View source for Existing name checking mechanisms

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 a “lookup” aggregator. 

(Testing and documentation in progress)
== Terminology ==
In the context of TETTRIs, we distinguish three types of "Target aggregators", i.e. online databases of organism names that offer services for the use cases defined in the TETTRIs project: Primary and secondary target aggregators and Repositories ("Lookup target aggregators"). See [https://wiki.bgbm.org/tettris/Global_or_regional_aggregators] for details.

See [[What is name matching?]] for general discussion on terminology and intent.

==[https://www.algaebase.org Algaebase]==
'''Type:''' primary<br/>
'''Scope:''' Global algae<br />
Currently no name matching, outdated copies included in OBIS, Global Names and ChecklistBank.<br />
A simple taxon match implementation is planned via [https://www.algaebase.org/api/ AlgaeBase API] in the framework of  [https://www.lifewatch.be Lifewatch - Thematic Service Taxonomy]<br />

==[https://www.anbg.gov.au/apni/ Australian Plant Name Index]==
'''Type:''' primary<br />
'''Scope:''' Australian plants<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 />

== [[https://www.catalogueoflife.org/ Catalogue of Life]] ==
'''Type:''' secondary<br/>
'''Scope:''' potentially all taxa but incomplete for some zoological groups (genera only) and for Algae<br/>
'''Software:''' Editions are integrated into Checklist Bank, see above and Global Names, see below.

==[https://www.checklistbank.org/tools/name-match Checklist Bank (GBIF & Catalogue of Life)]==
'''Type:''' lookup.<br/>
'''Scope:''' All taxa or specific groups, also geographically restricted, depending on the target dataset chosen<br />
'''Software updated:''' May 16, 2024 (frontend), May 21, 2024 (backend) (checked May 23, 2024)<br />
'''Codebase/Documentation:''' [https://api.checklistbank.org/ https://api.checklistbank.org/]<br />
'''Data updated:''' depending on target dataset<br />
'''Limitation:''' Direct input of list limited to 6000 names. (With file upload for asynchronous response not limited) <br />
'''Local ID input returned:''' YES<br />
'''Local Name input returned:''' YES<br />
'''Aggregator name ID returned:''' YES - in download only<br />
'''Interactive mode for partial matches:''' NO<br />
'''OpenRefine reconciliation API:''' No (but for OpenRefine possible with REST services)<br />
'''Other:''' Login with GBIF account is recommended (self-registration at [https://www.gbif.org/user/profile https://www.gbif.org/user/profile])<br />

==[https://europlusmed.org/ Euro+Med PlantBase]
'''Type:''' primary<br/>
'''Scope:''' European plants<br />
Currently no name matching, but included in PESI<br />

==[https://www.gbif.org/tools/species-lookup GBIF Taxonomic Backbone]==
'''Type:''' secondary<br/>
'''Scope:''' All taxa (GBIF taxonomic backbone)<br />
Software updated: <br />
'''Codebase/Documentation:''' see [https://www.gbif.org/developer/species Species API] <br />
'''Data updated:''' Current<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: <br />

==[https://verifier.globalnames.org/ Global Names Verifier]==
'''Type:''' lookup<br/>
'''Scope:''' defined by stored datasets - option to restrict matching to individual source dataset<br />
'''Software updated:''' active Nov. 2023<br />
'''Codebase/Documentation:''' https://github.com/gnames<br />
'''Data updated:''' Differs for stored datasets<br />
'''Limitation:''' 5000 names, at least in interactive mode<br />
Local ID input returned: <br />
Local Name input returned: <br />
Aggregator name ID returned: <br />
Interactive mode for partial matches: <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 />
'''TETTRIS Notes''' includes<br /> 
a 2021 Algabase set (but matching doesn’t work - [8/23]) <br />
an (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: http://www.indexfungorum.org/Names/NamesRecord.asp?RecordID=229900 <br />

==[https://www.indexfungorum.org/ Index Fungorum]==
'''Type:''' primary<br/>
'''Scope:''' Global fungi<br />
Currently no name matching, but included in Catalogue of Life and Global Names<br />

==[http://namematch.science.kew.org/ International Plant Name Index (IPNI)] <br />==
'''Type:''' primary<br/>
'''Scope:''' Vascular plants (POWO - IPNI offered but not working) <br />
'''Software updated:''' ? <br />
'''Codebase/Documentation''' ? <br />
'''Data updated:''' current <br />
'''Limitation:''' Not found - tested with 144.000 records<br />
'''Local ID input returned:''' YES <br />
'''Local Name input returned:''' YES<br />
'''Aggregator name ID returned:''' YES: IPNI-LSID<br />
'''Interactive mode for partial matches:''' NO<br />
'''OpenRefine reconciliation API:''' Yes - documentation: [https://data1.kew.org/reconciliation/help https://data1.kew.org/reconciliation/help]<br />
'''Other:'''<br />

==[https://lifewatch.be/e-lab LifeWatch]==
'''Type:''' lookup<br/>
Scope: <br />
Software updated: <br />
Codebase/Documentation <br />
Data updated: <br />
Limitation: <br />
Other: <br />
Local ID input returned: <br />
Local Name input returned: <br />
Aggregator name ID returned: <br />
Interactive mode for partial matches: <br />
'''OpenRefine reconciliation API:''' No <br />

==[https://www.eu-nomen.eu/portal/taxamatch.php PESI / eu-nomen]==
'''Type:''' secondary<br/>
'''Scope:''' European taxa <br />
'''Software updated:''' 2011?<br />
'''Codebase/Documentation:''' By refrence to components used (Taxamatch algorithm and scientific name parser)<br />
'''Data updated:''' 2014 <br />
'''Limitation:''' 5,000 names <br />
'''Local ID input returned:''' No <br />
'''Local Name input returned:''' Yes <br />
'''Aggregator name ID returned:''' Yes (as provided by the primary aggregator)<br />
'''Interactive mode for partial matches:''' Yes<br />
'''OpenRefine reconciliation API:''' No<br />
Other: <br />

==[https://tnrs.biendata.org/ TNRS Taxonomic Name Resolution Service] <br />==
'''Type:''' lookup<br/>
'''Scope:''' Plants, WFO and vascular plants WCVP - potentially more datasets could be included<br />
'''Software updated:''' v. 5.0 Feb. 24, 2021<br />
'''Codebase/Documentation:''' https://github.com/ojalaquellueva/TNRSapi<br />
'''Data updated:''' 2023<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:''' R package available<br />

==[https://legacy.tropicos.org/NameMatching.aspx Tropicos]==
'''Type:''' primary<br/>
'''Scope:''' Plants<br />
Software updated: <br />
Codebase/Documentation <br />
Data updated: <br />
Limitation: <br />
'''Local ID input returned:''' Yes<br />
'''Local Name input returned:''' Yes<br />
'''Aggregator name ID returned:''' Yes: Tropicos-ID<br />
'''Interactive mode for partial matches:''' No<br />
'''OpenRefine reconciliation API:''' No<br />
Other: <br />

==[https://list.worldfloraonline.org/matching.php World Flora Online WFO Plant List]==
'''Type:''' primary<br/>
'''Scope:''' Plants<br/>
'''Software updated:''' ongoing Sept. 2023 (not stated on website)<br />
'''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] <br />
'''Data updated:''' July 2023 (semiannual edition)<br />
'''Limitation:''' Not found - tested with 144.000 records<br />
'''Local ID input returned:''' Yes <br />
'''Local Name input returned:''' Yes <br />
'''Aggregator name ID returned:''' Yes - WFO-ID <br />
'''Interactive mode for partial matches:''' Yes <br />
'''OpenRefine reconciliation API:''' yes: [https://list.worldfloraonline.org/reconcile_index.php https://list.worldfloraonline.org/reconcile_index.php]<br />
'''Other:''' Service can be installed as local copy<br />
'''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]<br />

==[https://www.marinespecies.org/aphia.php?p=match WoRMS (World Register of Marine Species)]==
'''Type:''' primary.<br/>
'''Scope:''' Marine species <br />
Software updated: not stated<br />
Codebase/Documentation: <br />
'''Data updated:''' current<br />
'''Limitation:''' limited to 1500 names.<br />
Local ID input returned: NO<br />
Local Name input returned: YES<br />
'''Aggregator name ID returned:''' YES<br />
'''Interactive mode for partial matches:''' NO<br />
'''OpenRefine reconciliation API:''' No<br />
'''Other:''' Did not work on 2 April 2024<br />

==[https://docs.ropensci.org/taxize/articles/datasources.html ROpenSci taxize]==
'''Type:''' secondary.<br/>
'''Scope:''' Global <br />
Software updated: <br />
Codebase/Documentation: <br />
'''Data updated:''' <br />
'''Limitation:''' <br />
Local ID input returned: <br />
Local Name input returned: <br />
'''Aggregator name ID returned:''' YES<br />
'''Interactive mode for partial matches:''' NO<br />
'''OpenRefine reconciliation API:''' <br />
'''Other:''' <br />