Taxonomy Data Standard

Draft set of standards for Mineral Sciences taxonomy records.

About

The taxonomy module stores information about the classifications assigned to individual rock and meteorite specimens. Classifications are organized into an arbitrarily deep hierarchy (i.e., a given classification can have as many ancestors as needed, as opposed to Linnean classifications for biology where the number of available ranks is limited).

The hierarchy used by Mineral Sciences is ad hoc and has been compiled from multiple sources, including but not limited to the following:

  • British Geological Survey Rock Classification Scheme

  • Dana classification scheme

  • Igneous Rocks: A Classification and Glossary of Terms

  • IMS mineral list (for current mineral names)

  • Mindat (for varieties, synonyms, and archaic mineral names)

The Mineral Sciences taxonomy module includes records for a large number of classifications beyond rocks, minerals, and meteorites, including fossils, chemical compounds lacking formal names, and cultural objects.

A reasonable up-to-date version the complete taxonomic hierarchy can be browsed at http://adamancer.pythonanywhere.com/classification/id/10591819.

Standard

### Meets

A standard taxonomy record should contain the following fields:

  • Parent

  • Other > Other Rank

  • Other > Other Value

  • Scientific Name > Name

  • Currently Accepted Name > Currently Accepted?

  • Currently Accepted Name > Current Name

### Exceeds

To exceed standard, a taxonomy record must contain all the information required above and link to an authoritative record for the classification. Authoritative sources include the sources listed under About above. Not all valid classifications can meet this criteria for reasons discussed below.

Field definitions

  • Parent: a link to the next broadest classification

  • Other Rank: the type of material. This list is in flux, but the most common values include:

    • Rock

    • Mineral

    • Synonym

    • Variety

  • Other Value: the specific name of this classification

  • Name: a human-readable name, like you’d put on a label

  • Current name: a link to the currently valid name

Examples

Attachments to other records are in [brackets].

### Sapphire

  • Parent: [Corundum]

  • Other rank: Variety

  • Other value: Sapphire

  • Name: Corundum (var. sapphire)

  • Current name: [Corundum (var. sapphire)]

### Idocrase

For synonyms, the parent is the same as the current name.

  • Parent: [Vesuvianite]

  • Other rank: Synonym

  • Other value: Idocrase

  • Name: Idocrase

  • Current name: [Vesuvianite]

### Biotite granite

Rock names originally added to Paradox or SELGEM may be given as Primary, Modifier (e.g., “Granite, Biotite” for this example). New records should use the human-readable name instead, but the older records do not need to be corrected.

  • Parent: [Granite]

  • Other rank: Rock

  • Other value: Biotite granite

  • Name: Biotite granite

  • Current name: [Biotite granite]

Division-specific guidelines

### Mineralogy

  • Mineral varieties are expressed as Mineral (var. variety) in the scientific name field. This formulation is based on exhibit labels in GGM and works well for well for major varieties (for example, sapphire and emerald). It also makes it easier to perform simple searches for minerals (for example, a search for corundum would return sapphires and rubies without having to populate a synonym name in the identification grid). The syntax adopted here does present a few issues:

    • Microcrystalline forms of quartz (chalcedony, agate, etc.) do not play well with this scheme

    • Varieties that are not specific to a single mineral (for example, moonstone) must be explicitly defined for each mineral (for example, orthoclase (var. moonstone), albite (var. moonstone), etc.)

    • Varieties that contain the mineral name (e.g., titanian augite) should not use the Mineral (var. variety) syntax

### Petrology

The list of accepted igneous rock names contains around 400-500 entries, but that list is not exhaustive. Using major mineral phases as modifiers is a well-established practice in the field. As a result, the number of valid rock names is essentially infinite, which poses a significant problem for data management and the construction of a useful taxonomic hierarchy.

Classification of many rock types is challenging because many rocks can be placed at multiple locations within a hierarchy. There is no good solution for this issue without adopting a scheme that allows each record to have multiple parents.

Updating the parent

The taxonomy module is badly over-engineered, and it is not possible to assign a new parent to an existing record directly through the GUI. The easiest workaround makes use of the search-replace feature:

  • Open the Replace window by clicking Edit > Replace

  • Delete any existing rows in the Replace window

  • Click New in the bottom left corner to bring up the Substitution window and fill out the form as follows:

    • Set field to Parent or RanParentRef

    • Set text to find to .*

    • Set replace with using the green plus

    • Check the regular expression checkbox under Options

    • Click OK

  • In the Replace window, click Replace to update the parent of the current record

You can modify an existing substitution using the Properties button near the top of the Replace window. Tread carefully. Here are some common gotchas doing replacements in EMu:

  • All defined substitutions run when you click Replace or Replace All

  • When clicking Replace, the substitution will run on any highlighted records even if the current record is not highlighted. If no records are highlighted, the substitution will only affect the current record.

This workaround may be patched out of future versions EMu.