Progress of Colin’s 2013 Rubenstein Project (Ⅱ) —Glossary & Database Design
This article is to introduce some glossaries used or defined by us in this project and the work of database design.
Taxon is a taxonomic unit or group which may be named or not. A taxon encompasses all included taxa of lower rank and individual organisms. Taxonomic rank describes the level of a taxon in a taxonomic hierarchy for nomenclatural purposes. Each rank is either mandatory (e.g. kingdom, phylum, class, order, family, genus, species) or optional (e.g. subkingdom, subphylum, subclass, subfamily, subgenus, subspecies). Nominal taxon isa concept of a taxon which is denoted by an available name based on a name-bearing type.
(2) Taxon Concept
The scope of a taxon may differ from one taxonomists to another, and changes with new data. Each opinion as to what is intended by the name of a taxon is a ‘taxon concept’.
(3) Taxonomic Hierarchy
Taxa are arranged hierarchically from high rank to low rank, and compose a taxonomic hierarchy (or “taxonomic tree” and “taxonomic classification”) that reflects the view on classification. As well known, taxonomic hierarchy is usually tree-based and can be regarded as a special case of mathematical tree technically.
(4) Nominal Relation (NR)
Because of the inexact nature of taxonomy, different taxonomies may use different names for the same taxon concepts and the same name for different taxon concepts (Homonym). When compare two taxon concepts from different hierarchies, scientific names including accepted name and synonyms for the concepts usually provide important clues about the relationship between them, and that is named as Nominal Relation.
(5) Ancestor Relation (AR)
Ancestor Relation is defined to describe the relationship between two compared taxa by their parent paths.
(6) Descendant Relation (DR)
Descendant Relation is intended for assessing the similarity of the branches under the compared taxa.
(7) Taxon Link (TL)
Taxon Link is defined as a triple tuple (AR, NR, DR). It is the result of taxon to taxon comparison, and intended for representing the combined relationships among compared taxa.
(8) Compared Tree and Reference Tree
Just like subtraction, the hierarchy to be compared on the left of the comparator is regarded as compared tree (CT) and the hierarchy for comparing on the right of the operator is called reference tree (RT).
2. Database Design
(1) Data Requirements
According to the analysis of THC’s requirements (refer to Progress of Colin’s 2013 Rubenstein Project (Ⅰ)), the database should consider the following main data requirements:
1. The user information like username, password, self description, status.
2. The tree information like tree name, creator, created date, description of the tree.
3. The experiment information like name, creator, created date, compare tree, reference tree.
4. The result of comparison like similarity index, taxon links.
5. Taxon detail like scientific name, synonym, parents, rank.
This database will store as many as possible taxonomic trees (hierarchies) just like a forest, so it is named as “Taxonomic Forest” vividly. We will use MYSQL 5.0 or above as the database software.
(2) Tables & Relationship
Table 1 shows the main tables of “Taxonomic Forest”.
Table “experiment” is for storing detail information about experiment.
Table ‘synonyms’ is to store synonyms of taxon in ‘tree’.
Synonym is regarded as vice label for taxon.
Table ‘taxonlinks’ stores the relationships of taxa in compared trees.
It is for the result of tree comparison and computation.
Each record of ‘tree’ means a taxon including its propertis such as name, rank, position and so on.
'tree_info' stores information about tree.
It is for user management, and records the information for registered users.
Figure1 shows the relationship of these main tables (detail fields are not displayed for the security reason).
Fig 1 E-R Diagram of Database “Taxonomic Forest”
Relative article: Progress of Colin’s 2013 Rubenstein Project (Ⅰ)
This article is excerpted from “Database Design Specification for THC”
Author: Colin, 2013 EOL Rubenstein Fellow