Difference between revisions of "Existing name checking mechanisms"

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(Testing and documentation in progress)
 
(Testing and documentation in progress)
 
== Terminology ==
 
== Terminology ==
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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/>
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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.  
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'''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/>
 
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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/>
 
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'''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.
 
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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/>
 
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'''"Lookup" target aggregators (Repositories):''' 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)]==
 
==[https://www.checklistbank.org/tools/name-match Checklist Bank (GBIF & Catalogue of Life)]==

Revision as of 21:25, 23 January 2024

(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

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.

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

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

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:


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
Open Refine reconciliation service with step-by-step documentation: https://github.com/gnames/gnverifier/wiki/OpenRefine-readme
Local ID input returned:
Local Name input returned:
Aggregator name ID returned:
Interactive mode for partial matches:
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

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

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

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

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