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[bioontology-support] Problem loading EDAM into BioPortal

Trish Whetzel whetzel at stanford.edu
Fri May 14 13:27:50 PDT 2010


Thanks!


On May 14, 2010, at 1:25 PM, Kanjamala, Pradip P. wrote:

> FYI
>
> -----Original Message-----
> From: Kanjamala, Pradip P.
> Sent: Friday, May 14, 2010 11:51 AM
> To: 'Jon Ison'
> Subject: RE: Problem loading EDAM into BioPortal
>
> Hi Jon,
> Thank you for fixing the ontology. I took the liberty of overwriting  
> the
> last version of the ontology you submitted to BioPortal with the file
> you just sent me. The good news is that this version loads fine and
> visualizes in BioPortal. The url for visualization is
> http://bioportal.bioontology.org/visualize/42800
>
> Regards,
> Pradip
>
> -----Original Message-----
> From: Jon Ison [mailto:jison at ebi.ac.uk]
> Sent: Friday, May 14, 2010 11:22 AM
> To: Kanjamala, Pradip P.
> Subject: RE: Problem loading EDAM into BioPortal
>
> Many thanks Pradip
>
> I've attached a (hopefully) fixed version, following your suggestions.
>
> Would you mind trying again with it please?
>
> Cheers
>
> Jon
>
>
>
>> Hi Jon,
>> I noticed there was a mistake in the syntax in my example below.  
>> There
>> is not supposed to be a colon after the name of the relation, so
>> relationship: is_concern_of: EDAM:0000076 ! Undefined
>> Should actually be
>> relationship: is_concern_of EDAM:0000076 ! Undefined
>> i.e there is no : after is_concern_of
>>
>> I went ahead and updated your ontology and loaded it both in OBO Edit
>> and in LexEVS( the backend that BioPortal uses to serve up OBO
> content).
>> It is then that I noticed there is an issue with the hierarchy of the
>> ontology. The way the top node of an ontology is computed in OBO Edit
> is
>> based on finding all the concepts that do not have any outgoing
>> relations from them. In your case, every concept has a relation to
> some
>> other concept, and so both OBO Edit and LexEVS can not find a  
>> starting
>> point for a hierarchy tree.
>> The hierarchy is problematic in OBO since more than 1 relation can
>> participate in a hierarchy. Typically in most OBO ontologies, these
> are
>> is_a, part_of, develops_from etc. I am not sure if your intent was to
>> have the hierarchy based on just the is_a relation?
>> A solution I would propose is removing outgoing relations from just
> the
>> relations that you consider to be the top nodes. So, for example
>> [Term]
>> id: EDAM:0000002
>> name: Entity
>> namespace: entity
>> def: "Any biological thing (or part of a thing) with a physical
>> existence, a physical part, region or feature that can be mapped to
> such
>> a thing, a collection of such things or an observable phenonema or
>> occurence." [EDAM:EBI "EMBRACE definition"]
>> relationship: is_concern_of EDAM:0000003 ! Topic
>> relationship: has_identifier EDAM:0000842 ! Identifier
>> relationship: has_attribute EDAM:0000006 ! Data
>>
>> Would change to
>> [Term]
>> id: EDAM:0000002
>> name: Entity
>> namespace: entity
>> def: "Any biological thing (or part of a thing) with a physical
>> existence, a physical part, region or feature that can be mapped to
> such
>> a thing, a collection of such things or an observable phenonema or
>> occurence." [EDAM:EBI "EMBRACE definition"]
>>
>>
>> If you consider EDAM:0000002 to be one of the top nodes.
>>
>>
>> The only other thing that you may also want to look at is that there
> are
>> some duplicate relationship information in the ontology. I am pasting
>> the output from the LexEVS load that flags the duplicates.
>> 9 - warn - Fri May 14 09:24:50 CDT 2010 - Duplicate target found for
>> term[EDAM:0000043]: 'has_attribute' with value=EDAM:0000841 Exception
> -
>> null
>> 10 - warn - Fri May 14 09:24:50 CDT 2010 - Duplicate target found for
>> term[EDAM:0000045]: 'has_attribute' with value=EDAM:0000841 Exception
> -
>> null
>> 11 - warn - Fri May 14 09:24:50 CDT 2010 - Duplicate target found for
>> term[EDAM:0000046]: 'has_attribute' with value=EDAM:0000841 Exception
> -
>> null
>> 12 - warn - Fri May 14 09:24:50 CDT 2010 - Duplicate target found for
>> term[EDAM:0000693]: 'is_source_of' with value=EDAM:0000883  
>> Exception -
>> null
>> 13 - warn - Fri May 14 09:24:50 CDT 2010 - Duplicate target found for
>> term[EDAM:0000755]: 'has_identifier' with value=EDAM:0001056  
>> Exception
> -
>> null
>> 14 - warn - Fri May 14 09:24:50 CDT 2010 - Duplicate target found for
>> term[EDAM:0002161]: 'is_attribute_of' with value=EDAM:0000008
> Exception
>> - null
>> 15 - warn - Fri May 14 09:24:50 CDT 2010 - Duplicate target found for
>> term[EDAM:0000862]: 'is_attribute_of' with value=EDAM:0000008
> Exception
>> - null
>> 16 - warn - Fri May 14 09:24:50 CDT 2010 - Duplicate target found for
>> term[EDAM:0001003]: 'is_input_of' with value=EDAM:0000223 Exception -
>> null
>> 17 - warn - Fri May 14 09:24:50 CDT 2010 - Duplicate target found for
>> term[EDAM:0001004]: 'is_input_of' with value=EDAM:0000223 Exception -
>> null
>> 18 - warn - Fri May 14 09:24:50 CDT 2010 - Duplicate target found for
>> term[EDAM:0001023]: 'is_identifier_of' with value=EDAM:0001273
> Exception
>> - null
>> 19 - warn - Fri May 14 09:24:50 CDT 2010 - Duplicate target found for
>> term[EDAM:0001023]: 'is_identifier_of' with value=EDAM:0001270
> Exception
>> - null
>> 20 - warn - Fri May 14 09:24:50 CDT 2010 - Duplicate target found for
>> term[EDAM:0001023]: 'is_identifier_of' with value=EDAM:0001272
> Exception
>> - null
>> 21 - warn - Fri May 14 09:24:50 CDT 2010 - Duplicate target found for
>> term[EDAM:0001023]: 'is_identifier_of' with value=EDAM:0001273
> Exception
>> - null
>> 22 - warn - Fri May 14 09:24:50 CDT 2010 - Duplicate target found for
>> term[EDAM:0001052]: 'is_identifier_of' with value=EDAM:0000008
> Exception
>> - null
>> 23 - warn - Fri May 14 09:24:50 CDT 2010 - Duplicate target found for
>> term[EDAM:0001053]: 'is_identifier_of' with value=EDAM:0000008
> Exception
>> - null
>> 24 - warn - Fri May 14 09:24:50 CDT 2010 - Duplicate target found for
>> term[EDAM:0001304]: 'is_a' with value=EDAM:0001276 Exception - null
>> 25 - warn - Fri May 14 09:24:50 CDT 2010 - Duplicate target found for
>> term[EDAM:0001339]: 'is_a' with value=EDAM:0000857 Exception - null
>>
>>
>> I am attaching the updated ontology file in which I fixed the syntax
> of
>> the relationship field. I have not addressed the duplicate issue or
> the
>> issue of the hierarchy in the attached ontology file.
>>
>> Regards,
>> Pradip
>>
>>
>> -----Original Message-----
>> From: Jon Ison [mailto:jison at ebi.ac.uk]
>> Sent: Friday, May 14, 2010 4:38 AM
>> To: Kanjamala, Pradip P.
>> Cc: whetzel at stanford.edu
>> Subject: Re: Problem loading EDAM into BioPortal
>>
>> Hi Pradip (Trish)
>>
>> I've fixed those relationships down the line you suggest and uploaded
> a
>> new version.  I also
>> attach the file in case there's a problem.  Could you let me know
> please
>> if this one is OK?
>>
>> Cheers
>>
>> Jon
>>
>>
>>
>>> Hi Jon,
>>> I work at the Mayo Clinic and I am part of the BioPortal development
>>> team.
>>> I was investigating why your ontology wasn't getting parsed properly
>> on
>>> BioPortal. One thing I noticed was that in your ontology the
>>> relationship lines weren't starting with the keyword relationship.  
>>> So
>>> for example in the beta4 version of your ontology I see:
>>>
>>> [Term]
>>> id: EDAM:0000008
>>> name: Undefined
>>> namespace: entity
>>> def: "Debugging." [EDAM:EBI "EMBRACE definition"]
>>> is_a: EDAM:0000002 ! Entity
>>> is_concern_of: EDAM:0000076 ! Undefined
>>> has_identifier: EDAM:0000841 ! Undefined
>>> has_attribute: EDAM:0000841 ! Undefined
>>>
>>>
>>> I would have expected to see
>>>
>>> [Term]
>>> id: EDAM:0000008
>>> name: Undefined
>>> namespace: entity
>>> def: "Debugging." [EDAM:EBI "EMBRACE definition"]
>>> is_a: EDAM:0000002 ! Entity
>>> relationship: is_concern_of: EDAM:0000076 ! Undefined
>>> relationship: has_identifier: EDAM:0000841 ! Undefined
>>> relationship: has_attribute: EDAM:0000841 ! Undefined
>>>
>>>
>>> Our parser is based on the OBO 1.2 spec. I am not sure of there is a
>>> newer version of the spec that you are using to generate your
> content.
>>> Generally speaking we have had pretty good success in parsing  
>>> content
>>> generated using OBO Edit.
>>>
>>> The beta5 version of the ontology that you uploaded didn't seem to
>> have
>>> had any content. When I downloaded the file, the size was 0 bytes.
>>>
>>> Looking forward to hearing back from you.
>>>
>>> Regards,
>>> Pradip
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>




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