Extending the biogeographical model

Africamuseum6 (7?) June 2013

Workplan

Continue with database constructed so far Add fields for

Authority (name of the author, date, parentheses)

Classification Fields for different ranks

Synonymy Sources

Fields for classification Add fields to ‘species’ table for the main ranks:

Kingdom Phylum (=division) Class Order Family

Alternative: separate table Split taxonomy in genus/species, and family and above

Problem: not properly normalised, not good solution for long-term management of taxonomic register

Add field for authority

Add field for authority in the species table One text field, not structured further Too complex to be split up in separate

fields Optionally, add field for reference to

original description Ideally as a link to the sources table

Add table sources

Fields ID (=primary key, autonumber) Author Year Reference

Relations with sources table

Add ‘SourcesID’ link in Species table Add ‘SourcesID’ link in Distribution

table

Create relations between Sources and Species table Sources and distribution table

Add synonymy ‘Self-referential’ table

Record in table refers to other record in same table Needs status of the taxon described in the record

Create new fields: AcceptedID TaxonStatus (optionally link to separate table)

Create relation: AcceptedID link to ID of taxon table

Relations diagram - synonyms

One-to-many relationships

E.g. species in family: each species belongs to one, and only one family

Implement by listing the Primary Key of the ‘one’ side as a field in the table of the ‘many’ side

‘Foreign Key’ points at the right record in the ‘one’ side of the relationship

One-to-many relationships

(Many) species in (one) family

(Many) places/localitiesin (one) country

Many-to-many relationships?

Problem: we don’t have a ‘one’ side, there is no single record to refer to

Can not be implemented directly in SQL Needs extra table

To split up many-to-many in two one-to-many relations

Extra table takes pointers to both sides of the relationship

Many-to-many relationship

Example: ‘sources’ versus ‘species’ Source = literature, report, database…

One source refers to several species A species is referred to in many sources Create many-to-many table

Split the one many-to-many relationship in two one-to-many relationships

Many-to-many relationship

Relations diagram - complete

Present structure: Philosophy

Structure has to be as simple as possible But not any simpler!! Present structure is good short-term

solution, but not long-term Needs better alternative to represent

classification and hierarchy

Hierarchy: flat table

Every rank in the hierarchy is represented by a field in the table

Simplest solution Easy to create Easy to query

Hierarchy: flat table

Hierarchy: flat table

Problems not normalised!

Not a real problem if a quick-and-dirty solution is all that is needed

Difficult to maintain hierarchy in the long term

‘Standard’ problems with non-normalised database Possible conflicting information, inefficient storage…

Cfr MASDEA; too simple

Hierarchy: normalised tables

Every rank is represented by a separate table

Not very difficult to write a query to regenerate flat table

Every taxon can have additional information Extra fields with description…

Hierarchy: cascading tables

Hierarchy: normalised tables

Avantages Easy to maintain and query Normailised, possible to add information at any level

of the hierarchy Drawbacks

Ranks are hard-wired on the structure of the database New rank would require change of the structure of the

database And probably of the user interface, web interface…

Number of tables Lot of functionality duplicated

Taxonomic reality Ranks used depend on the taxonomic group

Botany: mainly infra-specific; zoology: mainly on higher levels

Many of the ranks are only sparsely used Needs for a more flexible system Much of the functionality is the same across

all ranks ‘parent’, synonymy Authority, description…

‘Open Hierarchy’ Possible to define new ranks without having

to rewrite the structure of the database All taxonomic names are stored in a field in

a single table; other fields indicate parent and rank

Many-to-one relation: a single parent, several descendants Include ID of parent in the record of the

descendant

Open Hierarchy Avantages

Completely normalised Flexible

Drawbacks Difficult to query classification

Queries of the type ‘all species of the Echinodermata’… Solution:

Recursive query ‘calculated field’ program

Synonymy

Every taxon can have several synonyms; in principle, only one valid name for any synonym Many-to-one relation: one valid name,

many synonymous names Include ID of the valid name in the record

of the synonymous nameOther fields for the type of synonymy…

Rest of the taxonomic model

Ranks should be in a separate table Information on the level of the rank

can be added Possibility of extra quality control

Rank of a parent as compared to rank of descendants

Rank of siblings should be same

Combine with rest

Previous work on geography and sources