We update the database as frequently as possible, but a ground rule is at least once a week.

Each publication in our database is manually analyzed and assigned a set of tags that allow for advanced filtering and analysis options.

Original publications on optogenetics are assigned the tags that describe which optogenetic switches have been implemented within the work presented in the publication (together with the information on which color of light activates them), in which host organism or cell line was this implementation done, and what kind of biological application(s), if any, were achieved through optogenetic control. Furthermore, in case two or more optogenetic switches were combined within a single optogenetic system, the publication is further tagged as Multichromatic. In addition, if the purpose of a publication was to compare the performance of multiple optogenetic switches, then it has a tag Benchmarking.

Review publications on optogenetics are assigned the tag Review and further tags of all optogenetic switches that the publication discusses. However, since the review publications often address a plethora of optogenetic switches, we display their switch tags only at the level of optogenetic switch classes. Note: Regardless of this display choice, the publication search engine still allows you to search at the precision of single optogenetic switch tags.

In addition to the optogenetic publications, our database also contains a set of basic research publications on optogenetic switch proteins. These publications provide further helpful information for optogeneticists, such as the 3D structure of the switch proteins or insights into the proteins’ switching mechanisms; hence the tag Background.

No, our database is actually supported by a rich ontology, which allows one to search for publications in many advanced ways, including

• synonyms (e.g. switch:"VVD" will give the same set of results as switch:"vivid", likewise if you search for host:"HEK293-T" instead of host:"HEK293T")
• parent relations (e.g. instead of for a single mouse host cell line or in vivo experiments in mice, one can search for host:"mouse" or host:"mammalian" and hence obtain all the publications matching the child-tags of these latter search options)
• classes (e.g. host:"rat hippocampal neurons" will give you the results that match this particular host cell line, but host:"neurons" will be able to find the publications that employ any neuronal type of host)

In case something does not function or look as it should, please report it to us by sending a message via our contact form or writing an email to hello@optobase.org. It is in everyone’s interest to make OptoBase as useful and reliable as possible.

Definitely! If you have any suggestions on how to further improve OptoBase, so that it will best serve the scientific community, we would be happy to hear them. Depending on the context and complexity of your suggested feature/tool, we can either arrange to implement it on our own, or set up a collaboration with you (make you a part of our OptoBase team).

If you use OptoBase for your optogenetics research work, or would like to mention it in your publication as a valuable resource for optogenetics, please, do not cite it as a website URL, but assign it a proper (measurable) credit by citing the paper within which it was formally presented:

K. Kolar, C. Knobloch, H. Stork, M. Žnidarič, W. Weber: OptoBase: A web platform for molecular optogenetics. ACS Synth. Biol. 2018; 7: 1825–1828. DOI: 10.1021/acssynbio.8b00120.