trait thesaurus for invertebrates and plants

[fdschneider]

Is there any news on how to access the trait thesaurus (T-SITA for invertebrate traits and TOP for plant traits)?

plants

It seems TOP has an own API, but no documentation at all. How do we proceed?

invertebrates

I don't see any possibility to download the scheme. Also, while screening through the responses of the survey and some dummy data that I received from different people, the T-SITA thesaurus does not capture all the traits reported by our data owners. I wonder if it is feasible to adopt it, but add more traits to the scheme and publish our version on BExIS. In any case, we would need their scheme as an xml file or data table.

other

other organism groups should set-up their own trait standards.

[fdschneider]

It seems there is no API exposed. Anyway, my plan now is to insert a simple data table to the R-script which contains a list of all 'accepted' traits. The following columns must be present in such a 'traitlist' object:

• traitName : contains a short and unique name of the trait (no spaces or points, just _ allowed)
• traitID : a numeric identifier for each trait
• type_of_data : defines the type of data to expect. Must be one of: numeric, factor, character, logical, integer .

optional columns can be

• measurementUnit
• factorLevels
• MaxAllowedValue & MinAllowedValue
• traitDescription
• extendedDescription
• example

Further columns can be present, e.g. for a hierarchical categorisation of traits, e.g. traitClass or traitType, that will not be handled by the R Script.

[fdschneider]

I got a reply from BETSI about how to axess the trait thesaurus.

Concerning your interest in the T-SITA. A way for giving you access to the T-SITA content is the following API :

if(id.equals("1"))
        //test existence of trait
if(id.equals("2"))
        //select all direct sons of a trait
if(id.equals("3"))
        //all qualitative traits
if(id.equals("4"))
        //all quantitive traits
if(id.equals("5"))
    //select trait real name
if(id.equals("6"))
        //test a trait is quantitative
if(id.equals("7"))
        //get synonym of a trait
if(id.equals("8"))
        //get all trait with unit interval (temporal traits)
if(id.equals("9"))
    //get all trait and synonyms with at least one synonym
if(id.equals("10"))
    //test a trait is interval

For use it replace the id in the following address

http://t-sita.cesab.org/BETSI_php.jsp?id=3 for categorical traits (3,4,8,9)
http://t-sita.cesab.org/BETSI_php.jsp?id=5&trait=Repulsive_glands for other trait information.

This API does not contain the definition of traits. For the moment, the additions, modifications..., of traits are made by human modifications directly on the web ressource by the administrators under the control of a french researcher community. Giving you a xml format does not fit our phylosophy which is to create a stable semantic reference. Nevertheless, if you have a precise idea of the way you want to use the T-SITA content we would be deligthed to find/propose you adapted solutions to your needs such as including defintions in the API etc...

[nadjasimons]

I actually just copy-pasted the traits from the hierarchy in the tree view . Those can now be found in the file "traitlist_T-SITA.csv". This list is however lacking any additional information which is associated with the trait and is only shown if one clicks on the trait.

[aostrow]

Hmpf, it seems that we don't get a (full and clean) list of invertebrates traits, or? Least of all not with the additional info (dataType, unit, ...) we want to the names. How about starting with a small subset of traits we know? We can use the derived BETSI-names as a standard for naming convention?

[fdschneider]

continued in #18