Research Article |
Corresponding author: Stefano Martellos ( martelst@units.it ) Academic editor: Stephen Boatwright
© 2020 Stefano Martellos, Fabrizio Bartolucci, Fabio Conti, Gabriele Galasso, Andrea Moro, Riccardo Pennesi, Lorenzo Peruzzi, Elena Pittao, Pier Luigi Nimis.
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Martellos S, Bartolucci F, Conti F, Galasso G, Moro A, Pennesi R, Peruzzi L, Pittao E, Nimis PL (2020) FlorItaly – the portal to the Flora of Italy. PhytoKeys 156: 55-71. https://doi.org/10.3897/phytokeys.156.54023
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Digital data concerning the flora of Italy are largely fragmented among different resources hosted on different platforms, and often with different data standards, which are neither connected by a common access point, nor by web services, thus constituting a relevant obstacle to data access and usage. Taxonomic incongruences add a further complication. This paper describes “FlorItaly”, an online information system which allows to access and query updated information on the checklist of the flora of Italy, aiming at becoming an aggregator for Italian botanical resources. “FlorItaly” was developed in a collaborative effort by more than 50 taxonomists, with the support of the Italian Botanical Society, and of Project “Dryades” (University of Trieste), to provide a better and reliable organization of botanical knowledge in Italy, as well as a relevant simplification for data retrieval, and a further stimulus towards a more collaborative approach in botanical research.
biodiversity data, checklist, floristics, taxonomic standard
Taxonomic checklists summarize the hitherto available knowledge of the biodiversity in a given area. They can be simple lists of names, or provide detailed information on each taxon. In well-explored areas, they are the basis for the development of a true flora, while in poorly known areas they provide a baseline for further investigation. Furthermore, checklists are also a mean for nomenclatural stability, providing a reliable taxonomic backbone. Checklists can potentially be of use for connecting information from different sources, ideally making biodiversity data interoperable through names (or Unique Identifiers – UIDs – associated with names). While being a fundamental tool for researchers, they can be relevant also for decision-makers, as they provide a baseline for informed decisions. National checklists are especially relevant, since environmental decisions are taken at national level. Being open-ended works, checklists can greatly benefit from a digital “publication”, which allows their updating with new information, continuously, or at regular intervals. Digital, online publication also makes a checklist more visible and accessible to target users (
The development of online plant data repositories, especially focused on taxonomic information as nomenclatural backbones, is the main aim of several international initiatives. In Europe, the Euro+Med PlantBase (
In Italy, efforts for the creation of a network of databases on the flora and vegetation of the country date back from far before the Rio Conference. As discussed by
This paper details the result of this effort, “FlorItaly”, which is accessible online at the address http://dryades.units.it/floritaly, and is being updated every six months.
The core of “FlorItaly” is a software written in PHP language, which works on data stored in a MySQL database, running on the servers of the Project “Dryades”, hosted at the Department of Life Sciences, University of Trieste. “FlorItaly” organizes nomenclatural and distribution data from the recent checklists of the Italian native and alien vascular flora and their subsequent updates, which are published every six months, and makes them interoperable with other resources.
The taxonomic circumscription of families follows
The main data source of “FlorItaly” are the two checklists of the native (
Distribution data (taken from the checklists, and expressed as presence-absence) are given for each of the 20 administrative regions of Italy (two enclave-countries Republic of San Marino and Vatican City State are not considered). When information on the occurrence of a given subspecies for a region is missing, only the occurrence at species level is reported. For each region, the presence and occurrence status of each taxon is provided by using the following categories: a) occurring, b) doubtfully occurring, c) no longer recorded (reliable historical record), d) extinct or possibly extinct, e) recorded by mistake, f) alien at regional and/or national level (casual, naturalized, invasive, undefined invasion status), g) Italian endemic (status attributed to those taxa occurring only in Italy, or in Italy and Corsica, or in Italy and Malta), h) cryptogenic, i.e. a doubtfully native taxon, whose origin in Italy is unknown, i) taxonomically doubtful, j) data deficient (unknown regional distribution; unknown alien status), k) archaeophyte, and l) neophyte. Occurrence status can also be provided at national level, when relevant, with the following categories: i) confirmed/not confirmed; ii) extinct; iii) doubtful; iv) data deficient; v) erroneously reported for the country); vi) endemic; vii) cryptogenic; viii) esoticity (neo- or archaeophyte). Presence and occurrence status at regional level are depicted in a distribution map (see description of a taxon page below), while those at national level are reported as textual information. A national standardized system was developed by
• casual: alien plants that may thrive and even produce offspring occasionally outside cultivation, but that usually disappear, since they are unable to form self-maintaining populations. Hence their persistence relies on repeated introductions;
• naturalized: alien plants that occur with self-maintaining populations without direct human intervention;
• invasive: alien plants that occur with self-maintaining populations without direct human intervention, and produce fertile offspring which can reach considerable distances from the parent individuals, thus being able to spread over a large area;
• archaeophytes: alien plants introduced to Italy before 1492 (approximate date corresponding to the discovery of America);
• neophytes: alien plants introduced to Italy after 1492.
Taxa involved in former domestication processes are separated into two categories:
• culton: plant distinct from its wild relative(s) and capable to conserve its taxonomic independence in cultivation only; records from the wild are regarded as casual occurrences;
• feral: wild plant originated from a culton escaped from domestication, and usually taxonomically distinct from its wild relative; it can either belong to the same taxon of the culton or to a different taxon.
Taxa at varietal rank were not considered; hybrids were considered only for the alien flora.
All of these data are released under a under a CC BY-SA 4.0 license.
“FlorItaly” makes the checklists data inter-operable with other resources (see below for a comprehensive list) which use the same taxonomy and the same UIDs of the checklist. This is achieved through:
• web services. “FlorItaly” uses a web service embedded into Wikiplantbase (
• direct querying to external databases, in the case of several “Dryades” resources. Since the developers of all the resources of “Dryades” and “FlorItaly” are the same, it was possible to directly access the other databases by querying through taxon name.
• auto-generated links, made to provide access to resources of
“FlorItaly” is accessible online since June 20th, 2018, at the address: http://dryades.units.it/floritaly. It has an average of 2,200 page views, and 220 unique visitors per day, and a total of ca. 1,100,000 page loads since its publication on the Internet. Users’ retention rate – calculated for March 2020 – is 61%.
“FlorItaly” has 3 query interfaces: 1) basic, 2) standard, and 3) advanced. In the second and third interface, users are allowed to combine several parameters in order to perform complex queries. The combination of parameters is transparent to the users, and makes use of the two logical operators OR (when two or more parameters are selected, if either is true, the complex expression is true) and AND (when two or more parameters are selected, all of them must be true for the complex expression to be true). The two operators are combined in the queries differently in each query interface (see below). All interfaces allow to query by taxon name. The query can be done by inputting an accepted name, a synonym, or part of their names. The query is case-insensitive, and no special characters are allowed (e.g., querying from a string followed by the character “*” will return no results, since the character “*” is read as text, and not as a “jolly” character). Each interface always returns a list of accepted names and/or synonyms, each giving access to a taxon page.
Basic query interface . It allows to quickly access all the information on each taxon, organized in “taxon pages”, which are dynamically generated from the database. When a synonym is typed as a query string, the thesaurus of synonyms is invoked, providing a link to the accepted name. For each query, a list of all synonyms, if present, is provided after the list of the accepted names. The basic interface also allows to filter the query by family (selecting one family from a drop-down menu). Furthermore, it permits to query the Thesaurus of Italian and local names of Project “Dryades”. When an Italian name is used as query string, the system provides a list of vernacular names together with the related scientific name(s). The latter give access to the taxon pages.
Standard query interface . This interface allows simple queries on national and regional floras by including/excluding: i) taxa known from reliable historical records only; ii) extinct taxa; iii) taxa reported by mistake; iv) taxa known from doubtful records only; v) alien taxa. The first four parameters are combined by the logical operator OR (in the same query users can include/exclude more than one of them). The last parameter (alien taxa) is combined with the others by logical operator AND. This interface can also display the results in the form of an image gallery.
Advanced query interface . This interface allows complex queries on the flora of the whole country, or on the floras of different Operational Geographical Units (OGUs), consisting of one or more administrative regions. If no OGU is selected, the system operates on the whole national flora, including extinct taxa, and those reported by mistake. For Italy, or for any other OGU, it is possible to refine the query by using the following seven groups of parameters:
A) occurrence status: 1) taxa known from reliable historical records only; 2) extinct taxa; 3) taxa reported by mistake; 4) taxa known from doubtful records only; 5) data deficient taxa (those recorded from Italy, but without sufficient knowledge on regional records);
B) alien status: 6) invasive; 7) naturalized; 8) casual; 9) other alien taxa (currently without invasiveness status); 10) cryptogenic taxa (doubtfully native);
C) alien, by period of introduction: 11) neophytes (since 1492); 12) archaeophytes (until 1492);
D) feral/culton status: 13) feral; 14) culton;
E) 15) Italian endemics;
F) 16) exclusive endemics (Italian endemics whose distribution is restricted to the selected OGU);
G) 17) taxonomically doubtful taxa.
Inside each group of parameters, the systems uses the logical operator OR, while among the groups the system uses the logical operator AND, as described for the standard query interface (see above).
The taxon pages, which are the final outcome of a query, display data from the checklist, and aggregate, or link different external resources (Fig.
Taxon page for Poa annua L. from FlorItaly [accessed on 18 June 2020]. The page lists taxon name, synonyms, distribution, also depicted in a distributional map, taxonomic position (in this case in the APG IV scheme), an image, links to external resources, Italian names, and a photo gallery.
At the top of the taxon page there is the accepted name, followed by synonyms, and the presence in the 20 administrative subdivisions of the country. Other information, such as whether the taxon is an archaeo-/neophyte, endemic, etc. are reported immediately below, when present.
This first block is followed by two external resources, a link to a cladogram, with the relative taxonomic information, and an image, which are displayed on the left. On the right of the page, a distribution map is dynamically generated by using the presence in the administrative regions, plus the other data on the taxon (e.g. whether it is an invasive).
The cladograms and the taxonomic information are external resources, deriving from an archive of cladograms from Project “Dryades”, which follows
These two sections are followed by a link to the I.P.F.I. database of Acta Plantarum, and a link to the Wikiplantbase Italy project. Each link reports the name of the resource, and its logo, and opens in a new page. Acta Plantarum is one of the most active groups of amateur botanists in Italy, and the resources present in the I.P.F.I. pages include digital images, altitudinal distribution, growth forms, etymology, discussions, etc. The Wikiplantbase initiatives (
At the bottom of the taxon page there is an image gallery, which currently derives from the archives of Project “Dryades”. However, since “FlorItaly” can be made interoperable with other resources, potentially other archives can be accessed, and integrated in the taxon pages (or linked as external resources). Images are displayed as thumbnails, and can be enlarged by a simple click. Each image is coupled with metadata that specify author, source, license of use, locality, and date of the shot, and any other metadata, when available. When the license is not specified, the author of the image reserves all rights. Approximately 80% of the images of Project “Dryades” are original, and released under a CC BY-SA 4.0 license, which means that anyone can use them, for any purpose, provided that author, source and license are mentioned.
Global access to biodiversity information is considered mandatory for research, and decision making since the UNESCO Conference of Rio outputs (
Given the relevance of the two checklists of native and alien vascular flora of Italy (
As far as sustainability of the system is concerned, “FlorItaly” will be maintained by the Department of Life Sciences of the University of Trieste, which will assure regular updates of software, and data. Furthermore, a backup instance of “FlorItaly” will be installed in the forthcoming LifeWatch (
While originally developed to target an academic audience, “FlorItaly” can be useful for a wider target audience, such as decision makers, and citizens, in the fields of formal education, life-long learning, and citizen science. Other resources (such as primary biodiversity repositories, a loci classici database, etc.) are planned to be made interoperable in “FlorItaly”. Furthermore, the system could be potentially connected to digital identification keys. Some keys have been already developed in the framework of Project “Dryades”, by using software FRIDA (