Fwd: [Biogeosdi] Re: Search on the GBIF REST services

Javier de la Torre jatorre at gmail.com
Wed Jun 27 22:19:08 CEST 2007


Here is a comment from Donald,

I have to say I have no idea why this statement is on the report...  
was like this in the previous too no?

Cheers.

Begin forwarded message:

> From: Donald Hobern <dhobern at gbif.org>
> Date: 27 de junio de 2007 12:17:27 GMT+02:00
> To: Javier de la Torre <jatorre at gmail.com>
> Subject: Re: [Biogeosdi] Re: Search on the GBIF REST services
>
> Thanks, Javier.
>
> I'll take a look.  By the way, the report says:
>
> */ GBIF data does not reference the original data providers
>
> Are you having a problem with this?  Every occurrence record (and  
> every taxon concept) is nested within a DataResource metadata  
> block, which is itself nested within a DataProvider block.  For  
> each you can use the appropriate web service (with the supplied key  
> values) to retrieve full information (including access points for  
> DataResources).
>
> If you need help, please let me know.
>
> Many thanks,
>
> Donald
>
> Javier de la Torre wrote:
>> jaja.
>>
>> Well,
>>
>> Let me send you the report as it is today. The doxygen still looks  
>> very bad, maybe is easier for you to just try the service  
>> interface we have for the code:
>>
>> http://omtest.cria.org.br/biogeosdi/backend/libs/amfphp/browser/
>>
>> The doxygen is here (we are working to clean it):
>>
>> http://omtest.cria.org.br/biogeosdi/doc/html/
>>
>> The two prototypes themselves can be found at:
>>
>> http://omtest.cria.org.br/biogeosdi/doc/html/
>>
>>
>> Have fun.
>>
>> Javier.
>>
>>
>>
>>
>> On 27/06/2007, at 10:36, Donald Hobern wrote:
>>
>>
>>
>>> Do you have any current presentation/document outlining what you  
>>> are doing in BioGeoSDI?  A web search tells me that you have  
>>> exceptionally well commented code...
>>>
>>>
>>>
>>> Donald
>>>
>>>
>>>
>>> Javier de la Torre wrote:
>>>
>>>> Buff... that is more than enough!!
>>>>
>>>> I suppose you also drop latitude=longitude=0 right?
>>>>
>>>>
>>>>
>>>> I think we have to change our report on this topic jeje.
>>>>
>>>>
>>>>
>>>> Cheers.
>>>>
>>>>
>>>>
>>>> On 26/06/2007, at 22:13, Donald Hobern wrote:
>>>>
>>>>
>>>>
>>>>> Right now the dodginess is only detected for records where we  
>>>>> interpret the Country name as a particular country and also  
>>>>> have coordinates and the coordinates do not intersect the  
>>>>> country.  In many cases we actually also determine that the  
>>>>> latitude is negated, the longitude is negated and/or the  
>>>>> latitude and longitude are transposed.
>>>>>
>>>>>
>>>>>
>>>>> Donald
>>>>>
>>>>>
>>>>>
>>>>> Tim Sutton wrote:
>>>>>
>>>>>> Hi
>>>>>>
>>>>>>
>>>>>>
>>>>>> Great stuff that we can now exclude dodgy / non existant  
>>>>>> occurrences -
>>>>>>
>>>>>> we could probably make th e second (coordinate issues) option  
>>>>>> user
>>>>>>
>>>>>> settable (or at the least a setting in our global config file).
>>>>>>
>>>>>>
>>>>>>
>>>>>> Regards
>>>>>>
>>>>>>
>>>>>>
>>>>>> Tim
>>>>>>
>>>>>>
>>>>>>
>>>>>> 2007/6/26, Javier de la Torre <jatorre at gmail.com>:
>>>>>>
>>>>>>> Great,
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> I will then uncomment the code :)
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Javier.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On 26/06/2007, at 17:24, Donald Hobern wrote:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> > Thanks, Javier - found the problem - will get the fix deployed
>>>>>>>
>>>>>>> > tomorrow.
>>>>>>>
>>>>>>> >
>>>>>>>
>>>>>>> > Best wishes,
>>>>>>>
>>>>>>> >
>>>>>>>
>>>>>>> > Donald
>>>>>>>
>>>>>>> >
>>>>>>>
>>>>>>> > Javier de la Torre wrote:
>>>>>>>
>>>>>>> >> Great Donald,
>>>>>>>
>>>>>>> >>
>>>>>>>
>>>>>>> >> We have now some comments to remove on the report about  
>>>>>>> the GBIF
>>>>>>>
>>>>>>> >> REST service ;)
>>>>>>>
>>>>>>> >>
>>>>>>>
>>>>>>> >> Still I have an issue when using the &coordinateissues=false
>>>>>>>
>>>>>>> >> parameter
>>>>>>>
>>>>>>> >>
>>>>>>>
>>>>>>> >> This URL returns 195 records:
>>>>>>>
>>>>>>> >> http://data.gbif.org/ws/rest/occurrence/list?
>>>>>>>
>>>>>>> >> format=brief&scientificname=Puma+concolor
>>>>>>>
>>>>>>> >>
>>>>>>>
>>>>>>> >> This one none:
>>>>>>>
>>>>>>> >> http://data.gbif.org/ws/rest/occurrence/list?
>>>>>>>
>>>>>>> >> format=brief&coordinateissues=false&scientificname=Puma 
>>>>>>> +concolor
>>>>>>>
>>>>>>> >>
>>>>>>>
>>>>>>> >>
>>>>>>>
>>>>>>> >> And I suppose not all coordinates are wrong no?
>>>>>>>
>>>>>>> >>
>>>>>>>
>>>>>>> >> Cheers.
>>>>>>>
>>>>>>> >>
>>>>>>>
>>>>>>> >>
>>>>>>>
>>>>>>> >> On 26/06/2007, at 14:29, Donald Hobern wrote:
>>>>>>>
>>>>>>> >>
>>>>>>>
>>>>>>> >>> Dear Javier,
>>>>>>>
>>>>>>> >>>
>>>>>>>
>>>>>>> >>> The structures are now stable.  Sorry not to have copied  
>>>>>>> you on
>>>>>>>
>>>>>>> >>> my emails on what was changing.  Adding  
>>>>>>> "&coordinatestatus=true"
>>>>>>>
>>>>>>> >>> should limit responses to those with coordinates.  You  
>>>>>>> can also
>>>>>>>
>>>>>>> >>> use "&coordinateissues=false" to exclude records where we  
>>>>>>> have
>>>>>>>
>>>>>>> >>> detected that the coordinates do not match the supplied  
>>>>>>> country
>>>>>>>
>>>>>>> >>> name.
>>>>>>>
>>>>>>> >>>
>>>>>>>
>>>>>>> >>> Donald
>>>>>>>
>>>>>>> >>>
>>>>>>>
>>>>>>> >>> Javier de la Torre wrote:
>>>>>>>
>>>>>>> >>>> Hey Donald,
>>>>>>>
>>>>>>> >>>>
>>>>>>>
>>>>>>> >>>> I am fixing some stuff on the prototype we did in Brasil  
>>>>>>> and I
>>>>>>>
>>>>>>> >>>> had to change my code to reflect the new format that the  
>>>>>>> rest
>>>>>>>
>>>>>>> >>>> services are sending now. Is this more or less stable now?
>>>>>>>
>>>>>>> >>>>
>>>>>>>
>>>>>>> >>>> And another question, would be possible to ask the  
>>>>>>> service to
>>>>>>>
>>>>>>> >>>> return only occurrences with coordinates. For us is not  
>>>>>>> of much
>>>>>>>
>>>>>>> >>>> use occurrences without coordinates.
>>>>>>>
>>>>>>> >>>>
>>>>>>>
>>>>>>> >>>> Thats the query I am trying
>>>>>>>
>>>>>>> >>>>
>>>>>>>
>>>>>>> >>>> http://newportal.gbif.org/ws/rest/occurrence/list?
>>>>>>>
>>>>>>> >>>>  
>>>>>>> format=brief&minLatitude=-90&maxLatitude=90&scientificname=Puma
>>>>>>>
>>>>>>> >>>> +concolor
>>>>>>>
>>>>>>> >>>>
>>>>>>>
>>>>>>> >>>> Thanks in advance.
>>>>>>>
>>>>>>> >>>>
>>>>>>>
>>>>>>> >>>> Javier.
>>>>>>>
>>>>>>> >>>>
>>>>>>>
>>>>>>> >>>>
>>>>>>>
>>>>>>> >>>>
>>>>>>>
>>>>>>> >>>
>>>>>>>
>>>>>>> >>> --
>>>>>>>
>>>>>>> >>> ------------------------------------------------------------
>>>>>>>
>>>>>>> >>> Donald Hobern (dhobern at gbif.org)
>>>>>>>
>>>>>>> >>> Deputy Director for Informatics Global Biodiversity  
>>>>>>> Information
>>>>>>>
>>>>>>> >>> Facility Secretariat Universitetsparken 15, DK-2100  
>>>>>>> Copenhagen,
>>>>>>>
>>>>>>> >>> Denmark
>>>>>>>
>>>>>>> >>> Tel: +45-35321483   Mobile: +45-28751483   Fax: +45-35321480
>>>>>>>
>>>>>>> >>> ------------------------------------------------------------
>>>>>>>
>>>>>>> >>>
>>>>>>>
>>>>>>> >>
>>>>>>>
>>>>>>> >>
>>>>>>>
>>>>>>> >>
>>>>>>>
>>>>>>> >
>>>>>>>
>>>>>>> > --
>>>>>>>
>>>>>>> > ------------------------------------------------------------
>>>>>>>
>>>>>>> > Donald Hobern (dhobern at gbif.org)
>>>>>>>
>>>>>>> > Deputy Director for Informatics Global Biodiversity  
>>>>>>> Information
>>>>>>>
>>>>>>> > Facility Secretariat Universitetsparken 15, DK-2100  
>>>>>>> Copenhagen,
>>>>>>>
>>>>>>> > Denmark
>>>>>>>
>>>>>>> > Tel: +45-35321483   Mobile: +45-28751483   Fax: +45-35321480
>>>>>>>
>>>>>>> > ------------------------------------------------------------
>>>>>>>
>>>>>>> >
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>>
>>>>>>> biogeosdi mailing list
>>>>>>>
>>>>>>> biogeosdi at lists.tdwg.org
>>>>>>>
>>>>>>> http://lists.tdwg.org/mailman/listinfo/biogeosdi
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>> -- 
>>> ------------------------------------------------------------
>>>
>>> Donald Hobern (dhobern at gbif.org)
>>>
>>> Deputy Director for Informatics Global Biodiversity Information  
>>> Facility Secretariat Universitetsparken 15, DK-2100 Copenhagen,  
>>> Denmark
>>>
>>> Tel: +45-35321483   Mobile: +45-28751483   Fax: +45-35321480
>>>
>>> ------------------------------------------------------------
>>>
>>>
>>>
>>
>>
>>
>
> -- 
> ------------------------------------------------------------
> Donald Hobern (dhobern at gbif.org)
> Deputy Director for Informatics
> Global Biodiversity Information Facility Secretariat
> Universitetsparken 15, DK-2100 Copenhagen, Denmark
> Tel: +45-35321483   Mobile: +45-28751483   Fax: +45-35321480
> ------------------------------------------------------------

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