[BioRuby] [Wg-phyloinformatics] bioruby classes for phyloxml support

[Diana Jaunzeikare]

On Tue, May 26, 2009 at 10:01 PM, Christian M Zmasek <czmasek at burnham.org>wrote:

> Hi:
>
> It's a great idea to look at TDWG's standards.
> But to me, these standards seem designed specifically for collections in
> museums and, not surprisingly, biodiversity applications. For the purposes
> of comparative genomics and related fields, these taxonomy concepts seem a
> little bit overkill.


I totally agree that TDWG is overkill. Here is rough overview what are the
data fields in TDWG standard. I agree that most of them are irrelevant for
applications not specific to taxonomic studies.

  * MetaData
  * Specimens []
    - id
    - Institution
    - Collection
    - SpecimenItem
  * Publications []
  * TaxonNames []
    - Rank
    - Canonical Name
    - CanonicalAutorship
    - PublishedIn
    - Year
    - MicroReference
    - Typification
    - SpellingCorrectionOf
    - Basionym
    - BasedOn
    - ConservedAgainst
    - LaterHomonymesOf
    - Sanctioned
    - ReplacementNameFor
    - PublicationStatus
    - ProviderLink
    - ProviderSpecificData
  * TaxonConcepts []
    - id
    - Name
    - Rank
    - AccordingTo
    - TaxonRelationships
    - SpecimenCircumscription
    - CharacterCircumscription
    - ProviderLink
  * TaxonRelationshipAssertions

Diana


>
> In my experience, taxonomy objects which can contain a scientific name, a
> common name, a mnemonic, and a (typed) identifier (which could be a Uniform
> Resource Name (URN) or a NCBI taxonomy id) are sufficient for most
> applications. This is pretty much what phyloXML's taxon element contains
> now. Of course, this does not mean that a potential taxonomy class in
> BioRuby has to follow the concept for phyloXML.
>
> What do you think?
>
> Christian
>
>
>
>
>
>
> Hilmar Lapp wrote:
>
>> On May 25, 2009, at 6:16 PM, Christian M Zmasek wrote:
>>
>>
>>
>>> I propose a taxonomy class with the following elements:
>>> -scientific name (e.g. Nematostella vectensis)
>>> -common name (e.g. starlet sea anemone)
>>> -code (or mnemonic, as used by swiss-port) (e.g. NEMVE)
>>> -rank (e.g. species)
>>>
>>> phyloxml also has a URI for taxonomies, but I am not sure if this is
>>> important for a general taxonomy class.
>>>
>>> On the other hand, a general taxonomy class might also have
>>> - authority (e.g. Stephenson, 1935)
>>> - aliases []
>>>
>>> (if these elements are considered important, they of course could be
>>> added to the next version of phyloxml)
>>>
>>>
>>
>>
>> Note that there is the Taxonomic Concepts Transfer Schema as a  ratified
>> TDWG standard, so if you really want to have a rich  representation of
>> taxonomic entities or concepts I wouldn't try to  roll my own.
>>
>> http://www.tdwg.org/standards/117/
>>
>> For lightweight taxonomic designation, there are taxonomic elements in
>>  Darwin Core:
>>
>> http://wiki.tdwg.org/DarwinCore
>>
>>        -hilmar
>>
>>
>
>