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} ], "person_or_org": { "family_name": "Ebeling", "given_name": "Christian", "name": "Ebeling, Christian", "type": "personal" } }, { "person_or_org": { "family_name": "Overmann", "given_name": "J\u00f6rg", "identifiers": [ { "identifier": "0000-0003-3909-7201", "scheme": "orcid" } ], "name": "Overmann, J\u00f6rg", "type": "personal" } }, { "affiliations": [ { "id": "02tyer376", "identifiers": [ { "identifier": "02tyer376", "scheme": "ror" }, { "identifier": "grid.420081.f", "scheme": "grid" }, { "identifier": "0000 0000 9247 8466", "scheme": "isni" } ], "name": "Leibniz Institute DSMZ \u2013 German Collection of Microorganisms and Cell Cultures" } ], "person_or_org": { "family_name": "Reimer", "given_name": "Lorenz Christian", "identifiers": [ { "identifier": "0000-0002-7805-0660", "scheme": "orcid" } ], "name": "Reimer, Lorenz Christian", "type": "personal" } } ], "description": "
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Presented at
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ELIXIR All Hands Meeting, 2025
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Abstract
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Since its initial release more than a decade ago, the bacterial diversity database BacDive (https://bacdive.dsmz.de) has grown tremendously in terms of content and functionality. Today, BacDive is a comprehensive resource covering the phenotypic diversity of prokaryotes with data on taxonomy, morphology, physiology, cultivation, and more. As the leading database for strain-level information on bacteria and archaea, it has been designated as an ELIXIR Core Data Resource and a Global Core Biodata Resource. These distinctions underscore its importance to the wider microbiological research community. As part of the newly established DSMZ Digital Diversity infrastructure, BacDive is now closely linked to several other databases of fundamental importance to the life sciences, including BRENDA, LPSN and SILVA. These databases will be further developed in a coordinated manner and benefit from frequent data exchange.

Here we present the current status and recent developments in BacDive. The database currently contains 2.7 million data points for 99,392 strains. This includes the world's largest collection of Analytical Profile Index (API) test results, which have now been fully integrated into the database and made searchable. Increasingly, the standardized high-quality data provided by BacDive is being used to train artificial intelligence models. The high-confidence genome-based predictions produced by our own models are now also being used to fill content gaps in the database. We further present a novel BacDive knowledge graph that provides powerful new search capabilities via a SPARQL endpoint to directly search and analyze the knowledge provided through BacDive in a standardized way, supported by a new descriptive ontology.
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", "publication_date": "2025-06-02", "publisher": "Zenodo", "resource_type": { "id": "poster", "title": { "de": "Poster", "en": "Poster" } }, "rights": [ { "description": { "en": "The Creative Commons Attribution license allows re-distribution and re-use of a licensed work on the condition that the creator is appropriately credited." }, "icon": "cc-by-icon", "id": "cc-by-4.0", "props": { "scheme": "spdx", "url": "https://creativecommons.org/licenses/by/4.0/legalcode" }, "title": { "en": "Creative Commons Attribution 4.0 International" } } ], "title": "BacDive - The core database for prokaryotic strain data" }, "parent": { "access": { "owned_by": { "user": "60428" }, "settings": { "accept_conditions_text": null, "allow_guest_requests": false, "allow_user_requests": false, "secret_link_expiration": 0 } }, "communities": { "default": "4e3e2057-2660-4cb1-90ed-87338908f00b", "entries": [ { "access": { "member_policy": "open", "members_visibility": "public", "record_submission_policy": "closed", "review_policy": "open", "visibility": "public" }, "children": { "allow": false }, "created": "2025-01-24T12:06:42.522984+00:00", "custom_fields": {}, "deletion_status": { "is_deleted": false, "status": "P" }, "id": "4e3e2057-2660-4cb1-90ed-87338908f00b", "links": {}, "metadata": { "curation_policy": "

Content must be associated with DSMZ Digital Diversity.

", "description": "DSMZ Digital Diversity is an integrated suite of scientific databases of fundamental importance to the life sciences. The databases include BRENDA, SILVA, LPSN, BacDive and TYGS, which are being developed in a highly coordinated manner.", "organizations": [ { "id": "01n6r0e97" } ], "page": "

The Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures establishes an integrated suite of scientific databases of fundamental relevance for the life sciences. The databases include BRENDA, SILVA, LPSN, BacDive and TYGS which are developed in a highly coordinated manner. A dedicated team of 22 scientists and software engineers builds a common research data infrastructure to significantly improve the access to a plethora of curated and standardized biological data. The resulting data platform DSMZ Digital Diversity will provide an integrated resource and will allow to link and comprehensively analyse the different types of scientific data from all domains of life sciences. 

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