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[bioontology-support] RANSUM

Trish Whetzel whetzel at stanford.edu
Wed Apr 21 13:10:59 PDT 2010


Hi Rob,

MP has been re-processed. I have not yet re-tested to confirm that the  
initial problem reported is now resolved.

Trish


On Apr 16, 2010, at 4:04 PM, Rob Tirrell wrote:

> mp is higher priority because it's used in examples. I'd say that's
> the only one really time sensitive
>
> Sent from my iPhone
>
> On Apr 16, 2010, at 15:56, Cherie H Youn <cyoun at stanford.edu> wrote:
>
>> Please let me know which ontologies that needs to be loaded ASAP
>> besides
>> Mammalian phenotype then I will have OPTRA populate them.
>>
>> 1) Here is the list of missing ontologies in OBS which exist in BP
>> with
>> VALID status.
>>
>> [Id: null, localOntologyId: 42594, ontology Name: Cereal plant trait,
>> version: 1.218, description: , virtualOntologyId: 1037, status: 3,
>> format:
>> OBO]
>> [Id: null, localOntologyId: 42596, ontology Name: C. elegans
>> phenotype,
>> version: 1.118, description: , virtualOntologyId: 1067, status: 3,
>> format:
>> OBO]
>> [Id: null, localOntologyId: 42592, ontology Name: Human disease,
>> version:
>> 1.170, description: , virtualOntologyId: 1009, status: 3, format:  
>> OBO]
>> [Id: null, localOntologyId: 40739, ontology Name: NIFSTD, version:
>> 1.4,
>> description: , virtualOntologyId: 1084, status: 3, format: OWL-DL]
>> [Id: null, localOntologyId: 42567, ontology Name: Mammalian  
>> phenotype,
>> version: 1.339, description: , virtualOntologyId: 1025, status: 3,
>> format:
>> OBO]
>> [Id: null, localOntologyId: 42593, ontology Name: Mosquito  
>> insecticide
>> resistance, version: 1.780, description: , virtualOntologyId: 1077,
>> status: 3, format: OBO]
>> [Id: null, localOntologyId: 42295, ontology Name: Read Codes,  
>> Clinical
>> Terms Version 3 (CTV3) , version: 1999, description: ,
>> virtualOntologyId:
>> 1427, status: 3, format: RRF]
>> [Id: null, localOntologyId: 42545, ontology Name: Health Level Seven,
>> version: 0230, description: , virtualOntologyId: 1450, status: 3,
>> format:
>> LEXGRID-XML]
>> Total Number of Missing Ontologies = 8
>>
>> ---
>> ---
>> --------------------------------------------------------------------
>> ---------------------------------------------------------------------
>> 2) Here is the list of missing ontologies in OBS which exist in BP
>> with
>> VALID & INVALID status.
>>
>> [Id: null, localOntologyId: 3155, ontology Name: NMR-instrument
>> specific
>> component of metabolomics investigations, version: See Remote Site,
>> description: , virtualOntologyId: 1033, status: 5, format: OWL]
>> [Id: null, localOntologyId: 3066, ontology Name: Loggerhead nesting,
>> version: See Remote Site, description: , virtualOntologyId: 1024,
>> status:
>> 5, format: OBO]
>> [Id: null, localOntologyId: 40892, ontology Name: Plant structure,
>> version: See Remote Site, description: , virtualOntologyId: 1108,
>> status:
>> 5, format: OBO]
>> [Id: null, localOntologyId: 38351, ontology Name: Molecule role (INOH
>> Protein name/family name ontology), version: See Remote Site,
>> description:
>> , virtualOntologyId: 1029, status: 5, format: OBO]
>> [Id: null, localOntologyId: 42594, ontology Name: Cereal plant trait,
>> version: 1.218, description: , virtualOntologyId: 1037, status: 3,
>> format:
>> OBO]
>> [Id: null, localOntologyId: 38371, ontology Name: Maize gross  
>> anatomy,
>> version: See Remote Site, description: , virtualOntologyId: 1050,
>> status:
>> 5, format: OBO]
>> [Id: null, localOntologyId: 38365, ontology Name: Cereal plant
>> development, version: See Remote Site, description: ,
>> virtualOntologyId:
>> 1047, status: 5, format: OBO]
>> [Id: null, localOntologyId: 40202, ontology Name: Breast Cancer
>> Grading
>> Ontology, version: 1.4, description: , virtualOntologyId: 1304,
>> status: 5,
>> format: OWL]
>> [Id: null, localOntologyId: 40724, ontology Name: Uber anatomy
>> ontology,
>> version: 1.70, description: , virtualOntologyId: 1111, status: 4,
>> format:
>> OBO]
>> [Id: null, localOntologyId: 38348, ontology Name: Physico-chemical
>> methods
>> and properties, version: See Remote Site, description: ,
>> virtualOntologyId: 1014, status: 5, format: OBO]
>> [Id: null, localOntologyId: 39727, ontology Name: Symptom Ontology,
>> version: See Remote Site, description: , virtualOntologyId: 1224,
>> status:
>> 5, format: OBO]
>> [Id: null, localOntologyId: 38360, ontology Name: OBO relationship
>> types,
>> version: 1.1, description: , virtualOntologyId: 1042, status: 4,
>> format:
>> OBO]
>> [Id: null, localOntologyId: 38347, ontology Name: eVOC (Expressed
>> Sequence
>> Annotation for Humans), version: See Remote Site, description: ,
>> virtualOntologyId: 1013, status: 5, format: OBO]
>> [Id: null, localOntologyId: 38346, ontology Name: Event (INOH pathway
>> ontology), version: See Remote Site, description: ,  
>> virtualOntologyId:
>> 1011, status: 5, format: OBO]
>> [Id: null, localOntologyId: 3036, ontology Name: Habronattus
>> courtship,
>> version: See Remote Site, description: , virtualOntologyId: 1020,
>> status:
>> 5, format: PROTEGE]
>> [Id: null, localOntologyId: 40893, ontology Name: Plant growth and
>> developmental stage, version: See Remote Site, description: ,
>> virtualOntologyId: 1038, status: 5, format: OBO]
>> [Id: null, localOntologyId: 42596, ontology Name: C. elegans
>> phenotype,
>> version: 1.118, description: , virtualOntologyId: 1067, status: 3,
>> format:
>> OBO]
>> [Id: null, localOntologyId: 39897, ontology Name: Lipid Ontology,
>> version:
>> See Remote Site, description: , virtualOntologyId: 1183, status: 5,
>> format: OWL]
>> [Id: null, localOntologyId: 38611, ontology Name: Skin Physiology
>> Ontology, version: 2.0, description: , virtualOntologyId: 1122,
>> status: 4,
>> format: OWL-DL]
>> [Id: null, localOntologyId: 42592, ontology Name: Human disease,
>> version:
>> 1.170, description: , virtualOntologyId: 1009, status: 3, format:  
>> OBO]
>> [Id: null, localOntologyId: 40739, ontology Name: NIFSTD, version:
>> 1.4,
>> description: , virtualOntologyId: 1084, status: 3, format: OWL-DL]
>> [Id: null, localOntologyId: 42567, ontology Name: Mammalian  
>> phenotype,
>> version: 1.339, description: , virtualOntologyId: 1025, status: 3,
>> format:
>> OBO]
>> [Id: null, localOntologyId: 2868, ontology Name: Animal natural
>> history
>> and life history, version: See Remote Site, description: ,
>> virtualOntologyId: 1002, status: 5, format: PROTEGE]
>> [Id: null, localOntologyId: 38241, ontology Name: Gene Regulation
>> Ontology, version: See Remote Site, description: , virtualOntologyId:
>> 1106, status: 5, format: OWL]
>> [Id: null, localOntologyId: 38364, ontology Name: Cereal plant gross
>> anatomy, version: See Remote Site, description: , virtualOntologyId:
>> 1001,
>> status: 5, format: OBO]
>> [Id: null, localOntologyId: 42593, ontology Name: Mosquito  
>> insecticide
>> resistance, version: 1.780, description: , virtualOntologyId: 1077,
>> status: 3, format: OBO]
>> [Id: null, localOntologyId: 40603, ontology Name: Infectious disease,
>> version: See Remote Site, description: , virtualOntologyId: 1092,
>> status:
>> 5, format: OWL]
>> [Id: null, localOntologyId: 40608, ontology Name: NIF Dysfunction,
>> version: See Remote Site, description: , virtualOntologyId: 1381,
>> status:
>> 5, format: OWL]
>> [Id: null, localOntologyId: 40730, ontology Name: NIF Cell, version:
>> See
>> Remote Site, description: , virtualOntologyId: 1402, status: 5,
>> format:
>> OWL]
>> [Id: null, localOntologyId: 40971, ontology Name: Ontology for  
>> General
>> Medical Science, version: See Remote Site, description: ,
>> virtualOntologyId: 1414, status: 5, format: OWL]
>> [Id: null, localOntologyId: 42167, ontology Name: Influenza Ontology,
>> version: See Remote Site, description: , virtualOntologyId: 1417,
>> status:
>> 5, format: OWL]
>> [Id: null, localOntologyId: 42228, ontology Name: Taxonomic rank
>> vocabulary, version: See Remote Site, description: ,
>> virtualOntologyId:
>> 1419, status: 5, format: OBO]
>> [Id: null, localOntologyId: 42295, ontology Name: Read Codes,  
>> Clinical
>> Terms Version 3 (CTV3) , version: 1999, description: ,
>> virtualOntologyId:
>> 1427, status: 3, format: RRF]
>> [Id: null, localOntologyId: 42477, ontology Name: Chemical  
>> Information
>> Ontology, version: See Remote Site, description: , virtualOntologyId:
>> 1444, status: 5, format: OWL]
>> [Id: null, localOntologyId: 42511, ontology Name: Software ontology,
>> version: See Remote Site, description: , virtualOntologyId: 1445,
>> status:
>> 5, format: OWL]
>> [Id: null, localOntologyId: 42545, ontology Name: Health Level Seven,
>> version: 0230, description: , virtualOntologyId: 1450, status: 3,
>> format:
>> LEXGRID-XML]
>> [Id: null, localOntologyId: 42581, ontology Name: Translational
>> Medicine
>> Ontology, version: r14, description: , virtualOntologyId: 1461,
>> status: 5,
>> format: OWL]
>>
>> Total Number of Missing Ontologies = 37
>>
>> -----Original Message-----
>> From: Natasha Noy [mailto:noy at stanford.edu]
>> Sent: Friday, April 16, 2010 3:18 PM
>> To: Rob Tirrell
>> Cc: support at bioontology.org; Cherie H Youn; Nigam Shah
>> Subject: Re: RANSUM
>>
>> I just talked to Cherie: apparently, the latest version of MP had a
>> parsing error when the synchronization with OBS happened.
>>
>> Cherie will do two things:
>> 1. Add the logic to her code that does the following: if OBS has data
>> for ontology X and the latest version of X in Bioportal has status
>> "Parsing error" or "Waiting to parse", keep the current OBS data  
>> for X
>> (currently, that data is deleted -- that's what happened with MP).
>> 2. Get a list of all ontologies that exist in Bioportal and have no
>> data in OBS. We will ask OPTRA to run synchronization for some or all
>> of  these ontologies ASAP.
>>
>> Natasha
>>
>>
>> On Apr 16, 2010, at 2:07 PM, Rob Tirrell wrote:
>>
>>> Hi - could you take a look at this issue? Thanks!
>>>
>>> Rob Tirrell
>>>
>>>
>>> ---------- Forwarded message ----------
>>> From: Nigam Shah <nigam at stanford.edu>
>>> Date: Fri, Apr 16, 2010 at 12:18
>>> Subject: Re: RANSUM
>>> To: Rob Tirrell <rpt at stanford.edu>
>>>
>>>
>>> Yes ... there was a lot of data corruption in the /obs
>>> ontologies ... Cherie Youn is fixing that. Send a request to
>> support at bioontology.org
>>> asking for MP in the /obs. It should be easy to include it.
>>>
>>> cc "Natasha Noy" <noy at stanford.edu> as well.
>>>
>>> --Nigam.
>>> PS: I am currently on leave, otherwise could have followed up  
>>> myself.
>>>
>>> On Fri, Apr 16, 2010 at 12:06 PM, Rob Tirrell <rpt at stanford.edu>
>>> wrote:
>>> hmmm... why would calls like rest.bioontology.org/bioportal/virtual/
>>> rootpath/1025/MP:0000001?email=example at example.org be failing? Is it
>>> because MP is not in rest.bioontology.org/obs/ontologies all of the
>>> sudden (it is in the other ontologies list)?
>>>
>>> Rob Tirrell
>>>
>>>
>>
> _______________________________________________
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Trish Whetzel, PhD
Outreach Coordinator
The National Center for Biomedical Ontology
Ph: 650-721-2378
whetzel at stanford.edu
http://www.bioontology.org



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