TaxonNamesModel v2.2
Contents
- 1 DiversityTaxonNames Information Model (version 2.2, 20. October 2009)
- 1.1 ER Diagrams
- 1.2 Organisation of the data
- 1.3 Description of the tables and columns:
- 1.3.1 Table: TaxonAcceptedName
- 1.3.2 Table: TaxonCommonName
- 1.3.3 Table: TaxonGeography
- 1.3.4 Table: TaxonHierarchy
- 1.3.5 Table: TaxonName
- 1.3.6 Table: TaxonNameExternalDatabase
- 1.3.7 Table: TaxonNameExternalID
- 1.3.8 Table: TaxonNameList
- 1.3.9 Table: TaxonNameListAnalysis
- 1.3.10 Table: TaxonNameListAnalysisCategory
- 1.3.11 Table: TaxonNameListAnalysisCategoryValue
- 1.3.12 Table: TaxonNameListArea
- 1.3.13 Table: TaxonNameListDistribution
- 1.3.14 Table: TaxonNameListReference
- 1.3.15 Table: TaxonNameProject
- 1.3.16 Table: TaxonSynonymy
DiversityTaxonNames Information Model (version 2.2, 20. October 2009)
By G. Hagedorn, M. Weiss, & D. Triebel 2009
Notes: The models currently reside in MS SQL Server, so knowledge of some SQL Server ER-diagram conventions will be helpful.
Besides the screen shots below, a Microsoft T-SQL-Script for the generation of the tables is provided.
Proposed citation:
G. Hagedorn, M. Weiss, & D. Triebel (2009). DiversityTaxonNames information model (version 2.2). http://www.diversityworkbench.net/Portal/TaxonNamesModel_v2.2.
ER Diagrams
Overview over the main entities and relations used in the database model
Some “housekeeping” fields for the documentation when and by whom the data were inserted or changed are not shown in the overview.
Organisation of the data
The data are organised in several groups, data connected with the name, data based on the opinion of an editor, the source of the data and the projects.
TaxonName and TaxonGeography are containing the nomenclatural information. Most items are expected to be undisputed nomenclatural facts. Some data items include editorial opinion (nomenclatural status, but also the accepted spelling which may involve orthographical or grammatical corrections as required by ICBN). However, it is expected that within a project agreement can be achieved on the information contained in TaxonName, i.e. collaborators can “correct” information without consultation.
The tables TaxonHierarchy, TaxonAcceptedName and TaxonSynonymy - represent a higher level of taxonomic opinion, where different editors and different digitized data sources need to be kept separate. This is achieved by making a “Project” attribute part of the primary key. Editors that wish to collaborate and form agreement may work in a single project, editors that desire to define separate opinions work in separate projects. Furthermore, if the opinion is based on published information, the reference and page number may be recorded (in ...RefText, ...RefID, ...RefDetail). The duality of representing editorial opinion and remaining true to a digitized sources causes some problems. For example, a species accepted in a referenced source may not longer be accepted by the project editors. To avoid a further complication of the model, the “IgnoreButKeepForReference” attribute (default “false”) may be set to “true”, indicating that the statement is true from the perspective of the referenced source, but should be ignored when representing editorial opinion.
TaxonHierarchy contains information about the hierarchical position of the taxa. For each project, a name may be referred to a single parent taxon. The attribute “NameParentID” may, however, be Null, in which case “HierarchyPositionIsUncertain” should be true. TaxonAcceptedName contains the accepted names (“valid or preferred taxon names”). For each project, a name in “TaxonName” may either be accepted (a corresponding record in “TaxonAcceptedName” exists) or not. Examples for not accepted names are synonyms of accepted names and nomenclaturally rejected names. TaxonSynonymy contains names, which are synonym to other names. Here a single name may be a synonym of multiple accepted names (“pro parte synonym”). The “pro parte” or corresponding sensu information is captured in the “ConceptSuffix” attribute, which is part of the primary key.
The tables TaxonNameList, TaxonNameListAnalysis, TaxonNameListAnalysisCategory, TaxonNameListArea, TaxonNameListDistribution, TaxonNameListReference contain informations about taxon list like checklists
TaxonNameExternalID and TaxonNameExternalDatabase document the sources of the names.
TaxonNameProject document the projects of the names.
Description of the tables and columns:
Table: TaxonAcceptedName
TaxonAcceptedName contains the accepted names ("valid or preferred taxon names"). For each project, a name in "TaxonName" may either be accepted (a corresponding record in "TaxonAcceptedName" exists) or not. Examples for not accepted names are synonyms of accepted names and nomenclaturally rejected names.
| Column | Data type | Description |
|---|---|---|
| ProjectID | int | Each project can have a different opinion regarding synonmy. Refers to the common project definition in the DiversityProjects module. DefaultValue: 0 |
| NameID | int | ID of the accepted name. Refers to the NameID of TaxonName (= foreign key). |
| IgnoreButKeepForReference | tinyint | If true, the record is ignored for all purposes of evaluation (because contradicted). It is kept only to maintain the cited reference. If no reference is given, it may be deleted instead. DefaultValue: 0 |
| ConceptSuffix | nvarchar (200) | Empty for default and primary concept; else 's. lat.', 's. str.', 'sec.', 'sensu Muell.', 'emend.' , '(Auct.)' etc. |
| ConceptNotes | nvarchar (500) | Notes on the concept of the name, e.g. incl. forms with black apothecia |
| RefURI | varchar (255) | ReferenceURI: Source publication where synonymization is published (not publication of name!) |
| RefText | nvarchar (255) | Free text, esp. where a RefURI is missing. Source publication where synonymization is published (not publication of name!) |
| RefDetail | nvarchar (255) | Esp. page number on which the synonymization is published |
| TypistsNotes | nvarchar (255) | An internal note of the responsible person concerning this synonymization. This information is NOT included in any report. |
Table: TaxonCommonName
TaxonCommonName contains the common names that are assigned to a scientific name.
| Column | Data type | Description |
|---|---|---|
| NameID | int | ID taxonomic name. Refers to the column NameID of the table TaxonName (= foreign key). |
| CommonName | nvarchar (300) | A common name of the taxonomic name |
| LanguageCode | nvarchar (50) | The 2-letter code of the language of the common name according to ISO |
| Notes | nvarchar (-1) | Notes about the common name |
Table: TaxonGeography
TaxonGeography is containing the information about the geographic distribution according to the protologue.
| Column | Data type | Description |
|---|---|---|
| NameID | int | ID of the name. Refers to the NameID of TaxonName (= foreign key). |
| PlaceURI | varchar (255) | URI (e.g. LSID) within e.g. the DiversityGazetteer for a place (which may have several names) as found in the protologue |
| PlaceNameCache | nvarchar (100) | The name of the place |
Table: TaxonHierarchy
TaxonHierarchy contains information about the hierarchical position of the taxa. For each project, a name may be referred to a single parent taxon. The attribute "NameParentID" may, however, be Null, in which case "HierarchyPositionIsUncertain" should be true.
| Column | Data type | Description |
|---|---|---|
| ProjectID | int | Each project can implement a different taxonomic hierarchy. Refers to the common project definition in the DiversityProjects module. DefaultValue: 0 |
| NameID | int | Unique NameID code of the higher taxon. Refers to the NameID code of LichenName (= foreign key). |
| IgnoreButKeepForReference | tinyint | If true, the record is ignored for all purposes of evaluation (because contradicted). It is kept only to maintain the cited reference. If no reference is given, it may be deleted instead. DefaultValue: 0 |
| NameParentID | int | Next higher taxon (e.g. the family or subfamily if this taxon is a genus) |
| HierarchyRefURI | varchar (255) | Reference URI: Source publication where the hierarchy is published (not publication of name!) as stored e.g. in DiversityReferences |
| HierarchyRefText | nvarchar (255) | Free citation, esp. where a HierarchyRefURI is missing. Source publication where the hierarchy is published (not publication of name!) |
| HierarchyRefDetail | nvarchar (255) | Esp. page number on which the hierarchy is published |
| HierarchyPositionIsUncertain | bit | If the position of this taxon within this taxonomic group is uncertain. DefaultValue: 0 |
| HierarchyTypistsNotes | nvarchar (255) | An internal note of the responsible person concerning this hierarchy. This information is NOT included in any report. |
| HierarchyListCache | nvarchar (1000) | CALCULATED FIELD: List of higher taxa for faster access: "div.; class; ord.; fam." |
Table: TaxonName
TaxonName is the nomenclatural information. Most items are expected to be undisputed nomenclatural facts. Some data items include editorial opinion (nomenclatural status, but also the accepted spelling which may involve orthographical or grammatical corrections as required by ICBN). However, it is expected that within a project agreement can be achieved on the information contained in TaxonName, i.e. collaborators can "correct" information without consultation.
| Column | Data type | Description |
|---|---|---|
| NameID | int | The ID of a name in DiversityTaxonNames_Fungi (primary key) |
| TaxonNameCache | nvarchar (255) | A full unique version of the name. Generated by the database, not entered by the user (candidate key) |
| Version | smallint | The version of a name record (revision number, internally filled by system) DefaultValue: (1) |
| BasedOnNameID | int | The Basionym of this name, resp. the NameID of the Basionym. A name is a Basionym, if NameID = BasionymID. |
| CreationType | nvarchar (50) | E.g.: taxon based on new type, combination based on a previously publ. name ('comb. nov.'), new name ('nom.nov.') introduced to replace a homonym (may occur for genera!), validation of previously invalidly publ. taxon name ('ex'), or unknown. |
| TaxonomicRank | nvarchar (50) | Taxonomic rank of the taxon (var., subsp., species, genus, family, order, etc.). The rank must be selected from the associated list of ranks (= TaxonomyRank) DefaultValue: N'sp.' |
| GenusOrSupragenericName | nvarchar (200) | If rank is above species: Name of taxon above species level (currently accepted spelling). Includes infrageneric taxon names, genera, families, etc. |
| SpeciesGenusNameID | int | If rank is species or below: NameID of the Genus name. Refers to same table with TaxonomicRank = genus. |
| InfragenericEpithet | nvarchar (200) | If rank below genus and above species: Name of infrageneric taxon above species level (currently accepted spelling). Includes subgenus, series, etc. |
| SpeciesEpithet | nvarchar (100) | The species name part of the species name, for example 'alba' in 'Abies alba'. |
| InfraspecificEpithet | nvarchar (100) | The epithet of the infraspecific entity |
| BasionymAuthors | nvarchar (100) | The authors of a newly created name. For all taxonomic ranks, only for 'comb. nov.' or 'nom. nov.': Author(s) of the basionym (will be displayed in '()', do not enter the parentheses), abbreviated according to authors standard |
| CombiningAuthors | nvarchar (255) | The names of the combining authors if the name is base on another older name (e.g. combined into a different genus) |
| PublishingAuthors | nvarchar (255) | If the authors of the taxon differ from the authors of the publication: the latter (...'in ' Publishing authors ... ) |
| SanctioningAuthor | nvarchar (100) | Sanctioning is a special instrument available for fungi to allow the starting date of taxonomy to be identical with higher plants, but preserve names used by Fries (Fr.) and Person (Pers.) |
| NonNomenclaturalNameSuffix | nvarchar (200) | A suffix for concept names not included in any nomenclatural code. If present fields for authors and typification must be empty and NomenclaturalCode set to 'not under code'. |
| IsRecombination | bit | True if the name is a recombination DefaultValue: (0) |
| IsHybrid | bit | If checked (or 'True'), the new taxon is a hybrid with or without a hybrid epithet. DefaultValue: (0) |
| HybridNameID1 | int | If IsHybrid is checked (or 'True'): Name of hybrid species 1. Refers to NomID code of publ. TaxonomyName (= foreign key). |
| HybridNameID2 | int | If IsHybrid is checked (or 'True'): Name of hybrid species 2. Refers to NomID code of publ. TaxonomyName (= foreign key). |
| HybridNameID3 | int | If IsHybrid is checked (or 'True'): Name of hybrid species 3. Refers to NomID code of publ. TaxonomyName (= foreign key). |
| HybridNameID4 | int | If IsHybrid is checked (or 'True'): Name of hybrid species 4. Refers to NomID code of publ. TaxonomyName (= foreign key). |
| ReferenceTitle | nvarchar (600) | The title of the publication where the name was published. Note this is only a cached value where ReferenceURI is present |
| ReferenceURI | varchar (255) | URI (e.g. LSID) of Reference, referes to table ReferenceTitle in Database DiversityReferences: Source publication where name is published |
| Volume | nvarchar (20) | The volume of the journal |
| Issue | nvarchar (255) | The issue of the literature |
| Pages | nvarchar (50) | The pages within the literature |
| DetailLocation | nvarchar (200) | Additional information like plates etc. |
| DayOfPubl | tinyint | The day when the name was published |
| MonthOfPubl | tinyint | The month when the name was published |
| YearOfPubl | smallint | The year when the name was published |
| DateOfPublSupplement | nvarchar (200) | Verbal or additional date information, e.g. 'end of summer 1985', 'first quarter', '1888-1892' |
| YearOnPubl | smallint | The year cited on the original paper as year of publication |
| DateOnPublSupplement | nvarchar (200) | Verbal or additional date information, e.g. 'end of summer 1985', 'first quarter', '1888-1892' |
| Protologue | nvarchar (-1) | Full text of the protologue. If protologue is provided in Latin and in another language
languages, both only the Latin or several languages may be stored together. |
| ProtologueURI | varchar (255) | URI of externally available Protologue information (scanned image, full text from external provider, etc.) |
| ProtologueResourceURI | varchar (255) | The ResourceID of an image of the protologue as stored in the module DiversityResources. Primary key of table Resource in the database DiversityResources.(= Foreign key) |
| NameUsageReferences | nvarchar (255) | Indexing volumes like Index of Fungi or any Name usage that caused this name to be added to the database |
| OriginalOrthography | nvarchar (255) | The original spelling of the name |
| NomenclaturalCode | nvarchar (50) | Code of Nomenclature under which this taxon was created: 'Bacteriology', 'Botany' (incl. Mycology), 'Zoology', 'Biocode' (for future use), 'Non nomenclatural name'. Default value: 'Botany' |
| NomenclaturalStatus | nvarchar (50) | Categories for effective/valid/legitimate... esp. 'nom. illeg.', 'nom. inval.', 'nom. nudum', etc. |
| NomenclaturalComment | nvarchar (-1) | Comments on the nomenclature. e.g. 'according to ICBN Art. 39.1' |
| Typification | nvarchar (50) | The status of the type specimen(s) as written in the protologue, e.g. holotype |
| TypificationDetails | nvarchar (255) | Details concerning the typification as written in the protologue, e.g. if just parts of a specimen were accepted as the type |
| TypificationReferenceTitle | nvarchar (255) | The title of the publication where the typification was published. Note this is only a cached value where Typification-LiteratureLink is present |
| TypificationReferenceURI | varchar (255) | URI (e.g. LSID) of Reference, refers to e.g DiversityReferences: Source publication where the typification is published |
| TypificationNotes | nvarchar (200) | Notes concerning the typification |
| TypeSubstrate | nvarchar (255) | The substrate the type was growing on as written in the protologue |
| TypeLocality | nvarchar (255) | The locality where the type was found as written in the protologue |
| TypeSpecimenNotes | nvarchar (200) | Notes about the type specimen, e.g. the herbarium where a type specimen is located, Collector, collection date/number, etc. |
| AnamorphTeleomorph | nvarchar (255) | If the name is related to a anamorph or a telemorph as written in the protologue |
| TypistNotes | nvarchar (200) | Additional notes and problems |
| RevisionLevel | nvarchar (50) | The level of the revision of the taxonomic name, e.g. 'unchecked', 'fully checked' |
| IgnoreButKeepForReference | bit | If true, the record is ignored for all purposes of evaluation (because contradicted). It is kept only to maintain the cited reference. If no reference is given, it may be deleted instead. DefaultValue: (0) |
| DataWithholdingReason | nvarchar (255) | If the dataset is withhold, the reason for withholding the data, otherwise null |
Table: TaxonNameExternalDatabase
TaxonNameExternalDatabase document the sources of the names.
| Column | Data type | Description |
|---|---|---|
| ExternalDatabaseID | int | An ID to identify an external data collection of plant names (primary key, the ID has no meaning outside of the DiversityWorkbench system) |
| ExternalDatabaseName | nvarchar (255) | The name of the data collection that has been integrated or can be linked to for further analysis |
| ExternalDatabaseVersion | nvarchar (255) | The version of this data collection (either official version number, or dates when the collection was integrated) |
| Rights | nvarchar (500) | A description of copyright agreements or permission to use data from the external database |
| ExternalDatabaseAuthors | nvarchar (200) | The persons or institutions responsible for the external database |
| ExternalDatabaseURI | nvarchar (300) | The URI of the database provider resp. the external database |
| ExternalDatabaseInstitution | nvarchar (300) | The institution responsible for the external database |
| InternalNotes | nvarchar (1500) | Additional notes concerning this data collection |
| ExternalAttribute_NameID | nvarchar (255) | The table and field name in the external data collection to which TaxonNameExternalID refers |
| PreferredSequence | tinyint | For selection in e.g. picklists: of several equal names only the name from the source with the lowest preferred sequence will be provided. |
| Disabled | bit | If this source should be disabled for selection of names e.g. in picklists |
Table: TaxonNameExternalID
TaxonNameExternalID document the source of a name together with the ID of the source.
| Column | Data type | Description |
|---|---|---|
| NameID | int | The ID of a name in DiversityTaxonNames (foreign key + part of primary key: the name string associated with NameID may occur in multiple external databases) |
| ExternalDatabaseID | int | The ID of an external taxonomic data collection as defined in TaxontNameExternalDatabase (foreign key + part of primary key) |
| ExternalNameURI | varchar (255) | The URI (e.g. a LSID) of the external name as defined in the external database |
Table: TaxonNameList
The table is containing the names listed in e.g. a checklist corresponding to the project.
| Column | Data type | Description |
|---|---|---|
| NameID | int | ID of the name. Refers to the NameID of TaxonName (= foreign key). |
| ProjectID | int | Each project may contain one taxon list. Refers to the common project definition in the DiversityProjects module. |
| Notes | nvarchar (-1) | A note concerning this entry. |
Table: TaxonNameListAnalysis
Analysis values for list entries in the database, "Red list category: R", "Time of observation: Sept. - Nov."
| Column | Data type | Description |
|---|---|---|
| NameID | int | ID of the name. Refers to the NameID of TaxonName (= foreign key). |
| ProjectID | int | Each project can may contain one taxon list. Refers to the common project definition in the DiversityProjects module. |
| AnalysisID | int | ID of the analysis (= foreign key) |
| AnalysisValue | nvarchar (255) | The result of the analysis |
| Notes | nvarchar (-1) | Notes concerning this analysis |
Table: TaxonNameListAnalysisCategory
Analysis types used within the database, e.g. "Red list category", "Frequency"
| Column | Data type | Description |
|---|---|---|
| AnalysisID | int | ID of the analysis (Primary key) |
| AnalysisParentID | int | Analysis ID of the parent analysis if it belongs to a certain type documented in this table |
| DisplayText | nvarchar (50) | Name of the analysis as e.g. shown in user interface |
| Description | nvarchar (-1) | Description of the analysis |
| AnalysisURI | varchar (255) | URI referring to an external documentation of the analysis |
| Notes | nvarchar (-1) | Notes concerning this analysis |
Table: TaxonNameListAnalysisCategoryValue
Value lists for analysis types with predefined values, e.g. "0, 1, 2, 3, ..." for Red list category. Includes description etc. for the values in the list.
| Column | Data type | Description |
|---|---|---|
| AnalysisID | int | ID of the analysis (Primary key) |
| AnalysisValue | nvarchar (255) | The categorized value of the analysis |
| Description | nvarchar (500) | Description of enumerated object, displayed in the user interface |
| DisplayText | nvarchar (50) | Short abbreviated description of the object, displayed in the user interface |
| DisplayOrder | smallint | The order in which the entries are displayed. The order may be changed at any time, but all values must be unique. |
| Notes | nvarchar (500) | Internal development notes about usage, definition, etc. of an enumerated object |
Table: TaxonNameListArea
The area defined for the whole taxon list
| Column | Data type | Description |
|---|---|---|
| ProjectID | int | Each project can have a different opinion regarding the parameters defined for a list. Refers to the common project definition in the DiversityProjects module. |
| PlaceURI | varchar (255) | URI or identifier for a place (which may have several names) derived from e.g. TDWG |
| PlaceNameCache | nvarchar (255) | The name of the place |
| Notes | nvarchar (-1) | An note concerning this entry. |
Table: TaxonNameListDistribution
The geographical distrbution for the organisms within the taxon list.
| Column | Data type | Description |
|---|---|---|
| NameID | int | ID of the name. Refers to the NameID of TaxonName (= foreign key). |
| ProjectID | int | Each project can may contain one taxon list. Refers to the common project definition in the DiversityProjects module. |
| PlaceURI | varchar (255) | URI or identifier for a place (which may have several names) derived from e.g. TDWG |
| PlaceNameCache | nvarchar (255) | The name of the place |
| Notes | nvarchar (-1) | Notes concerning this analysis |
Table: TaxonNameListReference
The reference where the taxon list resp. the name is published
| Column | Data type | Description |
|---|---|---|
| NameID | int | ID of the name. Refers to the NameID of TaxonName (= foreign key). |
| ProjectID | int | Each project can may contain one taxon list. Refers to the common project definition in the DiversityProjects module. |
| TaxonNameListRefText | nvarchar (255) | Free text, esp. where a TaxonNameListRefURI is missing. Source publication where distribution is published (not publication of name!) |
| TaxonNameListRefURI | varchar (255) | Reference URI: Source publication where the distribution is published (not publication of name!) as stored e.g. in DiversityReferences |
| TaxonNameListRefDetail | nvarchar (255) | Esp. page number on which the distribution is published |
| ReferenceType | nvarchar (50) | The type of the reference, e.g. a webpage |
| Notes | nvarchar (-1) | An note concerning this entry. |
Table: TaxonNameProject
TaxonNameProject documents the projects of the names and provides access to the data.
| Column | Data type | Description |
|---|---|---|
| NameID | int | The ID of a name in DiversityTaxonNames (foreign key + part of primary key: the name may occur in multiple projects) |
| ProjectID | int | ID of the project. Refers to the common project definition in the DiversityProjects module. DefaultValue: 0 |
Table: TaxonSynonymy
TaxonSynonymy contains names, which are synonym to other names. Here a single name may be a synonym of multiple accepted names ("pro parte synonym"). The "pro parte" or corresponding sensu information is captured in the "ConceptSuffix" attribute, which is part of the primary key.
| Column | Data type | Description |
|---|---|---|
| ProjectID | int | Each project can have a different opinion regarding synonmy. Refers to the common project definition in the DiversityProjects module. DefaultValue: (0) |
| NameID | int | ID of the synonymized name. Refers to the NameID of TaxonName (= foreign key). |
| SynNameID | int | The ID of the synonym to which this name has been assigned to. Refers to the NameID of TaxonName (= foreign key). |
| IgnoreButKeepForReference | tinyint | If true, the record is ignored for all purposes of evaluation (because contradicted). It is kept only to maintain the cited reference. If no reference is given, it may be deleted instead. DefaultValue: (0) |
| ConceptSuffix | nvarchar (200) | Empty for default and primary concept; else 's. lat.', 's. str.', 'sec.', 'sensu Muell.', 'emend.' , '(Auct.)' etc. |
| ConceptNotes | nvarchar (500) | Notes on the concept of the name, e.g. incl. forms with black apothecia |
| SynRefURI | varchar (255) | Reference URI: Source publication where synonymization is published (not publication of name!) as stored e.g. in DiversityReferences |
| SynRefText | nvarchar (255) | Free text, esp. where a SynRefURI is missing. Source publication where synonymization is published (not publication of name!) |
| SynRefDetail | nvarchar (255) | Esp. page number on which the synonymization is published |
| SynTypistsNotes | nvarchar (255) | An internal note of the responsible person concerning this synonymization. This information is NOT included in any report. |
| SynType | nvarchar (50) | Type of the synonymization, e.g. 'heterotypic', 'homotypic' DefaultValue: 'unknown' |
| SynIsUncertain | bit | If the synoymization is uncertain. Corresponding to =? for heterotypic synonyms and ? if the type of the synonymisation is unknown. Homotypic synonyms can not be uncertain. DefaultValue: (0) |
Footnotes: The following conventions and abbreviations have been used in the tables: Columns of primary key:underlined
