THE TAXONOMY MODULE: FunctionsTHE 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.].

NamingNamingName / epithet / author(s)Name / epithet / author(s)

TypificationTypificationCitations / type specimensCitations / type specimens

ClassificationClassificationMain / alternative / phylogeneticMain / alternative / phylogenetic

SynonymySynonymyHomotypic / heterotypicHomotypic / heterotypic

NomenclatureNomenclatureICBN / ICZNICBN / ICZN

CatalogueCataloguesupportsupport

ResearchResearchmodulemodule

Expanded use of data (web publishing, research) demands more complexExpanded use of data (web publishing, research) demands more complexinformation; differences between catalogue support and research are minorinformation; differences between catalogue support and research are minor

Name / epithet / author(s)Name / epithet / author(s)

Naming of catalogue units Naming of catalogue units (species and below) (species and below)

Naming of undetermined units at higher ranksNaming of undetermined units at higher ranks (genus, family, order, class, etc.) (genus, family, order, class, etc.)

Species level entries:Species level entries: Genus level entries: Genus level entries: Family level entries:Family level entries: Order level entries: Order level entries: Class level entries: Class level entries:

Using names as part of hierarchical classificationUsing names as part of hierarchical classification

THE TAXONOMY MODULE: NamingTHE TAXONOMY MODULE: Naming

100.000100.000 10.000 10.000

1.0001.0001001001010

Name elements stored on 3 tabsName elements stored on 3 tabs

Hybrids mixed with other namesHybrids mixed with other names

Overlap between tabsOverlap between tabs

Possibly superfluous fieldsPossibly superfluous fields

THE TAXONOMY MODULE: NamingTHE TAXONOMY MODULE: Naming

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

Citation

Name elements storedName elements stored on 2 tabs on 2 tabs Name string automaticName string automatic from second tab from second tab Tab switching and Tab switching and name strings name strings

Infraspecific ranks asInfraspecific ranks as defaults defaults Additional default ranksAdditional default ranks to accommodate ICZN to accommodate ICZN All principal nameAll principal name elements on single tab elements on single tab

THE TAXONOMY MODULE: NamingTHE TAXONOMY MODULE: Naming

THE TAXONOMY MODULE: TypificationTHE TAXONOMY MODULE: Typification

Potential overlap with data stored in CataloguePotential overlap with data stored in CatalogueCatalogue = customizable vs. Taxonomy module = standardizableCatalogue = customizable vs. Taxonomy module = standardizable

Typification data stored on Citations Tab - Taxa as types not possibleTypification data stored on Citations Tab - Taxa as types not possible

Status Reference Source Type

Holotype Kalb, Biblioth. Lichenol. 59: 16 (1984) Original

Status Reference Source Type

Lectotype McCarthy, Lichenologist 13: 32 (1999) Secondary

Allows typification at each levelAllows typification at each level Additional informationAdditional information

Rank selection could allow tab switching between specimen-basedRank selection could allow tab switching between specimen-based(species and below) and taxon-based (above species) typification(species and below) and taxon-based (above species) typification

THE TAXONOMY MODULE: TypificationTHE TAXONOMY MODULE: Typification

THE TAXONOMY MODULE: NomenclatureTHE TAXONOMY MODULE: Nomenclature

Inflexible data handlingInflexible data handling

Mixes nomenclatureMixes nomenclature with synonymywith synonymy

Possible attributes:Possible attributes:

IllegitimateIllegitimate= later homonym= later homonym= superfluous= superfluous

InvalidInvalid= nomen nudum= nomen nudum= no type= no type= no diagnosis= no diagnosis= no attribute (sp.n.)= no attribute (sp.n.)

Conserved nameConserved nameProposed conserved nameProposed conserved nameRejected nameRejected nameProposed rejected nameProposed rejected name

Flexible data handlingFlexible data handling Additional name informationAdditional name information

THE TAXONOMY MODULE: NomenclatureTHE TAXONOMY MODULE: Nomenclature

Diversity of nomenclatural attributes stored in dataDiversity of nomenclatural attributes stored in datainstead of being invariably reflected in field structureinstead of being invariably reflected in field structure

THE TAXONOMY MODULE: ClassificationTHE TAXONOMY MODULE: Classification

Should be part of data, not separate fieldShould be part of data, not separate field

Accommodate ranks preferably used by ICBN and ICZN by tab switching?Accommodate ranks preferably used by ICBN and ICZN by tab switching?How accommodate alternative and phylogenetic classifications?How accommodate alternative and phylogenetic classifications?

Alternative parent for each name recordAlternative parent for each name record PhylocodePhylocode

THE TAXONOMY MODULE: ClassificationTHE TAXONOMY MODULE: Classification

Current implementation allows for 1-parent-only relationshipsCurrent implementation allows for 1-parent-only relationshipsAlternative classifications laid out as lexica/thesauri?Alternative classifications laid out as lexica/thesauri?

Parent relationshipsParent relationships Do data have to be records (internal links)?Do data have to be records (internal links)?

THE TAXONOMY MODULE: ClassificationTHE TAXONOMY MODULE: Classification

Classification is reflected in unique parent relationships (n-1)Classification is reflected in unique parent relationships (n-1)Can these be populated/updated/changed by referring to external source?Can these be populated/updated/changed by referring to external source?

Homotypic Cluster Homotypic Cluster

Heterotypic Cluster

Pseudotsuga nigra

Pinus nigra

Picea nigra

Abies nigra

Synonymy Cluster

Illegitimate Names andOrthographic Variants

(all can have homotypic clusters!)

Pseudotsuga alba

Pinus alba

Picea alba

Abies alba

Leguminosae vs. Fabaceae(Accepted Alternative Names)

Gibberella vs. Fusarium(Alternative Pleomorphic Form-Names)

Lopadium epiphyllum vs. Lopadium epiphyllum(Homonymic Heterotypic Combination)

Heterotypic Alternative Names(all can have homotypic clusters!)

Data model to establishData model to establishfunctional synonymyfunctional synonymyclusters in taxonomyclusters in taxonomy

THE TAXONOMY MODULE: SynonymyTHE TAXONOMY MODULE: Synonymy

Abies alba(Isonym)

Picea alba(Superfluous Combination)

Abies thaxteri(Replaced Name)

Abies viridis(Alternative Name)

Abies conifera(Superfluous Name)

Pinus albus(Orthographic Variant)

Picea allba(Misspelling)

Bug in system?Bug in system?

THE TAXONOMY MODULE: SynonymyTHE TAXONOMY MODULE: Synonymy

Successfully establishing synonymy clusters depends on correct use of:Successfully establishing synonymy clusters depends on correct use of:Currently accepted? Is basionym? Kind of synonymy (Synonym status)Currently accepted? Is basionym? Kind of synonymy (Synonym status)

Separation between synonym types (separate tabs?)Separation between synonym types (separate tabs?)

THE TAXONOMY MODULE: SynonymyTHE TAXONOMY MODULE: Synonymy

Successfully establishing synonymy clusters depends on correct use of:Successfully establishing synonymy clusters depends on correct use of:Currently accepted? Is basionym? Kind of synonymy (Synonym status)Currently accepted? Is basionym? Kind of synonymy (Synonym status)

Security features?Security features?

THE TAXONOMY MODULE: FunctionsTHE 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.].

NamingNamingConsolidate tabs (cosmetic)Consolidate tabs (cosmetic)

TypificationTypificationAdd functionalityAdd functionality

ClassificationClassificationAdd alternative classificationAdd alternative classification

and external reference functionand external reference function

SynonymySynonymyFix bug and modify displayFix bug and modify display

to ensure functionalityto ensure functionality

NomenclatureNomenclatureModify and correctModify and correct

functionalityfunctionality