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[bioontology-support] RANSUM

Cherie H Youn cyoun at stanford.edu
Fri Apr 16 15:56:16 PDT 2010


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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