Schema linnaeancore.xsd


schema location:  F:\Data\sharedocs\linnaeancore.xsd
 
Elements  Complex types 
NameRecord  NameParentType 
NameRecordType 
SimpleBiostatusType 
SimpleCitationType 
VernacularNameType 


element NameRecord
diagram
annotation
documentation 
Container for all elements of a name record

complexType NameParentType
diagram

element NameParentType/NameURI
diagram

element NameParentType/NameLocalKey
diagram

element NameParentType/Parent
diagram

complexType NameRecordType
diagram

element NameRecordType/FullName
diagram
annotation
documentation 
The full name at any rank excluding the authors. Could be generated from hierarchical components. NB no point following ABCD in splitting name components for each code as I believe that is only necessitated because ABCD is for capturing the slacker use of names attached to specimens. Name providers have no excuse!

element NameRecordType/CanonicalName
diagram
annotation
documentation 
the correct spelling of the terminal element(s) at this rank. Normally a supra-specific mononomial, or an specific/infraspecific epithet but could be many words, e.g. hybrid formula, viral species name.

element NameRecordType/OriginalOrthograpy
diagram
annotation
documentation 
the spelling given by the author to terminal element if not accepted under code

element NameRecordType/BreedCultivarTradeName
diagram
annotation
documentation 
These can occur at any rank and are therefore treated as an extra 'label' attached at any rank. We should develop this more fully. ABCD is also lacking in this respect. We would be doing the multi-million dollar horticultural industry a favour by capturing trade names appropriately - and the model here and in ABCD is too simplistic. Trade Names are allocated by a registering authority on a country-basis and thus the same trade name can be applied to different taxa in different countries.

element NameRecordType/Rank
diagram
annotation
documentation 
It would be desirable to have this controlled by a vocabulary together with a sort code. Not sure that is achievable in an open system?  ranks are included 

element NameRecordType/Hierarchy
diagram
annotation
documentation 
two alternate mechanims. Either explicit flat hierarchy, or parent chain. Also allows infra-specific names to be captured explicity. This doesn't work elegantly. It would be better if names at all ranks were treated as part of a hierarchical chain but most systems aren't designed like that (except ours in NZ of course).

element NameRecordType/Hierarchy/FlatHierarchy
diagram
annotation
documentation 
Option: fill all or principal ranks and optionally provide keys

element NameRecordType/Hierarchy/FlatHierarchy/Empire
diagram

element NameRecordType/Hierarchy/FlatHierarchy/EmpireURI
diagram

element NameRecordType/Hierarchy/FlatHierarchy/Kingdom
diagram

element NameRecordType/Hierarchy/FlatHierarchy/KingdomURI
diagram

element NameRecordType/Hierarchy/FlatHierarchy/SubKingdom
diagram

element NameRecordType/Hierarchy/FlatHierarchy/SubKingdomURI
diagram

element NameRecordType/Hierarchy/FlatHierarchy/InfraKingdom
diagram

element NameRecordType/Hierarchy/FlatHierarchy/InfraKingdomURI
diagram

element NameRecordType/Hierarchy/FlatHierarchy/SuperPhylum
diagram

element NameRecordType/Hierarchy/FlatHierarchy/SuperPhylumURI
diagram

element NameRecordType/Hierarchy/FlatHierarchy/PhylumDivision
diagram

element NameRecordType/Hierarchy/FlatHierarchy/PhylumDivisionURI
diagram

element NameRecordType/Hierarchy/FlatHierarchy/SubPhylum
diagram

element NameRecordType/Hierarchy/FlatHierarchy/SubPhylumURI
diagram

element NameRecordType/Hierarchy/FlatHierarchy/InfraPhylum
diagram

element NameRecordType/Hierarchy/FlatHierarchy/InfraPhylumURI
diagram

element NameRecordType/Hierarchy/FlatHierarchy/Superclass
diagram

element NameRecordType/Hierarchy/FlatHierarchy/SuperclassURI
diagram

element NameRecordType/Hierarchy/FlatHierarchy/Class
diagram

element NameRecordType/Hierarchy/FlatHierarchy/ClassURI
diagram

element NameRecordType/Hierarchy/FlatHierarchy/SubClass
diagram

element NameRecordType/Hierarchy/FlatHierarchy/SubClassURI
diagram

element NameRecordType/Hierarchy/FlatHierarchy/SuperOrder
diagram

element NameRecordType/Hierarchy/FlatHierarchy/SuperOrderURI
diagram

element NameRecordType/Hierarchy/FlatHierarchy/Order
diagram

element NameRecordType/Hierarchy/FlatHierarchy/OrderURI
diagram

element NameRecordType/Hierarchy/FlatHierarchy/SubOrder
diagram

element NameRecordType/Hierarchy/FlatHierarchy/SubOrderURI
diagram

element NameRecordType/Hierarchy/FlatHierarchy/SuperFamily
diagram

element NameRecordType/Hierarchy/FlatHierarchy/SuperFamilyURI
diagram

element NameRecordType/Hierarchy/FlatHierarchy/Family
diagram

element NameRecordType/Hierarchy/FlatHierarchy/FamilyURI
diagram

element NameRecordType/Hierarchy/FlatHierarchy/SubFamily
diagram

element NameRecordType/Hierarchy/FlatHierarchy/SubFamilyURI
diagram

element NameRecordType/Hierarchy/FlatHierarchy/Tribe
diagram

element NameRecordType/Hierarchy/FlatHierarchy/TribeURI
diagram

element NameRecordType/Hierarchy/FlatHierarchy/Genus
diagram

element NameRecordType/Hierarchy/FlatHierarchy/GenusURI
diagram

element NameRecordType/Hierarchy/FlatHierarchy/Subgenus
diagram

element NameRecordType/Hierarchy/FlatHierarchy/SubgenusURI
diagram

element NameRecordType/Hierarchy/FlatHierarchy/Species
diagram

element NameRecordType/Hierarchy/FlatHierarchy/SpeciesURI
diagram

element NameRecordType/Hierarchy/FlatHierarchy/Infra-1Species
diagram
annotation
documentation 
Strictly varieties are not subordinate to species which means that successive infra-specific ranks cannot fit into a unique hiearchy. In addition the use of ranks below subspecies happens but is not governed by the codes. For bacteria and plant pathogenic fungi these tri-quadri-nomials are important. The mechanism here allows 3 level of hierarchy to species, eg puccinia alba subsp. alba var. deformans forma urticae. Might be a case here for including authors?

element NameRecordType/Hierarchy/FlatHierarchy/Infra-1SpeciesRank
diagram

element NameRecordType/Hierarchy/FlatHierarchy/Infra-1SpeciesURI
diagram

element NameRecordType/Hierarchy/FlatHierarchy/Infra-2Species
diagram

element NameRecordType/Hierarchy/FlatHierarchy/Infra-2SpeciesRank
diagram

element NameRecordType/Hierarchy/FlatHierarchy/Infra-2SpeciesURI
diagram

element NameRecordType/Hierarchy/ParentName
diagram
annotation
documentation 
Option: provide a parent linking key. Not sure if I'v egot the recursive mechanism correct here?

element NameRecordType/ProtonymAuthors
diagram
annotation
documentation 
The authors of the original name, B-P abrreviated or not for plant names, without brackets. I am usng Richard Pyles term 'protonym' for cross-code basionym equivalent.

element NameRecordType/ProtonymYear
diagram
annotation
documentation 
Necessary duplication with data in citation if present. In an ideal world ... 

element NameRecordType/ProtonymPageInLit
diagram
annotation
documentation 
The page/plate in which the protologue STARTS, i.e. it is not a pagination.

element NameRecordType/ProtonymIsInCitation
diagram
annotation
documentation 
name authors not same as lit authors 

element NameRecordType/ProtonymCitation
diagram
annotation
documentation 
Zoologists frequently have just original reference, and not combining reference. Will be duplicated if protonym reference given. Not sure how to handle this potential duplication?

element NameRecordType/ProtonymURI
diagram
annotation
documentation 
All these URI's need to be allocated by a central service. However, to be pragmatic, I suggest we use a semi-semantic URI of the form, say, provider.organization.country/localkey. Where localkey should itself preferably be non-semantic to the provider. Protonym URI Provides the link required to pull together MOST unambiguous synonyms. In the case of ICBN where Protonym equals Basionym there are some subtle rules for using nom. novs. 1) the original name is illegitimate in which case the nom. nov. has itself as a basionym and the replaced name is the illegitimate name. 2) a combination would result in a homonym or tautonym, in which case the nom. nov. has itself as a basionym and the replaced name is the original valid name. 3) a combination would result in a homonym or tautonym and the author selects the next available epithet in the priginal circumscription. In this case the basionym is that later name (even tho it is heterotypic!) and the replaced name is the original name. NB In this rare case linking names on the basionym INCLUDES AMBIGUOUS SYNONYMS.

element NameRecordType/ProtonymLocalKey
diagram
annotation
documentation 
Local primary keys are probably the only thing most providers have (at least I hope they do!). This allows a data-set to be internally linked and checked for self-consistency. In the absence of a provider-driven URI, the central aggregator can issue appropriate URI's for return to the provider. I think this mechanism would also be appropriate for issuing TaxonConcept URI's where, again, most providers won't have them, but they can be generated automatically on aggregation.

element NameRecordType/IsNovum
diagram
annotation
documentation 
Name is a nom. nov.

element NameRecordType/ReplacedNameURI
diagram
annotation
documentation 
In the case of nom. novs. a reference for the type bearing name - this required to fully group all objective synonyms

element NameRecordType/ReplacedNameLocalKey
diagram

element NameRecordType/CombinationAuthors
diagram
annotation
documentation 
The authors of the original name, BP abrreviated or not for plant names, and without brackets

element NameRecordType/CombinationYear
diagram

element NameRecordType/CombinationPageInLit
diagram
annotation
documentation 
May also be a plate/figure

element NameRecordType/CombinationIsInCitation
diagram

element NameRecordType/CombinationCitation
diagram

element NameRecordType/Nomenclature
diagram
annotation
documentation 
The nomenclatural status of this name

element NameRecordType/Nomenclature/NomenclaturalCode
diagram
annotation
documentation 
The code to which name has been submitted for scrutiny. Do I need to make this 1 to many to cover ambiregnal names? Also, don't have the official abbreviations at hand.

element NameRecordType/Nomenclature/NomenclaturalStatus
diagram
annotation
documentation 
See attributes

element NameRecordType/Nomenclature/RuleConsidered
diagram
annotation
documentation 
The article in the code in question that is commented on below

element NameRecordType/Nomenclature/StatusQualification
diagram
annotation
documentation 
possibly need some vocabulary here, e.g. superfluous

element NameRecordType/Nomenclature/CodeEdition
diagram
annotation
documentation 
Article numbering changes according to edition of the code

element NameRecordType/Nomenclature/BlockingNames
diagram
annotation
documentation 
The names having priority which block the use of this name

element NameRecordType/Nomenclature/BlockingNames/NameURI
diagram

element NameRecordType/Nomenclature/BlockingNames/NameLocalKey
diagram

element NameRecordType/Nomenclature/BlockingNames/BlockingString
diagram
annotation
documentation 
placeholder for blocking name(s) if not referenced

element NameRecordType/Nomenclature/NomenclaturalNote
diagram
annotation
documentation 
nom. conf. etc

element NameRecordType/Nomenclature/NomenclaturalSources
diagram
annotation
documentation 
The literature used to determine the nomenclatural status.

element NameRecordType/EditorialStatus
diagram
annotation
documentation 
The current status of the record from an editorial persepective

element NameRecordType/EditorialStatus/LiteratureSources
diagram
annotation
documentation 
The sources of literarature used to compile the record other than protologue and those mentioned against nomenclatural status

element NameRecordType/EditorialStatus/Editors
diagram
annotation
documentation 
The people who compiled the data

element NameRecordType/EditorialStatus/EditorialNotes
diagram
annotation
documentation 
Notes on compilation

element NameRecordType/EditorialStatus/Status
diagram
annotation
documentation 
what sources were checked in compilation

element NameRecordType/TypeCollection
diagram
annotation
documentation 
not really nomenclatural - but useful. Should only be populated if this record is a protonym record. Not sure how to XML code that? 

element NameRecordType/TypeCollection/InstitutionCode
diagram
annotation
documentation 
The IndexHerbariorum or equivalent unique designation of the collection

element NameRecordType/TypeCollection/AccessionNumber
diagram
annotation
documentation 
The accession number of the type in the institute

element NameRecordType/TypeCollection/TypeStatus
diagram
annotation
documentation 
See attributes. Need to be careful here. We only need type desigantions that say something about nomenclatural status - any many don't, e.g. kelptotype etc.

element NameRecordType/TypeCollection/CountryOfOrigin
diagram
annotation
documentation 
ISO country. Where the type was collected. Strictly a job for collection databases but many name dbs hold this data so let's use it.

element NameRecordType/IsProParte
diagram
annotation
documentation 
This name is based on part of the same type as another name - possibly referenced below

element NameRecordType/ProParteOfNameURI
diagram
annotation
documentation 
 NB pro-parte names have this nomenclatural type-linkage that needs storing in a nomenclatural record.

element NameRecordType/ProParteOfNameLocalKey
diagram

element NameRecordType/IsAutonym
diagram
annotation
documentation 
i.e. this name doesn't really exist but many name providers will have them acting as placeholders for attaching data. Unfortunately an autonym is a Taxon Concept as it implies a different circumsciption to the parent name. I am not including misapplications here for the same reason, but I don't see how to avoid registering autonyms because it is a different 'string'!

element NameRecordType/IsHybridGraft
diagram

element NameRecordType/HybridGraftNames
diagram
annotation
documentation 
Plant hybrids and grafts may be referred to by a 'nothotaxon' name for the hybrid formula. there is a need to capture the grammar of this formula, i.e. to  specify the sex and order of component names which constitute the hybrid (effectively the 'partial' objective synonyms for the hybrid).

element NameRecordType/HybridGraftNames/IsNothoTaxonName
diagram
annotation
documentation 
This name is a nothotaxon name

element NameRecordType/HybridGraftNames/HybridFormula
diagram

element NameRecordType/HybridGraftNames/HybridFormula/Sex
diagram

element NameRecordType/HybridGraftNames/HybridFormula/NameURI
diagram

element NameRecordType/HybridGraftNames/HybridFormula/Level
diagram
annotation
documentation 
provides mechanisms of grouping inter-hybrid names

element NameRecordType/IsAnamorph
diagram
annotation
documentation 
Name applies to an anamorphic taxon: art 59 ICBN. Whilst the ICBN continues to allow two names for the same organism then we must provide a linking mechanism.

element NameRecordType/TeleomorphNameURI
diagram
annotation
documentation 
Unambiguous link between anamorph/teleomoprh names for same taxon currently allowed under ICBN

element NameRecordType/TeleomorphNameLocalKey
diagram

element NameRecordType/SimpleBiostatus
diagram
annotation
documentation 
Not nomenclature but probably best placed here and many providers will have this data attached to 'names' and not concepts, largely because the national/international lists deal with names and not concepts.

element NameRecordType/VernacularNames
diagram
annotation
documentation 
Not nomenclature but also probably best placed here.

element NameRecordType/ThisNameURI
diagram

element NameRecordType/ThisNameLocalKey
diagram

element NameRecordType/ThisNameProvider
diagram
annotation
documentation 
The nomenclator source of information. I suggest this refelects the non-semantic part of the providers URI. We need a mechanism for registering these.

element NameRecordType/RecordCreatedDate
diagram

element NameRecordType/RecordUpdatedDate
diagram

complexType SimpleBiostatusType
diagram

element SimpleBiostatusType/Indigenous
diagram
annotation
documentation 
This needs coding better - it's not saying what I want. There is a simple hierarchy of terms here.

element SimpleBiostatusType/Indigenous/IsEndemic
diagram

element SimpleBiostatusType/Alien
diagram

element SimpleBiostatusType/Alien/AlienStatus
diagram

element SimpleBiostatusType/IsExtinct
diagram

element SimpleBiostatusType/ListStatus
diagram
annotation
documentation 
Status in a published list, eg CITES

element SimpleBiostatusType/ListCitation
diagram

element SimpleBiostatusType/Region
diagram
annotation
documentation 
ISO Country

complexType SimpleCitationType
diagram

element SimpleCitationType/ArticleType
diagram

element SimpleCitationType/FreeFormCitation
diagram
annotation
documentation 
for article type equals freeform. Many name citations will be of this form

element SimpleCitationType/CitationURL
diagram
annotation
documentation 
The web-based location of the article

element SimpleCitationType/SeriesTitle
diagram
annotation
documentation 
Series are occasional book publications under a single editor/institution/title

element SimpleCitationType/SeriesTitleEnglish
diagram

element SimpleCitationType/SeriesEditor
diagram

element SimpleCitationType/BookTitle
diagram

element SimpleCitationType/BookLanguage
diagram
annotation
documentation 
ISO Language

element SimpleCitationType/BookTitleEnglish
diagram
annotation
documentation 
Maybe imperialistic? Need a mechanism for multi-language translations.

element SimpleCitationType/BookEditorAuthor
diagram

element SimpleCitationType/BookVolPartInSeries
diagram

element SimpleCitationType/BookPagination
diagram
annotation
documentation 
Includes forward, appendices, index and plates/figures

element SimpleCitationType/BookPublicationYear
diagram
annotation
documentation 
year on the publication

element SimpleCitationType/BookPublicationDate
diagram
annotation
documentation 
date of publication, or year of publication if different to stated year. Need ABCD vague date format.

element SimpleCitationType/BookPublisher
diagram

element SimpleCitationType/BookPublicationPlace
diagram

element SimpleCitationType/BookISBN
diagram

element SimpleCitationType/ChapterTitle
diagram

element SimpleCitationType/ChapterLanguage
diagram
annotation
documentation 
ISO Language

element SimpleCitationType/ChapterTitleEnglish
diagram

element SimpleCitationType/ChapterNumber
diagram

element SimpleCitationType/ChapterPagination
diagram

element SimpleCitationType/JournalTitle
diagram
annotation
documentation 
We really need BPH and TL2 as standard disctionaries to drive these titles

element SimpleCitationType/JournalPublishers
diagram

element SimpleCitationType/JournalPublicationPlace
diagram

element SimpleCitationType/JournalISSN
diagram

element SimpleCitationType/ArticleAuthor
diagram

element SimpleCitationType/ArticleTitle
diagram

element SimpleCitationType/ArticleLanguage
diagram

element SimpleCitationType/ArticleTitleEnglish
diagram

element SimpleCitationType/ArticlePublicationYear
diagram

element SimpleCitationType/ArticlePublicationDate
diagram

element SimpleCitationType/ArticlePagination
diagram

element SimpleCitationType/ArticleJournalVolume
diagram

element SimpleCitationType/ArticleJournalPart
diagram

element SimpleCitationType/ArticleDOI
diagram

complexType VernacularNameType
diagram

element VernacularNameType/CountryOfApplication
diagram

element VernacularNameType/ISOCountryOfApplication
diagram
annotation
documentation 
ISO Country

element VernacularNameType/ProvinceOfApplication
diagram

element VernacularNameType/ISOProvinceOfApplication
diagram
annotation
documentation 
ISO 2nd level

element VernacularNameType/OriginalName
diagram
annotation
documentation 
Vernacular name in the original language

element VernacularNameType/OriginalLanguage
diagram
annotation
documentation 
ISO Language

element VernacularNameType/EnglishTranslation
diagram
annotation
documentation 
I guess we really need a many-language mechanism. This is a bit imperalistic! But then the international language of science is english?

element VernacularNameType/RomanTransliteration
diagram

element VernacularNameType/Qualifier
diagram


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