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

Dan Bolser dan.bolser at
Thu Feb 27 15:47:47 PST 2014

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

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'.


On 27 February 2014 23:39, Ray Fergerson <ray.fergerson at> 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]
> Sent: Thursday, February 27, 2014 3:05 PM
> To: Ray Fergerson
> Cc: support at 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>
> wrote:
>>> ------------------
>>> Most of the fields (like with/include_synonyms) aren't explicitly
>>> documented here:
>>> 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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