Diversity Workbench: Schema for DiversityTaxonomy, version 'draft 0.5'.
Document last revised on 16.Feb.2001 13:23
Copyright 2001 G. Hagedorn. All rights reserved.
Suggestions how to correct or improve the schema are welcome! 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. Unique ID code for the nomenclatural name (primary key). Taxonomic rank of the taxon (var., subsp., species, genus, family, order, etc.). The rank must be selected from the associated list of ranks (= TaxonomyRank). If rank is above species: Name of taxon above species level (currently accepted spelling). Includes infrageneric taxon names, genera, families, etc. If rank is species or below: NomID code of the Genus name. Refers to TaxonomyName (= foreign key) where TaxonomicRank = genus. If rank is species or below: Species epithet, for example 'alba' in 'Abies alba Miller' (currently accepted spelling). T: New taxon; C: new combination based on a previously publ. other name ('comb. nov.'), N: new name ('nom.nov.') introduced to replace a homonym (may occur for genera!), V: validation of previously invalidly published taxon name ('ex'), or U: for unknown. Basionym if CreationType is 'comb. nov.' or replacement ('nom. nov.'), of another name based on the same type material. Refers to ID code of TaxonomyName (= foreign key). Validated name if CreationType is validation ('ex') of another name based on the same type material. Refers to ID code of TaxonomyName (= foreign key). If rank is infraspecific: Infraspecific epithet (currently accepted spelling). Note: the rank is known from required attribute TaxonomicRank in TaxonomyName (= the supertype entity). If rank is infraspecific: The infraspecific name is an autonym (example: 'Abies alba Miller ssp. alba'; normal infraspecific example: 'Abies alba ssp. nebrodensis (Lojac.) Nitz.', note the placement of author names!). For all taxonomic ranks: Author(s) of the taxon, abbreviated according to authors standard, including basionym authors in '()', validating authors ('ex'), optionally including sanctioning authors or "in" authors. 'sensu' or 'emend.' author, or 's.str.'/'s.lat.'. Provided as sep. attribute to simplify later changes (multiple taxon concepts can be based on a single name, so this really belongs into a separate entity). Compare 'potential taxon' sensu Berendsohn! If rank is suprageneric: Type genus of taxon. Refers to the ID code of TaxonomyName (= foreign key). If rank is genus or infrageneric: Type species of genus or infrageneric taxon. Refers to the ID code of TaxonomyName (= foreign key). If rank is species or below: Information on deposition of type material in a collection, entered exactly as written in the protologue (original taxon description). If rank is species or below: Optional information on the geographic location of type material, entered exactly as written in the protologue (i.e. not as known from type specimen studied elsewhere!). If rank is species or below: Optional information on substrate (anorganic, or living/dead plant, animal, or fungus) of type material, entered exactly as written in the protologue (i.e. not as known from type specimen studied elsewhere!). If rank is species or below: Optional information on collector(s) of type material (separate multiple collectors with a ";"), entered exactly as written in the protologue (i.e. not as known from type specimen studied elsewhere!). If rank is species or below: Optional further information on type material, esp. collection date and number, entered exactly as written in the protologue (i.e. not as known from type specimen studied elsewhere!). If rank is genus: Checked (or true) -> this an anamorph genus, containing asexual forms only (relevant for fungi). The information can also be obtained from the taxonomic hierarchy; it is always added here to be available when the hierarchy is incomplete. 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. Reference ID of the original description/protologue. Refers to the ID code of the main ReferenceTitle table in the reference module (= foreign key). Calculated: cached reference description, obtained through the ProtologueRefID from the references subsystems. First page of protologue (original description) in the reference. 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. Original spelling of taxonomic name in the protologue publication. Recorded only, if different from current taxon name. Taxonomic placement (e.g. family or division) mentioned in the original description. This is NOT the current taxonomic placement! Optional: The full text of the Latin description/diagnosis in the protologue. Optional: The full text of the original description/diagnosis 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. Optional: A secondary reference indexing this taxon, e.g. Saccardo, Index of Fungi, etc. Entered as text, not as reference ID! If imported from another database: The name of the database system or provider. Otherwise empty. If imported from another database: An ID value to later re-identify the record in that database may be stored here. Empty for published names, filled w. the name of the responsible person for unpublished ('inedited') names entered in the database. These may not appear in any reports, until specifically requested for a report that will be used to publish the name. Problem with data entry (not with the taxon). 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. Date and time when record was first entered (typed or imported) into this system. 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. Calculated: Like NameCache, but italic and plain text is formatted using xhtml markup (<i>/</i>). 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. 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'). Taxonomy: Secondary action, affecting the status of a taxon. Examples are neo-, lecto- or epitypifications and conservation/rejection. Unique ID for this record. The taxon concerning this action. Refers to the NomID code of TaxonomyName (= foreign key). Type of nomenclatural action: conservation, rejection, neo-, lecto- or epitypification, emendation. The sanctioning of a name should not be recorded here. Additional information regarding the typification or conservation/rejection. 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). Calculated: cached reference description, obtained through the RefID from the references subsystems. Relevant detail in a nomenclatural action reference; usually number of the page on which the action is described. 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. Date and time when record was first entered (typed or imported) into this system. Only for typification actions: A user readable description of the specimen to which the typification refers (collection acronym + storage code / name under which specimen is stored). Only for typification actions: If a specimen collection database subsystem is available, the relevant specimen unit identifier in that system is stored here (added in addition to a user readable TypificationSpecimenDescription). Taxonomy: Opinion or comment relating to the status (valid, accepted, etc.) of a nomenclatural name. Unique ID code for the opinion (primary key). Note that the combination of NomID, ProjectMarker, and Responsible must also be unique and not null (candidate key). The taxon this opinion refers to. Refers to the NomID code of TaxonomyName (= foreign key). Each project can have a different opinion regarding synonmy. Refers to the common project definition in the user module. The person responsible for this opinion/assessment on a taxon. Status of taxonomic name: A=accepted, D=Doubtful, E=Excluded, etc. Synonyms of accepted taxa should have status A. The report may be grouped by this attributes. List of known type specimens, use a '!' after collection name/abbreviation to indicate that this material has been studied by the responsible person. Included in the report. Taxonomic remarks that will be output after the taxon in a report. An internal note of the responsible person concerning this name. This information is NOT included in any report. If the opinion is based on a publication: the reference ID of that work. If the opinion is based on a publication: the reference description of that work. If the opinion is based on a publication: relevant detail; usually page number where the opinion is published. A temporary marker or keyword 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. A temporary marker or keyword 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. Temporary problem with data entry (not with the taxon, cmp. ReportedNote/InternalNote for permanent notes on problems). Name of user responsible for a first plausibility or consistency check. User and Date are automatically filled if 'Original check' performed directly. Date and time when plausibility/consistency was checked (i.e. data entry rules and spelling errors checked, no comparison with original publication). Name of user responsible for comparison of taxon record with original publication. Date and time when entry was compared with the original publication. 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. Date and time when record was first entered (typed or imported) into this system. Taxonomy: Synonymization of species. Each responsible user can create an independent system. Each project can have a different opinion regarding synonmy. Refers to the common project definition in the user module. Synonym name. Refers to the NomID code of TaxonomyName (= foreign key). 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! Accepted name within a project. Refers to the NomID code of TaxonomyName (= foreign key). 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. An internal note of the responsible person concerning this synonymization. This information is NOT included in any report. 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). If the synonymization is based on a publication: the reference description of that work. If the synonymization is based on a publication: relevant detail; usually page number where the synonymization is published. The person responsible for this synonymy opinion. 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. Date and time when record was first entered (typed or imported) into this system. Taxonomy: Hierarchy above the species. Each responsible user can create an independent taxonomic system. Each project can implement a different taxonomic hierarchy. Refers to the common project definition in the user module. Unique ID code of the higher taxon. Refers to the NomID code of TaxonomyName (= foreign key). Next higher taxon (e.g. the family or subfamily if this taxon is a genus). Taxonomic remarks that will be output after the taxon in a report. An internal note of the responsible person concerning this taxon. This information is NOT included in any report. If the classification is based on a publication: the reference ID of that work. If the classification is based on a publication: the reference description of that work. If the classification is based on a publication: relevant detail; usually page number where the opinion is published. The person responsible for grouping this taxon into a higher taxon. 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. Date and time when record was first entered (typed or imported) into this system. CALCULATED FIELD: List of higher taxa for faster access: "div.; class; ord.; fam.". Taxonomy: A technical log of changes of taxonomic or nomenclatural information maintained automatically by the database (user, date, entities & attributes affected). The ID of the taxon that was changed by the user. Refers to the NomID code of TaxonomyName (= foreign key). Attributes and data affected by changes, details of changes. Name of user who last updated the record. This is the operator (or typist) name, which may be different from the person responsible. Date and time of last update of the record. (system attribute used in database replication). (system attribute used in database replication). (system attribute used in database replication). Taxonomy: Specimen (esp. type specimens) that have been studied or shall be cited in a taxonomic monograph. Unique ID for the record (primary key). All cited specimens must refer to a taxonomic opinion that defines a NomID, project marker, and responsible scientist (foreign key). Standard abbreviation of the specimen collection from which the studied specimen was obtained (e.g. 'B' for Berlin herbarium). Used only when a specimen record is available in a compatible collection database subsystem; refers to CollectionSpecimenID in that system (foreign key). Type, holotype, syntype, paratype, isotype, lectotype, neotype, epitype, etc. Annotation regarding the studied specimen that will be output after the taxon in a report. An internal note of the responsible person concerning the studied specimen. This information is NOT included in any report. False = the specimen is known to exist, but has not (perhaps not yet) been studied by the person named under Responsible. False = the information on the studied specimen is suppressed in reports, but can be maintained in the database. Taxonomy: tax. ranks ranging from subforma to superregnum. The logical order of ranks (and display order), can be tested to find false hierarchizations or combinations Do not change the code, it is used in several restriction queries! A unique user readable code for the taxonomic rank that is used in TaxonomyName. Single line description of the rank. Output elements for the rank, stored as a list of two elements (prefix string-semicolon-postfix string). Internal development notes regarding the taxonomic rank. (potential root element for the namespace of current database subsystem)