View source for Existing name checking mechanisms

(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:<br/>
'''Primary target aggregators:''' These are aggregators that offer comprehensive taxonomic coverage for a certain group of organisms, globally or with a European geographic coverage. As a role, they offer more in depth information compared to the other types of aggregators. They may contain data from literature, from smaller-scale aggregators or sometimes even original data. TETTRIs here focuses sites directly driven by the respective taxonomic community: For Fungi: Index Fungorum / Species Fungorum (IF). For vascular plants and bryophytes: World Flora Online Plant List (WFO) and for Europe, Euro+Med PlantBase. IF is also contributing to CoL and PESI, Euro+Med to PESI (and it will use WFO Name IDs), and WFO Plant List will in the future probably contribute to CoL, too. The question of identifying appropriate community datasets for animal groups and for Algae is being discussed. <br/>
Species Fungorum and Euro+Med do not provide their own name matching services. However, since the CoL Services essentially are also covering ChecklistBank, versions of these datasets deposited in a standard format there can be accessed directly by singling them out as target datasets.<br/> 
'''Secondary Target Aggregators:''' These are aggregators that offer comprehensive taxonomic coverage of names and taxa irrespective of the taxonomic group, with either global (Catalogue of Life) or European (PESI/EU-nomen) geographic coverage. Their records are mostly contributed by secondary aggregators representing a certain taxonomic group. In contrast to "Lookup" aggregators, they provide a single classification of name usage, either as synonyms, accepted taxon names or for some reason unplaced names. 
Primary target aggregators are the principal components of the TETTRIs taxonomic backbone. TETTRIs focuses on Catalogue of Life and PESI/EU-nomen as a Primary Target Aggregators. <br/>
'''"Lookup" target aggregators:''' These are services that provide access to a multitude of stored datasets, which may be updated or rather out-of-date. They are of interest for name discovery and to identify where a designation comes from. However, TETTRIs focusses here on GBIF Checklist Bank and on Global Names and both offer a service to match names against specific datasets – this essentially renders them (indirect) secondary target aggregators. 
 
==[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 23 (frontend), June 23 (backend) (checked August 15, 2023)<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 not limited) <br />
'''Other:''' Login with GBIF account is recommended (self-registration at [https://www.gbif.org/user/profile https://www.gbif.org/user/profile])<br />
'''Local ID input returned:''' NO (checked August 16, 2023)<br />
'''Local Name input returned:''' YES<br />
'''Aggregator name ID returned:''' YES - in download only<br />
'''Interactive mode for partial matches:''' NO<br />

== Catalogue of Life ==
'''Type:''' Secondary
'''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.

==[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 />
'''Other:''' Service can be installed as local copy<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 />

==[https://www.eu-nomen.eu/portal/taxamatch.php PESI]==
'''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 />
Other: <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 />

==[https://lifewatch.be/en/e-lab LifeWatch]==
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 />


==[https://verifier.globalnames.org/ Global Names]==
Contains options to restrict matching to certain source dataset, among them: <br />
a 2021 Algabase set (but matching doesn’t work) <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 />
'''Scope:''' defined by stored datasets<br />
Software updated: <br />
Codebase/Documentation <br />
Data updated: <br />
'''Limitation:''' 5000 names, at least in interactive mode<br />
'''Other:''' Offers a kind of query language that seems to be very flexible<br />
Local ID input returned: <br />
Local Name input returned: <br />
Aggregator name ID returned: <br />
Interactive mode for partial matches: <br />


==[http://namematch.science.kew.org/ Kew (IPNI)] <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 />
'''Other:''' OpenRefine Interface? <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

==[https://tnrs.biendata.org/ TNRS Taxonomic Name Resolution Service] <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 />
'''Other:''' R package available<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

==[https://legacy.tropicos.org/NameMatching.aspx Tropicos]==
'''Scope:''' Plants<br />
Software updated: <br />
Codebase/Documentation <br />
Data updated: <br />
Limitation: <br />
Other: <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 />

==[https://www.gbif.org/tools/species-lookup GBIF Taxonomic Backbone]==
'''Scope:''' All taxa<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 />