characters/states and measurements and other hoary problems

Thu Aug 3 15:58:21 CEST 2000

Dear List'eners

attached find DDST Specifications.htm. See if this works.

Cheers - k
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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.<font=
 size=3D-1>

<hr WIDTH=3D"100%">
<dir>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}
<dir>[
 ID {Unique (in the context of this treatment)
number for the contributor}
 Name {contributor=92s name}
 Contact details {contributor=92s address, email=
 etc}
 Private notes {internal notes on=
 contributor}7
 ]</dir>
Attribution {ID of principal treatment builder - this is
the default attribution unless a lower-level item is specifically=
 attributed}1
 List of sources
<dir>[
 ID {Number for the source}
 Description {e.g. reference, description of=
 specimen
set etc}
 ]</dir>
Principal Source {ID of the principal (default) source for
the data}1
 Treatment attachments {General information topics=
 applicable
to the treatment as a whole}
<dir>[
 Attachment name
 Attachment type {e.g.=
 xml,html,txt,rtf,jpeg,gif}
 Attachment path/URL
 Public attachment notes7
 Private attachment notes7
 ]</dir>
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}
<dir>[
 Name {name string for a character set}
 ]</dir>
Character List {required unless an external lexicon resource
has been specified above}
<dir>[
 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=92s
ID from the Contributors list}
 Source1 (reference to a source=92s ID from=
 the
Sources
list)
 Collated Character source {path name for another=
 treatment
that contains lower-level data for this character}
<dir>Collation rule name {Name of a collation rule
as defined in the Collation Rules list}2</dir>
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
<dir>[
 attachment name
 attachment type
 attachment path/URL
 Public notes7
 Private notes7
 ]</dir>
Private notes {internal notes for=
 character}7
 Character State List
<dir>[
 Character state name | Character state ID
 Character dependencies (down)
 Character state attachments
<dir>[
 attachment name
 attachment type
 attachment path/URL
 Public notes7
 Private notes7
 ]</dir>
Private notes7
 ]</dir>
]</dir>
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}
<dir>[
 name
 ]</dir>
Taxon List
<dir>[
 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
<dir>[
 attachment name
 attachment type
 attachment path/URL
 Public notes7
 Private notes7
 ]</dir>
Private notes7
 ]</dir>
Item Data {This will hold the "score matrix"}
<dir>Taxon Name|ID/Character=
 Name|ID6
<dir>Character Name|ID/Taxon=
 Name|ID6
<dir>State Name|ID
<dir>Score {normally present, rare, present by=
 misinterpretation
etc}
 Score Attribution1
 Public Notes7
 Private Notes7</dir>
</dir>
</dir>
</dir>
</dir>

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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.
<dir>e.g.
Leaves
<dir>margins
teeth
<dir>orientation }only these have
shape } properties</dir>
</dir>
</dir>
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
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