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feat: removed NCBI access from lesson 8 #30

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finstermeier merged 1 commit into from
May 12, 2026
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feat: removed NCBI access from lesson 8 #30

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96 changes: 0 additions & 96 deletions lessons/lesson_08.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -301,102 +301,6 @@
" break"
]
},
{
"cell_type": "markdown",
"id": "0fc324f7",
"metadata": {},
"source": [
"# Accessing NCBI\n",
"- WARNING: NCBI can and will block your institute, if you misuse this, even unintentionally, but they will try to reach you first.\n",
"- NCBI guidelines: https://www.ncbi.nlm.nih.gov/books/NBK25497/\n",
"- In brief:\n",
" - For more than 100 consecutive requests in a row, do that at a weekend or outside of US peak times\n",
" - No more than 3 queries per second\n",
" - **IMPORTANT**: always provide a valid email address for contacting you! \n",
" - Entrez allows you to search and download large amounts of data. Save those files rather than downloading them over and over again!\n",
" - Use alternatives to download large datasets, i.e. ftp server for all bacterial genomes etc.\n"
]
},
{
"cell_type": "markdown",
"id": "a65f491c",
"metadata": {},
"source": [
"- Allows programmatic database search similar to website\n",
"- Multiple databases are supported, i.e. nucleotide, pubmed\n",
"- Will return identifiers for downloading / accessing data"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "6d52bf4d",
"metadata": {},
"outputs": [],
"source": [
"from Bio import SeqIO\n",
"from Bio import Entrez\n",
"\n",
"Entrez.email = \"finstermeier@mpusp.mpg.de\"\n",
"handle = Entrez.esearch(db=\"pubmed\", term=\"biopython\")\n",
"record = Entrez.read(handle)\n",
"print(record[\"IdList\"][:5])"
]
},
{
"cell_type": "markdown",
"id": "e428202c",
"metadata": {},
"source": [
"- Available databases: https://www.ncbi.nlm.nih.gov/books/NBK25497/table/chapter2.T._entrez_unique_identifiers_ui/?report=objectonly\n",
"- Keywords for search term can be found here: https://www.ncbi.nlm.nih.gov/books/NBK49540/\n",
"- Overview of available databases and parameters:\n",
" - https://www.ncbi.nlm.nih.gov/books/NBK25499/table/chapter4.T._valid_values_of__retmode_and/?report=objectonly\n"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "d94519b6",
"metadata": {},
"outputs": [],
"source": [
"handle = Entrez.esearch(\n",
" db=\"nucleotide\", term=\"Cypripedioideae[Orgn] AND matK[Gene]\", idtype=\"acc\"\n",
")\n",
"record = Entrez.read(handle)\n",
"print(record[\"IdList\"][:5])"
]
},
{
"cell_type": "markdown",
"id": "4fd85ecd",
"metadata": {},
"source": [
"# Downloading from NCBI"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "6d794ccd",
"metadata": {},
"outputs": [],
"source": [
"with Entrez.efetch(\n",
" db=\"nucleotide\", rettype=\"gb\", retmode=\"text\", id=\"6273291\"\n",
") as handle:\n",
" seq_record = SeqIO.read(handle, \"gb\") # using \"gb\" as an alias for \"genbank\"\n",
" print(f\"{seq_record.id} with {len(seq_record.features)} features\")\n",
"\n",
"\n",
"with Entrez.efetch(\n",
" db=\"nucleotide\", rettype=\"gb\", retmode=\"text\", id=\"6273291, 6273290, 6273289\"\n",
") as handle:\n",
" for seq_record in SeqIO.parse(handle, \"gb\"):\n",
" print(f\"{seq_record.id}: {seq_record.description[:50]}...\")"
]
},
{
"cell_type": "markdown",
"id": "0642bc14",
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