This is a documentation of an earlier, more detailed model for nomenclature and taxonomy that has not been further pursued. In it, the TaxonomyName entity is formulated as a supertype-subtype structure. The common attributes are in the supertype TaxonomyName and 4 exclusive subtypes exist for higher taxa (TaxonomyHigherTaxa), genera (TaxonomyGenus), infrageneric taxa (TaxonomyInfraGenericTaxon), and infraspecific taxa and species (TaxonomySpecies; this could have been separated into two subtypes again). Each entity of TaxonomyName must have exactly one these four subtype entities linked to it.
Note that the introduction of a supertype is not only an implementation issue (to implement common attributes only once), but also deduced from the requirement that a single ID must be provided for all taxa, regardless of rank. If the taxonomy database subsystem is used from other subsystems, in many cases (e.g. identification of specimen, morphological descriptions) the same link may point to taxa ranging from infraspecific taxa to family or even higher. For example, it is indeed possible that an identification can only assert that the species must belong to Basidiomycetes.
The advantage of the model using entities as subtype is that the relationship between the subtypes can be defined in more detail. For example the genus or higher taxon type can only be a species of genus, respectively. However, since the relational database management systems used (Jet and SQL Server) do not support supertype/subtype explicitly, and since the aim of the model is relative simplicity, rather than completeness, the supertype and subtype attributes have been combined in all newer models into the single entity TaxonomyName. The basic supertype-subtype structure is maintained, albeit simplified and less visible in the new model: Instead of linking entities, groups of attributes must be used alternatively.
An empty Microsoft Access 2000 database implementing this model is provided for archiving purposes. See the selfextracting archive DiversityTaxonomy_SupertypeSubtype.exe.
Gregor Hagedorn, 11.Jan.2001.
Entity relationship diagram of DiversityTaxonomy (supertype-subtype version, archived Jan. 2001)
(You can click on the entities to go to the attribute tables.)
Taxonomy: Supertype entity, providing a nomenclatural ID for all names introduced as taxa (infraspecific, species, genus, family, etc.). Contains only objective information; all scientific opinion is placed in ...Opinion, ...Synonymy, & ...Hierarchy.
| Name | Type | Description / Default value & validation | Rqrd./Index | |
|---|---|---|---|---|
| NomID | Autonumber | Unique ID code for the nomenclatural name. Default value: GenUniqueID() |
- | I (U) |
| TaxonomicRank | Text (20) | Taxonomic rank of the taxon (var., subsp., species, genus, family, order, etc.). | R | I |
| ConceptSuffix | Text (255) | 'sensu' or 'emend.' author, 's.str.'/'s.lat.'. This attribute does not really belong here, since multiple taxon concepts can be based on a single name. Provided as sep. attribute to simplify later changes. Compare 'potential taxon' sensu Berendsohn! | - | - |
| ProtologueReportedCitation | Text (255) | Optional text of citation; used only when default reference description is unsatisfactorily (esp. abbreviated tax. literature book titles, exsiccata references). If present, this information is used in preference over the ProtologueRefDescription. | - | - |
| ProtologueRefID | Text (20) | Reference ID of the original description/protologue. Refers to the ID code of the main ReferenceTitle table in the reference module (= foreign key). | - | I |
| ProtologueRefDescriptionCache | Text (255) | Calculated: cached reference description, obtained through the ProtologueRefID from the references subsystems. | - | - |
| ProtologueRefPage | Text (50) | First page of protologue (original description) in the reference. | - | - |
| ProtologueRefReprintPagination | Boolean | If checked (or 'True'), the true page number of the protologue page is unknown and only a reprint page number (pagination starting w. 1...) can be given. In tax. monographs this situation is often indicated by 'extr.' or 'extractum' after the page number. | R | - |
| OriginalNameSpelling | Text (255) | Original spelling of taxonomic name in the protologue publication, if different from current taxon name. | - | - |
| OriginalTaxonPlacement | Text (255) | Taxonomic placement (e.g. family or division) mentioned in the original description. This is NOT the current taxonomic placement! | - | - |
| OriginalDiagnosisLatin | Memo | Optional: The full text of the Latin description/diagnosis in the protologue. | - | - |
| OriginalDiagnosisOther | Memo | Optional: The full text of the original description in the protologue, if a diagnosis in another language than Latin was provided. To be entered into the database only if no copyright is violated. | - | - |
| IndexingReference | Text (255) | Optional: A secondary reference indexing this taxon, e.g. Saccardo, Index of Fungi, etc. Entered as text, not as reference ID! | - | - |
| ImportedFrom | Text (255) | If imported from another database: The name of the database system or provider. Otherwise empty. | - | - |
| ImportedID | Text (255) | If imported from another database: An ID value to later re-identify the record in that database may be stored here. | - | - |
| Problem | Text (255) | Problem with data entry (not with the taxon). | - | - |
| LogCreated_User | Text (255) | Name of user who first entered (typed or imported) the data. This is the operator (or typist) name, which may be different from the person responsible. | R | - |
| LogCreated_Date | Date/Time | Date and time when record was first entered (typed or imported) into this system. Default value: Now() |
R | - |
| NameCache | Text (255) | Calculated: Full, standardized name for the new taxon, calculated from genus, species and infraspecific epithet and authors. The value is unique, since it includes the author for higher taxa (genera, families) as well as for species. | R | I (U) |
| NameCache_html | Text (255) | Calculated: Like NameCache, but italic and plain text is formatted using xhtml markup (/). | R | - |
| NameCache_NoAuthors | Text (255) | Calculated: Like NameCache, but without any authors. Duplicates may occur here, and taxa with homonyms can be detected using this attribute. Where no homonyms are found, names from other data sources may be compared based on this field alone. | R | I |
| NameCache_inverted | Text (255) | Calculated: Like NameCache, but for species or infraspecific taxa the lowest rank name is printed first ('species-epitheton, Genus' or 'variety (var.) species-epitheton, Genus'). | R | I (U) |
| Relation type: | Fields involved | |||
| Referential integrity | TaxonomyName.NomID « TaxonomyHierarchy.Parent_NomID | |||
| Updates cascade, one-to-one | TaxonomyName.NomID « TaxonomyInfraGenericTaxon.InfraGenericID | |||
| Deletions cascade | TaxonomyName.NomID « TaxonomyActionOnName.NomID | |||
| Deletions cascade, one-to-one | TaxonomyName.NomID « TaxonomyGenus.GenusID | |||
| Referential integrity | TaxonomyName.NomID « TaxonomyHierarchy.NomID | |||
| Deletions cascade, one-to-one | TaxonomyName.NomID « TaxonomyHigherTaxon.HigherTaxonID | |||
| Referential integrity | TaxonomyName.NomID « TaxonomyOpinion.NomID | |||
| Deletions cascade, one-to-one | TaxonomyName.NomID « TaxonomySpecies.SpeciesID | |||
Taxonomy: Nomenclatural information relating to the introduction of infrageneric taxa (between species and genus). This is a subtype of the supertype entity TaxonomyName.
| Name | Type | Description / Default value & validation | Rqrd./Index | |
|---|---|---|---|---|
| InfraGenericID | Long | Unique ID code of the higher taxon. Refers to the NomID code of TaxonomyName (= foreign key). | R | I (U)/I (U) |
| InfraGenericTaxonName | Text (255) | Name of taxon above species level, excluding genera (currently accepted spelling). | R | I (U) |
| TaxonAuthors | Text (255) | Author of the taxon. | - | - |
| TypeSpecies_NomID | Long | Type species of infrageneric taxon. Refers to the ID code of TaxonomyName (= foreign key). | - | I/I |
| Relation type: | Fields involved | |||
| Updates cascade, one-to-one | TaxonomyName.NomID « TaxonomyInfraGenericTaxon.InfraGenericID | |||
| Updates cascade | TaxonomySpecies.SpeciesID « TaxonomyInfraGenericTaxon.TypeSpecies_NomID | |||
Taxonomy: Nomenclatural information relating to the introduction of a genus. This is a subtype of the supertype entity TaxonomyName.
| Name | Type | Description / Default value & validation | Rqrd./Index | |
|---|---|---|---|---|
| GenusID | Long | Unique ID code of the genus. Refers to the NomID code of TaxonomyName (= foreign key). | R | I (U)/I (U) |
| GenusName | Text (255) | Genus name (currently accepted spelling). | R | I (U) |
| GenusAuthors | Text (255) | Author of the genus. | - | - |
| TypeSpecies_NomID | Long | Type species of genus. Refers to the ID code of TaxonomyName (= foreign key). | - | I/I |
| AsexualGenus | Boolean | Checked (or true): The genus is an anamorph genus, containing asexual forms only (relevant for fungi). This information can often also be obtained from the taxonomic hierarchy; it is added here to be available when the hierarchy is yet unfinished. Default value: Null |
- | - |
| Relation type: | Fields involved | |||
| Referential integrity | TaxonomyGenus.GenusID « TaxonomyHigherTaxon.TypeGenus_NomID | |||
| Referential integrity | TaxonomyGenus.GenusID « TaxonomySpecies.Genus_NomID | |||
| Referential integrity | TaxonomySpecies.SpeciesID « TaxonomyGenus.TypeSpecies_NomID | |||
| Deletions cascade, one-to-one | TaxonomyName.NomID « TaxonomyGenus.GenusID | |||
Taxonomy: Nomenclatural information relating to the introduction of scientific specific and subspecific names. This is a subtype of the supertype entity TaxonomyName.
| Name | Type | Description / Default value & validation | Rqrd./Index | |
|---|---|---|---|---|
| SpeciesID | Long | Unique ID code of the species/infraspecific taxon. Refers to the NomID code of TaxonomyName (= foreign key). | - | I (U)/I (U) |
| Genus_NomID | Long | Genus name. Refers to the ID code of TaxonomyGenus (= foreign key). | R | I/I |
| SpeciesEpithet | Text (255) | Species epithet, for example 'alba' in 'Abies alba Miller' (currently accepted spelling). | R | I |
| SpeciesAuthor | Text (255) | Authors of the species, abbreviated according to authors standard (empty for infraspecific taxa except autonyms; autonym example: 'Abies alba Miller ssp. alba'; infraspecific example: 'Abies alba ssp. nebrodensis (Lojac.) Nitz.'). | - | - |
| InfraspecificName | Text (255) | Infraspecific epitheton (currently accepted spelling). Note: the rank is known from required attribute TaxonomicRank in TaxonomyName (= the supertype entity). | - | I |
| InfraspecificAuthor | Text (255) | Authors of the infraspecific name (empty for infraspecific autonyms like Abies alba alba). | - | - |
| CreationType | Text (1) | T: New taxon; C: new combination based on a previously published other name, N: new name ('nom.nov.') introduced to replace a homonym, V: validation of previously invalidly published taxon name, or U: for unknown. Default value: "U" |
R | - |
| Basionym_NomID | Long | Basionym. Filled only if the new name is a combination, replacement, or validation based on another name and has the same type material. Refers to the ID code of TaxonomyName (= foreign key). | - | I/I |
| ProtologueTypeInformation | Text (255) | Information on deposition/location of type material, entered exactly as mentioned in the protologue (original taxon description). | - | - |
| Relation type: | Fields involved | |||
| Referential integrity | TaxonomyGenus.GenusID « TaxonomySpecies.Genus_NomID | |||
| Referential integrity | TaxonomySpecies.SpeciesID « TaxonomyGenus.TypeSpecies_NomID | |||
| Updates cascade | TaxonomySpecies.SpeciesID « TaxonomyInfraGenericTaxon.TypeSpecies_NomID | |||
| Referential integrity | TaxonomySpecies.SpeciesID « TaxonomySpecies.Basionym_NomID | |||
| Referential integrity | TaxonomySpecies.SpeciesID « TaxonomySynonymy.Accepted_NomID | |||
| Referential integrity | TaxonomySpecies.SpeciesID « TaxonomySynonymy.Syn_NomID | |||
| Deletions cascade, one-to-one | TaxonomyName.NomID « TaxonomySpecies.SpeciesID | |||
Taxonomy: Secondary action, affecting the status of a taxon. Examples are neo-, lecto- or epitypifications and conservation/rejection.
| Name | Type | Description / Default value & validation | Rqrd./Index | |
|---|---|---|---|---|
| ActionID | Autonumber | Unique ID for this record. | - | I (U) |
| NomID | Long | The taxon concerning this action. Refers to the NomID code of TaxonomyName (= foreign key). | R | I/I |
| ActionType | Text (1) | Type of nomenclatural action: conservation, rejection, neo-, lecto- or epitypification, emendation. The sanctioning of a name should not be recorded here. | R | - |
| InternalNote | Memo | Additional information regarding the typification or conservation/rejection. | - | - |
| RefID | Text (20) | Reference ID of the reference containing the nomenclatural action defined in ActionType. Refers to the ID code of the main ReferenceTitle table in the reference module (= foreign key). | R | I |
| RefDescriptionCache | Text (255) | Calculated: cached reference description, obtained through the RefID from the references subsystems. | - | - |
| RefPage | Text (50) | Relevant detail in a nomenclatural action reference; usually number of the page on which the action is described. | - | - |
| LogCreated_User | Text (255) | Name of user who first entered (typed or imported) the data. This is the operator (or typist) name, which may be different from the person responsible. | R | - |
| LogCreated_Date | Date/Time | Date and time when record was first entered (typed or imported) into this system. Default value: Now() |
R | - |
| Relation type: | Fields involved | |||
| Deletions cascade | TaxonomyName.NomID « TaxonomyActionOnName.NomID | |||
Taxonomy: Opinion or comment relating to the status (valid, accepted, etc.) of a nomenclatural name.
| Name | Type | Description / Default value & validation | Rqrd./Index | |
|---|---|---|---|---|
| NomID | Long | The taxon this opinion refers to. Refers to the NomID code of TaxonomyName (= foreign key). | - | I |
| ProjectMarker | Text (255) | Each project can have a different opinion regarding synonmy. Refers to the common project definition in the user module. | R | I (UM) |
| Responsible | Text (255) | The person responsible for this opinion/assessment on a taxon. Validation rule: Not Is Null, validation message: Any opinion must be signed by a responsible person. |
R | - |
| Status | Text (1) | Status of taxonomic name: A=accepted, D=Doubtful, E=Excluded, etc. | - | I |
| UserMarker1 | Text (255) | A temporary marker assigned by user for searching and sorting purposes while a group is reviewed. Any information can be entered here, but it will be visible only internally. | - | I |
| UserMarker2 | Text (255) | A temporary marker assigned by user for searching and sorting purposes while a group is reviewed. Any information can be entered here, but it will be visible only internally. | - | I |
| TypeInformation | Text (255) | List of known type collections, use a '!' after collection name/abbreviation to indicate that this material has been studied by the responsible person. | - | - |
| ReportedNote | Memo | Taxonomic remarks that will be output after the taxon in a report. | - | - |
| InternalNote | Memo | An internal note of the responsible person concerning this name. This information is NOT included in any report. | R | - |
| RefID | Text (20) | If the opinion is based on a publication: the reference ID of that work. | - | I |
| RefDescriptionCache | Text (255) | If the opinion is based on a publication: the reference description of that work. | - | - |
| RefPage | Text (50) | If the opinion is based on a publication: relevant detail; usually page number where the opinion is published. | - | - |
| Problem | Text (255) | Temporary problem with data entry (not with the taxon, cmp. ReportedNote/InternalNote for permanent notes on problems). | - | - |
| CheckPlausible_User | Text (255) | Name of user responsible for a first plausibility or consistency check. User and Date are automatically filled if 'Original check' performed directly. | - | - |
| CheckPlausible_Date | Date/Time | Date and time when plausibility/consistency was checked (i.e. data entry rules and spelling errors checked, no comparison with original publication). | - | - |
| CheckOriginal_User | Text (255) | Name of user responsible for comparison of taxon record with original publication. | - | - |
| CheckOriginal_Date | Date/Time | Date and time when entry was compared with the original publication. | - | - |
| LogCreated_User | Text (255) | Name of user who first entered (typed or imported) the data. This is the operator (or typist) name, which may be different from the person responsible. | R | - |
| LogCreated_Date | Date/Time | Date and time when record was first entered (typed or imported) into this system. Default value: Now() |
R | - |
| Relation type: | Fields involved | |||
| Referential integrity | TaxonomyName.NomID « TaxonomyOpinion.NomID | |||
Taxonomy: Synonymization of species. Each responsible user can create an independent system.
| Name | Type | Description / Default value & validation | Rqrd./Index | |
|---|---|---|---|---|
| ProjectMarker | Text (255) | Each project can have a different opinion regarding synonmy. Refers to the common project definition in the user module. | R | I (UM) |
| Syn_NomID | Long | Synonym name. Refers to the NomID code of TaxonomyName (= foreign key). | R | I |
| ProParteSynID | Byte | 0 = only a single accepted name is possible for a given synonym. 1..255 = multiple valid names are allowed for pro parte ('p.p.') synonyms. Use 1 for the first pro parte name, 2 for the second, and so on. Please do not use 0 for 1st, 2nd, etc. name! Default value: 0 |
R | - |
| Accepted_NomID | Long | Accepted name within a project. Refers to the NomID code of TaxonomyName (= foreign key). | R | I/I |
| ObligateSynonym | Boolean | True (= checked) indicates an obligate synonym, based on the same type; False (= empty) a facultative (or taxonomic) synonym. Null (= gray checkbox) indicates that the synonymization status could not be decided. Default value: Null |
- | - |
| SynonymyTypeCache | Text (1) | @@ Teleomorph?? Unknown?? Type of Synonymy: Normal synonym (N), anamorph of a teleomorph (A), or synanamorph (S). Calculated from AsexualGenus marker in the Genus. | - | - |
| InternalNote | Memo | An internal note of the responsible person concerning this synonymization. This information is NOT included in any report. | R | - |
| RefID | Text (20) | If the synonymization is based on a publication: the reference ID of that work. Refers to the ID code of the main ReferenceTitle table in the reference module (= foreign key). | - | I |
| RefDescriptionCache | Text (255) | If the synonymization is based on a publication: the reference description of that work. | - | - |
| RefPage | Text (50) | If the synonymization is based on a publication: relevant detail; usually page number where the synonymization is published. | - | - |
| LogCreated_User | Text (255) | Name of user who first entered (typed or imported) the data. This is the operator (or typist) name, which may be different from the person responsible. | R | - |
| LogCreated_Date | Date/Time | Date and time when record was first entered (typed or imported) into this system. Default value: Now() |
R | - |
| Relation type: | Fields involved | |||
| Referential integrity | TaxonomySpecies.SpeciesID « TaxonomySynonymy.Accepted_NomID | |||
| Referential integrity | TaxonomySpecies.SpeciesID « TaxonomySynonymy.Syn_NomID | |||
Taxonomy: Hierarchy above the species. Each responsible user can create an independent taxonomic system.
| Name | Type | Description / Default value & validation | Rqrd./Index | |
|---|---|---|---|---|
| ProjectMarker | Text (255) | Each project can implement a different taxonomic hierarchy. Refers to the common project definition in the user module. | - | I (UM) |
| NomID | Long | Unique ID code of the higher taxon. Refers to the NomID code of TaxonomyName (= foreign key). | - | I/I |
| Parent_NomID | Long | Next higher taxon (e.g. the family or subfamily if this taxon is a genus). | R | I/I |
| ReportedNote | Text (255) | Taxonomic remarks that will be output after the taxon in a report. | - | - |
| InternalNote | Memo | An internal note of the responsible person concerning this taxon. This information is NOT included in any report. | - | - |
| RefID | Text (20) | If the classification is based on a publication: the reference ID of that work. | - | I |
| RefDescriptionCache | Text (255) | If the classification is based on a publication: the reference description of that work. | - | - |
| RefPage | Text (50) | If the classification is based on a publication: relevant detail; usually page number where the opinion is published. | - | - |
| LogCreated_User | Text (255) | Name of user who first entered (typed or imported) the data. This is the operator (or typist) name, which may be different from the person responsible. | - | - |
| LogCreated_Date | Date/Time | Date and time when record was first entered (typed or imported) into this system. Default value: Now() |
- | - |
| HierarchyListCache | Text (255) | CALCULATED FIELD: List of higher taxa for faster access: "div.; class; ord.; fam.". | - | - |
| Relation type: | Fields involved | |||
| Referential integrity | TaxonomyName.NomID « TaxonomyHierarchy.Parent_NomID | |||
| Referential integrity | TaxonomyName.NomID « TaxonomyHierarchy.NomID | |||
Taxonomy: A technical log of changes of taxonomic or nomenclatural information maintained automatically by the database (user, date, entities & attributes affected).
| Name | Type | Description / Default value & validation | Rqrd./Index | |
|---|---|---|---|---|
| NomID | Long | The ID of the taxon that was changed by the user. Refers to the NomID code of TaxonomyName (= foreign key). | R | I |
| Changes | Memo | Attributes and data affected by changes, details of changes. | R | - |
| LogUpdated_User | Text (255) | Name of user who last updated the record. This is the operator (or typist) name, which may be different from the person responsible. | R | - |
| LogUpdated_Date | Date/Time | Date and time of last update of the record. | R | I (UM) |
| s_GUID | GUID | (system attribute used in database replication). Default value: GenGUID() |
- | I (U) |
| s_Generation | Long | (system attribute used in database replication). | - | I |
| s_Lineage | OLE Object | (system attribute used in database replication). | - | - |
Taxonomy: Nomenclatural information relating to the introduction of higher taxa (above the genus). This is a subtype of the supertype entity TaxonomyName.
| Name | Type | Description / Default value & validation | Rqrd./Index | |
|---|---|---|---|---|
| HigherTaxonID | Long | Unique ID code of the higher taxon. Refers to the NomID code of TaxonomyName (= foreign key). | R | I (U)/I (U) |
| HigherTaxonName | Text (255) | Name of taxon above species level, excluding genera (currently accepted spelling). | R | I (U) |
| TaxonAuthors | Text (255) | Author of the taxon. | - | - |
| TypeGenus_NomID | Long | Type genus of taxon. Refers to the ID code of TaxonomyName (= foreign key). | - | I/I |
| Relation type: | Fields involved | |||
| Referential integrity | TaxonomyGenus.GenusID « TaxonomyHigherTaxon.TypeGenus_NomID | |||
| Deletions cascade, one-to-one | TaxonomyName.NomID « TaxonomyHigherTaxon.HigherTaxonID | |||
Footnotes: The following abbreviations have been used in the tables: R: It is required to enter data in this field. I: The field is indexed to allow fast searching. different types of indices are denoted by additional letters in parentheses: U = unique index, N = Null values are ignored in the index, M = the index contains more than one attribute. Note that all attributes that are part of the primary key index are underlined in the first column.
Documentation last revised on 19.Jan.2001 02:15, last page update: 2005-03-30.