What is Ontogrator and how does it work?

An ontology is the next step above a controlled vocabulary. It is a collection of terms, with precise definitions, and of the relationships between terms. Ontogrator is a demonstration of how ontologies can be used to automatically generate user interfaces for browsing data sets. 

Behind the scenes there is a database which knows about the ontologies. It has been generated by feeding text from the source data into the Terminizer service which scans the text looking for known ontogical terms. The power of ontology-based annotations raises from the conserved relationship between terms; for instance if you searched for rRNA sequences obtained from the marine environment with simple keyword search, you would not be able to retrieve sequences obtained from hydrothermal vents. An ontology retains the information that a hydrothermal vent is also included in the marine environment, hence will return the respective sequences as well. 

SSU and LSU rRNA sequences have been annotated using four different ontologies; taxonomy (uBio) anatomy (MIAA), gazetteer (GAZ) and environment (EnvO); based on the country, isolation source, host, strain and publication title of each sequence entry.

Please note that the SSU and LSU databases have not been separated in the Ontogrator browser. Please also be aware that the Ontogrator is still in test version – the accuracy of the annotations has not been assessed yet!

Click here to test the Ontogrator...

1. Select SILVA tab

2. To search for sequences from a specific organism-associated habitat, a country or a certain environment, you can use the anatomy, gazetteer and environment browsers respectively. For example, to search for sequences obtained from sand you should follow the path "environmental feature > geographic feature > physiographic feature > rock > sand" in the environment browser.

3. It is also possible to join search terms from different browsers. To search for sequences obtained from marine sediments in Norway, you should select Norway from the Gazetteer browser, and follow the path "environmental matter > sediment > marine sediment" in the environment browser.

4. Finally, you can also search for a term of choice within the search fields of different browsers. To search for sequences obtained from the intestine, you can type "intestine" in the anatomy browser search field.

5. To go back to the SILVA browser for a selected sequence, simply just click on the accession number on the left side!