fbd2fa45-56c0-474c-9b8f-73cebae018dd 1.0 PROTO: Pollen-flora Record Overlapping Tool 2025-11-09 The Pollen-flora Record Overlapping Tool (PROTO) is a web application designed to establish a link between user-input pollen taxa and floras. As palynology uses both regular taxonomic classification and a discipline-specific morphotype-based classification to identify pollen grains, it is necessary to establish a common currency between the two to bridge them to plant species. By providing a user interface to input pollen taxa from GBIF’s backbone taxonomy (for regular taxa) and compiled sources (for pollen morphotypes), the tool aims to explore plant biodiversity through pollen by linking input pollen taxa with a flora that is either user-input, retrieved from GBIF’s observational datasets by specifying a set of coordinates and a radius around them, or a combination of the two. The tool automatically matches pollen taxa with plant species in the flora via unique GBIF taxon identifiers, and attributes a percentage score to each pollen taxon and each plant species based on the proportion of total matches they account for. PROTO was designed to infer species-level plant biodiversity of the past through fossil pollen and establish a taxonomically explicit pollen morphotype backbone, but is applicable to modern pollen record as well, as no time constraint is required. Lorenzo Braga University of Modena and Reggio Emilia lorenzo.braga@unimore.it Luca Garusi Freelancer m4r10.v4r10@gmail.com Lorenzo Braga University of Modena and Reggio Emilia lorenzo.braga@unimore.it Lorenzo Braga University of Modena and Reggio Emilia lorenzo.braga@unimore.it Anna Maria Mercuri University of Modena and Reggio Emilia annamaria.mercuri@unimore.it Assunta Florenzano University of Modena and Reggio Emilia assunta.florenzano@unimore.it Jessica Zappa University of Modena and Reggio Emilia jessica.zappa@unimore.it 3.0.1 https://metadatacatalogue.lifewatch.eu/srv/api/records/fbd2fa45-56c0-474c-9b8f-73cebae018dd/attachments/proto_logo_horizontal.png proto_logo_horizontal.png pollen biodiversity taxonomy ecology paleoecology Attribution-NonCommercial-NoDerivatives 4.0 International License. https://protoflora.net/tool/ WWW:LINK-1.0-http--link Home page https://doi.org/10.48372/08we-rg47 WWW:LINK-1.0-http--link DOI Species/Genus/Family-level pollen taxa input or morphotype pollen taxa input Species/Genus/Family dedicated buttons provide a programmatic interface to the GBIF Backbone Taxonomy, allowing the retrieval and input of pollen taxa corresponding to accepted species, genera, and families covered by the GBIF Backbone Taxonomy. Reference-specific dedicated buttons provide an interface to PROTO’s underlying pollen morphotype database, allowing the input of pollen morphotypes from the respective pollen identification manuals and references that are compiled in the database. Each morphotype includes a set of species-, genus-, or family-level taxa listed in the original reference, all of which are linked to their accepted GBIF taxon identifier. A .csv or .tsv file can be input via a dedicated button. It must be formatted as a four-column table: Type (“Species”, “Genus”, “Family” for GBIF backbone taxa; name of the first author of the reference for pollen morphotypes); Name (species binomial name for GBIF backbone taxa; pollen morphotype name for pollen morphotypes), ID (unique GBIF taxon identifier for GBIF backbone taxa; the pollen morphotype’s internal PROTO identifier for pollen morphotypes), and Level (“-” for GBIF backbone taxa; hierarchical level of the pollen morphotype for pollen morphotypes). ID and Level for morphotypes can be viewed in PROTO’s pollen morphotype database. A .csv template or savestate of loaded data can be exported via a dedicated button. Flora input An interface to import a user-defined flora as a .csv file. It must be structured as a table with three columns: GBIF ID (unique GBIF taxon identifier); GBIF URL (URL of the GBIF taxon webpage); Name (taxon binomial name). A flora can also be retrieved from observations via GBIF API by inputting a set of decimal-degree coordinates and a radius around them. In this case, contributing datasets are output to ensure compliance with citation guidelines. A combination of a user-defined flora and a GBIF-retrieved flora can be loaded by first inputting the user-defined flora and then fetching a flora from GBIF observations via GBIF API. A .csv template or savestate of loaded data can be exported via a dedicated button. Pollen taxa and flora overlap An interface to compute GBIF ID-based overlap between the input pollen taxa and flora, and calculate taxon-specific scores representing the proportion of total matches a pollen taxon or species in the flora accounts for. An operation log can be displayed to monitor data processing. Results can be viewed in the webpage, exported as .csv file, or exported as .pdf file. User guide A static webpage displaying a manual for the usage of the tool. Pollen Types References A static webpage displaying a list of identification manuals and references currently covered in PROTO’s internal pollen type database. Pollen Type Database https://protoflora.net/tool/db_browser_v3.php An interface that allows users to search PROTO’s underlying pollen morphotype database. It allows to search pollen morphotypes or taxa therein, both in the whole database at once or in a single identification manual/reference. Information presented is a table listing: species’ binomial names; pollen morphotype(s) they are included in; their GBIF unique identifier and their GBIF taxon page; the internal PROTO identifier of the pollen morphotype(s) they are included in; a flag to indicate if they are selectable as pollen morphotypes (pollen morphotypes exactly corresponding to a single species, genus, or family must be input as GBIF backbone taxa); and the database table they are contained in (whose name is indicative of the original source of the pollen type). If the whole database is searched, an additional column explictly listing the original reference is added to the table. Taxonomic match Taxonomic atlas Data harmonisation Data analysis data classification