Treatment level

Draft Specifications for a Descriptive Data Standard for Taxonomy

Version History:

Version 1.0 February 24, 2000, K.Thiele

Version 1.1 revised July 18, 2000, K.Thiele

General Requirements

The DDST will be a data file structure that allows the capture and management of all types of data required for describing the morphology and anatomy of an organism or taxon. All data and metadata needed will be stored in one file, structured into several blocks (character lists, taxon lists, items data etc.).

One file will comprise one treatment, the basic unit of which is one or more characters describing one or more taxa or individuals.

The DDST will support the following:

External lexica: these are externally-referenced lists of characters and states, or taxa, shared between several treatments. Lexica may be used without modification, or with one or more characters, states or taxa added internally (e.g. global vs local characters).

Collation of data: data in the DDST may be captured and managed at several levels. One treatment (see above for definition of treatment) may store descriptive data for individual specimens, another may store data for species-level taxa, while another may store data for higher-level taxa. These individual treatments may be linked into a nested hierarchy, with specified collation rules allowing collation of data up the hierarchy, and passing of data down the hierarchy. Thus, some characters in the species-level treatment may be scored directly in that treatment, while others will collate data (e.g. leaf measurements) from items in the specimen-level treatment. Conversely, some characters may be scored in a genus-level treatment, and these become implicitly true for all taxa in a linked species-level treatment.

Rich Attribution: all data elements in the DDST may be fully attributed to a source (e.g. contributor, published reference, specimen etc). Attribution will be optional at any level. Attribution will allow data-tracking and house-keepng, especially in circumstances when several contributors work on one treatment.

The list of data elements below is structured using tabbed levels. Items tabbed across one level and enclosed in square parentheses are replicable within the higher level.

Items in bold are required within their level (although the higher-level structure to which they belong may not be required)

Comments are in curly parentheses.

Note that this draft specification does not imply any particular structure for the data file used. It should be read as a list of required data elements for the final specification.

Treatment Name {Free-text title for the treatment}
Description {Free-text description of the treatment}
Treatment build/revision number {A real numeric e.g. 4.1 used for version control}
Treatment build/revision date {Date string (standardised format?)}
Contributors List {List of contributors to the treatment, including the principal builder} [
ID {Unique (in the context of this treatment) number for the contributor}
Name {contributor’s name}
Contact details {contributor’s address, email etc}
Private notes {internal notes on contributor}⁷
] Attribution {ID of principal treatment builder - this is the default attribution unless a lower-level item is specifically attributed}¹
List of sources [
ID {Number for the source}
Description {e.g. reference, description of specimen set etc}
] Principal Source {ID of the principal (default) source for the data}¹
Treatment attachments {General information topics applicable to the treatment as a whole} [
Attachment name
Attachment type {e.g. xml,html,txt,rtf,jpeg,gif}
Attachment path/URL
Public attachment notes⁷
Private attachment notes⁷
] Private treatment notes {internal freeform notes for treatment}⁷
Character list source {path to an external lexicon that defines the character list for the treatment}
Character set names list {list of set names for characters} [
Name {name string for a character set}
] Character List {required unless an external lexicon resource has been specified above} [
Character Name³
Character ID
Set membership {list of sets to which the character belongs; a character must be able to belong to more than one set}
Attribution¹{reference to a contributor’s ID from the Contributors list}
Source¹ (reference to a source’s ID from the Sources list)
Collated Character source {path name for another treatment that contains lower-level data for this character} Collation rule name {Name of a collation rule as defined in the Collation Rules list}² Character type {ordered multistate, unordered multistate etc}
Character dependencies (up)⁴
Applies To list (or global/restricted type definition, then leave it to program to extract)⁵
Character attachments [
attachment name
attachment type
attachment path/URL
Public notes⁷
Private notes⁷
] Private notes {internal notes for character}⁷
Character State List [
Character state name | Character state ID
Character dependencies (down)
Character state attachments [
attachment name
attachment type
attachment path/URL
Public notes⁷
Private notes⁷
] Private notes⁷
] ] Taxon list source {path to an external resource that defines the taxon list for the treatment}
Taxon set names {defines a list of allowable names for taxon sets} [
name
] Taxon List [
Name | Taxon ID
Taxon set membership {list of sets to which the taxon belongs; a taxon must be able to belong to more than one set?}
Taxon attribution¹
Taxon attachments [
attachment name
attachment type
attachment path/URL
Public notes⁷
Private notes⁷
] Private notes⁷
] Item Data {This will hold the "score matrix"} Taxon Name|ID/Character Name|ID⁶ Character Name|ID/Taxon Name|ID⁶ State Name|ID Score {normally present, rare, present by misinterpretation etc}
Score Attribution¹
Public Notes⁷
Private Notes⁷

^{1 Attribution and sources for an item datum overides
that for a character or taxon, which override that for the treatment as
a whole. Attribution for characters and taxa are equivalent and additive.}

^{2 Treatments are nestable. That is, one treatment
may contain data on specimens, a higher-level treatment on taxa. The higher-level
treatment gathers information for some characters from lower-level treatments,
using a specified collation rule. Collation rules will be specified externally
to the treatment, and will cover e.g. how to merge scores, calculate values,
deal with conflicts in source data etc}

^{3 Character names may be hierarchically nested. Character
properties (e.g. sets, dependencies, attachments) are only specified for
the lowest level characters.}

^e.g.

^Leaves

^margins

^teeth

^{orientation }only these have}

^{shape } properties}

^{4 Dependencies may be defined either up or down (but
not both?). An up dependency lists the character states that make this
character inapplicable; a down dependency lists characters that become
inapplicable when this state is chosen.}

^{5 The idea here is to specify a subset of taxa for
which this character is scored, or to specify that the character is non-global,
then leave it to the parsing program to determine the taxon list. This
feature would be used by future identification programs that employ the
Progressive Revelation model.}

^{6 The item data may be stored as the equivalent of
either a taxon-state matrix or a state-taxon matrix, depending upon whether
taxa are nested within characters or characters are nested within taxa.
There will need to be a way of specifying which of these is operative.}

^{7 Public Notes are available for parsing, Private
Notes are not, and are designed for private housekeeping within the treatment}