All life taxonomy projects

Why do we not have a single standard all-life taxonomy by now?

These are personal impressions! Verify all information before repeating.

High level points:

• Different taxonomies serve different applications. E.g. NCBI must have unidentified organisms, while CoL cannot have unidentified organisms.
• With one or two exceptions, each taxonomy is the work of a single person, often in a part-time or even volunteer capacity
• These people talk to one another sometimes, but do not generally have the time to engage in serious coordination efforts
• There are taxonomic data exchange standards (notably Darwin Core Archive), which aid export and import efforts, but they are not universally adopted, and does not in itself lead to taxonomies being more similar to one another
• The TDWG conferences used to be mostly about taxonomic data exchange, but they have now shifted to occurrence data. At the 2016 conference there was almost no discussion of taxonomy.

Major all-life taxonomy projects

Catalogue of Life

• Application: Aims to be a standard, authoritative unified species checklist and taxonomy
• Small staff (1-2 people??) supported by licensing fees
• Aggregates information from 100+ separate taxonomic efforts - divide and conquer approach
• URL for download, but restrictive terms of use apply when retrieved
• Only nomenclaturally valid names are admitted. No temporary or ad hoc taxon names
• Some people complain that it's incomplete and out of date. But you would expect that given the project's desire for quality.

ITIS

• Application: serves needs of government agencies?
• US Government ? level of support not clear
• Feeds into Catalogue of Life somehow?

Species 2000

• Predecessor of / somehow related to Catalogue of Life ?

GBIF backbone taxonomy

• Application: Aims to cover all species names occurring in GBIF occurrence records
• Maintained part time by a single staff member at GBIF (I believe)
• Same as CoL from family level up; from family down, an automated synthesis of 100+ 'checklists'
• Therefore, many more names than CoL.
• Lacks information important to application, e.g. nomenclatural status (valid vs. invalid names), extinct, bibliographic references

IRMNG

• Application: comprehensive list of genera, helpful in detecting and sorting out genus name ambiguities; has been expanded to species
• Maintained by a single person, now retired, but continuing on in a volunteer (or consulting?) capacity
• Good authority and provenance information

NCBI Taxonomy

• Application: used for indexing and annotating the molecular sequences in Genbank
• Maintained by staff at NIH (5 people??? I don't know)
• The only entries are ones for which there is sequence data. That excludes the vast majority of species that are in CoL and GBIF
• Includes a vast number of entries for unidentified or poorly described taxa.
• Emphasis is on taxonomy, not nomenclature. Information on classification is usually detailed and good, e.g. showing intermediate groupings not occurring in traditional taxonomies, and information on authorities (who published a species description and when) is usually missing; you need to go to CoL or IRMNG for that.

uBio

• Application: ?
• No longer maintained, but still available via Global Names project
• Used by phylopic and Data Dryad

IUCN Red List

• Application: species conservation
• Controlled by restrictive terms of use

Systema Naturae 2000

• Application: bring Linnaeus up to date? research needed

Wikidata

• Application: general reference work. research needed

Wikispecies

• Application: general references work. research needed
• Not to be confused with wikidata. Separate projects, different people

Union4

• This was published, once, with a list of distinguished authors, but never documented either regarding method or content

Open Tree Reference Taxonomy (not to be consused with Open Tree synthetic tree)

• Application: aggregator of phylogenetic tree
• Maintained by one person, under Open Tree grant, which is ending soon
• Algorithmic combination of several sources
• Includes NCBI so that all sequences are covered, and includes GBIF for wider coverage
• Does not do its own curation, except under duress

OneZoom

• Almost entirely based on Open Tree taxonomy
• Minor changes such as substituting a better mammals subtree

Encyclopedia of Life

• EOL does not have its own taxonomy; it relies on outside sources for taxonomic information.

Undoubtedly there are others.

Species databases (non-taxonomic)

ION

• Commercial list of all species names used for indexing the literature

Zoobank

• Open database used by ICZN for species name registration
• Run by one person

'Regional' taxonomies

Plants and fungi are big groups of 100,000 species or more; fish is something like 16,000, amphibians and birds maybe 8,000 each. Of course the smaller a list, the easier it is to maintain.

The Plant List

• Application: comprehensive checklist of all plant species worldwide
• Developed under grant; not maintained but followon project is proposed

Index Fungorum / Species Fungorum

• Maintained by a single person, who lost his funding recently - database is now at Kew, future uncertain
• Competes with Mycobank...

Fishbase

• An excellent resource - very well curated, up to date.
• I know nothing about their staff or funding, but somebody is putting a lot of TLC into it.

Amhibiaweb

• Also very high quality, current

IOC World Bird Names

• High quality, current

Algaebase

• Maintained by single person who is using it as a source of income
• Very much not open

LSPN (Bacteria)

• Nomenclaturally authoritative checklist
• The work of a single person, I believe
• Access license costs money, I believe

and hundreds of others.