(copy the [oor-dev] list on this conversation, so the exchange is
archived there too. ...Tx.) (01)
---------- Forwarded message ----------
From: kenb <kenb@xxxxxxxxxxx>
Date: Wed, Mar 13, 2013 at 7:11 AM
Subject: Re: Ontology summit hackathon: submission of Ontohub-OOPS!
Integration proposal
To: Till Mossakowski <Till.Mossakowski@xxxxxxx>
Cc: Peter Yim <peter.yim@xxxxxxxx>, María Poveda
<mpoveda@xxxxxxxxxxxxxxxxxxxxxx>, Mike Dean <mdean@xxxxxxx>, Ontology
Summit 2013 <ontology-summit@xxxxxxxxxxxxxxxx>, Ontohub
<ontohub@xxxxxxxxxxxxxxxxxxxxxxxx> (02)
The API is currently a REST API and is the same as BioPortal, see: (03)
http://www.bioontology.org/wiki/index.php/NCBO_REST_services (04)
As you noted, the plan is to specify the repository content using an
ontology. To this end, BioPortal has been developing a SPARQL
endpoint that is still being tested. It is documented at: (05)
http://www.bioontology.org/wiki/index.php/SPARQL_BioPortal (06)
When that is completed, it could form the basis for an OOR SPARQL
endpoint. This should take care of expressing the query method of the
API in terms of an ontology. However, the rest of the API is in REST
(no pun intended) which is far from being ontology-based. (07)
To base the rest of the API on an ontology, I analyzed the API and
expressed it in terms of SOAP. Here is the proposed WSDL for OOR: (08)
http://www.ccs.neu.edu/home/kenb/oor/OORService.wsdl (09)
I also expressed it in terms of Java: (010)
http://www.ccs.neu.edu/home/kenb/oor/OORI.java (011)
One can support both SOAP and REST simultaneously with the same server
using my soaprest package, but this has not yet been done for OOR. (012)
Moreover, the WSDL is based on an earlier version of BioPortal, so it
is no longer fully compatible with the OOR instances. However, the
WSDL is reasonably close. (013)
I hope this helps clarify the situation. Let me know if you have any
other questions. (014)
Best regards, (015)
-- Ken (016)
On Wed, 13 Mar 2013, Till Mossakowski wrote: (017)
> Dear all,
>
> we have just discussed this issue at our local Ontohub meeting.
> We think that developing the API is good idea (we will need an OOPS! API
>anyway, since we do not want to machine-interpret the HTML), and also like
>possibility (2).
> The following question arose: where can we find the current version of the
>OOR API?
> And another one: on some slides, I have read that the API will be based on an
>ontology. Is this ontology available?
>
> All the best,
> Till
>
> Am 12.03.2013 17:54, schrieb Peter Yim:
>>
>> Dear Till, Maria and All,
>>
>>
>> Further to our Mar-5 Hackathon-Clinics proposal preparation confcall ...
>> ref.http://ontolog.cim3.net/forum/ontology-summit/2013-03/msg00005.html#nid07
>>
>> Along the line of the "Ontology Evaluation Tool and Ontology
>> Repository integration," we did talk another possible "OOR-OOPS!"
>> project.
>>
>> I discussed with KenBaclawski and MikeDean on the possibilities of either:
>>
>> (1) work a proposal, aiming mainly towards developing the API that
>> will allow services like OOPS! to be integrated with OOR and Ontohub
>> (since they supposedly share the same architecture) ... or,
>>
>> (2) forgo the submission of another proposal, but instead, suggest
>> that we incorporate the above goal into the two proposals that are
>> already in - namely, the OOR-KEEPER & Ontohub-OOPS! proposals - ref.
>>
>http://ontolog.cim3.net/cgi-bin/wiki.pl?OntologySummit2013_Hackathon_Clinics#nid3O5I
>>
>> Our consensus was to go with (2).
>>
>> What do you think? .Till, Maria and All
>> ... attn: principals in featured ontology evaluation tools and
>> ontology repositories, please chime in. You are most welcome to join
>> in this API development hack (please indicate interest!)
>>
>>
>> Regards. =ppy
>> -- (018)
>> On Fri, Mar 8, 2013 at 1:18 PM, Till Mossakowski
>> <Till.Mossakowski@xxxxxxx> wrote:
>>>
>>> Dear Peter, Mike,
>>>
>>> please find below the submission of the Ontohub-OOPS! Integration proposal
>>> for the hackathon. Do you need a PDF, or can the ASCII text below directly
>>> be copied into the Wiki?
>>>
>>> All the best,
>>> Till
>>>
>>
>>> * a Title of proposed project (prefix it with "Hackathon," "Ontology
>>> Clinic-A/B" or "Application Clinic")
>>>
>>> Ontohub-OOPS! Integration
>>>
>>> * an Abstract describing the project work
>>>
>>> The project aims at the integration of OOPS! [1] into the Ontohub.org [2,3]
>>> platform. A user of Ontohub.org would see a button "evaluate with OOPS!".
>>> Then Ontohub.org would call the OOPS! webservice (or even a local
>>> installation of OOPS!), and display the results. The results should also be
>>> displayed in a per-class and per-property way in Ontohub.
>>>
>>> * Collaborators involved names of individuals, affiliations, their
>>> roles in the project, their tasks, etc.
>>>
>>> María Poveda, Universidad Politécnica de Madrid, Spain
>>> Till Mossakowsi, DFKI GmbH Bremen, Germany
>>> Oliver Kutz, University of Bremen, Germany
>>> several students, University of Bremen, Germany
>>>
>>> * Objectives / Goals ... especially as they relate to the Summit and the
>>> "Ontology Evaluation" theme
>>>
>>> Ontohub.org is a distributed heterogeneous ontology repository that aims at
>>> implementing the open ontology repository architecture [4]. OOPS! is a web
>>> service detecting some of the most common pitfalls appearing when developing
>>> ontologies. When combined, the result will be a web-based repository storing
>>> the feedback provided by OOPS! for many OWL ontologies, making it
>>> web-searchable and versioned. This means that the evolution of ontologies
>>> according to the feedback can be traced.
>>> This hackathon project will provide as well very useful feedback to improve
>>> OOPS!, maybe by including new cases or analysis false positive we might get
>>> and making it more precise.
>>>
>>> * expected Deliverable(s)
>>>
>>> - code in the Ontohub code repository [2] providing the described
>>> functionality
>>> - functionality provided online at Ontohub.org
>>>
>>> * Remarks ... (anything pertinent)
>>> * Resource / References
>>>
>>> [1] http://www.oeg-upm.net/oops/
>>> [2] http://www.ontohub.org
>>> [3] https://github.com/ontohub/ontohub/
>>> [4] http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository
>>>
>>>
>>> --
>>> Prof. Dr. Till Mossakowski Cartesium, room 2.51 Phone +49-421-218-64226
>>> DFKI GmbH Bremen Fax +49-421-218-9864226
>>> Cyber-Physical Systems Till.Mossakowski@xxxxxxx
>>> Enrique-Schmidt-Str. 5, D-28359 Bremen
>>> http://www.informatik.uni-bremen.de/~till/
>>>
>>> Deutsches Forschungszentrum fuer Kuenstliche Intelligenz GmbH
>>> principal office, *not* the address for mail etc.!!!:
>>> Trippstadter Str. 122, D-67663 Kaiserslautern
>>> management board: Prof. Wolfgang Wahlster (chair), Dr. Walter Olthoff
>>> supervisory board: Prof. Hans A. Aukes (chair)
>>> Amtsgericht Kaiserslautern, HRB 2313
>
>
>
> --
> Prof. Dr. Till Mossakowski Cartesium, room 2.51 Phone +49-421-218-64226
> DFKI GmbH Bremen Fax +49-421-218-9864226
> Cyber-Physical Systems Till.Mossakowski@xxxxxxx
> Enrique-Schmidt-Str. 5, D-28359 Bremen
> http://www.informatik.uni-bremen.de/~till/
>
> Deutsches Forschungszentrum fuer Kuenstliche Intelligenz GmbH
> principal office, *not* the address for mail etc.!!!:
> Trippstadter Str. 122, D-67663 Kaiserslautern
> management board: Prof. Wolfgang Wahlster (chair), Dr. Walter Olthoff
> supervisory board: Prof. Hans A. Aukes (chair)
> Amtsgericht Kaiserslautern, HRB 2313 (019)
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