The Schema Tool
The Schema Tool has been discussed so far
only in the article Diederich,
Fortuner & Milton, 2000. A uniform representation
for the
plan of organization of nematodes of the order Tylenchida, Nematology
2(8): 805-822. This article states that:
In the future Genisys database, each
concept will be represented in
a text file using a specified syntax. Generally speaking, this
will
not be seen by any user. A designer will normally refer to the
syntax
only to see what can be represented by the concept. Both user and
designer will normally interact with the schema via a tool for building
and displaying the schema. This schema tool will also provide
some
automatic operations such as generating standard synonyms for a
particular
concept. Finally, each concept will be used within the database
itself,
often as the field name for the structure in question.
The Schema Tool will implement the various name extensions discussed in
the present page.
1. Perspectives
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.
A schema tool should automatically generate a name and common
synonyms.
Synonyms are indicated after a sign '=' and they have the following
form:
<structure-name> <type> = <type> of the
<structure-name>
as in:
Spermatheca Cross-section = Cross-section of the Spermatheca.
The schema tool will by default show the hierarchical representation
of the actual structures. Thus one would see Spermatheca in the
hierarchy,
but not its perspectives. However, the user or designer can opt
to
examine the perspectives of any structure and then the existing
perspectives
and their properties would be displayed. The designer can add
perspectives
to any structure, as needed to enter data.
Since perspectives have basic properties, within the database itself
<structure-name> <type> will serve as its database
name. From
the Entity-Relationship model (Chen, 1976), both entities and
relationships
between entities are ultimately represented in the database as if
relationships
were also entities. The reason is that both entities and
relationships
have properties.
2. Junctions
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
A schema tool should automatically generate a name and common
synonyms
of the following form:
= Junction of the
<structure-name1> and the <structure-name2>
= Junction of the <structure-name2> and <structure-name1>
= <structure-name1> <structure-name2> junction
= <structure-name2> <structure-name1> junction
which for the example above would automatically generate:
'Junction' Procorpus / Median bulb
= Junction of the Procorpus and the Median bulb
= Junction of the Median bulb and the Procorpus
= Procorpus Median bulb junction
= Median bulb Procorpus junction
As in the case of perspectives, junctions would appear in the schema
tool at the user's/designer's option when viewing the hierarchy of
structures.
Within the database, junctions would be treated similarly to
perspectives
since junctions have properties as well. The name of the field in
the database would be 'Junction of the <structure-name1> and the
<structure-name2>'
3. Overlaps
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.
An example of the syntax (including an existing synonym)
in the schema is:
'Overlap'
Intestine/Anus
= Post-rectal sac
The schema tool will also automatically generate the following
synonyms
as well.
Overlap of the
<structure-name2>
by the <structure-name1>
as in:
Overlap of the Anus by the
Intestine
Unlike what we saw with Junctions, the order of the two structures
is
important as it would be meaningless to create a synonym such as
Overlap
of the Intestine by the Anus.
If a particular name, such as Post-rectal sac, is specified and used
by the authors for an overlap, this name will be used in the database
to
represent an entity with properties. If no name exists in the
literature,
then the first synonym would serve as the name used in the
database.
In terms of displaying overlaps in the hierarchy of structures,
overlaps
would be handled in the same way as junctions and perspectives.
4. Groupings or aggregations
Some structures that are separated in the database may be used by some
authors as a single structure, which has properties attached to it.
The textual representation has the following
syntax:
'Grouping' <structure-name-1> + ... +
<structure-name-m>
= <name>
= <synonym1>
= ...
= <synonym n>
The name and synonyms must be specified, as none will automatically
be generated by the schema tool. Since a grouping has basic
properties
with states or values, and since a grouping is a relationship between
two
or more structures, it is converted by the Schema Tool to the entity
name in the database
using the specified <name>.
5. Structure contained in
several superstructures
Some structures are not entirely contained inside or are not part of
a single superstructure but they continue over several
structures.
One example is the oesophageal lumen, a tube that starts at the base of
the stylet, continues through the various parts of the oesophagus and
opens
into the intestinal lumen.
Body envelopes and by others in Genital systemA partial substructure
consists of three or more components: 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).
Since properties can be attached to
the structure as it relates to its containing
superstructure, field names in the database would have to be generated
from each combination, i.e., the name in the database would have the
form:
<structure-name-1> within <structure-name-i>, i
=
2, ..., n,
as in:
Lumen within the Procorpus
Lumen within the Median bulb
Lumen within the Isthmus
Lumen within the Oesophageal glands
6. Multiple systems for one structure
Some structures (e.g., male caudal alae) can be placed in one system by
some authors and in another system by other authors (e.g., caudal alae
in either Body envelopes or in Male Genital system). We placed the
structure in one of the possible system and we used
the relationship 'Also in' to indicate its secondary location.
The textual representation has the following
syntax:
[In system 1:] <structure name>, the term 'Also in', >system 2
name>
For example:
Body envelopes / ... / Caudal alae ('Also in' Cuticle)
The schema tool will automatically display the structure name when it
is queried about the secondary structure.
7. Muscular and glandular systems
The muscular system includes some muscles whose physiological functions
that belong in other systems. For example, the stylet muscles,
digestive sphincters, vaginal
and spicule muscles belong to other systems (digestive
system, genital system). Same thing with the glandular system.
The textual representation has the following
syntax:
To be defined later.
The schema tool will use database
'views' to display on demand the lists of structures comprising the
glandular
system or the muscular system.
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.
The textual representation has the following
syntax:
'Also in' relationships are used
to support the 'external morphology' view.
The textual representation has the following
syntax:
To be defined later.
The schema tool will use database
'views' to display on demand the lists of structures comprising the
glandular
system or the muscular system.
9.1 Basic properties
depending on the observation material used
The
textual representation has the following syntax:
<structure
name>, basic property name, <specifying wording>
For
example: Face view, shape - by LM, by SEM
The corresponding function in the Schema Tool will be defined later.
9.2. Basic property
"position relative to"
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}
The corresponding function in the Schema
Tool will be defined later.