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[bioontology-support] RANSUM

Rob Tirrell rpt at stanford.edu
Wed Apr 21 18:50:13 PDT 2010


It looks to be working! Thanks, again, for your help!
Rob Tirrell


On Wed, Apr 21, 2010 at 13:10, Trish Whetzel <whetzel at stanford.edu> wrote:

> 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 <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
>
>
>
>
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>
>
>  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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