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

Ray Fergerson ray.fergerson at stanford.edu
Thu Feb 27 12:31:31 PST 2014


<changing the cc list>

1) Just a gripe, but... for exploratory purposes, could you give free
access to some small number of queries from a given IP per day, requiring
the apikey only for 'high volume' use? It's a pain to share links in
emails and to explore from the examples when you constantly have to paste
your key into the URL.

RWF: Once the API key is set in your browser it will get remembered for 2
weeks. This is documented at the very top of:

http://data.bioontology.org/documentation
--------

2) More importantly, this URL breaks:
http://data.bioontology.org/search?apikey={paste-your-api-here!}&exact_mat
ch=true&include=all&q=computer+science

It works fine if you remove 'include=all'. I'm just looking for a list of
fields I can grab per term. Specifically I'm looking for the old
'definition' field... Ah... include=definition :-)

RWF: include=all on search is broken and a known bug. It will be fixed in
the release next week. You don't need an include to get definitions
though. They are returned by default. The example query on the
documentation (melanoma) returns definitions for terms. If you scroll down
just a bit on the first returned page you can see terms that include
definitions.

--------------------
This query reports nothing (apparently):
http://data.bioontology.org/search?apikey={convinced-yet?}&exact_match=tru
e&q=variant+calling&with_synonyms=true

while I'd expect it to turn up this information:
http://bioportal.bioontology.org/ontologies/EDAM?p=classes&conceptid=http%
3A%2F%2Fedamontology.org%2Foperation_3227

RWF: another known bug. "exact_match" currently does not work with
synonyms. Will try to get this fixed for next week too. There is no
with_synonyms switch. You always get them now.

------------------
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).

-------------------
Am I doing something wrong, or are there still issues with the service? If
I migrate all my code, how long until I'm asked to move everything again?

RWF: Well the project has been going for 8 years and this is the first API
revision. As they say, past history is no guarantee of future performance,
but it would not be unreasonable to plan on reworking your code in another
8 years.

Seriously though, we realize that it is a lot of work for our user
community to adapt to a changing API. We have not made this change lightly
and a lot of effort has gone into it. Initial feedback has been pretty
positive wrt the old system. We are continuing to work on it and improve
it and we are committed to getting all of the bugs out.

-----------------------
It's a bit annoying to be told to move imminently to a service that seems
to have bugs and/or missing documentation (sorry if this is just me being
dumb).

RWF: We believe that most of the documentation is there. The new system
does have bugs but the old system had bugs too. You may have either just
not encountered them or have worked around them.  We notified people in
October that the API would be changed. Thus we have provided almost 6
months for a switchover. This seems pretty reasonable as these things go.



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