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[bioontology-support] RANSUM

Rob Tirrell r.tirrell at gmail.com
Fri Apr 16 16:04:24 PDT 2010


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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