulation | Search terms |
|---|---|---|
| "алкоголь и похудение" | Влияние потребления алкоголя на массу тела | `alcohol consumption body weight adiposity` |
| "пробиотики от депрессии" | Эффект пробиотиков на симптомы депрессии | `probiotics depression mood mental health` |
| "кофе вреден для сердца?" | Связь кофеина с сердечно-сосудистыми заболеваниями | `coffee caffeine cardiovascular risk` |
| "таблетки от бессонницы" | Фармакологическое лечение инсомнии | `pharmacological treatment insomnia` |
| "правда ли что сахар вызывает рак" | Связь потребления сахара с онкологическими заболеваниями | `sugar intake cancer risk` |

---

## Step 1 — Translate query to English

All APIs are English-only. After Step 0 clarification, translate the final search terms.

Examples:
- "интервальное голодание" → "intermittent fasting"
- "микробиом кишечника" → "gut microbiome"
- "клинические испытания метформина" → "metformin clinical trials"

Use the translated English terms for all API calls below.

---

## Step 2 — Classify and pick platform(s)

| Query type | Platform |
|---|---|
| General question ("does X help with Y?", "evidence for...") | Semantic Scholar |
| Clinical trials, RCTs, systematic reviews, medical/disease | PubMed |
| Direct PMID provided (`PMID: 12345678`) | PubMed fetch |
| Latest preprints in biology or medicine | bioRxiv / medRxiv |
| Psychology, neuroscience, cognitive science, behavior | Semantic Scholar |
| Direct DOI provided (e.g. `10.1101/...`) | bioRxiv API |
| "Clinical trials", "ongoing trial", "phase 3", "испытания" | ClinicalTrials.gov |
| Broad topic — use both | PubMed + Semantic Scholar |

---

## Platform Instructions

### Semantic Scholar (broad search, psychology, health questions)

**Search:**
```
GET https://api.semanticscholar.org/graph/v1/paper/search?query={URL_ENCODED_QUERY}&fields=title,abstract,tldr,year,authors,citationCount,venue&limit=5
```

**By paper ID (S2 ID or DOI):**
```
GET https://api.semanticscholar.org/graph/v1/paper/{ID}?fields=title,abstract,tldr,year,authors,citationCount,externalIds
```

- Response includes `tldr.text` — a 1-sentence AI summary. **Prefer `tldr.text` over abstract when available.**
- `citationCount` indicates paper influence — highlight highly cited papers
- If response is 429 (rate limit) → fall back to **OpenAlex** (see below), then PubMed

---

### OpenAlex (fallback for Semantic Scholar, 250M+ papers)

Use when Semantic Scholar returns 429 or empty results.

```
GET https://api.openalex.org/works?search={URL_ENCODED_QUERY}&per-page=5&select=title,abstract_inverted_index,publication_year,authorships,cited_by_count,primary_location&mailto=research@example.com
```

- `abstract_inverted_index` is an inverted index — reconstruct the abstract by sorting keys by their position values:
  ```
  { "word": [pos1, pos2], ... } → sort all (word, pos) pairs by pos → join words
  ```
- `primary_location.source.display_name` = journal name
- `authorships[0].author.display_name` = first author

---

### PubMed (medical, clinical, NIH database)

**Step 1 — Search for PMIDs:**
```
GET https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term={URL_ENCODED_QUERY}&retmax=5&retmode=json&tool=claude-skill&email=research@example.com
```

To prioritize high-quality evidence, append publication type filters:
- Meta-analyses: add `+AND+Meta-Analysis[pt]`
- RCTs: add `+AND+Randomized+Controlled+Trial[pt]`
- Reviews: add `+AND+Review[pt]`

**Step 2 — Fetch abstracts by PMID(s):**
```
GET https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id={COMMA_SEPARATED_PMIDS}&rettype=abstract&retmode=text&tool=claude-skill&email=research@example.com
```

- If direct PMID provided, skip Step 1 and go straight to efetch
- Response is plain text. Look for `PT` lines (Publication Type) to extract study type for badges (see Step 4)

---

### bioRxiv / medRxiv (preprints)

**By DOI:**
```
GET https://api.biorxiv.org/details/{server}/{DOI}/na
```
Where `{server}` = `biorxiv` or `medrxiv`

**Recent papers by date range:**
```
GET https://api.biorxiv.org/details/{server}/{YYYY-MM-DD}/{YYYY-MM-DD}
```
Filter by category: append `?category={topic}` (e.g. `neuroscience`, `cell_biology`, `epidemiology`)

Response is JSON with `abstract` field in each item.

---

### ClinicalTrials.gov (active and completed clinical trials)

Use when user asks about trials, ongoing studies, drug testing, or phase 1/2/3.

```
GET https://clinicaltrials.gov/api/v2/studies?query.term={URL_ENCODED_QUERY}&pageSize=5&format=json
```

Key fields from response (`studies[].protocolSection`):
- `identificationModule.nctId` → trial ID (e.g. NCT04727359)
- `identificationModule.briefTitle` → trial name
- `statusModule.overallStatus` → Recruiting / Completed / Active, not recruiting
- `designModule.phases` → ["PHASE2", "PHASE3"]
- `descriptionModule.briefSummary` → short description
- `statusModule.startDateStruct.date` → start date

Trial link: `https://clinicaltrials.gov/study/{NCTId}`

---

## Step 3 — Fetch and parse results

Extract from whichever platform(s) used:
- Title
- Authors (first author + et al.)
- Year / date
- TLDR or abstract summary
- Citation count (if available)
- Publication type (for badge)
- Link to paper / trial

---

## Step 4 — Present results

### Study type badge (from PubMed `PT` field or inferred):

| Publication Type | Badge |
|---|---|
| Meta-Analysis | 📊 Мета-анализ |
| Randomized Controlled Trial | 🔬 РКИ |
| Systematic Review | 📋 Систематический обзор |
| Review | 📖 Обзор |
| Clinical Trial | 🏥 Клиническое испытание |
| Preprint | 📄 Препринт |
| Other | 🧪 Исследование |

### Paper format:

```
## [Badge] [Title] (Year)
**Авторы:** First Author et al.
**Журнал:** Journal/venue
**Цитирований:** N

[tldr.text if available — otherwise 2-3 sentence summary of key findings]

🔗 Link
```

### ClinicalTrials format:

```
## 🏥 [Trial Title]
**Статус:** Recruiting / Completed / Active
**Фаза:** Phase 2 / Phase 3
**Начало:** Date

[Brief summary 1-2 sentences]

🔗 https://clinicaltrials.gov/study/{NCTId}
```

If multiple results, list top 3–5 ranked by relevance and citation count.

### After listing papers — add synthesis block:

```
---
## Что говорит наука

[2-4 sentences synthesizing the overall evidence: is there consensus or conflict,
what is the effect size / strength of evidence, practical takeaway if any.
If evidence is weak or mixed, say so clearly.]
```

---

## Error handling

- **429 from Semantic Scholar** → fall back to OpenAlex, then PubMed
- **OpenAlex empty or irrelevant** → fall back to PubMed
- **Empty results on PubMed** → simplify query (remove qualifiers), retry with broader terms
- **404 from bioRxiv** → paper not found, suggest checking the DOI
- **No abstracts in PubMed** → return title + authors from esummary endpoint:
  ```
  GET https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&id={PMID}&retmode=json
  ```
- **ClinicalTrials 0 results** → suggest trying broader terms or checking manually at clinicaltrials.gov