Type Strain Genome Server
Summary

The TYGS has an API for the programmatic download of results:

BEFORE YOU START USING THE API: Please note that the underlying computing resources are limited. That is, please do not write scripts that run large-scale analyses via the TYGS by splitting larger datasets into chunks that comply with the current upload cap (i.e. please avoid "request bombing"). That way, you would block resources other users would want to use as well. If you want to run large-scale TYGS analyses, please contact the TYGS team. Whenever possible and deemed reasonable, we frequently offer to run large-scale analyses as part of a scientific collaboration - just ask! If you establish a script-based access to the TYGS, please use the TYGS resources in a considerate way, i.e., do not query the API a dozen of times a minute but rather check the status of your jobs only once or twice an hour. The best way would be to wait for the automated response email which is delivered upon finalization of your request.

The following API call will return the status of your job in JSON format. Once the finalization_date is set, the job is done.

https://tygs.dsmz.de/user_requests/show/status/<GUID>

'<GUID>' has to be replaced by the respective TYGS request guid.

Example

The following API call will return the identification results of your job (Table 2) in JSON format:

https://tygs.dsmz.de/user_results/show/identification_table_json/<GUID>

'<GUID>' has to be replaced by the respective TYGS request guid.

Example

The following API call will return the dDDH results of your job (Table 3) in JSON format:

https://tygs.dsmz.de/user_results/show/digital_ddh_json/<GUID>

'<GUID>' has to be replaced by the respective TYGS request guid.

Example

The following API call will return the strain table of your job (Table 4) in JSON format:

https://tygs.dsmz.de/user_results/show/strain_table_json/<GUID>

'<GUID>' has to be replaced by the respective TYGS request guid.

Example

Download of literature (i.e., original species descriptions of the type strains included in a particular TYGS job) in BibTex format ...

... with species names italicized via LaTeX formatting commands:

https://tygs.dsmz.de/user_results/show/bibtex/<GUID>

Example

... with species names italicized via HTML formatting commands:

https://tygs.dsmz.de/user_results/show/bibtex_with_html/<GUID>

Example

In both cases '<GUID>' has to be replaced by the respective TYGS request guid.

Download of trees (either based on 16S rRNA gene sequence or genome-scale data):

16S tree in Newick format:

https://tygs.dsmz.de/user_phylogenies/16S/newick_by_guid/<GUID>

Example

Genome-scale tree in Newick format:

https://tygs.dsmz.de/user_phylogenies/genome/newick_by_guid/<GUID>

Example

In all cases '<GUID>' has to be replaced by the respective TYGS request guid.

Download of trees (either based on 16S rRNA gene sequence or genome-scale data):

16S tree in PhyloXML format:

https://tygs.dsmz.de/user_phylogenies/16S/phyloxmlannot_by_guid/<GUID>

Example*

Genome-scale tree in PhyloXML format

https://tygs.dsmz.de/user_phylogenies/genome/phyloxmlannot_by_guid/<GUID>

Example*

Proteome-scale tree in PhyloXML format (if tree was ordered via the result page before)

https://tygs.dsmz.de/user_phylogenies/proteome/phyloxmlannot_by_guid/<GUID>

Example*

In all cases '<GUID>' has to be replaced by the respective TYGS request guid.

* If you are viewing the PhyloXML examples in your browser, you have to switch to page source mode to actually see the XML.