[BioRuby] [Wg-phyloinformatics] bioruby classes for phyloxml support
Diana Jaunzeikare
rozziite at gmail.com
Wed May 27 02:51:48 UTC 2009
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
>>
>>
>
>
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