Difference between revisions of "Name matching services"
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| − | + | 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.<br /> | |
| − | The following results from the TNLS (Taxonomic Name Linking Services) | + | The following results from the TNLS (Taxonomic Name Linking Services) TETTRIs Satellite Project provide an important overview of name service functionality:<br/> |
[https://docs.google.com/spreadsheets/d/1QKvytrNa8TxYY63cfxzttd9tSUAN-xeF8TY3vG-J5gs/edit?gid=0#gid=0 Overview of input parameters of aggregator services]<br /> | [https://docs.google.com/spreadsheets/d/1QKvytrNa8TxYY63cfxzttd9tSUAN-xeF8TY3vG-J5gs/edit?gid=0#gid=0 Overview of input parameters of aggregator services]<br /> | ||
| − | [https://docs.google.com/spreadsheets/d/1QKvytrNa8TxYY63cfxzttd9tSUAN-xeF8TY3vG-J5gs/edit?gid=223152038#gid=223152038 Overview of output fields of aggregator services] | + | [https://docs.google.com/spreadsheets/d/1QKvytrNa8TxYY63cfxzttd9tSUAN-xeF8TY3vG-J5gs/edit?gid=223152038#gid=223152038 Overview of output fields of aggregator services]<br> |
| + | We distinguish between services that act upon repositories of taxonomic datasets and single-dataset services. | ||
| − | == | + | =Repository services= |
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==[https://www.checklistbank.org/tools/name-match Checklist Bank (GBIF & Catalogue of Life)]== | ==[https://www.checklistbank.org/tools/name-match Checklist Bank (GBIF & Catalogue of Life)]== | ||
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'''Interactive mode for partial matches:''' NO<br /> | '''Interactive mode for partial matches:''' NO<br /> | ||
'''OpenRefine reconciliation API:''' NO (but for OpenRefine possible with REST services)<br /> | '''OpenRefine reconciliation API:''' NO (but for OpenRefine possible with REST services)<br /> | ||
| − | '''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])<br /> | + | '''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])<br /> |
| − | + | Offers the possibility to match datasets in repository against other such datasets. | |
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==[https://verifier.globalnames.org/ Global Names Verifier]== | ==[https://verifier.globalnames.org/ Global Names Verifier]== | ||
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'''OpenRefine reconciliation API:''' YES, with step-by-step documentation: https://github.com/gnames/gnverifier/wiki/OpenRefine-readme <br /> | '''OpenRefine reconciliation API:''' YES, with step-by-step documentation: https://github.com/gnames/gnverifier/wiki/OpenRefine-readme <br /> | ||
'''Other:''' Offers a kind of query language that seems to be very flexible<br /> | '''Other:''' Offers a kind of query language that seems to be very flexible<br /> | ||
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| − | + | ==[https://tnrs.biendata.org/ TNRS Taxonomic Name Resolution Service] also: http://tnrs.iplantcollaborative.org/ <br />== | |
| − | + | '''Taxonomic scope:''' Plants, WFO and vascular plants WCVP - potentially more datasets could be included<br /> | |
| + | '''Geographic scope:''' Global<br /> | ||
| + | '''Software updated:''' v. 5.0 Feb. 24, 2021<br /> | ||
| + | '''Codebase/Documentation:''' https://github.com/ojalaquellueva/TNRSapi and https://github.com/iPlantCollaborativeOpenSource/TNRS/.<br /> | ||
| + | '''Data updated:''' 2023 (2024)<br /> | ||
| + | '''Limitation:''' Pasting 5000 names; API-processing unlimited (in batches of 5000)<br /> | ||
| + | '''Local ID input returned:''' NO <br /> | ||
| + | '''Local Name input returned:''' YES<br /> | ||
| + | '''Aggregator name ID returned:''' NO<br /> | ||
| + | '''Interactive mode for partial matches:''' YES<br /> | ||
| + | '''OpenRefine reconciliation API:''' NO<br /> | ||
| + | '''Other:''' API and R package available<br /> | ||
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| + | =Single-dataset name matching services= | ||
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| + | ==[https://www.anbg.gov.au/apni/ Australian Plant Name Index]== | ||
| + | '''Taxonomic scope:''' Plants<br /> | ||
| + | '''Geographic scope:''' Australia<br /> | ||
| + | Software updated: ?<br /> | ||
| + | Codebase/Documentation: ?<br /> | ||
| + | Data updated: ?<br /> | ||
| + | '''Limitation:''' not stated, check with nearly 21,000 names ended in server error [23 may 2024]<br /> | ||
| + | '''Local ID input returned:''' NO<br /> | ||
| + | Local Name input returned: <br /> | ||
| + | Aggregator name ID returned: <br /> | ||
| + | '''Interactive mode for partial matches:''' NO <br /> | ||
| + | '''OpenRefine reconciliation API:''' NO<br /> | ||
| + | '''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]<br /> | ||
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| + | ==[https://www.gbif.org/tools/species-lookup GBIF Taxonomic Backbone]== | ||
| + | '''Taxonomic scope:''' All taxa <br /> | ||
| + | '''Geographic scope:''' global<br /> | ||
| + | '''Software updated:''' current<br /> | ||
| + | '''Codebase/Documentation:''' see [https://www.gbif.org/developer/species Species API] <br /> | ||
| + | '''Data updated:''' August 28, 2023 (no further updates, but will stay online; will most probably be replaced by COL eXtended edition)<br /> | ||
| + | '''Limitation:''' 6000 records<br /> | ||
| + | '''Local ID input returned:''' YES <br /> | ||
| + | '''Local Name input returned:''' YES<br /> | ||
| + | '''Aggregator name ID returned:''' NO<br /> | ||
| + | '''Interactive mode for partial matches:''' NO<br /> | ||
| + | '''OpenRefine reconciliation API:''' NO<br /> | ||
| + | '''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. <br /> | ||
==[http://namematch.science.kew.org/ International Plant Name Index (IPNI)] <br />== | ==[http://namematch.science.kew.org/ International Plant Name Index (IPNI)] <br />== | ||
| − | '''Taxonomic scope:''' Vascular plants (source: POWO | + | '''Taxonomic scope:''' Vascular plants (source: POWO; IPNI offered but not working) <br /> |
'''Geographic scope:''' Global<br /> | '''Geographic scope:''' Global<br /> | ||
Software updated: ? <br /> | Software updated: ? <br /> | ||
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'''OpenRefine reconciliation API:''' n/a <br /> | '''OpenRefine reconciliation API:''' n/a <br /> | ||
Other: <br /> | Other: <br /> | ||
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==[https://legacy.tropicos.org/NameMatching.aspx Tropicos]== | ==[https://legacy.tropicos.org/NameMatching.aspx Tropicos]== | ||
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'''Interactive mode for partial matches:''' NO<br /> | '''Interactive mode for partial matches:''' NO<br /> | ||
'''OpenRefine reconciliation API:''' NO<br /> | '''OpenRefine reconciliation API:''' NO<br /> | ||
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| + | =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. | ||
Latest revision as of 15:55, 28 September 2025
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 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:
Overview of input parameters of aggregator services
Overview of output fields of aggregator services
We distinguish between services that act upon repositories of taxonomic datasets and single-dataset services.
Contents
Repository services
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)
Offers the possibility to match datasets in repository against other such datasets.
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
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
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
GBIF Taxonomic Backbone
Taxonomic scope: All taxa
Geographic scope: global
Software updated: current
Codebase/Documentation: see 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.
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
Refers to Global Names for name matching.
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:
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 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
R-packages that include name matching
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 (“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.
