|
|
| (20 intermediate revisions by the same user not shown) |
| Line 1: |
Line 1: |
| − | 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.
| + | The content of this page has been moved and split into a page listing [[Taxonomic datasets]] and a list of [[Name matching services]]. |
| − | | |
| − | (Testing and documentation in progress)
| |
| − | == Terminology ==
| |
| − | See [[What is name matching?]] for general discussion on terminology and intent.
| |
| − | The following results from the TNLS (Taxonomic Name Linking Services) 3PP (TETTRIs third party project) provide an important overview:<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://www.algaebase.org Algaebase]==
| |
| − | | |
| − | '''Taxonomic scope:''' Algae<br />
| |
| − | '''Geographic scope:''' global<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| − | Currently no name matching, outdated copies included in OBIS, Global Names and ChecklistBank.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]==
| |
| − | '''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 />
| |
| − | | |
| − | == [[https://www.catalogueoflife.org/ Catalogue of Life]] ==
| |
| − | '''Taxonomic scope:''' All taxa but incomplete for some zoological groups (genera only) and for Algae<br />
| |
| − | '''Geographic scope:''' global<br />
| |
| − | '''Software:''' Editions are integrated into Checklist Bank and Global Names, see below.
| |
| − | | |
| − | ==[https://www.checklistbank.org/tools/name-match Checklist Bank (GBIF & Catalogue of Life)]==
| |
| − | '''Taxonomic scope:''' All taxa or specific groups depending on the target dataset chosen <br />
| |
| − | '''Geographic scope:''' Global or specific areas, 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, required for file upload (self-registration at [https://www.gbif.org/user/profile https://www.gbif.org/user/profile])<br />
| |
| − | | |
| − | ==[https://europlusmed.org/ Euro+Med PlantBase]==
| |
| − | '''Taxonomic scope:''' Plants <br />
| |
| − | '''Geographic scope:''' Europe and the Mediterranean area (see [https://europlusmed.org/explanations https://europlusmed.org/explanations] for details and a map <br />
| |
| − | Currently no name matching, but included in PESI (see below)<br />
| |
| − | | |
| − | ==[https://www.gbif.org/tools/species-lookup GBIF Taxonomic Backbone]==
| |
| − | '''Taxonomic scope:''' All taxa but incomplete for some zoological groups (genera only) and for Algae<br />
| |
| − | '''Geographic scope:''' global<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 Feb. 2025<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:''' No<br />
| |
| − | '''Local Name input returned:''' Yes<br />
| |
| − | '''Aggregator name ID returned:''' Yes (may be taxon ID)<br />
| |
| − | '''Interactive mode for partial matches:''' No<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 />
| |
| − | | |
| − | ==[https://www.itis.gov/ Integrated Taxonomic Information System - ITIS]==
| |
| − | '''Type:'''Secondary <br/>
| |
| − | '''Scope:'''Plants, animals, fungi, and microbes of North America and the world<br />
| |
| − | Currently (Feb 25,2025) no access to [https://www.itis.gov/taxmatch.html Taxamatch service]
| |
| − | | |
| − | ==[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://docs.ropensci.org/taxize/articles/datasources.html ROpenSci taxize]==
| |
| − | '''Type:''' lookup<br/>
| |
| − | '''Scope:''' Global <br />
| |
| − | Software updated: Feb 2025<br />
| |
| − | Codebase/Documentation: https://github.com/ropensci/taxize/<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 />
| |
| − | | |
| − | ==[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 (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 />
| |
| − | | |
| − | ==[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 />
| |
| − | | |
| − | ==World Checklist of Vascular Plants (WCVP)==
| |
| − | '''Type:''' primary<br/>
| |
| − | '''Scope:''' Vascular Plants<br/>
| |
| − | Currently no name matching, but updated versions are included in TNRS and in ChecklistBank<br />
| |
| − | '''Other:''' R-Package [https://matildabrown.github.io/rWCVP/articles/rWCVP.html rWCVP]. [https://nph.onlinelibrary.wiley.com/doi/10.1111/nph.18919 See Brown & al. 2023.]
| |
| − | | |
| − | ==[https://list.worldfloraonline.org/matching.php World Flora Online WFO Plant List]==
| |
| − | '''Type:''' primary<br/>
| |
| − | '''Scope:''' Plants<br/>
| |
| − | '''Software updated:''' ongoing February 2024 (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:''' December 2024 (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 (AphiaID)<br />
| |
| − | '''Interactive mode for partial matches:''' NO<br />
| |
| − | '''OpenRefine reconciliation API:''' No<br />
| |
