BioColour Library collects chemical fingerprints in Chemical fact sheets. A chemical compound fragment may have multiple names in the scientific literary, and consequently, a chemical fact sheet may show multiple chemical names per fact sheet. For each chemical compound fragment, the sheet collates data from the library under sections Basics, Sources, References, and Analysis results. The Basics-section lists a category, IUPAC-name, chemical formula, exact mass, molecular weight, and structure drawing. The Sources-section collects and links all taxonomy entries the chemical compound fragment has been analysed in along with links to the specific analysis results shown further down the fact sheet. Note that listing a source here does not necessarily mean that the chemical compound fragment was present in the sample – an analysis studying its presence has been performed. The next section, References, lists the scientific literature that reported these findings. This section is intended as a quick reference to check if a certain article is cited for this chemical fragment. These references are also cited in individually the last section per analysis. The last section, Analysis results, collects all analysis results in the BioColour Library. An analysis result in this section may contain masses obtained with mass spectrometry and their measurement modes. It may also contain peak wavelengths of UV/Vis spectrometry. These results are followed by measurement device descriptions identifying the mass spectrometer setups or UV/Vis detectors. The measurement device descriptions are followed by sample preparation descriptions and notes including organism, collection dates, drying and material storage temperatures, extraction and extract handling.
BioColour Library provides multiple ways to access Chemical fact sheets. The simplest way to access a sheet for a specific compound is to use the “Search by name” option in the “Chemical fact sheets”-menu on the top of the site. Searches by origin, mass spectrometry masses and UV/Vis peak wavelengths are other simple query tools located in the same menu.
The search by name query searches for chemical compound fragments by name. The Match-option controls how the input should match the names in the library: option “contains” includes all matches that contain the given name as a substring within the name while “exact” requires the name in the library to match exactly what was given. Both match modes are case-insensitive, i.e., inputs “Quercetin”, “querCetin”, and “QUERCETIN” would match the same entry in exact-mode. The option toggle “Include synonyms” includes in the results listing chemical compound fragments that the library considers synonymous with name being queried. The option toggle “Include without analysis” lists also names that are not related to any analysis result in the library.
Submit-button will perform the query. The results are listed below the Submit-button in three columns: Compound, Taxonomy, and Analysis. The entries in the first column are links to the named chemical compound fragment’s Chemical fact sheet, while entries in the second column are links to the taxonomy the named chemical compound fragment was analysed from. The final column links directly to the relevant analysis result on the Chemical fact sheet.
The search by chemical compound fragment origin query searches for chemical compound fragments by their samples’ origin descriptions. A search condition has seven parts: common name, genus, species, part, form, growth, and planter. The common name refers to non-scientific names of organisms, f. ex., alder, webcap, or woad. Genus and species work together to form a scientific name of form “G. Species” that is, to query chemical compound fragments analysed from, f. ex., Isatis tinctoria, one would input “Isatis” in the genus-field and “tinctoria” in the species-field. Part-field is dropdown list of organism parts like leaves, stems, or roots [In the current version, 2024-11-22, this field is empty]. The form-field refers to sample preparation – the organism may have been used, f. ex., as a whole, chopped, crushed, or dried. It is a multi-selection dropdown field [In the current version, 2024-11-22, this field has buggy behaviour in the user interface]. Growth-field is a dropdown menu of options “cultivated”, “wild”, or “unspecified”, and refers to the growth conditions of the organism. Planter-field is a dropdown menu of options “indoors”, “outdoors”, and “unspecified”.
The query results are tabulated below the Submit-button. The table has three columns: Compound, Taxonomy, and Analysis. The entries in the first column are links to the named chemical compound fragment’s Chemical fact sheet, while entries in the second column are links to the taxonomy fact sheets the named chemical compound fragment was analysed from. The final column links directly to the relevant analysis result on the Chemical fact sheet.
The search by MS mass query searches for chemical compound fragments by their analysed masses from mass spectrometry. A search condition has four parts: detector type, detection mode, mass and error margin. Detector type is a dropdown menu containing all detectors known to the BioColour Library. Detection mode contains options “[M⁺ H]⁺”, ”M⁺”, ”MS²⁺”, ”MS³⁺” , ”[M⁻ H]⁻”, ”MS²⁻”, and ”MS³⁻”.The value and error margin fields take singular values. Multiple conditions can be used by adding new search condition with “Add row”-button, while a search condition can be removed with “Remove”-button. Multiple conditions must all match at the same time, i.e., the library will perform an AND-query. The query can be performed with “Submit”-button.
This query view is intended for exact or near exact queries. That is, to query exact mass, set the exact mass on the value-field and set error margin at 0, while an approximate query should set an expected mass in the value field and an acceptable error margin in the error margin -field. Querying masses within a range is slightly inconvenient: f. ex. querying masses within a range 290 – 310, set the value-field to 300 and error margin at 10.
The query results are tabulated below the Submit-button. The table has four columns: Compound, Taxonomy, Detectors, and Mode and masses. The first column, Compound, names the chemical compound fragment as a link to its chemical fact sheet. The second column, Taxonomy, links to the taxonomy the named chemical compound fragment was analysed from. This column may have multiple entries per one chemical compound fragment if it has been analysed in multiple sources. The third column, Detectors, describes the mass spectrometer configuration and detectors, while the last column, Mode and masses, lists all masses detected for the chemical compound fragment in the queried mode.
The search by UV/Vis peaks query searches for chemical compound fragments by their analysed UV/Vis peaks. A search condition has three parts: detector type, value and error margin. Detector type is a dropdown menu containing all UV/Vis detectors known to the BioColour Library. The value and error margin fields take singular values. Multiple conditions can be used by adding new search condition with “Add row”-button, while a search condition can be removed with “Remove”-button. Multiple conditions must all match at the same time, i.e., the library will perform an AND-query. The query can be performed with “Submit”-button.
The query view is intended for exact or near exact queries. That is, to query exact peak wavelength, set the exact peak wavelength in the value-field and set error margin at 0, while an approximate query should set an expected peak wavelength in the value-field and an acceptable error margin within the error margin -field. Querying peak wavelengths within a range is slightly inconvenient: f. ex., querying peak wavelengths within a range 360 – 400 nm, set the value-field to 380 nm and error margin at 20.
The query results are tabulated below the Submit-button. The table has four columns: Compound, Taxonomy, Detectors, and Peaks. The first column, Compound, names the chemical compound fragment as a link to its chemical fact sheet. The second column, Taxonomy, links to the taxonomy the named chemical compound fragment was analysed from. This column may have multiple entries per one chemical compound fragment if it has been analysed in multiple sources. The third column, Detectors, describes the UV/Vis measurement configuration and detectors, while the last column, Peaks, lists all UV/Vis peaks detected for the chemical compound fragment with the selected detectors.
BioColour Library collects taxonomic information in Taxonomy fact sheets. Like in case of chemical compound fragments, organisms may have multiple taxonomic classifications. Unlike chemical fact sheets, each of these alternative classifications have separate taxonomy fact sheets. When a taxonomic classification is in use and in accepted status, a blue pill with text “accepted name” appears on the main title of a taxonomy sheet. When the classification is obsolete, a grey pill with text “secondary name” will appear instead.
A taxonomy sheet collates data from the library under sections Nomenclature, Genealogy, Distribution, Macromorpology, Chemicals, Images, Colour swatches, and References. The Nomenclature section collects naming information: subsection Taxonomy lists the taxonomy hierarchy. The hierarchy consists of 11 levels: kingdom, order, family, genus, section, species, subspecies, variety, form, cultivar and strain. Each level down to species shows a link to taxonomy browser, which allows quick listing of other taxonomy fact sheets at the same level. Subsection Binomial synonyms collects a list of alternative scientific names of the current organism. Each of them opens a separate taxonomy fact sheet for that name. These sheets may contain analysis results from literature that used that name. The last subsection, Common names, lists non-scientific names of organism in multiple languages. The second section, Genealogy, is divided into two subsections: Genetics shows information on chromosome pair counts, parentage background, ploidy levels, and species identifier DNA, while Subspecies lists entries that are below the current taxon in the taxonomic hierarchy as links to their own taxonomy fact sheets. Distribution section shows the distribution maps of the organism. Macromorphology section shows macroscopic morphological descriptions of the organism including surface, colour and shape for stems, leaves, flowers and other part specific characteristics. Chemicals section lists all chemical compound fragments analysed from samples of the described organism and links them to the appropriate chemical fact sheet, additionally the system also links to the individual analysis results on those fact sheets. Images section contains an image gallery of photographs of the organism, f. ex., photographs of herbarium samples. Colour swatches section collects results from dyeing experiments performed with the organism. These colour swatches should indicate what colours are possible to produce from the organism with some specific dyed material and dyeing parameters. Note that the database does not contain chemical analyses of these dyeings – this part of the database purely for showcasing achieved dyeing results! References sections lists scientific literary that forms the basis of each taxonomy fact sheet.
The biocolour palette of BioColour Library consists of results from dye experimentation. Each experiment records dye source on organism level, dyed material, mordant, and notes from the dying process. Colour measurements include CIELAB-colour coordinates and reflectance spectra. These are shown in dyed sample detail view accessible through three different colour visualisation views.
The CIELAB plot view plots the CIELAB colour coordinates in a 3D scatter plot with L*, a* and b* as the three axes. The plot is dynamic and can be rotated and zoomed in and out. Clicking any of the sample points opens a modal dialog asking the user if they want to see the detailed information described earlier for the sample or return to the plot and select a different sample.
The palette view shows a 26 x 26 grid of the dyed sample colours available in the BioColour Library. This palette grid is static and offers no user actions aside from the detail view. Clicking any of the colour tiles opens the detailed sample view represented by that tile.
The swatches-view represents the dyed sample colours like collection of paint cards. Each dyed sample colour card has a Details-button that opens the detailed information view. The swatches-view is dynamic and allows colour filtering based on user-specified parameters: above the colour cards is a colour chooser and a colour difference slider. Together these define a point and a spherical radius in the CIELAB colour space and all colour points within this sphere will be shown in the view and colour points outside the sphere will be hidden.