THE TAXONOMY MODULE: Functions

1. Naming Name / epithet / author(s) Typification Citations / type specimens Catalogue support Nomenclature ICBN / ICZN Research module Classification Main / alternative / phylogenetic Synonymy Homotypic / heterotypic Expanded use of data (web publishing, research) demands more complex information; differences between catalogue support and research are minor THE TAXONOMY MODULE: Functions • Eremothecella calamicola Syd. • (Arthoniales: Arthoniaceae) • Sydow & Sydow, Ann. Mycol. 15: 236. 1917; Sérusiaux, • Syst. Ascomycetum 11: 42. 1992. — Type. Philippines, • Baker 3367 (holotype, S). — Arthonia calamicola (Syd.) • R. Sant.; Arthoniopsis calamicola (Syd.) Szatala. • Nematidia tenella Stirt. [nom. inval., ICBN Art. 32, 36–37]. • Arthonia mycoporoides Vain. • Santessonia bactridiifolii Bat. & Cavalc. [nom. illeg., ICBN Art. 52.2; non Santessonia bacrtidiifolii Stirt.].

2. THE TAXONOMY MODULE: Naming • Name / epithet / author(s) • Naming of catalogue units (species and below) • Naming of undetermined units at higher ranks (genus, family, order, class, etc.)Species level entries: Genus level entries: Family level entries: Order level entries: Class level entries: • Using names as part of hierarchical classification 100.000 10.0001.00010010

3. Name elements stored on 3 tabs • Hybrids mixed with other names • Overlap between tabs • Possibly superfluous fields THE TAXONOMY MODULE: Naming

4. Citation • Infraspecific ranks as defaults • Additional default ranks to accommodate ICZN • All principal name elements on single tab Citation Kind Verified by Date verified Primary G. Tonkovich 12/09/2005 Santesson, Symb. Bot. Ups. 12(1): 214 (1952) Monograph J. Buschbom 01/01/2005 THE TAXONOMY MODULE: Naming • Name elements stored on 2 tabs • Name string automatic from second tab • Tab switching and name strings

5. THE TAXONOMY MODULE: Typification Typification data stored on Citations Tab - Taxa as types not possible Potential overlap with data stored in Catalogue Catalogue = customizable vs. Taxonomy module = standardizable

6. Status Reference Source Type Lectotype McCarthy, Lichenologist 13: 32 (1999) Secondary Status Reference Source Type Holotype Kalb, Biblioth. Lichenol. 59: 16 (1984) Original THE TAXONOMY MODULE: Typification Allows typification at each level Additional information Rank selection could allow tab switching between specimen-based (species and below) and taxon-based (above species) typification

7. Mixes nomenclature with synonymy Inflexible data handling THE TAXONOMY MODULE: Nomenclature Possible attributes: Illegitimate = later homonym = superfluous Invalid = nomen nudum = no type = no diagnosis = no attribute (sp.n.) Conserved name Proposed conserved name Rejected name Proposed rejected name

8. THE TAXONOMY MODULE: Nomenclature Flexible data handling Additional name information Diversity of nomenclatural attributes stored in data instead of being invariably reflected in field structure

9. THE TAXONOMY MODULE: Classification Should be part of data, not separate field Accommodate ranks preferably used by ICBN and ICZN by tab switching? How accommodate alternative and phylogenetic classifications?

10. THE TAXONOMY MODULE: Classification Alternative parent for each name record Phylocode Current implementation allows for 1-parent-only relationships Alternative classifications laid out as lexica/thesauri?

11. THE TAXONOMY MODULE: Classification Parent relationships Do data have to be records (internal links)? Classification is reflected in unique parent relationships (n-1) Can these be populated/updated/changed by referring to external source?

12. THE TAXONOMY MODULE: Synonymy Pinus albus (Orthographic Variant) Synonymy Cluster Picea allba (Misspelling) Pseudotsuga alba Pseudotsuga nigra Pinus alba Pinus nigra Picea alba (Superfluous Combination) Picea alba Picea nigra Abies thaxteri (Replaced Name) Abies alba Abies nigra Abies conifera (Superfluous Name) Heterotypic Cluster Homotypic Cluster Homotypic Cluster Abies alba (Isonym) Abies viridis (Alternative Name) Leguminosae vs. Fabaceae (Accepted Alternative Names) Illegitimate Names and Orthographic Variants (all can have homotypic clusters!) Gibberella vs. Fusarium (Alternative Pleomorphic Form-Names) Lopadium epiphyllum vs. Lopadium epiphyllum (Homonymic Heterotypic Combination) Data model to establish functional synonymy clusters in taxonomy Heterotypic Alternative Names(all can have homotypic clusters!)

13. THE TAXONOMY MODULE: Synonymy Bug in system? Successfully establishing synonymy clusters depends on correct use of: Currently accepted? Is basionym? Kind of synonymy (Synonym status)

14. THE TAXONOMY MODULE: Synonymy Separation between synonym types (separate tabs?) Security features? Successfully establishing synonymy clusters depends on correct use of: Currently accepted? Is basionym? Kind of synonymy (Synonym status)

15. THE TAXONOMY MODULE: Functions Naming Consolidate tabs (cosmetic) Typification Add functionality • Eremothecella calamicola Syd. • (Arthoniales: Arthoniaceae) • Sydow & Sydow, Ann. Mycol. 15: 236. 1917; Sérusiaux, • Syst. Ascomycetum 11: 42. 1992. — Type. Philippines, • Baker 3367 (holotype, S). — Arthonia calamicola (Syd.) • R. Sant.; Arthoniopsis calamicola (Syd.) Szatala. • Nematidia tenella Stirt. [nom. inval., ICBN Art. 32, 36–37]. • Arthonia mycoporoides Vain. • Santessonia bactridiifolii Bat. & Cavalc. [nom. illeg., ICBN Art. 52.2; non Santessonia bacrtidiifolii Stirt.]. Nomenclature Modify and correct functionality Classification Add alternative classification and external reference function Synonymy Fix bug and modify display to ensure functionality