Existing name checking mechanisms

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: Primary and secondary target aggregators and Repositories ("Lookup target aggregators"). See [1] for details.

Checklist Bank (GBIF & Catalogue of Life)

Type: lookup.
Scope: All taxa or specific groups, also geographically restricted, depending on the target dataset chosen
Software updated: May 23 (frontend), June 23 (backend) (checked August 15, 2023)
Codebase/Documentation: https://api.checklistbank.org/
Data updated: depending on target dataset
Limitation: Direct input of list limited to 6000 names. (With file upload not limited)
Other: Login with GBIF account is recommended (self-registration at https://www.gbif.org/user/profile)
Local ID input returned: NO (checked August 16, 2023)
Local Name input returned: YES
Aggregator name ID returned: YES - in download only
Interactive mode for partial matches: NO
OpenRefine reconciliation API: No

Catalogue of Life

Type: Secondary Scope: potentially all taxa but incomplete for some zoological groups (genera only) and for Algae
Software: Editions are integrated into Checklist Bank, see above and Global Names, see below.

World Flora Online WFO Plant List

Type: Primary
Scope: Plants
Software updated: ongoing Sept. 2023 (not stated on website)
Codebase/Documentation: GraphQL API, Name Matching REST API, Reconciliation API
Data updated: July 2023 (semiannual edition)
Limitation: Not found - tested with 144.000 records
Other: Service can be installed as local copy
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

PESI

Type: Secondary
Scope: European taxa
Software updated: 2011?
Codebase/Documentation: By refrence to components used (Taxamatch algorithm and scientific name parser)
Data updated: 2014
Limitation: 5,000 names
Other:
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

LifeWatch

Scope:
Software updated:
Codebase/Documentation
Data updated:
Limitation:
Other:
Local ID input returned:
Local Name input returned:
Aggregator name ID returned:
Interactive mode for partial matches:
OpenRefine reconciliation API: No

Global Names

Type: Lookup
Scope: defined by stored datasets - option to restrict matching to individual source dataset
Software updated: active Nov. 2023
Codebase/Documentation: https://github.com/gnames
Data updated: Differs for stored datasets
Limitation: 5000 names, at least in interactive mode
Other: Offers a kind of query language that seems to be very flexible
Local ID input returned:
Local Name input returned:
Aggregator name ID returned:
Interactive mode for partial matches:
OpenRefine reconciliation API: yes, with step-by-step documentation: https://github.com/gnames/gnverifier/wiki/OpenRefine-readme
TETTRIS Notes includes
a 2021 Algabase set (but matching doesn’t work - [8/23])
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

Kew (IPNI)

Scope: Vascular plants (POWO - IPNI offered but not working)
Software updated: ?
Codebase/Documentation ?
Data updated: current
Limitation: Not found - tested with 144.000 records
Other: OpenRefine Interface?
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

TNRS Taxonomic Name Resolution Service

Scope: Plants, WFO and vascular plants WCVP - potentially more datasets could be included
Software updated: v. 5.0 Feb. 24, 2021
Codebase/Documentation: https://github.com/ojalaquellueva/TNRSapi
Data updated: 2023
Limitation: Pasting 5000 names; API-processing unlimited (in batches of 5000)
Other: R package available
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

Tropicos

Scope: Plants
Software updated:
Codebase/Documentation
Data updated:
Limitation:
Other:
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

GBIF Taxonomic Backbone

Scope: All taxa (GBIF taxonomic backbone)
Software updated:
Codebase/Documentation: see Species API
Data updated: Current
Limitation: 6000 records
Other:
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