News

Taxonomy-based media search

Thanks to the integration of MycoBank and ITIS data, it is now also possible to find eukaryotic species in the taxonomy search. Of course, only taxonomic ranks for which we have culture media can be found. Since taxonomy is a controversial topic, here are some disclaimers, which you can also find on the site itself:

Disclaimer

The taxonomy search is intended to assist in finding media from closely related strains. It does not show a state-of-the-art representation of the taxonomy, nor does it claim to be complete or up-to-date.

We obtain the taxonomy from external sources, i.e. LPSN for prokaryotes, MycoBank for fungi, and ITIS for everything else. However, we update the database at irregular intervals, so do not expect everything to be up-to-date.

We show only a simplified taxonomy, which contains only the ranks given in the dropdown. For the sake of simplicity, we omit further ranks such as subfamily.

Furthermore, we reserve the right to change the taxonomy independently if there are scientific reasons that lead us to do so.

Thanks to the kind permission of CCAP, we were able to add more than 100 new media and over 3000 new strains. As a result, MediaDive now supports new organism groups such as algae and protists. The organisms are now also further subdivided, which is why you can now search for e.g. cyanobacteria or diatoms on the strain page.

We have made it official and are pleased to present our publication to you. We have worked hard to bring you the best cultivation media. If MediaDive supports you in your work, we would be grateful if you cite us.

Koblitz, J., Halama, P., Spring, S., Thiel, V., Baschien, C., Hahnke, R., Pester, M., Overmann, J. and Reimer, L. (2022) MediaDive: the expert-curated cultivation media database. Nucleic Acids Research http://dx.doi.org/10.1093/nar/gkac803

Did you know that the DSMZ media in MediaDive are maintained by experts? We have developed an internal curation interface to ensure that the media in the database are always up to date. But until now, it was exclusively reserved for employees at the DSMZ to add media to the database. For this reason, we have developed the Medium builder.

The Medium builder is a tool kit that allows you to easily add your own medium to the database. To do this, you can either create a new medium from scratch or import an existing one. Once published, your medium will be given its own medium number and added to the list of media so you can share and reference it with ease.

Already one of the first versions of MediaDive had a working API (Application Programming Interface) that allowed developers to interface with our database. However, this API was very rudimentary and literally undocumented. For this reason, we completely revamped our API, adding new entry points and revising the existing ones. We also added detailed documentation. You can find it by clicking on this logo:

For a long time, the working title of this database was BacMedia, in reference to its sister database BacDive. However, since this suggested that this database would only contain media for bacteria, we decided to rename it in the last few meters before release. After all, nothing is further from our minds than to discriminate against all the (at this point) 408 media for archaea, yeasts, fungi, and phages.

To make a long story short, we decided to rename the database to MediaDive.

As a result, the database also got a new outfit right away. Thereby we show more our affiliation to the DSMZ and its mission for digital diversity. There was also a new logo for MediaDive to match the new web design on the one hand and also to capture the character of linked data on the other.

• Database update: 57 new media and 577 new strains were added.
• The web interface was optimized and adapted.
• Media were partially curated and optimized by experts for the new format.
• We added light to the modifications.

• We added a taxonomy based search to find media from closely related strains. Check it out!
• We have improved the Medium finder! You can now include gases and solutions into your search and you will receive more information. Additionally, we added the whole new Solution finder .
• We have improved the adjustment of the final volume of the medium.
• We added webpage tours to a couple of pages. Whenever you see this icon: , click on the button and discover all functionalities of the page.

• We added strain-specific modifications to our media. Check them out!
• We added more download options (e.g. for ingredients, media, solutions, etc).
• We integrated BacDive metadata on the media pages.
• We improved our PDFs drastically. You can now also influence the final volume and select a strain for the medium.
• We improved our interfaces and added more links to the pages. Single ingredients and solutions now have their own page.
• We added German as a language and translated most parts of the website. Change language