noamteyssier / ggetrs

Efficient querying of biological databases

Hello!

I'm Noam Teyssier, a Bioinformatics PhD Candidate in the Kampmann Lab and Goodarzi Lab at UCSF.

I work at the intersection of functional genomics, machine learning, dynamical modeling, and systems biology in the context of neurodegenerative diseases.

I highly value open source and try to share all the tools I've developed during my own research.

ggetrs's Issues

Convert async to blocking sync

this will make all the pyo3 conversions much easier.

enrichr library search

returns all libraries in the enrichr database

alphafold - rust request

ARCHS4 - tissue

Should split this into two different submodules

Include an NCBI query interface

blat - Python API

http error code handling for ensembl-search

setup code coverage with codecov

set up python interpreter with maturin

seq - rust request

alphafold - Python API

Set up all APIs as constants

Include ARCHS4 Commandline and python API in README

Integration with ChEMBL

Symbol to Ensembl ID Translation

Should do this in a batched way with: https://rest.ensembl.org/documentation/info/symbol_post

Restructure repos

Example:

module
├── mod.rs
├── submodule.rs        # CLI
├── python.rs           # Python interface
├── functions           # Functions
│   ├── mod.rs
│   ├── some_func_1.rs
│   └── some_func_2.rs
└── types                # Return Types and Enums
    ├── mod.rs
    ├── some_type_1.rs
    └── some_type_2.rs

info - Python API

ref - rust request

add ensembl search cli and python usage to readme

exhaustive linting

blast - Python API

seq - Python API

add more information from NCBI query request

enrichr gene-library search

return all libraries that a gene is a member of

enrichr - python API

Integration with PANTHER

http://pantherdb.org/services/openAPISpec.jsp

search - rust request

Integration with HOCOMOCO

https://hocomoco11.autosome.org/api_description

reorder results for ensembl lookup results

Convert Uniprot query results container to hashmap for better interface with ensembl lookup

archs4 - rust request

Integration with ZINC

info - rust request

Implement `search` with a single mysql command

Can chain together the query before sending it.

Would send in a single time as opposed to multiple queries.

SELECT * from ... WHERE description LIKE {} OR description LIKE {}

interface for ensembl lookup

need both the ID and the symbol lookup

ref - Python API

blat - rust request

add python module for ensembl database query

add direct database as option for ensembl search

Integration with GeneCards

enrichr - rust request

Uniprot module

Generic query

Add taxonomy information to `uniprot query`

Integration with GSE GEO

Download GEO with accession + potentially read them into dataframes.

https://www.ncbi.nlm.nih.gov/geo/info/geo_paccess.html

ensembl release

small function to get the last ensembl release version

search - Python API

Integration with STRING

blast - rust request

database query for ensembl

parse through the sql database and return all available databases

essentially a wrapper around

SHOW databases

but could filter by species

SHOW databases LIKE '%{species_name}%'

archs4 - python API