About BacMap 3.0

BacMap 3.0 is the world's largest atlas of annotated bacterial genomes, providing researchers with an interactive platform for exploring bacterial diversity at genomic, metabolic, and phylogenetic scales. The database integrates detailed genome annotations, gene and metabolite information, metabolic pathways, and high-quality visualizations within a unified, user-friendly environment. Through powerful search, browsing, and filtering tools, users can seamlessly navigate among genomes, genes, metabolites, pathways, and phylogenetic relationships, enabling both broad comparative analyses and organism-specific investigations. BacMap 3.0 combines comprehensive biological data with interactive genome and pathway viewers to support genome annotation, comparative genomics, metabolomics, and microbial research.

Overview

BacMap integrates genome annotations, taxonomy, metabolic pathways,metabolite information, and phylogenetic relationships into one resource.

What You Can Do

Browse bacterial genomes, explore pathways, view annotations, and compareorganisms across diverse bacterial taxa.

Features

• Genome collection
• Genome visualization
• Pathway exploration
• Gene and metabolite annotation
• Taxonomic browsing
• Search and filtering

API

We are currently working on developing an API for BacMap.

Please contact rkruger@ualberta.ca (Ray) or metabolomicsinnovations@gmail.com (MII) for more information.

Cite BacMap

1. To be published 2027

2. Cruz J, Liu Y, Liang Y, Zhou Y, Wilson M, Dennis JJ, Stothard P, Van Domselaar G, Wishart DS. BacMap: an up-to-date electronic atlas of annotated bacterial genomes. Nucleic Acids Res. 2012 Jan;40(Database issue):D599-604.

3. Stothard, P., Van Domselaar, G., Shrivastava, S., Guo, A., O'Neill, B., Cruz, J., Ellison, M., & Wishart, D. S. (2005). BacMap: an interactive picture atlas of annotated bacterial genomes. Nucleic acids research, 33(Database issue), D317–D320. https://doi.org/10.1093/nar/gki075

Contact

Questions, suggestions, or feedback are welcome. Please visit the Contact Us page for more information.

FAIR Compliance

BacMap is FAIR. Specifically it is:

FINDABLE:

• F1. meta(data) are assigned a globally unique and eternally persistent identifier.
  Each bacterial genome in BacMap is assigned a globally unique identifier. This identifier is searchable within the database and associated with the genome and its metadata. The identifier is also associated with downloadable data from the database.
• F2. data are described with rich metadata.
  All data in BacMap are described with rich metadata. Every bacterial genome is described in detail, including its taxonomy, organism and strain information, genome statistics, gene annotations, morphology, physiology, metabolic pathways, and associated biological information. Scientific references and external database identifiers are provided where available.
• F3. meta(data) are registered or indexed in a searchable resource.
  All data and metadata in BacMap are indexed, viewable, and searchable through the BacMap database at bacmap.ca.

ACCESSIBLE:

• A1. (meta)data are retrievable by their identifier using a standardized communications protocol.
  All data and metadata in BacMap are retrievable through the website using their associated identifiers. Genome sequences, annotations, and other data can be downloaded through BacMap in standardized formats using standard internet communications protocols. ul li A1.1 the protocol is open, free, and universally implementable.
  The BacMap website is open and free, and its data download operations are compatible with modern web browsers. Downloadable genome and annotation data are provided in commonly used, machine-readable formats. li A1.2 the protocol allows for an authentication and authorization procedure, where necessary.
  No authentication or authorization is required to access or download publicly available BacMap data.
• A2 metadata are accessible, even when the data are no longer available.
  BacMap metadata are associated with persistent genome identifiers, accession numbers, and links to external databases, helping ensure that the associated information remains accessible beyond the lifetime of the project.

INTEROPERABLE:

• I1. (meta)data use a formal, accessible, shared, and broadly applicable language for knowledge representation.
  BacMap data and metadata are provided using established genome data formats, identifiers, nomenclature, and standards used by the bacterial genomics community.
• I2. (meta)data use vocabularies that follow FAIR principles.
  BacMap uses established taxonomic nomenclature, genome identifiers, accession numbers, and standardized biological terminology.
• I3. (meta)data include qualified references to other (meta)data.
  BacMap data and metadata include accession numbers, scientific references, and links to external databases and related biological information.

RE-USABLE:

• R1. (meta)data have a plurality of accurate and relevant attributes.
  BacMap bacterial genomes are described using a wide range of relevant attributes, including taxonomy, genome information, gene annotations, morphology, physiology, metabolic pathways, and other biological information. ul li R1.1 (meta)data are released with a clear and accessible data usage license.
  BacMap data are made available for download under the terms and conditions specified by BacMap and its underlying data sources. li R1.2 (meta)data are associated with their provenance.
  BacMap data include source information, accession numbers, references, and links to external databases where applicable. li R1.3 (meta)data meet domain-relevant community standards.
  BacMap data and metadata use established standards, identifiers, nomenclature, and data formats used by the bacterial genomics and bioinformatics communities.

Funders

This work was supported by the Canada Foundation for Innovation (CFI MSIF #42495), Genome Alberta, a division of Genome Canada, Genome Canada and the Canada Research Chairs Program (CRC Tier 1 #100628). Additional support was provided by the Natural Sciences and Engineering Research Council of Canada (NSERC) through a Discovery Grant (NSERC RGPIN-2025-04867), the NSERC Brockhouse Canada Prize (NSERC BCPIR-590317-2024) and the NSERC Gerhard Herzberg Canada Gold Medal (NSERC GLDSU 601838-2025).