https://github.com/cfsan-biostatistics/ncbi-pathogen-api-docs
Repository for samizdat about NCBI's undocumented Pathogen API.
https://github.com/cfsan-biostatistics/ncbi-pathogen-api-docs
Science Score: 10.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
○CITATION.cff file
-
○codemeta.json file
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○.zenodo.json file
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○DOI references
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✓Academic publication links
Links to: ncbi.nlm.nih.gov -
○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (4.3%) to scientific vocabulary
Last synced: 10 months ago
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Repository
Repository for samizdat about NCBI's undocumented Pathogen API.
Basic Info
- Host: GitHub
- Owner: CFSAN-Biostatistics
- Language: Shell
- Default Branch: main
- Size: 4.88 KB
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- Stars: 0
- Watchers: 8
- Forks: 1
- Open Issues: 0
- Releases: 0
Created over 5 years ago
· Last pushed over 5 years ago
https://github.com/CFSAN-Biostatistics/ncbi-pathogen-api-docs/blob/main/
# ncbi-pathogen-api-docs
Repository for [samizdat](http://www.catb.org/jargon/html/S/samizdat.html) about NCBI's undocumented Pathogen API.
*note* For large batch jobs, please download from the ftp site and run operations locally.
ftp://ftp.ncbi.nlm.nih.gov/pathogen/
## API Endpoint URL
[https://www.ncbi.nlm.nih.gov/Structure/pathogen/tree/tree_srv.cgi](https://www.ncbi.nlm.nih.gov/Structure/pathogen/tree/tree_srv.cgi)
# Parameters
## Action
### getneighbors
Retrieve neighboring nodes in the tree within `distance` from `accessions`.
[https://www.ncbi.nlm.nih.gov/Structure/pathogen/tree/tree_srv.cgi?action=getneighbors&distance=4&accessions=PDT000608728.1,SAMN13035591,PDT000608727.1,FSIS21821478,qqq](https://www.ncbi.nlm.nih.gov/Structure/pathogen/tree/tree_srv.cgi?action=getneighbors&distance=4&accessions=PDT000608728.1,SAMN13035591,PDT000608727.1,FSIS21821478,qqq)
# Schema
JSON Schema to follow if we can figure out what it is.
# Using APIs
```python
import requests # seriously, use requests
accessions = [
'PDT000608728.1',
'SAMN13035591',
'PDT000608727.1',
'FSIS21821478',
'qqq'
]
response = requests.get(
"https://www.ncbi.nlm.nih.gov/Structure/pathogen/tree/tree_srv.cgi",
params=dict(
action='getneighbors',
distance=4,
accessions=",".join(accessions)
)
)
records = response.json()
```
Owner
- Name: CFSAN (Center for Food Safety and Applied Nutrition)
- Login: CFSAN-Biostatistics
- Kind: organization
- Website: https://www.fda.gov/about-fda/fda-organization/center-food-safety-and-applied-nutrition-cfsan
- Repositories: 18
- Profile: https://github.com/CFSAN-Biostatistics
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