Difference between revisions of "Name matching services"
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== Terminology == | == Terminology == | ||
See [[What is name matching?]] for general discussion on terminology and intent.<br /> | See [[What is name matching?]] for 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] | ||
| + | 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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a 2021 Algabase set (but matching doesn’t work - [8/23]) <br /> | a 2021 Algabase set (but matching doesn’t work - [8/23]) <br /> | ||
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 http://www.indexfungorum.org/Names/NamesRecord.asp?RecordID=229900] <br /> | 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 http://www.indexfungorum.org/Names/NamesRecord.asp?RecordID=229900] <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]== | ||
Revision as of 15:11, 22 September 2025
Contents
- 1 Terminology
- 2 Checklist Bank (GBIF & Catalogue of Life)
- 3 Global Names Verifier
- 4 TNRS Taxonomic Name Resolution Service also: http://tnrs.iplantcollaborative.org/
- 5 Australian Plant Name Index
- 6 GBIF Taxonomic Backbone
- 7 International Plant Name Index (IPNI)
- 8 LifeWatch
- 9 PESI / eu-nomen
- 10 ROpenSci taxize
- 11 Tropicos
- 12 World Flora Online WFO Plant List
- 13 WoRMS (World Register of Marine Species)
Terminology
See What is name matching? for 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.
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
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
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
