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markusha77 merged 3 commits into from
Mar 25, 2026
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feat: update research skills part 7 #53

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5a5f122
feat: update research skills part 7 (20 folders)
SixiangH Mar 16, 2026
2ccc724
Update external audit preparation guidance in SKILL.md
sixiang-svg Mar 21, 2026
8aeafe7
Remove redundant safety implementation sections
sixiang-svg Mar 21, 2026
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239 changes: 6 additions & 233 deletions skills/Research/pubmed-database/SKILL.md
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Original file line number Diff line number Diff line change
@@ -1,8 +1,12 @@
---
category: Research
id: pubmed-database
name: PubMed Database
description: Guidance and answers for pubmed database.
description: Search and retrieve metadata, citations, and abstracts from the PubMed database for biomedical and life sciences research.
category: Research
requires: []
examples:
- Search PubMed for recent clinical trials on immunotherapy for cancer.
- Retrieve metadata and citations for a specific PMID from PubMed.
---
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# Biopython: Computational Molecular Biology in Python
Expand Down Expand Up @@ -44,28 +48,15 @@ Biopython is organized into modular sub-packages, each addressing specific bioin

Install Biopython using pip (requires Python 3 and NumPy):

```python
uv pip install biopython
```

For NCBI database access, always set your email address (required by NCBI):

```python
from Bio import Entrez
Entrez.email = "your.email@example.com"

# Optional: API key for higher rate limits (10 req/s instead of 3 req/s)
Entrez.api_key = "your_api_key_here"
```

## Using This Skill

This skill provides comprehensive documentation organized by functionality area. When working on a task, consult the relevant reference documentation:

### 1. Sequence Handling (Bio.Seq & Bio.SeqIO)

**Reference:** `references/sequence_io.md`

Use for:
- Creating and manipulating biological sequences
- Reading and writing sequence files (FASTA, GenBank, FASTQ, etc.)
Expand All @@ -74,90 +65,35 @@ Use for:
- Sequence translation, transcription, and reverse complement
- Working with SeqRecord objects

**Quick example:**
```python
from Bio import SeqIO

# Read sequences from FASTA file
for record in SeqIO.parse("sequences.fasta", "fasta"):
print(f"{record.id}: {len(record.seq)} bp")

# Convert GenBank to FASTA
SeqIO.convert("input.gb", "genbank", "output.fasta", "fasta")
```

### 2. Alignment Analysis (Bio.Align & Bio.AlignIO)

**Reference:** `references/alignment.md`

Use for:
- Pairwise sequence alignment (global and local)
- Reading and writing multiple sequence alignments
- Using substitution matrices (BLOSUM, PAM)
- Calculating alignment statistics
- Customizing alignment parameters

**Quick example:**
```python
from Bio import Align

# Pairwise alignment
aligner = Align.PairwiseAligner()
aligner.mode = 'global'
alignments = aligner.align("ACCGGT", "ACGGT")
print(alignments[0])
```

### 3. Database Access (Bio.Entrez)

**Reference:** `references/databases.md`

Use for:
- Searching NCBI databases (PubMed, GenBank, Protein, Gene, etc.)
- Downloading sequences and records
- Fetching publication information
- Finding related records across databases
- Batch downloading with proper rate limiting

**Quick example:**
```python
from Bio import Entrez
Entrez.email = "your.email@example.com"

# Search PubMed
handle = Entrez.esearch(db="pubmed", term="biopython", retmax=10)
results = Entrez.read(handle)
handle.close()
print(f"Found {results['Count']} results")
```

### 4. BLAST Operations (Bio.Blast)

**Reference:** `references/blast.md`

Use for:
- Running BLAST searches via NCBI web services
- Running local BLAST searches
- Parsing BLAST XML output
- Filtering results by E-value or identity
- Extracting hit sequences

**Quick example:**
```python
from Bio.Blast import NCBIWWW, NCBIXML

# Run BLAST search
result_handle = NCBIWWW.qblast("blastn", "nt", "ATCGATCGATCG")
blast_record = NCBIXML.read(result_handle)

# Display top hits
for alignment in blast_record.alignments[:5]:
print(f"{alignment.title}: E-value={alignment.hsps[0].expect}")
```

### 5. Structural Bioinformatics (Bio.PDB)

**Reference:** `references/structure.md`

Use for:
- Parsing PDB and mmCIF structure files
Expand All @@ -167,24 +103,9 @@ Use for:
- Structure superimposition and RMSD calculation
- Extracting sequences from structures

**Quick example:**
```python
from Bio.PDB import PDBParser

# Parse structure
parser = PDBParser(QUIET=True)
structure = parser.get_structure("1crn", "1crn.pdb")

# Calculate distance between alpha carbons
chain = structure[0]["A"]
distance = chain[10]["CA"] - chain[20]["CA"]
print(f"Distance: {distance:.2f} Å")
```

### 6. Phylogenetics (Bio.Phylo)

**Reference:** `references/phylogenetics.md`

Use for:
- Reading and writing phylogenetic trees (Newick, NEXUS, phyloXML)
- Building trees from distance matrices or alignments
Expand All @@ -193,23 +114,9 @@ Use for:
- Creating consensus trees
- Visualizing trees

**Quick example:**
```python
from Bio import Phylo

# Read and visualize tree
tree = Phylo.read("tree.nwk", "newick")
Phylo.draw_ascii(tree)

# Calculate distance
distance = tree.distance("Species_A", "Species_B")
print(f"Distance: {distance:.3f}")
```

### 7. Advanced Features

**Reference:** `references/advanced.md`

Use for:
- **Sequence motifs** (Bio.motifs) - Finding and analyzing motif patterns
- **Population genetics** (Bio.PopGen) - GenePop files, Fst calculations, Hardy-Weinberg tests
Expand All @@ -218,15 +125,6 @@ Use for:
- **Clustering** (Bio.Cluster) - K-means and hierarchical clustering
- **Genome diagrams** (GenomeDiagram) - Visualizing genomic features

**Quick example:**
```python
from Bio.SeqUtils import gc_fraction, molecular_weight
from Bio.Seq import Seq

seq = Seq("ATCGATCGATCG")
print(f"GC content: {gc_fraction(seq):.2%}")
print(f"Molecular weight: {molecular_weight(seq, seq_type='DNA'):.2f} g/mol")
```

## General Workflow Guidelines

Expand All @@ -239,136 +137,33 @@ When a user asks about a specific Biopython task:
3. **Extract relevant code patterns** and adapt them to the user's specific needs
4. **Combine multiple modules** when the task requires it

Example search patterns for reference files:
```bash
# Find information about specific functions
grep -n "SeqIO.parse" references/sequence_io.md

# Find examples of specific tasks
grep -n "BLAST" references/blast.md

# Find information about specific concepts
grep -n "alignment" references/alignment.md
```

### Writing Biopython Code

Follow these principles when writing Biopython code:

1. **Import modules explicitly**
```python
from Bio import SeqIO, Entrez
from Bio.Seq import Seq
```

2. **Set Entrez email** when using NCBI databases
```python
Entrez.email = "your.email@example.com"
```

3. **Use appropriate file formats** - Check which format best suits the task
```python
# Common formats: "fasta", "genbank", "fastq", "clustal", "phylip"
```

4. **Handle files properly** - Close handles after use or use context managers
```python
with open("file.fasta") as handle:
records = SeqIO.parse(handle, "fasta")
```

5. **Use iterators for large files** - Avoid loading everything into memory
```python
for record in SeqIO.parse("large_file.fasta", "fasta"):
# Process one record at a time
```

6. **Handle errors gracefully** - Network operations and file parsing can fail
```python
try:
handle = Entrez.efetch(db="nucleotide", id=accession)
except HTTPError as e:
print(f"Error: {e}")
```

## Common Patterns

### Pattern 1: Fetch Sequence from GenBank

```python
from Bio import Entrez, SeqIO

Entrez.email = "your.email@example.com"

# Fetch sequence
handle = Entrez.efetch(db="nucleotide", id="EU490707", rettype="gb", retmode="text")
record = SeqIO.read(handle, "genbank")
handle.close()

print(f"Description: {record.description}")
print(f"Sequence length: {len(record.seq)}")
```

### Pattern 2: Sequence Analysis Pipeline

```python
from Bio import SeqIO
from Bio.SeqUtils import gc_fraction

for record in SeqIO.parse("sequences.fasta", "fasta"):
# Calculate statistics
gc = gc_fraction(record.seq)
length = len(record.seq)

# Find ORFs, translate, etc.
protein = record.seq.translate()

print(f"{record.id}: {length} bp, GC={gc:.2%}")
```

### Pattern 3: BLAST and Fetch Top Hits

```python
from Bio.Blast import NCBIWWW, NCBIXML
from Bio import Entrez, SeqIO

Entrez.email = "your.email@example.com"

# Run BLAST
result_handle = NCBIWWW.qblast("blastn", "nt", sequence)
blast_record = NCBIXML.read(result_handle)

# Get top hit accessions
accessions = [aln.accession for aln in blast_record.alignments[:5]]

# Fetch sequences
for acc in accessions:
handle = Entrez.efetch(db="nucleotide", id=acc, rettype="fasta", retmode="text")
record = SeqIO.read(handle, "fasta")
handle.close()
print(f">{record.description}")
```

### Pattern 4: Build Phylogenetic Tree from Sequences

```python
from Bio import AlignIO, Phylo
from Bio.Phylo.TreeConstruction import DistanceCalculator, DistanceTreeConstructor

# Read alignment
alignment = AlignIO.read("alignment.fasta", "fasta")

# Calculate distances
calculator = DistanceCalculator("identity")
dm = calculator.get_distance(alignment)

# Build tree
constructor = DistanceTreeConstructor()
tree = constructor.nj(dm)

# Visualize
Phylo.draw_ascii(tree)
```

## Best Practices

Expand Down Expand Up @@ -403,28 +198,6 @@ Phylo.draw_ascii(tree)
### Issue: PDB parser warnings
**Solution:** Use `PDBParser(QUIET=True)` to suppress warnings, or investigate structure quality.

## Additional Resources

- **Official Documentation**: https://biopython.org/docs/latest/
- **Tutorial**: https://biopython.org/docs/latest/Tutorial/
- **Cookbook**: https://biopython.org/docs/latest/Tutorial/ (advanced examples)
- **GitHub**: https://github.com/biopython/biopython
- **Mailing List**: biopython@biopython.org

## Quick Reference

To locate information in reference files, use these search patterns:

```bash
# Search for specific functions
grep -n "function_name" references/*.md

# Find examples of specific tasks
grep -n "example" references/sequence_io.md

# Find all occurrences of a module
grep -n "Bio.Seq" references/*.md
```

## Summary

Expand Down
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