Introduction


Welcome to the documentation for our web application BIOMX-DB. This page will guide you through the key features and functionalities of the application.
BIOMX-DB was created to enhance the current curated Mexican natural product database BIOFACQUIM, which was last updated in 2023. Here you can find the most recent compilation of this dabase which currently holds over 605 molecules!
Molecular data is displayed in BIOMX-DB mainly in two ways:

  • By Molecular cards:
    which contain only the most basic molecular information, like common name and source of extraction along with a picture of the molecule.
  • By Molecular records:
    which comprise all of the information known on the molecule, like the molecule´s physico-chemical characteristics, geographical data, its reference in scientific literature, the biological source of extraction, etc..

    • Features


    • Molecular Gallery:
      • Intended for users to explore the database without a specific molecule in mind, the molecular gallery allows users to navigate through molecular cards.
      • If the user wishes to expand on the cards, a click would allow the user to consult more information about the molecule by redirecting the user to the molecular record.
      • This functionality prevails even through the search pages.

    • Search by name:
      • Using the 'search by name' search bar, the user can find all records in BIOFACQUIM´s database that match the searched word with the common name of the molecule. This feature is not case sensitive.

    • Search by source of extraction:
      • Find specific molecules in BIOFACQUIM's database based on the taxonomical kingdom of the organism from which the natural product was originally extracted.

    • Search by potential bioactivity:
      • Find specific molecules in BIOFACQUIM's database based on their potential bioactivity. The bioactivities were determined by the molecules´ activities over certain receptors.
      • For more details about the values of the reported activities, the cited referenced in the molecular record can be consulted.

    • Search by chemical descriptors
      • Find specific molecules in BIOFACQUIM's database based on their Lipinki and Berg descriptors.
      • To filter by physico-chemical descriptors just use the sliders to define the minimun and maximum desired values, and then click 'search'. All records complying with the selected criteria should appear in a few seconds

    • Similarity Search:
      • By using the similarity search filter, users are redirected to a page where they can draw any desired molecule by using the molsoft plugin.
      • Records in BIOFACQUIM's database are then retrieved in descending order according to the common scoring function 'Tanimoto coefficient'.
      • Currently, the Tanimoto coefficient is calculated using MACCs fingerprints, but future releases plan to allow users to choose the type of molecular fingerprint to use.

    BIOFACQUI's Data Curation Process


    The database for BIOMX DB was based on BIOFACQUIM´s latest dataset release (2023) which comprises a 605-compound version instead of the 400-version released in 2019. Downloaded from: https://www.difacquim.com/d-databases/
    This dataset was enriched by calculating each molecule´s Lipinski and Berg Descriptors along with their corresponding fingerprints in the form of MACCS keys. The two-dimensional descriptors and the fingerprints were calculated using RDKit as it is described in the python library documentation Since MongoDB was chosen as a storage platform, and it stores documents in the form of keys and values, the entries of the CSV file had to be transformed into JSON objects.

    Download the database (605 molecules)

    How to cite us

    You can find all scripts and github code in the published paper at:

    1. F. Martínez-Urrutia, J. L. Medina-Franco, Molecular Informatics 2024, e202400060. https://doi.org/10.1002/minf.202400060

    Additionally please cite the original paper where BIOFACQUIM was firstly introduced

    1. B. A. Pilón-Jiménez, F. I. Saldívar-González, B. I. Díaz-Eufracio, and J. L. Medina-Franco, “BIOFACQUIM: A Mexican compound database of natural products”, Biomolecules, vol. 9, no. 1, 2019, doi: 10.3390/biom9010031