What is name matching?

What is name matching?

The process of combining biodiversity data from multiple sources currently starts with matching of the Latin name strings for the organisms used in each dataset. Studies often contain names that can not be unambiguously matched or miss out some names entirely. When combining datasets, between 10% and 20% of names will fail to match perfectly and may need some human interaction or accepted error. With datasets of many thousands of species this soon becomes a major hurdle that has to be crossed every time datasets are used in analyses and is exasperated when more than two datasets are used.

It is better if study data can be matched once, at source, then linked on unambiguous name IDs rather than by matching potentially ambiguous name strings.

What is discussed here is name matching not matching to a specific taxon which is a subsequent process. Firstly we identify the name that string of characters applies to then we check which taxon that name applies to within a specific classification. See Potential caveats for discussion.

How Latin names are ambiguous

It is worthwhile to summarise some of the mechanisms whereby scientific names can be ambiguous either because different strings of characters refer to the same published name or the same string of characters refers to a different published name.

Homonyms

Homonyms are names that are spelt the same but refer to different things. Under the codes of nomenclature one of the names will always have presidence over another but because there have not been universal name registries it has not been possible to prevent creation of duplicate names. In the strict sense homonym means the full name, including the author(s) names, are identical. Homonym is often used in a looser sense of just applying to the words that make up the name, excluding the author string. This is because author strings are often not standardised or omitted entirely. Homonyms may occur within or between codes, that is the same name string may be used for two plants or for a plant and an animal. Furthermore there are two types of homonyms:

Isonyms

Isonyms occur when a name is based on the same type specimen but published in multiple places. The majority of isonyms are created by the author publishing the name again (perhaps in a paper and in a flora, fauna or catalogue) and so have the same author(s). There is no scope for taxonomic confusion in botany and the only scope for nomenclatural confusion caused by isonyms is citing the wrong reference as a place of original publication. In zoology the name string may have different dates thus causing matching failures even though the intent of the author(s) was to name the same taxon.

True Homonyms

True homonyms are names based on different type specimens and, usually, published by different authors. If they are published by different authors (homonym in the loose sense) and the author(s) names are included in the full name then they should not be ambiguous during matching however author(s) names may be omitted, causing false matches, or use nonstandard forms, causing false mismatches. Because the useage of species epithets in different genera (new combination in botany) are not required in zoology the potential for ambiguity is higher.

Author(s) String variation

Most ambiguity caused by identically spelt scientific names can be resolved if the author(s) of the name are included in the full name. Unfortunately this is fraught with difficulties in real data.

1. The author(s) are frequently omitted. If material is created for a general audience then inclusion of author(s) names can be considered confusing especially if the scientific (Latin) form of the name is being used in addition to a well known vernacular name. When data is being shared within a specialist scientific community who only work on a few species then the author(s) are omitted because there is no chance of confusion in that particular research context. Omission has also been influenced by legacy systems having restrictions on the length of data fields and on encoding errors that occur prior to widespread adoption of UTF-8. Author names may include accented characters but taxon names should only include common characters from the original ASSCII code page.
2. The zoological code of nomenclature does not consider the author(s) to be part of the name and inclusion is only customary although usually advisable. It is recommended on first use in a publication. Zoologists do not include the names of authors of new combinations (species placed in different genera). Botanist are more consistent in use of authors but do not include the year of publication of a name which is customary in zoology.
3. Standard author abbreviations are not mandated in either botany or zoology although in botany there is a more establish convention to use the author abbreviations as maintained by IPNI and also community curated in Wikidata property P428.

Orthographical variants

Permitted spelling variations and corrections.

Errors

Only at the end do we get to stochastic or unforced errors. These may occur when a name is mistyped by a human or through OCR failure.

Potential for Automation

FIXME

An automated system can't differentiate between identically spelt names without taking context into account.

No system can match a name against a list that doesn't contain that name. The "Add to dictionary?" option will need human intervention or approval.