Difference between revisions of "Existing name checking mechanisms"

Revision as of 10:39, 4 July 2025

In the following we list (in alphabetical order) large scale aggregators of taxonomic information that either provide name matching services themselves or are indirectly accessible for name checking by means of one of the repository services.

(Testing and documentation in progress)

Terminology

See What is name matching? for general discussion on terminology and intent.
The following results from the TNLS (Taxonomic Name Linking Services) 3PP (TETTRIs third party project) provide an important overview:
Overview of input parameters of aggregator services
Overview of output fields of aggregator services

Algaebase

Taxonomic scope: Algae
Geographic scope: Global
Currently no name matching, outdated copies included in Global Names and ChecklistBank, recent version in WoRMS.
A simple taxon match implementation is planned via AlgaeBase API in the framework of Lifewatch - Thematic Service Taxonomy

Australian Plant Name Index

Taxonomic scope: Plants
Geographic scope: Australia
Software updated: ?
Codebase/Documentation: ?
Data updated: ?
Limitation: not stated, check with nearly 21,000 names ended in server error [23 may 2024]
Local ID input returned: NO
Local Name input returned:
Aggregator name ID returned:
Interactive mode for partial matches: NO
OpenRefine reconciliation API: NO
Other: APCalign: an R package workflow and app for aligning and updating flora names to the Australian Plant Census

Botanical Information and Ecology Network (BIEN)

Taxonomic scope: Plants
For Name matching see TNRS below.

Catalogue of Life (COL)

Taxonomic scope: All taxa but incomplete for some zoological groups (genera only) and for parts of the Algae. The "eXtended release" with gaps filled from other datasets.
Geographic scope: Global
Software: Editions are integrated into Checklist Bank and Global Names, see below.

Checklist Bank (GBIF & Catalogue of Life)

Taxonomic scope: All taxa or specific groups depending on the target dataset chosen
Geographic scope: Global or specific areas, depending on the target dataset chosen
Software updated: current (last checked june 26, 2025)
Codebase/Documentation: https://www.checklistbank.org/about/API
Data updated: depending on target dataset
Limitation: Direct input of list limited to 6000 names. (With file upload for asynchronous response not limited)
Local ID input returned: YES
Local Name input returned: YES
Aggregator name ID returned: YES - in download only
Interactive mode for partial matches: NO
OpenRefine reconciliation API: NO (but for OpenRefine possible with REST services)
Other: Login with GBIF account is recommended, required for file upload (self-registration at https://www.gbif.org/user/profile)

Euro+Med PlantBase

Taxonomic scope: Plants
Geographic scope: Europe and the Mediterranean area (see https://europlusmed.org/explanations for details and a map
Currently no name matching, but included in PESI (see below)

GBIF Taxonomic Backbone

Taxonomic scope: All taxa but incomplete for some zoological groups (genera only) and for Algae
Geographic scope: global
Software updated: current
Codebase/Documentation: see Species API
Data updated: August 28, 2023 (is being replaced by COL eXtended edition)
Limitation: 6000 records
Local ID input returned: YES
Local Name input returned: YES
Aggregator name ID returned: NO
Interactive mode for partial matches: NO
OpenRefine reconciliation API: NO
Other:

Global Names Verifier

Taxonomic scope: defined by stored datasets - option to restrict matching to individual source dataset
Geographic scope: global (cross datasets or with global datasets) or restricted by choice of dataset
Software updated: active Feb. 2025
Codebase/Documentation: https://github.com/gnames
Codebase/Documentation: https://resolver.globalnames.org/api
Data updated: Differs for stored datasets
Limitation: 5000 names, at least in interactive mode
Local ID input returned: NO
Local Name input returned: YES
Aggregator name ID returned: YES (may be a taxon ID)
Interactive mode for partial matches: NO
OpenRefine reconciliation API: YES, with step-by-step documentation: https://github.com/gnames/gnverifier/wiki/OpenRefine-readme
Other: Offers a kind of query language that seems to be very flexible
TETTRIS Notes includes:
a 2021 Algabase set (but matching doesn’t work - [8/23])
a (supposedly) up to date Index Fungorum search – the output (HTML, JSON, CSV, TSV) contains a UUID in the „id“ field which is not the „Index Fungorum UUID“, probably a Global Names UUID. But the field „RecordID“ is the „Index Fungorum Registration Identifier“ which in a URL resolves to the name page, e.g.: http://www.indexfungorum.org/Names/NamesRecord.asp?RecordID=229900

Index Fungorum

Taxonomic scope: Fungi
Geographic scope: Global
Currently no name matching, but included in Catalogue of Life and Global Names

==Integrated Taxonomic Information System - ITIS, Taxamatch service Taxonomic scope: Plants, animals, fungi, and microbes
Geographic scope: "North America and the World"
Currently (June 18,2025) access via Firefox not working properly.

International Plant Name Index (IPNI)

Taxonomic scope: Vascular plants (source: POWO - IPNI offered but not working)
Geographic scope: Global
Software updated: ?
Codebase/Documentation ?
Data updated: current
Limitation: Not found - tested with 144.000 records
Local ID input returned: YES
Local Name input returned: YES
Aggregator name ID returned: YES: IPNI-LSID
Interactive mode for partial matches: NO
OpenRefine reconciliation API: YES - documentation: https://data1.kew.org/reconciliation/help
Other:

LifeWatch

Scope:
Software updated:
Codebase/Documentation
Data updated:
Limitation:
Other:
Local ID input returned:
Local Name input returned:
Aggregator name ID returned:
Interactive mode for partial matches:
OpenRefine reconciliation API: NO

PESI / eu-nomen

Taxonomic scope: All taxa
Geographic scope: Europe
Software updated: 2011?
Codebase/Documentation: By reference to components used (Taxamatch algorithm and scientific name parser)
Data updated: 2014
Limitation: 5,000 names
Local ID input returned: NO
Local Name input returned: YES
Aggregator name ID returned: YES (as provided by the primary aggregator)
Interactive mode for partial matches: YES
OpenRefine reconciliation API: NO
Other:

ROpenSci taxize

Taxonomic scope: All taxa or specific groups, depending on dataset used
Geographic scope: Global or regional, depending on dataset used
Software updated: Feb 2025
Codebase/Documentation: https://github.com/ropensci/taxize/
Data updated:
Limitation:
Local ID input returned:
Local Name input returned:
Aggregator name ID returned: YES
Interactive mode for partial matches: NO
OpenRefine reconciliation API: n/a
Other:

TNRS Taxonomic Name Resolution Service also: http://tnrs.iplantcollaborative.org/

Taxonomic scope: Plants, WFO and vascular plants WCVP - potentially more datasets could be included
Geographic scope: Global
Software updated: v. 5.0 Feb. 24, 2021
Codebase/Documentation: https://github.com/ojalaquellueva/TNRSapi and https://github.com/iPlantCollaborativeOpenSource/TNRS/.
Data updated: 2023 (2024)
Limitation: Pasting 5000 names; API-processing unlimited (in batches of 5000)
Local ID input returned: NO
Local Name input returned: YES
Aggregator name ID returned: NO
Interactive mode for partial matches: YES
OpenRefine reconciliation API: NO
Other: API and R package available

Tropicos

Taxonomic scope: Plants
Geographic scope: Global
Software updated:
Codebase/Documentation
Data updated: Current
Limitation:
Local ID input returned: YES
Local Name input returned: YES
Aggregator name ID returned: YES: Tropicos-ID
Interactive mode for partial matches: NO
OpenRefine reconciliation API: NO
Other:

World Checklist of Vascular Plants (WCVP)

Taxonomic scope: Vascular plants
Geographic scope: Global
Currently no name matching, but updated versions are included in TNRS and in ChecklistBank
Other: R-Package rWCVP. See Brown & al. 2023.

World Flora Online WFO Plant List

Taxonomic scope: Plants
Geographic scope: Global
Software updated: ongoing June 2025 (not stated on website)
Codebase/Documentation: GraphQL API, Name Matching REST API, Reconciliation API
Data updated: December 2024 (semiannual edition)
Limitation: Not found - tested with 144.000 records
Local ID input returned: YES
Local Name input returned: YES
Aggregator name ID returned: YES - WFO-ID
Interactive mode for partial matches: YES
OpenRefine reconciliation API: YES: https://list.worldfloraonline.org/reconcile_index.php
Other: Service can be installed as local copy
Other: R-Package World Flora - see https://cran.r-project.org/web/packages/WorldFlora/index.html

WoRMS (World Register of Marine Species)

Scope: Marine species (global)
Software updated: not stated
Codebase/Documentation:
Data updated: current
Limitation: limited to 1500 names.
Local ID input returned: NO
Local Name input returned: YES
Aggregator name ID returned: YES (AphiaID)
Interactive mode for partial matches: NO
OpenRefine reconciliation API: NO