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[bioontology-support] Final Notice on NCBO BioPortal Old REST API Phaseout

Ray Fergerson ray.fergerson at stanford.edu
Fri Feb 28 10:54:49 PST 2014


Dan,

I completely agree with you. This sentence is way too much "geek speak".
We will revise this to something more understandable.

Ray

-----Original Message-----
From: Dan Bolser [mailto:dan.bolser at gmail.com] 
Sent: Thursday, February 27, 2014 3:48 PM
To: Ray Fergerson
Cc: support at bioontology.org Support
Subject: Re: [bioontology-support] Final Notice on NCBO BioPortal Old REST
API Phaseout

Sorry Ray, I was seeing it there. I got lost in the document and saw the
sub-heading 'Search Parameters' and thought I was looking at search.

Thanks for the clarifications and sorry for being dumb.

Overall I have to say that I'm finding the documentation page a bit
confusing. For example, can you explain what this means:

"This API uses hypermedia to expose relationships between media types.
The state of the application is driven by navigating these links."

This is literally the first sentence on the documentation page, and I
can't understand what it even relates to. Wikipedia says 'Hypermedia is
used as a logical extension of the term hypertext in which graphics,
audio, video, plain text and hyperlinks intertwine to create a generally
non-linear medium of information.' Generally I prefer linear information,
but I still don't understand how this relates to 'the state of the
application'.


Cheers,
Dan.


On 27 February 2014 23:39, Ray Fergerson <ray.fergerson at stanford.edu>
wrote:
> I'm afraid that I am lost. I don't see that "include_synonyms" is 
> listed as a parameter on the search function documentation. Perhaps we 
> are looking at a different page...  It is listed under the "resource
index"
> topic but this is entirely different.
>
> Ray
>
> -----Original Message-----
> From: Dan Bolser [mailto:dan.bolser at gmail.com]
> Sent: Thursday, February 27, 2014 3:05 PM
> To: Ray Fergerson
> Cc: support at bioontology.org Support
> Subject: Re: [bioontology-support] Final Notice on NCBO BioPortal Old 
> REST API Phaseout
>
> Why is it listed as a parameter on that page?
>
> On 27 February 2014 22:52, Ray Fergerson <ray.fergerson at stanford.edu>
> wrote:
>>> ------------------
>>> Most of the fields (like with/include_synonyms) aren't explicitly 
>>> documented here:
>>> http://data.bioontology.org/documentation
>>>
>>> RWF: the fields that are there are documented. There is currently no 
>>> include_synonyms switch. You always get synonyms back (except for 
>>> the exact_match bug, described above).
>>
>> Where is include_synonyms documented? What does it do? Setting 
>> 'include_synonyms=false' doesn't seem to affect the fields returned...
>> Is it changing what fields gets searched? You could document that...
>> Actually, it doesn't even affect the number of results returned, so I 
>> can't even guess what it's doing.
>>
>>
>> RWF: The reason that "include_synonyms" is not documented is that it 
>> does not exist. There is no such parameter in the new system. Search 
>> always looks at synonyms. Synonym matches appear lower in the search 
>> results than preferred name matches but they are there.
>>
>> If this behavior turns out to be a problem for some users then we may 
>> implement a "do not include synonyms" parameter. For the moment 
>> though no one has asked for one and we have no plans.
>>
>> Ray


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