bold codecorrespond to database objects:
Proteinsare represented with a name, common aliases, amino acid sequence, external accession IDs (currently GenBank, UniProt, Protein Data Bank, and NCBI Identical Protein Groups), aggregation type, photochromicity/switch type, and required cofactors (e.g. biliverdin). Every protein has a
primary reference(that introduced the protein),
additional references( limited to those that further characterize the protein), and the NCBI taxonomy ID for the
parental organismfrom which the protein was evolved (e.g. 6100 for Aequorea victoria). Protein
lineagesare stored as recursively as parent-child relationships between two proteins, along with the mutation that generates the child sequence from the parent.
Excerptsare snippets of text from
referencesthat convey key information about a
proteinthat is otherwise difficult to capture within the current database schema, and appear on both the corresponding protein and reference pages.
proteincan have one or more
statesthat represent the protein in a certain intrinsic condition (e.g. pre/post photoactivation or photoconversion) or under a certain environmental condition (e.g. pH, calcium, etc.).
Stateshave typical fluorescence characteristics such as
fluorescence lifetime, and full
spectradata (stored as an array of wavelength/value pairs, along with metadata describing, for instance, the pH or solvent under which the spectra was measured).
Transitionsrepresent conversions between two
statesin response to some stimulus, such as irradiation with a certain wavelength.
Bleach measurementscapture information about the photostability of a given protein
stateunder one set of experimental conditions (such as microscope modality, light source and filter spectra, illumination power, temperature, fusion protein, cell type, etc.) along with the
referencethat made the measurement.
OSER measurementsare quantifications of the monomericity of the protein (Costantini et al 2012), taken from a given
Referencesare stored as DOIs, and corresponding metadata (such as title,
authors, date, journal, etc.) is pulled from Crossref. Every reference and author object has a dedicated page showing the corresponding
references, respectively, attributed to that object.
microscopes. Microscopes are stored as collections of
optical configurations, each of which comprises a set of filters,
light source, and
camera, all of which are associated with a