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[bioontology-support] [BioPortal] Feedback from Shaker El-Sappagh

Jennifer Leigh Vendetti vendetti at stanford.edu
Wed May 10 15:47:41 PDT 2017


Hello Dr. El-Sappagh,

There are a couple of issues with regard to why your latest upload did not parse.


1).  As previously stated by John Graybeal, your ontology file has some annotation properties with IRIs that contain colon characters, which is invalid.  You had corrected most of the occurrences, but there were still three left on lines 27, 25345, and 182239.  In other words, this IRI:

http://www.co-ode.org/ontologies/ont.owl#DDO:0000002

… needed to be changed to use an underscore in the last fragment, like so:

http://www.co-ode.org/ontologies/ont.owl#DDO_0000002

I made these corrections manually in the ontology file on our server.


2).  I found a bug in our code that deals with ontologies that are submitted to BioPortal in ZIP format.  We should process all of the ontology files contained in the ZIP file, but the code currently only processes ontologies that are imported via valid import statements in the top-level ontology file.  In your case, the DMTO.owl file has an unresolvable import statement of:

<Import>http://www.owl-ontologies.com/OntoFood.owl</Import>

As a workaround, I opened your top-level ontology in the Protege ontology editor, and merged all of the ontologies into a single OWL file.  I uploaded this merged version to BioPortal and reprocessed the ontology so that it’s now fully parsed and available to browse in BioPortal:

http://bioportal.bioontology.org/ontologies/DMTO

If you object to this workaround, there are two options:

- Correct the import statement in DMTO.owl to use a resolvable import statement for OntoFood.owl and upload a new version.
- Wait until we fix the bug in our code that handles ontologies in ZIP format.


Kind regards,
Jennifer


> 
>> On May 10, 2017, at 8:05 AM, Shaker El-Sappagh <shaker_elsapagh at yahoo.com> wrote:
>> 
>> Hello Professor John,
>> I hope you are fine. Finally and after hard works, I have finished the DMTO. It is the most comprehensive and complete diabetes ontology ever. I have handled the previously mentioned issues of "_" in place of ":" and the date data type. 
>> Please I have an important request from you. I have to submit the paper of this ontology, but DMTO version on BioPortal is not working and not complete. So, I am asking about the time the new ontology will be in a stable state and on the portal. 
>> I know that it is difficult, but I am sure that you will help me. 
>> 
>> Thank you very much. The attached in my ZIP file for the ontology and its imported materials. I have not uploaded it on the BioPortal until you check it. If you see that I have to upload it, please just tell me, and I will do it. 
>>  
>> Waiting for your reply.
>> 
>> Best Regards.
>> 
>> Shaker El-Sappagh, Ph.D. 
>> ------------------------------------------------
>> Information Systems Dept. 
>> Faculty of Computers and Information.
>> Mansura University.
>> Email: Shaker_elsapagh at yahoo.com, sh.elsappagh at gmail.com. 
>> 
>> 
>> On Wednesday, May 3, 2017 11:57 PM, John Graybeal <jgraybeal at stanford.edu> wrote:
>> 
>> 
>> Hi Shaker,
>> 
>> That sounds good. We on BioPortal are probably not the best people to advise on ontology best practices; the Protege mail list is excellent for those types of questions. 
>> 
>> But I note that you don't have to include an ontology in order to just re-use its concepts, so that might be a way to simplify if you don't have to leverage the assertions. 
>> 
>> John
>> 
>> From: Shaker El-Sappagh <shaker_elsapagh at yahoo.com>
>> Sent: Wednesday, May 3, 2017 12:15:28 PM
>> To: John Graybeal
>> Subject: Re: [bioontology-support] [BioPortal] Feedback from Shaker El-Sappagh
>>  
>> Hello,
>> Thank you. I will make replacement for the ":" to be "_" in all the ontology classes. I will change the date datatype to be of type string to solve the problem of formatting. This will be done in my upcoming version of DMTO.
>> 
>> One thing that I do not understand. I have sent you the DMTO with all of its imported ontologies. Regarding the OntoFood, because the ontology is big, I have imported only my needed classes using a manual way. As a result, we have to bind the version of OntoFood which I sent to you with DMTO. I really do not know how to solve this problem. But I have to mention that, if we import the original OntoFood from BioPortal in DMTO, the ontology will not work as intended.
>> 
>> Regards.
>>  
>> Shaker El-Sappagh, Ph.D. 
>> ------------------------------------------------
>> Information Systems Dept. 
>> Faculty of Computers and Information.
>> Mansura University.
>> Email: Shaker_elsapagh at yahoo.com, sh.elsappagh at gmail.com. 
>> 
>> 
>> On Wednesday, May 3, 2017 8:42 PM, John Graybeal <jgraybeal at stanford.edu> wrote:
>> 
>> 
>> Hello,
>> 
>> I think using "_" in place of ":" is only an issue for those six IRIs (wherever they are used in your ontology). There is further discussion of this on the issue thread, but simply doing the replacement may solve your problem.
>> 
>> The only other issue that I know of is the location of the imported OntoFood ontology. The original location is no longer working, so you should change your referenced URI for it as I previously suggested.
>> 
>> We are testing a version of these changes and will let you know how it turns out, but I think you should have success. Please let us know.
>> 
>> John
>> 
>> 
>>> On May 3, 2017, at 12:47 AM, Shaker El-Sappagh <shaker_elsapagh at yahoo.com> wrote:
>>> 
>>> Thank you very much.
>>> I will send you a new version of the ontology, and I will try to solve some of these issues as I can such as the issue of Date and the one of "_" in place of ":". However, I can not and do not understand the other issues.
>>> 
>>> Thank you again.
>>>  
>>> Shaker El-Sappagh, Ph.D. 
>>> ------------------------------------------------
>>> Information Systems Dept. 
>>> Faculty of Computers and Information.
>>> Mansura University.
>>> Email: Shaker_elsapagh at yahoo.com, sh.elsappagh at gmail.com. 
>>> 
>>> 
>>> On Wednesday, May 3, 2017 4:40 AM, John Graybeal <jgraybeal at stanford.edu> wrote:
>>> 
>>> 
>>> Continuing to keep in touch…
>>> 
>>> I have enlisted the help of a colleague to work with us on investigating this further. 
>>> 
>>> I agree that, since the ontology parses in Protege, the place to start solving this problem is BioPortal. 
>>> 
>>> Can you tell me, did you fix the ontology to resolve the two other issues we saw?  These issues were identified by the Protege log, but did not produce any UI errors (not sure why they did not get flagged). They were: (a) dc:date is not of the correct xsd:dateTime format "2017-3-27" is not one of the accepted formats; (b) the location of the imported OntoFood ontology appears to be wrong ("http://www.owl-ontologies.com/OntoFood.owl" does not resolve; you could point to http://data.bioontology.org/ontologies/OF/submissions/1/ as a source for this ontology.) 
>>> 
>>> What I meant by looking at your ontology is to see if you can tell whether there is anything special about those 6 classes, that are causing problems as we described in the ticket. For example, we have determined that those 6 properties are defined as IRI in the ontology, but all the other properties are defined as AbbreviatedIri. I believe it is not strictly legal to include a colon in an IRI, even though Protege does not detect this as an error.
>>> 
>>>>  Caused by: org.semanticweb.owlapi.rdf.rdfxml.renderer.IllegalElementNameException: 
>>>>https://bioportal.bioontology.org/ontologies/DMTO.owl#DMTO:0000081
>>>>https://bioportal.bioontology.org/ontologies/DMTO.owl#DMTO:0001649
>>>>http://www.co-ode.org/ontologies/ont.owl#DDO:0000002
>>>>https://bioportal.bioontology.org/ontologies/DMTO.owl#DMTO:0000051
>>>>https://bioportal.bioontology.org/ontologies/DMTO.owl#DMTO:0000909
>>>>https://bioportal.bioontology.org/ontologies/DMTO.owl#DMTO:0000079
>>> If we have time we will try to test this at our end, but as you are in a hurry, I think you can fix this yourself by creating an appropriate prefix in the header, or changing these IRIs to use _ instead of : .
>>> 
>>> I will let you know if we are able to confirm this repair takes care of the problem. 
>>> 
>>> John
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>>  
>>>> On May 1, 2017, at 9:51 AM, Shaker El-Sappagh <shaker_elsapagh at yahoo.com> wrote:
>>>> 
>>>> Dear Professor John,
>>>> Thank you very much for your kind email and help. I am sorry about the problems in the ontology. Actually, I have other two ontologies on Bioportal DDO and SCTO. Syntactically, DMTO is not different from them. I have not sent the DMTO ontology to Bioportal before making parsing in protege and the ontology is totally free of any errors. I have not worked with OWLAPI before and I have no experience with it. So, I do not know what can I do to help in the process. 
>>>> 
>>>> Please keep in touch.
>>>> Thank you again.
>>>> Best Regards.
>>>> 
>>>>  
>>>> Shaker El-Sappagh, Ph.D. 
>>>> ------------------------------------------------
>>>> Information Systems Dept. 
>>>> Faculty of Computers and Information.
>>>> Mansura University.
>>>> Email: Shaker_elsapagh at yahoo.com, sh.elsappagh at gmail.com. 
>>>> 
>>>> 
>>>> On Monday, May 1, 2017 7:08 PM, John Graybeal <jgraybeal at stanford.edu> wrote:
>>>> 
>>>> 
>>>> Hello again Dr. El-Sappagh,
>>>> 
>>>> I am sorry that I do not have better news for you so far, but here is detailed information about the status, as you have requested. We are committed to finding a working solution, while recognizing that we may not be able to meet your turnaround needs.
>>>> 
>>>> As is shown in the github ticket, we have reviewed the software source of this error. We believe it results from the pre-processing that takes place in the owlapi_wrapper library, and have tested some changes to that code. Unfortunately, that introduced other issues, and further research is needed. 
>>>> 
>>>> Our primary analyst is out this week, and will return next week. I think there are 3 paths that could be pursued:
>>>>  (1) Analyze and repair the root cause of the problem (this will likely take some time, and core assumptions in our use of the OWL API may preclude a clean solution);
>>>>  (2) As a workaround, create a separate processing path just for your ontology (which may prove unfeasible for similar reasons); or
>>>>  (3) See if minor modifications to your ontology could make it parse successfully.
>>>> 
>>>> Unfortunately, we are not resourced to pursue options (1) or (2) full-time, so we are not able to project how long this analysis might take. For this reason, I think option (3) might be a good tactic to allow you to make progress. Would you please have a look at the comments in the GitHub issue, and see if you can help suggest some specific changes to the ontology to get us to a working upload?
>>>> 
>>>> John
>>>> 
>>>> 
>>>> 
>>>>> Begin forwarded message:
>>>>> 
>>>>> From: John Graybeal <jgraybeal at stanford.edu>
>>>>> Subject: Re: [bioontology-support] [BioPortal] Feedback from Shaker El-Sappagh
>>>>> Date: May 1, 2017 at 8:32:57 AM PDT
>>>>> To: "<support at bioontology.org>" <support at bioontology.org>
>>>>> Cc: shaker_elsapagh at yahoo.com
>>>>> 
>>>>> Hello Shaker,
>>>>> 
>>>>> We have been working extensively to isolate BioPortal's problem processing your ontology, as described in https://github.com/ncbo/bioportal-project/issues/16. I'll contact you offline to discuss the status in greater detail.
>>>>> 
>>>>> John
>>>>> 
>>>>> 
>>>>>> On Apr 28, 2017, at 12:43 AM, support at bioontology.org wrote:
>>>>>> 
>>>>>> Name: Shaker El-Sappagh
>>>>>> Email: shaker_elsapagh at yahoo.com
>>>>>> Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FDMTO
>>>>>> 
>>>>>> Feedback:
>>>>>> Please, I need to know the status of my DMTO ontology. I have sent it for a long time, but I can not browse it until now.
>>>>>> Thanks very much.
>>>>>> 
>>>>>> _______________________________________________
>>>>>> bioontology-support mailing list
>>>>>> bioontology-support at lists.stanford.edu
>>>>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>>>> 
>>>> 
>>> 
>>> ========================
>>> John Graybeal
>>> Technical Program Manager
>>> Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
>>> Stanford Center for Biomedical Informatics Research
>>> 650-736-1632  
>>> skype: graybealski
>>> 
>>> 
>>> 
>>> 
>> 
>> ========================
>> John Graybeal
>> Technical Program Manager
>> Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
>> Stanford Center for Biomedical Informatics Research
>> 650-736-1632  
>> skype: graybealski
>> 
>> 
>> 
>> 
>> 
>> 
>> <DMTO.zip>
> 
> ========================
> John Graybeal
> Technical Program Manager
> Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
> Stanford Center for Biomedical Informatics Research
> 650-736-1632  
> skype: graybealski
> 
> 



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