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[bioontology-support] BP Mapping not working, why?

Mobed, Ketty Ketty.Mobed at ucsf.edu
Mon Jan 9 10:28:05 PST 2012


Thanks Trish.

Yes, hopefully once I resolve the issue with Protege, I will have a few (not many) more mappings in the next day or so.

Ketty
________________________________________
From: Trish Whetzel [whetzel at stanford.edu]
Sent: Monday, January 09, 2012 10:25 AM
To: Mobed, Ketty
Cc: Lakshminarayanan, Prakash; Wynden, Rob; Rekapalli, Hari; support at bioontology.org Support
Subject: Re: [bioontology-support] BP Mapping not working, why?

Hi Ketty,

Thanks for reviewing, the duplicates are now removed. Will you have additional mappings to load in the next few weeks before our next release?

Cheers,
Trish

PS - adding the user support mailing list back into the thread to close the loop


On Jan 9, 2012, at 9:59 AM, Mobed, Ketty wrote:

> Hi Trish, thanks very much.
>
> Everything looks okay other than 'Black' and 'White' are mapped twice, so one of each needs to be deleted.
>
> Thanks again,
> Ketty
> ________________________________________
> From: Trish Whetzel [whetzel at stanford.edu]
> Sent: Sunday, January 08, 2012 9:49 PM
> To: Mobed, Ketty
> Cc: Lakshminarayanan, Prakash; Wynden, Rob; Rekapalli, Hari
> Subject: Re: [bioontology-support] BP Mapping not working, why?
>
> Hi Ketty,
>
> For the time being, since there were very few mappings to upload and the UI is working for me I uploaded the mappings. Let me know if they look ok and if you can move to your next step in preparation for your demo.
>
> Trish
>
>
> On Jan 8, 2012, at 6:52 PM, Mobed, Ketty wrote:
>
>> Hi all,
>>
>> so just to give you an update. I had a webex call with Trish today where I showed her the issue I have been having. Unfortunately we weren't able to troubleshoot it and so we discussed that I put together a worksheet (attached) where I would indicate which terms in HOM-DATASRC_ORTHO would have to be mapped to HOM_ORTHO.
>>
>> Prakash, Trish was hoping that you could develop and incorporate the mapping scripts based on the worksheet I have attached. She could do it as well, but has other projects on her hands that she needs to get done as well. Please let her know whether you can do it or not. Thank very much!
>>
>> I have also come across another issue in Protege, which i need to communicate with Martin/Natasha tomorrow. This means that the Fusion, Decompression and Revision columns will not be available to be mapped in BP.
>>
>> Ketty
>>
>> ________________________________________
>> From: Trish Whetzel [whetzel at stanford.edu]
>> Sent: Sunday, January 08, 2012 7:16 AM
>> To: Mobed, Ketty
>> Cc: Wynden, Rob; Rekapalli, Hari; Lakshminarayanan, Prakash; support at bioontology.org Support
>> Subject: Re: [bioontology-support] BP Mapping not working, why?
>>
>> Hi Ketty,
>>
>> I've been testing a few things since your last email and this one. Below are my observations and how I was able to create the mappings based on the email I've been drafting this morning.
>> -------
>>
>> I was able to create a mapping between the term "Asian" in HOM-DATASRC-ORTHO and HOM-ORTHO, however I did run into a few issues. Here are the steps I followed, issues I encountered, and what I did to resolve the issue. Overall, I believe there is a caching issue in the Mapping UI and have reported these bugs.
>>
>> To create the mapping, I used the "Jump To" function to navigate to the term "Asian" in HOM-ORTHO and then clicked on the "Term Mappings" tab and then the button "Create New Mapping". This opened the Mappings window  with the "Map From" information displayed. If I tried to use the term search first in the "Map To" section of the window, in some instances the response was "No results found". This then locked the functionality of the "Map To" section of the window so I was not able to either select an ontology or use the term search. To resolve this issue in Firefox, Safari, and Chrome I used the browser controls (Ctrl-R/Cmd-R for Mac) to refresh the window.  This did close the Mapping window, but the ontology tree was still highlighted on the term "Asian". After re-opening the "Term Mappings" tab, the functionality in the "Map To" section was restored. Once restored, I did not have to refresh the Mappings tab again in the few instances I tried to create other new mappings.
>>
>> Using IE (Mac with VMWare to run IE), if I encountered the error "No results found" I was not able to resolve the issue using the browser controls to refresh the window. In this case I had already navigated to the term of interest in the ontology tree view using the "Jump To" function. However, if I expanded the tree using the (+) icons or opened the "Term Mappings" tab without using the "Jump To" I was then able to use the functionality within the Mappings window.
>>
>> In addition to using the Web interface to create mappings, you can also use the "Create Mapping" Web service [1]. How many mappings do you have to create, what information do you have for each mapping pair, and what format is the data (e.g. a tab-delimited file)?
>>
>> Trish
>>
>>
>> [1] http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service#Create_a_new_mapping
>>
>>
>>
>> On Jan 8, 2012, at 6:42 AM, Mobed, Ketty wrote:
>>
>>> OK, I tried again and here is what I encountered:
>>>
>>> Trish, thanks, first of all I saw that you created mappings between HOM-DATASRC-ORTHO and HOM-ORTHO and the term 'Asian' and 'Asian'. So I tried to replicate that between 'White' and 'White', but wasn't able to. Then I tried a couple of different other ontologies and I was able to pull up and could have mapped the term 'White' from the HOM-HARVARD and the HOMERUN ontologies, but wasn't able to pull up the term 'White' from the HOM-EPIC or HOM-UCARE ontologies. There is something going on but don't know what.
>>>
>>> Thanks,
>>> Ketty
>>> ________________________________
>>> From: Wynden, Rob
>>> Sent: Saturday, January 07, 2012 6:06 PM
>>> To: Mobed, Ketty; Trish Whetzel
>>> Cc: Rekapalli, Hari; Lakshminarayanan, Prakash; support at bioontology.org Support
>>> Subject: Re: [bioontology-support] BP Mapping not working, why?
>>>
>>> Ketty,
>>>
>>> Can you search by ID instead if by name?
>>>
>>> Rob
>>>
>>>
>>> Sent from my HTC
>>>
>>> ----- Reply message -----
>>> From: "Mobed, Ketty" <Ketty.Mobed at ucsf.edu>
>>> To: "Trish Whetzel" <whetzel at stanford.edu>
>>> Cc: "Wynden, Rob" <Rob.Wynden at ucsf.edu>, "Rekapalli, Hari" <Hari.Rekapalli at ucsf.edu>, "Lakshminarayanan, Prakash" <Prakash.Lakshminarayanan at ucsf.edu>, "support at bioontology.org Support" <support at bioontology.org>
>>> Subject: [bioontology-support] BP Mapping not working, why?
>>> Date: Sat, Jan 7, 2012 5:34 pm
>>>
>>>
>>>
>>> Hi Trish,
>>>
>>> this is the problem I am having, everything is okay until I get to the new Map window. So for instance I want to 'Map From' HOM-DATASRC-ORTHO the pulled up term 'Asian' to 'Asian' in the 'Map To' HOM-ORTHO ontology. But when I type in Asian into the line, it tells me that there are 'No results found'. Why is that? Basically any term that I know exists in the HOM-ORTHO ontology it tells me that 'No results found'. Maybe I am doing something wrong.
>>>
>>> Thanks,
>>> Ketty
>>>
>>> If it is hard to figure it out this way, could I maybe call you tomorrow? Thanks.
>>> ________________________________
>>> From: Trish Whetzel [whetzel at stanford.edu]
>>> Sent: Saturday, January 07, 2012 12:23 PM
>>> To: Mobed, Ketty
>>> Cc: Wynden, Rob; Rekapalli, Hari; Lakshminarayanan, Prakash; support at bioontology.org Support
>>> Subject: Re: [bioontology-support] BP Mapping not working, why?
>>>
>>> I am able to create new mappings between ontologies ID #s 1697 (HOM-ORTHO) and 1698 (HOM-DATASRC-ORTHO). As a test (using Mac/Firefox) I was able to map "0000000rev" as a bidirectional mapping to "Demographics" and all relevant UI components are displaying the new mapping information, i.e. the Term Mappings tab, the BioPortal Home page "Latest Mappings" section and the Mappings page.
>>>
>>> Trish
>>>
>>>
>>> On Jan 7, 2012, at 12:05 PM, Trish Whetzel wrote:
>>>
>>> Hi Ketty,
>>>
>>> Can you tell me a bit more about the steps you were performing and what browser you are using? We can talk via Skype/phone if that is easier.
>>>
>>> Trish
>>>
>>>
>>> On Jan 7, 2012, at 11:08 AM, Mobed, Ketty wrote:
>>>
>>> Hi Trish,
>>>
>>> first off Happy New Year!
>>>
>>> I have come across a critical issue regarding required mappings between 2 new ontologies ID #s 1697 (HOM-ORTHO) and 1698 (HOM-DATASRC-ORTHO). In previous mapping tasks I was able to pull up the correct mapping node. That was with the old mapping interface. This time, with the new mapping interface, I have not been able to bring up any node in the other ontology (Map to:) that would make sense. Am I doing anything wrong? Your quick guidance is required as we have a hard deadline in the beginning of this week to do a demo.
>>>
>>> Thanks,
>>> Ketty
>>> ________________________________
>>> From: Trish Whetzel [whetzel at stanford.edu]
>>> Sent: Sunday, October 23, 2011 1:22 PM
>>> To: Mobed, Ketty
>>> Subject: Re: UCSF-EPIC duplicate entries
>>>
>>> The duplicate entry is removed.
>>>
>>> Trish
>>>
>>>
>>> On Oct 18, 2011, at 12:01 PM, Mobed, Ketty wrote:
>>>
>>> Hi Trish,
>>>
>>> yes please, delete one of them. I got an error message yesterday when uploading, so I uploaded it again resulting in 2 copies of the ontology.
>>>
>>> Thanks,
>>> Ketty
>>> ________________________________
>>> From: Trish Whetzel [whetzel at stanford.edu]
>>> Sent: Tuesday, October 18, 2011 8:47 AM
>>> To: Mobed, Ketty
>>> Subject: UCSF-EPIC duplicate entries
>>>
>>> Hi Ketty,
>>>
>>> There are two entries on the "Browse" page for UCSF-EPIC, should one of these be removed?
>>>
>>> Trish
>>>
>>> http://bioportal.bioontology.org/ontologies/1677
>>> http://bioportal.bioontology.org/ontologies/1678
>>>
>>>
>>> Trish Whetzel, PhD
>>> Outreach Coordinator
>>> The National Center for Biomedical Ontology
>>> Ph: 650-721-2378
>>> http://www.bioontology.org
>>>
>>> Now on Twitter: http://twitter.com/#!/bioontology
>>> and "Like" us on Facebook: http://www.facebook.com/pages/National-Center-for-Biomedical-Ontology/127444774011153
>>>
>>>
>>> Trish Whetzel, PhD
>>> Outreach Coordinator
>>> The National Center for Biomedical Ontology
>>> Ph: 650-721-2378
>>> http://www.bioontology.org
>>>
>>> Now on Twitter: http://twitter.com/#!/bioontology
>>> and "Like" us on Facebook: http://www.facebook.com/pages/National-Center-for-Biomedical-Ontology/127444774011153
>>>
>>>
>>>
>>> Trish Whetzel, PhD
>>> Outreach Coordinator
>>> The National Center for Biomedical Ontology
>>> Ph: 650-721-2378
>>> http://www.bioontology.org<http://www.bioontology.org/>
>>>
>>> Now on Twitter: http://twitter.com/#!/bioontology
>>> and "Like" us on Facebook: http://www.facebook.com/pages/National-Center-for-Biomedical-Ontology/127444774011153
>>>
>>> _______________________________________________
>>> bioontology-support mailing list
>>> bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>>
>>>
>>>
>>
>>
>> <HOM_ORTHO_term_mappings.xls>
>
>
>





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