Curated Optogenetic Publication Database

Review only	search only for review papers	Review
Exclude reviews	exclude review papers from the search
Benchmarking	search only for papers that benchmark different optogenetic switches	Benchmarking
Background only	search only for basic research papers on photoreceptors	Background
Exclude background	exclude basic research papers on photoreceptors
Multichromatic	search only for papers that combine multiple optogenetic switches within a single optogenetic system	Multichromatic
Time frame	search only within a specified time frame

`color:`	search by the color of a switch-inducing light `color:blue`	Light color
`switch:`	search by an optogenetic switch `switch:"PhyB/PIF6"`	Switch name
`host:`	search by the host cell line or organism of a designed optogenetic system `host:"mouse in vivo"`	Host name
`application:`	search by the type of biological application of an optogenetic system `application:"cell death"` note: Find The Application tool provides you with the same function, but in a guided way, together with an overview of all the available type options	Biological application
`""`	exact match / multi-worded term `switch:"CRY2/CIB1"` finds results with CRY2/CIB1 only typing only `switch:CRY2/CIB1` would find results with either CRY2 or CIB1, i.e. CRY2/CIB1, CRY2/CRY2 and CRY2olig
`()`	group terms for operators `switch:(AsLOV2 VVD FKF1/GI)` finds publications with all specified elements
`AND`	logical operator "and" `switch:"PhyB/PIF" AND host:"in vivo"`
`OR`	logical operator "or" `HEK293T OR CHO-K1`
`-`	exclude a term from the query `PHYB -PIF3` show results with PHYB but exclude PIF3
`*`	wildcard search `switch:PHY*` finds results containing PhyB or PhyA -based switches

Search feature	Query example(s)	Query explanation
OptoBase ontology enables the search engine to recognize common synonyms	`host:HEK293T` `host:HEK293-T` `host:"HEK293 T"`	Search for optogenetic systems implemented in the HEK293T cell line. All the queries return the same result. Note: multi-word terms have to be put in quotations marks, e.g. "HEK293 T", to be processed correctly.
OptoBase ontology allows one to search by common denominators	`switch:phytochromes host:mouse`	Search for phytochrome-based optogenetic systems implemented either in mice or in any mouse cell line.
	`host:neuron`	Search for optogetic systems implemented in any neuronal cell line, regardless of its source organism.
To omit a specific tag, place a - right in front of its category	`color:blue -switch:”CRY2/CIB1”`	Search for blue light-inducible systems, but omit CRY2/CIB1 switch. Note: Slash-separated terms are multi-word terms and thus have to be written in quotation marks, e.g. "CRY2/CIB1".
	`transport -host:bacteria`	Search for publications with the word transport in their title or abstract, but omit the ones presenting optogenetic systems implemented in bacteria.
OptoBase ontology enables the search engine to recognize common synonyms	`switch:("PhyB/PIF6" OR "UVR8/COP1")`	Search for optogenetic systems based on either the PhyB/PIF6 or the UVR8/COP1 switch. Note: the default logical operator of the search engine is AND.