worms: Search World Register of Marine Species (WoRMS)

In ropensci/taxizesoap: Taxonomic Information from Around the Soap Web

Search World Register of Marine Species (WoRMS)

Description

Paging in worms_* functions: Where available, you an use the offset parameter to give the first record to return. The max records to return is 50, which you can not change. If there are more than 50 records, you can do the same request, but set offset=51, for example.

Details

WORMS has a SOAP API. We store the machine generated API specification in the package as the object worms_iface. However, you can update the spec if you want using worms_gen_iface, then pass the output of that fxn to the iface parameter of worms_* functions.

The following functions are available to interact with WoRMS:

• worms_gen_iface Generate new WoRMS SOAP API interface.

• worms_children Get immediate children from a WoRMS ID.

• worms_common Get common (vernacular) names from a WoRMS ID.

• worms_extid Get external IDs from a WoRMS ID, E.g., get an NCBI identifier.

• worms_hierarchy Get complete taxonomic hierarchy from a WoRMS ID.

• worms_name Get scientific name from a WoRMS ID.

• worms_records Get WoRMS records from a WoRMS ID, an external ID, a scientific name, a common name, or a start- or end-date.

• worms_sources Get sources (references) for taxa from a WoRMS ID.

• worms_synonyms Get scientific name synonyms from a WoRMS ID.

Each WoRMS record (row in the output of most worms_ functions) has the same output columns:

• AphiaID: unique and persistent identifier within WoRMS. Primary key in the database.

• url: HTTP URL to the AphiaRecord

• scientificname: the full scientific name without authorship

• authority: the authorship information for the scientificname formatted according to the conventions of the applicable nomenclaturalCode

• rank: the taxonomic rank of the most specific name in the scientificname

• status: the status of the use of the scientificname as a label for a taxon. Requires taxonomic opinion to define the scope of a taxon

• unacceptreason: the reason why a scientificname is unaccepted

• valid_AphiaID: the AphiaID (for the scientificname) of the currently accepted taxon

• valid_name: the scientificname of the currently accepted taxon

• valid_authority: the authorship information for the scientificname of the currently accepted taxon

• kingdom: the full scientific name of the kingdom in which the taxon is classified

• phylum: the full scientific name of the phylum or division in which the taxon is classified

• class: the full scientific name of the class in which the taxon is classified

• order: the full scientific name of the order in which the taxon is classified

• family: the full scientific name of the family in which the taxon is classified

• genus: the full scientific name of the genus in which the taxon is classified

• citation: a bibliographic reference for the resource as a statement indicating how this record should be cited (attributed) when used

• lsid: LifeScience Identifier. Persistent GUID for an AphiaID

• isMarine: a boolean flag indicating whether the taxon is a marine organism, i.e. can be found in/above sea water. Possible values: 0/1/NULL

• isBrackish: a boolean flag indicating whether the taxon occurrs in brackish habitats. Possible values: 0/1/NULL

• isFreshwater: a boolean flag indicating whether the taxon occurrs in freshwater habitats, i.e. can be found in/above rivers or lakes. Possible values: 0/1/NULL

• isTerrestrial: a boolean flag indicating the taxon is a terrestial organism, i.e. occurrs on land as opposed to the sea. Possible values: 0/1/NULL

• isExtinct: a flag indicating an extinct organism. Possible values: 0/1/NUL

• match_type: Type of match. Possible values: exact/like/phonetic/near_1/near_2

• modified: The most recent date-time in GMT on which the resource was changed

References

http://www.marinespecies.org/

ropensci/taxizesoap documentation built on May 18, 2022, 7:33 p.m.