worrms R package

worrms is a R client for the World Register of Marine Species REST webservices ( http://www.marinespecies.org/rest).

The aim of a World Register of Marine Species (WoRMS) is to provide an authoritative and comprehensive list of names of marine organisms, including information on synonymy. While the highest priority goes to valid names, other names in use are included so that this register can serve as a guide to interpret taxonomic literature.

The content of WoRMS is controlled by taxonomic and thematic experts, not by database managers. WoRMS has an editorial management system where each taxonomic group is represented by an expert who has the authority over the content, and is responsible for controlling the quality of the information. Each of these main taxonomic editors can invite several specialists of smaller groups within their area of responsibility to join them.

Date ( Creation): 2017-01-13

Date ( Revision): 2020-07-08

Status: On going / operational

Author

rOpenSci - Scott Chamberlain

Resource provider

Flanders Marine Institute (VLIZ) - WoRMS Team

Custodian

rOpenSci - Scott Chamberlain

Keywords: marine species

Keywords: register

Keywords: synonymy

Keywords: taxon match

Keywords: taxonomic classification

Keywords: scientific name

Keywords: R

Keywords: taxonomy

Access constraints: License

Use limitation: https://github.com/ropensci/worrms/blob/master/LICENSE.md

OnLine resource: WoRMS Website (
WWW:LINK-1.0-http--link
)

OnLine resource: worrms Github (
WWW:LINK-1.0-http--link
)

OnLine resource: worrms CRAN (
WWW:LINK-1.0-http--link
)

OnLine resource: Package website (
WWW:LINK-1.0-http--link
)

Operation name: Aphia platform

Web site: http://www.marinespecies.org/about.php#what_is_aphia

Description: The Aphia platform is an infrastructure designed to capture taxonomic and related data and information, and includes an online editing environment. It is the core platform that underpins the World Register of Marine Species (WoRMS) and all its related global, regional and thematic species databases, but it also allows the storage of non-marine data. The Aphia platform is an MS SQL database, containing over 400 fields spread over more than 80 related tables. Content-wise, the Aphia structure can roughly be divided into 10 modules: taxonomy, distribution, traits, specimen information, vernacular names, notes, links, images, identification keys and sources.

Function: Aphia uses unique and stable identifiers for each available name in the database, through Life Science Identifiers (LSIDs). The system allows the storage of accepted and unaccepted names and it documents the relationship between names. This makes it a very powerful tool for taxonomic quality control, and also allows the linking of different pieces of information through scientific names, within the Aphia platform and in relation to externally-hosted databases.

Operation name: WoRMS webservices

Description: The web services of WoRMS allow to access the Aphia platform with REST and other protocols.

A non exhaustive list of applications:

- get the AphiaID for your taxon

- check the spelling of your taxa

- get the authority for your taxa

- get the full classification for your taxa

- resolve your unaccepted names to accepted ones

- get all synonyms for a taxon

- fuzzy/near match your species list

- resolve a common name/vernacular to a scientific name

- get the common name(s)/vernacular(s) for a taxon

- get the sources/references for a taxon

- get the WoRMS citation for a taxon

- get the direct children for a taxon

- get all taxa modified during a time interval

- get an external identifier for a taxon

- get the AphiaID for an external identifier/database

- get all distributions for a taxon

- get all attributes for a taxon

Function: As a user or developer you can use the WoRMS webservice to feed your own application with standard WoRMS data.

Topic Category: Species distribution

Service Category: data analysis

Service Category: data processing

Service Language: eng

Service TRL: TRL 9 – Actual system proven in operational environment

Service Funding: worrms is developed and maintained by the rOpenSci project. rOpenSci is a Sponsored Project of NumFOCUS, a 501(c)(3) nonprofit charity in the United States. NumFOCUS provides rOpenSci with fiscal, legal, and administrative support to help ensure the health and sustainability of the project. Visit numfocus.org for more information.

worrms relies on the web services offered by WoRMS. The maintenance and further development of WoRMS relies on financial contributions, the time contributed by its editorial board, and support of its host institution: VLIZ. WoRMS is currently funded through the LifeWatch Belgium project.