Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] Coriell Cell Line

James Malone malone at ebi.ac.uk
Thu Mar 10 13:46:26 PST 2011


Hi,

Ah yes, this is the inferred saved view from Protege 4 which has kept the
asserted is_a directly under cell line as well as the inference moving
them further down the tree. I'll give P3 a go tomorrow with a couple of
reasons to see if it's any better.

Cheers,

James


> Hi James,
>
> The Explore link was removed since trying to view the tree hierarchy
> resulted in an error. We are still exploring options for displaying large
> numbers of sibling terms, however it was suggested that the ontology be
> classified with another classifier since one of the branches includes
> 28,000 siblings that are not re-organized following the classification. Is
> there another classifier you can run over the ontology?
>
> Trish
>
>
> On Mar 10, 2011, at 1:43 AM, James Malone wrote:
>
>> Hi Trish,
>>
>> I see the Coriell ontology is not visible in BioPortal - any update on
>> this?
>>
>> Cheers,
>>
>> James
>>
>>
>> On 07/03/2011 18:16, Trish Whetzel wrote:
>>> Thanks, also I see in Protege that there is a branch with ~2800 sibling
>>> terms. Is that the intended hierarchy?
>>>
>>> Trish
>>>
>>>
>>> On Mar 5, 2011, at 1:00 AM, James Malone wrote:
>>>
>>>> Hi Trish,
>>>>
>>>> Ah interesting. Actually everytime I tried to "submit" I got a sorry
>>>> we
>>>> have an encountered an error page, so I assumed it had not be uploaded
>>>> hence the mutliple uploads. You're right in that they are the same
>>>> thing
>>>> so please feel to remove all but one copies. Not sure if this is an
>>>> issue
>>>> but the Coriell is quite big - about 70MB. It loads in Protege ok,
>>>> though
>>>> takes a little while.
>>>>
>>>> Cheers,
>>>>
>>>> James
>>>>
>>>>
>>>>
>>>>> Hi James,
>>>>>
>>>>> I saw the upload of the Coriell Cell Line ontology and noticed there
>>>>> are a
>>>>> few problems. One is that there are multiple uploads of the ontology
>>>>> as
>>>>> separate entries on the Browse page. Was the ontology file uploaded
>>>>> the
>>>>> same file in all cases and if so, can the other entries be removed
>>>>> therefore leaving only one entry on the Browse page? Were the
>>>>> separate
>>>>> entries on the Browse page the result of separate ontology
>>>>> submissions?
>>>>>
>>>>> Also, although the Explore link is displayed there is an error in
>>>>> visualizing the ontology. We are looking into this.
>>>>>
>>>>> Trish
>>>>>
>>>>>
>>>>>
>>>>
>>>> --
>>>> European Bioinformatics Institute,
>>>> Wellcome Trust Genome Campus,
>>>> Hinxton,
>>>> Cambridge, CB10 1SD,
>>>> United Kingdom
>>>> Tel: + 44 (0) 1223 494 676
>>>> Fax: + 44 (0) 1223 492 468
>>>>
>>
>>
>> --
>> European Bioinformatics Institute,
>> Wellcome Trust Genome Campus,
>> Cambridge, CB10 1SD,
>> United Kingdom
>> Tel: + 44 (0) 1223 494 676
>> Fax: + 44 (0) 1223 494 468
>>
>
>


-- 
European Bioinformatics Institute,
Wellcome Trust Genome Campus,
Hinxton,
Cambridge, CB10 1SD,
United Kingdom
Tel: + 44 (0) 1223 494 676
Fax: + 44 (0) 1223 492 468




More information about the bioontology-support mailing list