SynoSpecies

About SynoSpecies

SynoSpecies is a tool developed by FactsMission AG to leverage the RDF data provided by Plazi. The RDF data of all treatments is stored in an AllegroGraph triple store allowing SPARQL queries over the data. SynoSpecies allows manually writing and submitting such queries in the advanced mode and send such queries in the background when using the easier interface.

SynoSpecies is an Open Source application running purely in the browser, the source code is available on GitHub.

About Plazi

Plazi is an association supporting and promoting the development of persistent and openly accessible digital taxonomic literature. To this end Plazi will:

Maintain a digital taxonomic literature repository to enable archiving of taxonomic treatments.
Enhance submitted taxonomic treatments by creating TaxonX and Taxpub XML versions.
Participate in the development of new models for publishing taxonomic treatments in order to maximize interoperability with other relevant cyberinfrastructure components (e.g., name servers, biodiversity resources, etc...)
Advocate and educate about the vital importance of maintaining free and open access to scientific discourse and data

About FactsMission

FactsMission offers consulting and development services to create, process, store, publish, and consume linked data.

FactsMission helps you provide data in such a way that it can be easily used as the foundation of different applications as well as linked to as an authoritative source.

FactsMission helps you grow communities around your data to maximize its impact and increase your organization’s influence.

Explanation of the Interface

Search

SynoSpecies supports using any of the following as search terms:

A human readable taxon name in the form Genus, Genus species, or Genus species infraspecific.
The input field will offer auto-complete suggestions for this.
A URI for a taxon-name or taxon-concept, i.e. a URI starting with http://taxon-name.plazi.org/ or http://taxon-concept.plazi.org/.
(You can find these by expanding any of the search results by clicking the )
A URI for a Catalogue of Life-taxon, i.e. a URI starting with https://www.catalogueoflife.org/data/taxon/.

Options

If the “Show CoL-synonyms” option is disabled, SynoSpecies will not follow -synonyms listed in the Catalogue of Life. They will still be shown if they are found via treatment citations. Use this option if you get too many deprecated synonyms otherwise.

If the “Include subtaxa of search term” option is enabled, SynoSpecies will also search for all taxa that are subtaxa of the search term. For example, with this option enabled, a search for “Mini” will also include “Mini ature, “Mini mum”, and “Mini scule”, as if you also searched for these.

If the “Do not search for Synonyms” option is enabled, SynoSpecies will look up only the search term (and possibly its subtaxa), but it will not show any other synonyms. This is usually faster, and can be useful if you are only interested in the treatments for a specific taxon.

These options are added to the URL parameters, so if you bookmark or share a given search this preserves the options used.

Timeline

The Timeline visualizes the data in a two-dimensional grid. Here, the rows correspond to taxon names and the columns correspond to years of treatments.

Usually, one row corresponds to one taxon and one authority. However, if there are multiple authorities given for a taxon (or if some treatments omit the authority entirely), The taxon is split into multiple rows with the top row used for authority-less citations and underneath one row per authority. In such cases, the / buttons can be used to collapse/expand the taxon into one row. If there are many authorities given for one taxon, the row will be collapsed by default.

Hint: To quickly scroll to a given taxon in the list below, click its name on the left.

In the right half of the Timeline, we find a visualization of all treatments found, grouped by year. A yellow bar always indicates a single treatment. Hover over one to reveal its authors. If there are multiple treatments in one year, they can be collapsed into one blue bar showing aggregate counts of the icons. Clicking a blue bar or the buttons next to the year number will expand the year to show all its treatments.

If there are entries of the Catalogue of Life found, the corresponding synonym-relationships are shown in the first column as there is no date information here. Here too is a blue bar used for the collapsed (union) state, and (when expanded) separate yellow bars for each accepted name and its synonyms.

Other Notes

In some rare cases, mostly with viruses, entries the Catalogue of Life is missing explict dwc:genericName and dwc:specificEpithet annotaions. In this case, it is no longer possible for synospecies to correlate the Catalogue of Life-entry with the corresponding Plazi entry. To indicate this, the name of the (Catalogue of Life) taxon is surrounded with quotation marks.

Icons

This indicates a defines-relationship between a treatment and a taxon: “This treatment defines (e.g. as ‘sp. nov.’) a new Taxon.”

This indicates a treats-relationship between a treatment and a taxon: “The taxon the treatment is about. SynoSpecies interprets this as an assertion that this name is valid.”

This indicates a deprecates-relationship between a treatment and a taxon: “Synonym(s) cited in the treatment.”

This indicates a cites-relationship between a treatment and a taxon: “Other taxa cited in the treatment. These citations are not considered synonyms by SynoSpecies.”

This is used if no defining treatment could be found in the plazi dataset as a stand-in for the defining treatment implied by the given authority.

This indicates that the Catalogue of Life considers this an accepted name.

This indicates that the Catalogue of Life considers this a synonym or combination.

This indicates Plantae. It is only shown in the Timeline if there are multiple kingdoms present in the result.

This indicates Animalia. —“—

This indicates Bacteria. —“—

This indicates Fungi. —“—

This indicates a missing kingdom. —“—

– A green tint is used to highlight homonyms.

Used for treatments with figures. They are shown when the treatment is expanded.

Used for treatments with cited materials. They are shown when the treatment is expanded.

This is used as decoration next to the vernacular or common names of a taxon.

This is used for the button which expands the details for a taxon. Additionally, this is used as decoration next to the justification (“Why this name was found by SynoSpecies.”)

This is used for the button which expands the details for a treatment, Catalogue of Life entry, and to expand rows or columns in the Timeline.

Collapse details, row, or column.

This indicates a link which will open in a new tab.

The Wikidata logo, Wikipedia 'W' icon, Wikispecies logo, and Wikimedia Commons logo are used for links to the respective sites.