SCHEMA
for the Nematode Order TYLENCHIDA

The Tylenchida schema

Discussion on the schema concept in Genisys

Diederich, 1997. Basic properties for biological databases: Character development and support. Mathl Comput. Modelling 25(10): 109-127
Diederich, Fortuner & Milton, 1997. Construction and integration of large character sets for nematode morpho-anatomical data. Fundam. appl. Nematol. 20(5): 409-424.
Diederich, Fortuner & Milton, 2000. Genisys and computer-assisted identification of nematodes. Nematology 2(1): 17-30
Diederich, Fortuner & Milton, 2000. A uniform representation for the plan of organisation of nematodes of the order Tylenchida. Nematology 2(8): 805-822.
Fortuner, 2002. Uniformity and representation of taxonomic and other characters and semi-automatic extraction using computer tools. Nematology 4(5): 583-591.

The Schema tool
Once a database is created according to the concepts described in the articles above and in the text below, a Schema tool will make it possible to use its data.  Such a tool has never been created, or even fully described, but some of its functions are discussed in a separate page (schema tool).

Explanations of name extensions
(modified from Diederich, Fortuner & Milton, 2000. A uniform representation for the plan of organization of nematodes of the order Tylenchida,
Nematology 2(8): 805-822.)

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. 

 

 

2.  Junctions

 

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

 

 

3.  Overlaps

 

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. 

 

4.  Groupings

 

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.

8. External morphology

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}

 





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