Science Score: 20.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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○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 -
✓Committers with academic emails
3 of 6 committers (50.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (10.6%) to scientific vocabulary
Repository
Bioinformatics data-mining
Basic Info
Statistics
- Stars: 1
- Watchers: 5
- Forks: 8
- Open Issues: 7
- Releases: 0
Metadata Files
README.md
BioMine
This is a toolkit to handle variant and clinical data (see variant classes). Web accessions are included through the webapi class for
- ClinicalTrials.gov
- NCBI Entrez services
- Ensembl ReST API
- ExAC (Harvard) ReST API
The webapi parent class can be used to more easily create classes for other URL-based web services as well.
The variant classes can be used independently of the webapi's, and they include many useful functions to conform to HGVS variant representations. The BioMine toolkit is used in other software, such as CharGer.
Installation
This package works with Python 2.7. To install:
pip install .
All dependencies should automatically install.
Note to developers
Please be aware of site's crawler limitations (robots.txt) & rate limitations when creating new classes for web services. Failure to do so can result in IP banning or denial of service.
Modules
Web API - general
Parent class of the included ReST APIs, web services, and HTML
Example to print this readme from github:
site = webAPI.webAPI( "https://github.com/" , "AdamDS/" )
site.action = "WebAPIs"
site.submit()
page = site.parseHTMLResponse()
readme = page.getElementById( 'readme' )
print readme.innerHTML
Clinical Trials - HTML
Based on ClinicalTrials.gov
NCBI: Entrez - service
Based on NCBI's Entrez Programming Utilities (E-utilities)
Search ClinVar
searchClinVar - search terms for ClinVar
returns requests response object
searchPubMed - search terms for PubMed
returns requests response object
NCBI: PubChem - ReST
Based on NCBI's Power User Gateway for PubChem
Compound Synonyms
compoundSynonyms - single compound lookup
returns tab delimited string (searched compound '\t' synonym)
compoundsSynonyms - array of compounds lookup
returns tab delimited array (searched compound '\t' synonym)
compoundsSynonyms2File - array of compounds lookup and write to file
no return
Ensembl: Variant Effect Predictor - ReST
Based on Ensembl's VEP annotator
HGVS genomic variant annotation
Use GRCh37 or GRCh38
Switch to GRCh37 or GRCh38
useGRCh37 - switches to annotation by GRCh37
useGRCh38 - switches to annotation by GRCh38
Annotate HGVS Notation with Genomic Variant
tab delimited annotation as: HGVS notation, chr, start, stop, ref, var, strand, classification
annotateHGVSScalar2Response - annotate a single mutation
returns request response as JSONP
annotateHGVSScalar2tsv - annotate a single mutation
returns dictionary with tsv annotation and error message
annotateHGVSScalarResponse2tsv - annotate a single mutation from response
returns dictionary with tsv annotation and error message
annotateHGVSArray2Dict - annotate an array of mutations
returns dictionary of HGVS notated mutations (key)/ response as JSONP (values)
annotateHGVSArray2tsv - annotate an array of mutations
returns dictionary with tsv annotations and error messages
annotatedHGVSDict2tsv - annotate a dictionary of mutations of mutations (key)/ responses (values)
returns dictionary with tsv annotations and error messages
annotateHGVSArray2File - annotate an array of mutations
no return
ExAC - HTML
Based on [ExAC Browser Beta](exac.broadinstitute.org/)
Variants
getAlleleFrequency - retrieves allele frequency of a variant
returns a number of the given variant
Owner
- Name: Adam D Scott
- Login: AdamDS
- Kind: user
- Location: St. Louis, MO
- Repositories: 25
- Profile: https://github.com/AdamDS
A scientist.
GitHub Events
Total
Last Year
Committers
Last synced: almost 3 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Adam David Scott | a****m@a****m | 114 |
| Adam_D_Scott | a****t@w****u | 8 |
| Amila_Weerasinghe | a****a@w****u | 2 |
| Meng Wang | w****5@g****m | 2 |
| Adam D Scott | a****t@g****u | 1 |
| amilacsw | a****w@g****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: about 1 year ago
All Time
- Total issues: 3
- Total pull requests: 7
- Average time to close issues: 2 months
- Average time to close pull requests: about 1 month
- Total issue authors: 2
- Total pull request authors: 4
- Average comments per issue: 0.33
- Average comments per pull request: 0.14
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- mmoisse (2)
- AdamDS (1)
Pull Request Authors
- mmoisse (4)
- fernanda-rodrigues (1)
- ralic (1)
- icebert (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 2
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Total downloads:
- pypi 89 last-month
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Total dependent packages: 0
(may contain duplicates) -
Total dependent repositories: 0
(may contain duplicates) - Total versions: 10
- Total maintainers: 2
spack.io: py-biomine
Bioinformatics data-mining.
- Homepage: https://github.com/AdamDS/BioMine
- License: []
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Latest release: 0.9.5
published over 4 years ago
Rankings
Maintainers (1)
pypi.org: biomine
Bioinformatics data-mining
- Homepage: https://github.com/AdamDS/BioMine
- Documentation: https://biomine.readthedocs.io/
- License: MIT
-
Latest release: 0.9.5
published about 8 years ago