biodb - biodb, a library and a development framework for connecting to chemical and biological databases

The biodb package provides access to standard remote chemical and biological databases (ChEBI, KEGG, HMDB, ...), as well as to in-house local database files (CSV, SQLite), with easy retrieval of entries, access to web services, search of compounds by mass and/or name, and mass spectra matching for LCMS and MSMS. Its architecture as a development framework facilitates the development of new database connectors for local projects or inside separate published packages.

Last updated 4 months ago

softwareinfrastructuredataimportkeggbiologycheminformaticschemistrydatabasescpp

7.85 score 11 stars 6 dependents 24 scripts 514 downloads

biodbChebi - biodbChebi, a library for connecting to the ChEBI Database

The biodbChebi library provides access to the ChEBI Database, using biodb package framework. It allows to retrieve entries by their accession number. Web services can be accessed for searching the database by name, mass or other fields.

Last updated 4 months ago

softwareinfrastructuredataimport

4.78 score 2 stars 1 dependents 3 scripts 208 downloads

biodbHmdb - biodbHmdb, a library for connecting to the HMDB Database

The biodbHmdb library is an extension of the biodb framework package that provides access to the HMDB Metabolites database. It allows to download the whole HMDB Metabolites database locally, access entries and search for entries by name or description. A future version of this package will also include a search by mass and mass spectra annotation.

Last updated 4 months ago

softwareinfrastructuredataimportcpp

4.30 score 2 stars 2 scripts 202 downloads

biodbUniprot - biodbUniprot, a library for connecting to the Uniprot Database

The biodbUniprot library is an extension of the biodb framework package. It provides access to the UniProt database. It allows to retrieve entries by their accession number, and run web service queries for searching for entries.

Last updated 4 months ago

softwareinfrastructuredataimport

4.30 score 2 stars 3 scripts 170 downloads

biodbNcbi - biodbNcbi, a library for connecting to NCBI Databases.

The biodbNcbi library provides access to the NCBI databases CCDS, Gene, Pubchem Comp and Pubchem Subst, using biodb package framework. It allows to retrieve entries by their accession number. Web services can be accessed for searching the database by name or mass.

Last updated 4 months ago

softwareinfrastructuredataimport

4.00 score 1 stars 1 scripts 172 downloads

biodbNci - biodbNci, a library for connecting to biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database

The biodbNci library is an extension of the biodb framework package. It provides access to biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database. It allows to retrieve entries by their accession number, and run specific web services.

Last updated 4 months ago

softwareinfrastructuredataimportcpp

4.00 score 2 scripts 208 downloads

sched - Request Scheduler

Offers classes and functions to contact web servers while enforcing scheduling rules required by the sites. The URL class makes it easy to construct a URL by providing parameters as a vector. The Request class allows to describes SOAP (Simple Object Access Protocol) or standard requests: URL, method (POST or GET), header, body. The Scheduler class controls the request frequency for each server address by mean of rules (Rule class). The RequestResult class permits to get the request status to handle error cases and the content.

Last updated 5 months ago

2.78 score 2 scripts 189 downloads