Please find below some
explanations for the following name extensions used in the Tylenchida
schema:
Perspectives
Junctions
Overlaps
Groupings
Structures contained in more than
one superstructures
Multiple systems for one structure
Muscular and glandular systems
External morphology
Name extensions
attached to basic property names
1. Perspectives
Biological structures can be seen from various perspectives: face view, lateral view, posterior view, and cross-section after dissection. Some basic properties attached to a structure will differ depending on how the structure to be described is viewed. For example, a cylindroid organ such as the spermatheca of many species will be seen as a rectangle in lateral view but as a circle in cross section. The shape and dimensions of this structure are quite different in lateral and in face views.
The schema includes only one structure, the Spermatheca, with various perspectives. (We called this concept 'perspective' instead of 'view' because the latter already has a specific meaning in database design.)
Note that in the case of a cylindroid organ such as the spermatheca, the width in lateral view is equal to the diameter in cross section. The uniformity of representation we enforce makes it possible to enter this relationship only once, and make it valid for all cylindrical structures:
If structure shape = cylindrical
then structure lateral view, width = structure cross section, diameter.
This is a state-based relationship as discussed by Diederich (1997) and Diederich et al. (1998). In other cases, the various perspectives are specific for a particular organ.
When a
structure is described according to several perspectives, the one
the most frequently used by the authors (often the one with the greater
number
of basic properties attached to it) is called the primary perspective
and is
used by default for the structure. The secondary perspective is
explicitly noted as a perspective. The list of structures
includes two
entries. For example:
Spermatheca
and
'Perspective - Cross-section' Spermatheca
In
lateral view (default), the spermatheca is seen as a roundish or a
rectangular organ. When rectangular, its length and its width
will be
entered as:
Spermatheca
shape
rectangular
length (specific value)
width (specific value)
Most spermathecae are rounded in cross section, which means that, in
cross
section, they do not have a length and a width but a diameter. It
is
possible to enter a value for this diameter:
'Perspective
- Cross-section' Spermatheca
shape circular
diameter (specific value)
A perspective consists of three components: the term
'Perspective', its
type, and the name of a structure. The textual representation has
the
following syntax:
'Perspective - <type>'
<structure-name>
where <type> is one of {Face view = Anterior view,
Lateral
view, Cross-section, Posterior view} and <structure-name> is the
name of
the principal view, i.e., the structure.
In some cases, the place where two structures meet may have some properties, but it is not a real structure. For example, the median bulb is a spherical structure that lies between two cylindrical structures, the procorpus and the isthmus. The junctions between these structures may have some characteristics that need to be described (e.g., bulb fused with procorpus vs. bulb clearly set-off by a constriction). A junction is a relationship between two structures. In database practice this is a relationship between entities.
The schema adds a new concept called 'junction'. For example:
Oesophagus
Procorpus
'Junction' Procorpus / Median bulb
Median bulb
This arrangement clearly differentiates the real substructures,
procorpus and
median bulb, from their junction.
The concept of 'junction' is used only when the point where two organs meet is an imaginary line such as the junction between Procorpus and Median bulb, which has no specific name in the literature. Generally speaking, a junction becomes a structure in its own right when it is a clearly distinct part, that is, when it would continue to exist if the adjacent structures were to be dissected out. Such 'junctions' are generally given a name of their own in the literature, e.g., Cardia is a true structure located at the junction between Oesophagus and Intestine.
A
junction consists of three components: the term 'Junction', and the
names of two structures. The textual representation has the
following
syntax:
'Junction' <structure-name1>/<structure-name2>
as shown in the example:
'Junction' Procorpus / Median bulb
In some nematodes, some organs continue past other organs and such 'overlaps' have properties of their own, in particular a length. However, it would be wrong to describe them as separate substructures, because they are not individualized organs: an overlap is only a part of a well-individualized superstructure and it is recognized (and described) only by virtue of this superstructure being longer than usual. For example, oesophageal glands can stop short of the beginning of the intestine, or they can be longer and extending over the intestine in a 'glandular overlap'.
In other cases, the overlap is formed when an organ is folded over itself. For example, in some nematode species, the very long ovary is folded and its end overlaps its beginning.
The
schema describes these types of situation as 'overlaps', for
example:
Oesophageal
glands
'Overlap' Oesophageal glands/Intestine = Glandular overlap
Intestine
Ovary
Flexure
of
ovary
'Overlap' Ovary /Ovary
An overlap consists of three or more components: the term 'Overlap', the names of the overlapping structures including the same name repeated when a structure overlaps itself, the name of the overlap if it has one in the literature, and synonyms of the name if they exist.
The
textual representation has the following syntax:
'Overlap'
<structure-name1>/<structure-name2> = <name>
=
<synonym
1>
=
...
=
<synonym
n>.
where the <name> and the synonyms are specified by the
schema
designer.
In the nematode body, authors describe a 'head', often bulbous and offset from the 'neck', the part of the body that continues to the end of the oesophagus, and a 'tail', the part of the body posterior to the anus. The part between the end of oesophagus and the anus, i.e., between the neck and the tail, does not have a proper name and can be named the 'body proper' (Fig. 5).
Thus,
the external morphology includes the following structures and
substructures:
Body
Head
'Junction' Head/Neck
Neck
Body proper
Tail
(Note that the junctions between neck and body proper and between body
proper
and tail are not included because, so far, no basic properties have
been
described for these by the authors. It would be easy to add them
should
the need arise.)
However,
the
description of species in one of the families of
Tylenchida, Heteroderidae, often separates the neck (with the head)
from the
rest of the body, i.e., Body proper + Tail (Fig. 5). Basic
properties
such as length or shape are described for these two body parts and
there must
be a structure to which these basic properties can be attached in the
database. We preferred to include such aggregation of structures
as
'groupings':
'Grouping' Head + Neck
'Grouping' Body proper + Tail = Body behind the neck = Spherical part
of body
Other groupings may be used some day in future descriptions, which would avoid adding to the list of structures.
The
textual representation has the following syntax:
'Grouping' <structure-name-1> + ... +
<structure-name-m>
= <name>
= <synonym1>
= ...
= <synonym n>
5. Structures contained in more than one superstructure
Some structures are not entirely contained inside or are not part of a single superstructure but they continue over several structures. For example, the oesophageal lumen starts at the base of the stylet, continues through the various parts of the oesophagus, and opens into the intestinal lumen.
The schema adds a new concept called 'within' to be used as follows with the single structure 'oesophageal lumen':
Oesophagus = Pharynx = (Esophagus)
Lumen = Oesophageal lumen
'Within' Procorpus
'Within' Median bulb
'Within' Isthmus
'Within' Oesophageal glands
The textual representation has the following syntax: the name of a
structure,
the term 'Within', and the names of the partially containing
superstructures as
in:
<structure-name
1>
'Within' <structure-name 2>
...
'Within' <structure-name
n>
where the first-named structure (structure-name 1) is within the
second-named
ones (structure-names 2 to n).
6. Multiple systems
for one structure
In the schema, the various structures are grouped within the traditional morphological "systems": digestive system, genital system, and the like. Usually there is little difficulty in determining this for most structures. In other cases, the situation is more ambiguous. For example, the caudal alae are cuticular folds that are used as male secondary sexual organs (Fig. 4, C). This structure could be placed by some authors in Body envelopes and by others in Genital system.
In the
schema, caudal alae are placed under Secondary male sexual
organs, in the male genital system (because their primary physiological
function is reproduction), but some users may not realize this and look
for
this structure under Cuticle, in Body envelopes. The schema uses
the
relationship 'Also in' to indicate this secondary location:
Caudal alae ('Also in' Cuticle)
7. Muscular and glandular systems
The Tylenchida schema does not include all of the systems generally considered in a plan of organization. For example, it does not have a glandular system, because glands are part of various physiological systems, particularly the digestive and genital systems. Also, the schema includes in the muscular system only the muscles that are connected with locomotion, i.e., the somatic muscles. There are other muscles (stylet muscles, digestive sphincters, vaginal and spicule muscles, etc.), but they belong to other systems (digestive system, genital system).
Some users may want to look at all the glands or all the muscles that exist in nematodes. To avoid duplicating structures [which would occur if the schema included, e.g., two copies of vagina sphincter, one in the female genital system and the other in the muscular system], the schema includes each muscle and each gland within the system associated with its major physiological function (e.g., Vagina sphincter with Female genital system) while database 'views' can be used to display on demand the lists of structures comprising the glandular system or the muscular system.
Note: the current version of the schema does not include such 'views'. They will be added later.
Some structures in various internal systems open to the outside and these openings must appear in the external morphology, under the corresponding body parts.
'Also in'
relationships are used to support
the 'external morphology' view. For example, the phasmid is a
chemosensory organ that opens in the lateral field, generally on the
tail or
somewhere along the body (Fig. 4, B). As its primary function is
sensory,
it is placed in the nervous system, but a 'Also in' relationship links
it to
the lateral field. Interestingly, lateral fields also are part of
an
internal system (under Cuticle in Body envelopes), but a second 'Also
in' makes
them viewable with the external morphology:
Phasmids
Phasmid opening ('Also in' Lateral fields)
Lateral field ('Also in' Body)
'Also in' is different from the other relationships in the sense that it is just used by the schema tool to display the structure in another location(s) in the schema, but not to create virtual structure names such as Junction of the Procorpus and the Median bulb.
9. Name extensions attached to basic property names
9.1 Basic properties depending on the observation material used
In some instances, the value of a property depends on the material used to record it. For example, the number of cuticle layers as seen with a transmission microscope and with a scanning electron microscope are not the same. Name extensions are used also in such cases.
The textual representation has the following syntax:
<structure name>, basic property name, <specifying wording>
For example: Face view, shape - by LM, by SEM
In other cases, the value of a character depends on the location where it is observed on the body. For example, the number of ornamentation on the posterior edge of annuli depends on the position of the annuli considered.
Posterior edge ornamentations, number per annulus, - { on anterior end, on neck, on body, on posterior end}
9.2. Basic property "position relative to"
The basic property ' position relative to' attached to a particular structure (1) requires the name of another structure (2), because the position of structure 1 is described in relation to structure 2.
The textual representation has the following syntax:
<structure name 1>, the words 'position relative to', and <structure name 2>
Example:
Labial disc, position relative to - {Lip region}