TETTRIs - User contributions [en]

Name matching services

2025-12-10T15:47:27Z

WikiSysop: fixed linking issue

These are online services that let users compare their lists of scientific organism names against [[Taxonomic_datasets|reference datasets]]. Because user needs can vary widely, selecting both an appropriate dataset and a suitable name-matching service requires careful consideration before deciding on the most appropriate [[End-user workflows for name matching|workflow]]. Also see [[What is name matching?]] for a general discussion on terminology and intent. 
The following results from the TNLS (Taxonomic Name Linking Services) TETTRIs Satellite Project provide an important overview of name service functionality: 
[https://docs.google.com/spreadsheets/d/1QKvytrNa8TxYY63cfxzttd9tSUAN-xeF8TY3vG-J5gs/edit?gid=0#gid=0 Overview of input parameters of aggregator services] 
[https://docs.google.com/spreadsheets/d/1QKvytrNa8TxYY63cfxzttd9tSUAN-xeF8TY3vG-J5gs/edit?gid=223152038#gid=223152038 Overview of output fields of aggregator services] 
We distinguish between services that act upon repositories of taxonomic datasets and single-dataset services.

=Repository services=

==[https://www.checklistbank.org/tools/name-match 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 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 https://www.gbif.org/user/profile]) 
Offers the possibility to match datasets in repository against other such datasets.

==[https://verifier.globalnames.org/ 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 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 

==[https://tnrs.biendata.org/ 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 

=Single-dataset name matching services=

==[https://www.anbg.gov.au/apni/ 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:''' [https://www.biorxiv.org/content/10.1101/2024.02.02.578715v1 APCalign: an R package workflow and app for aligning and updating flora names to the Australian Plant Census] 

==[https://www.gbif.org/tools/species-lookup GBIF Taxonomic Backbone]==
'''Taxonomic scope:''' All taxa 
'''Geographic scope:''' global 
'''Software updated:''' current 
'''Codebase/Documentation:''' see [https://www.gbif.org/developer/species Species API] 
'''Data updated:''' August 28, 2023 (no further updates, but will stay online; will most probably be 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:''' "Multi-taxonomy" mode in preparation - will allow to match against other taxonomies (e.g. COL eXtended edition). Matching Service including data will be downloadable as a Docker image. 

==[http://namematch.science.kew.org/ 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 https://data1.kew.org/reconciliation/help] 
Other: 

==[https://lifewatch.be/e-lab LifeWatch]==
Refers to Global Names for name matching.

==[https://www.eu-nomen.eu/portal/taxamatch.php 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: 

==[https://docs.ropensci.org/taxize/articles/datasources.html 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: 

==[https://legacy.tropicos.org/NameMatching.aspx 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: 

==[https://list.worldfloraonline.org/matching.php World Flora Online WFO Plant List]==
'''Taxonomic scope:''' Plants 
'''Geographic scope:''' Global 
'''Software updated:''' ongoing June 2025 (not stated on website) 
'''Codebase/Documentation:''' [https://list.worldfloraonline.org/gql_index.php GraphQL API], [https://list.worldfloraonline.org/matching_rest.php Name Matching REST API], [https://list.worldfloraonline.org/reconcile_index.php 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 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 https://cran.r-project.org/web/packages/WorldFlora/index.html] 

==[https://www.marinespecies.org/aphia.php?p=match 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 

=R-packages that include name matching=
[https://doi.org/10.1111/2041-210X.13802 Grenié & al. (2022)] cover this subject in detail, identifying a number of packages providing direct or indirect access to online taxonomic datasets. They also point to an application [https://mgrenie.shinyapps.io/taxharmonizexplorer/ (“taxharmonizeexplorer")] that should aid R-users to select tools and datasets. The website for the app lists and graphically depicts the relationship between taxonomic datasets and R-packages (as of end of July 2025, it covers 68 packages). If this tool continues to be updated, it should be the primary source for R-programmers to identify useful packages for name matching, and apply these in a workflow detailed in Grenié & al.’s paper.

What is name matching

2025-12-09T10:42:14Z

WikiSysop: created redirect for URL without special character replacement

#REDIRECT [[What is name matching?]]

Workpackage 2

2025-11-28T17:30:10Z

WikiSysop: added outcome of the

== [https://tettris.eu/ TETTRIs] Workpackage 2: "Connecting local and European taxonomies" ==

TETTRIs' task 2.2 responsible for the wiki started in 2023. We will gradually incorporate project results as they become available.

=== Our mission (project deliverables): ===
'''"Functional workflow for mapping local taxonomies established and documented" (Task 2.2)'''

This is to document and enhance the mapping of local taxon lists (or scientific data holdings containing lists of taxon names) to global and European aggregators of scientific names and taxa. Local lists are here understood to range from spreadsheets maintained by individual researchers to large databases containing taxonomic checklists for countries or entire regions of the world (e.g. the European plant checklist Euro+Med PlantBase). Scientific names are used to document multiple kinds of properties of organisms, the mapping process serves to unite this information while at the same time ensuring that '''[[potential caveats]]''' in the direct linking of names (and their synonyms) can be identified. The initial step in that process is matching the local name with the names in the aggregated lists. 
So why would the administrators of local lists want to relate their name data to global or regional aggregators, for example to [https://www.catalogueoflife.org/ Catalogue of Life], [https://wfoplantlist.org/plant-list/ World Flora Online Plant List] or
[https://www.eu-nomen.eu/portal/ EU-Nomen]? We are collecting such '''[[use cases for name matching]]''' and from that we are proposing [[Aggregator_services_wish_list|mechanisms to improve name matching and other services]] provided by the target aggregator systems. For end-users, we strive to document [[End-user workflows for name matching|recipe-like workflows]] covering different use cases.
 
This task will also be supported by two [https://tettris.eu/3pp/ 3PP third party projects (3PP)] funded by TETTRIs that address TETTRIs Topic 2: "Improving access to local taxon lists and taxon-related scientific data through pragmatic name-mapping workflows": [https://tettris.eu/3rd-party-projects/isedge/ iSedge] and particularly [https://tettris.eu/3rd-party-projects/test-2/ Taxonomic Name Linking Services - TNLS].

'''"Functional optimised EU Nomen processes and services up and running" (Task 2.1)'''

[https://www.eu-nomen.eu/portal/ EU-Nomen] is the first all-taxa inventory for European species, initially assembled by the EU-funded PESI project (Pan European Species Inventory Infrastructure). EU-Nomen is an aggregated data set allowing queries and name matching via the Internet. The central database is hosted and web access maintained by the [https://www.vliz.be/nl Vlaams Instituut voor de Zee (VLIZ)]. The content consists of several largely complementary European taxonomic datasets, each of which is maintained by a specialised taxonomic community: Fungi from [https://www.indexfungorum.org/ Index Fungorum] / [https://www.speciesfungorum.org/ Species Fungorum], Marine organisms from the [https://www.marbef.org/data/erms.php European Register of Marine Species] ERMS, Animals from [https://fauna-eu.org/ Fauna Europaea], and Plants from [https://europlusmed.org/ Euro+Med PlantBase]. Merging these datasets is the responsibility of the [https://www.bgbm.org/en/biodiversity-informatics Zentrum für Biodiversitätsinformatik und Sammlungsdatenintegration] (ZBS) in Berlin. TETTRIs will streamline the process of merging these datasets in order to enable regular updating of the EU-nomen services. It will foster the provision of globally unique identifiers provided by the source datasets. In collaboration with the [https://www.nhm-wien.ac.at/ Naturhistorisches Museum] in Vienna, special attention will also be given to common taxon names, as they are the key to data access by a broader public. 
This task will directly improve the data content of EU-Nomen (PESI), which is the principal European target for mapping taxon names.

=== Project milestones: ===
'''"MS4 Agreed strategy for mapping local taxonomies (31 May 2024)" (Task 2.2)''' [https://tettris.eu/wp-content/uploads/2024/07/TETTRIs-MS4-Agreed-strategy-for-mapping-local-taxonomies-.docx.pdf Download PDF]

Strategy for synchronising taxonomies agreed and documented

'''"MS3 Taxonomic Resolution Platform up and running (30 Nov 2024)" (Task 2.3)'''

Taxonomic Resolution Engine is available and linked to backbone services

=== Outcomes of the TNLS Satellite Project ===
* Hyam, R., Vanhoorne, B., Berendsohn, W. G., Müller, A., Lamote, M., & De Paepe, B. (2025). '''TNLS: Taxonomic activity notification service'''. Royal Botanic Garden Edinburgh (RBGE); Flanders Marine Institute (VLIZ). https://doi.org/10.5281/zenodo.17588932

* Hyam, R., Vanhoorne, B., Berendsohn, W. G., Müller, A., & Lyssens, L. (2025). '''TNLS: Common name matching specification'''. Royal Botanic Garden Edinburgh (RBGE); Flanders Marine Institute (VLIZ). https://doi.org/10.5281/zenodo.17670579

MediaWiki:Sidebar

2023-08-24T15:29:03Z

WikiSysop: added link to TETTRIs Website

MediaWiki:Common.css

2023-08-24T15:14:37Z

WikiSysop: a bit more space for the logo

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MediaWiki:Mainpage

2023-07-24T08:01:04Z

WikiSysop: Created page with "Workpackage 2"

Workpackage 2