Type Strain Genome Server

TYGS Application Programming Interface TYGS API

Summary

The main purpose of the TYGS API is to allow for a programmatic download of results.

BEFORE YOU START USING THE API:

Please note that the underlying computing resources are of course 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"). This would not only be an inefficient workaround solution, you would also potentially block resources other users would want to use as well.

  • That is, 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 on specialized in-house computing hardware as part of a scientific collaboration - just ask!
  • If you just want to run a slightly larger analysis somewhere between e.g. 20 and 70 genomes, please read the dedicated FAQ item.
Once you have established 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 job(s) only once or twice an hour. As soon as the job is finalized, you can proceed to query the actual result data.

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>

Example GUID: 3da2e199-82af-440d-b178-f3fda71cc299

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

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

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

Example GUID: 3da2e199-82af-440d-b178-f3fda71cc299

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

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>

Example GUID: 3da2e199-82af-440d-b178-f3fda71cc299

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

A tab-separated tabular file (tsv format) can be obtained via this API call:

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

Example GUID: 3da2e199-82af-440d-b178-f3fda71cc299

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

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>

Example GUID: 3da2e199-82af-440d-b178-f3fda71cc299

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

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 GUID: 3da2e199-82af-440d-b178-f3fda71cc299
... with species names italicized via HTML formatting commands:

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

Example GUID: 3da2e199-82af-440d-b178-f3fda71cc299
In both cases '<GUID>' has to be replaced by the respective TYGS request guid.

16S rRNA gene sequence tree in Newick format:

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

Example GUID: 29ae139a-3a41-4571-a19b-809af76a3ec5

Genome-scale tree in Newick format:

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

Example GUID: 29ae139a-3a41-4571-a19b-809af76a3ec5

Proteome-scale tree in Newick format:

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

Example GUID: 29ae139a-3a41-4571-a19b-809af76a3ec5

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

16S rRNA gene sequence tree in PhyloXML format:

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

Example* GUID: 29ae139a-3a41-4571-a19b-809af76a3ec5

Genome-scale tree in PhyloXML format:

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

Example* GUID: 29ae139a-3a41-4571-a19b-809af76a3ec5

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

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

Example* GUID: 29ae139a-3a41-4571-a19b-809af76a3ec5

Note: 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.