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[bioontology-support] Feedback

Ray Fergerson ray.fergerson at stanford.edu
Wed Jun 15 12:39:14 PDT 2011


Barry,

 

Kinetoplast  appears twice in the tree because it has two asserted
parents: genome and sequence_collection. The latter is logically redundant
since genome is already a subclass of sequence_collection.  Nevertheless
since this relation is asserted we show it.

 

BioPortal does have a bug that causes UI hangs with two terms with the
same id are visible in the tree. We are working on this and it should be
fixed in the next release (roughly end of month). 

 

Ray

 

name: kinetoplast
alt_id: SO:0000826
def: "A kinetoplast is an interlocked network of thousands of minicircles
and tens of maxi circles, located near the base of the flagellum of some
protozoan species." [PMID:8395055]
synonym: "kinetoplast_chromosome" EXACT []
xref: http://en.wikipedia.org/wiki/Kinetoplast "wiki"
is_a: SO:0001026 ! implied link automatically realized ! genome
is_a: SO:0001260 ! sequence_collection
intersection_of: SO:0001260 ! sequence_collection
intersection_of: has_part SO:0000742 ! maxicircle
intersection_of: has_part SO:0000980 ! minicircle

 

Ray

From: Barry Smith [mailto:phismith at buffalo.edu] 
Sent: Tuesday, June 14, 2011 4:45 PM
To: Ray Fergerson
Subject: Re: [bioontology-support] Feedback

 

image.png

Ray

There are still bugs here.

1. When I try to open kinetoplast (for the fourth time now) it freezes my
browser (see above)

2. Since there is only one SO term kinetoplast, two such terms should not
appear when SO is opened in bioportal.

I think.

Barry

 

On Tue, Jun 14, 2011 at 5:11 PM, Ray Fergerson
<ray.fergerson at stanford.edu> wrote:

Barry,

The NIFSTD owl ontology imports owl versions of both GO and SO (along with
a large number of other ontologies). The SO ontology version being
imported does have a unique term defined for kinetoplast which is distinct
from the one in GO. The details from the original files are given below.

(Big thanks to Tania for digging this out of the files.)

Ray

------------------

ID: http://purl.org/obo/owl/GO#GO_0020023
Location:
http://ontology.neuinfo.org/NIF/BiomaterialEntities/cellular_component.owl

Declaration:

<owl:Class rdf:about="http://purl.org/obo/owl/GO#GO_0020023">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
 >kinetoplast</rdfs:label>
....

--------------------

ID: http://purl.org/obo/owl/SO#SO_0000741
Location: http://ontology.neuinfo.org/NIF/BiomaterialEntities/sequence.owl

Declaration:

<owl:Class rdf:about="http://purl.org/obo/owl/SO#SO_0000741">
<oboInOwl:hasAlternativeId
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
 >SO:0000826</oboInOwl:hasAlternativeId>
<oboInOwl:hasExactSynonym>
<oboInOwl:Synonym>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
 >kinetoplast_chromosome</rdfs:label>
</oboInOwl:Synonym>
</oboInOwl:hasExactSynonym>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
 >kinetoplast</rdfs:label>
....


> -----Original Message-----
> From: Barry Smith [mailto:phismith at buffalo.edu]
> Sent: Saturday, June 04, 2011 5:20 AM
> To: Ray Fergerson
> Cc: support at bioontology.org; karen.eilbeck at genetics.utah.edu
> Subject: Re: [bioontology-support] Feedback
>
> Ray
> It seems that there is something wrong with the way SO is being
> imported into Bioportal. There are no SO terms with GO ideas.
>
> >> Name : Barry Smith
> >> Comment:
> >> In Sequence Types and Features the term 'kinetoplast' occurs twice;
> >
>
> On Fri, Jun 3, 2011 at 7:58 PM, Ray Fergerson
> <ray.fergerson at stanford.edu> wrote:
> > Barry,
> >
> > The duplicate terms show up because there are in fact two terms with
> > distinct identifiers with the same label in NIFSTD. One has id:
> > so:SO_0000741 and the other go:GO_0020023.
> >
> > Ray
> >

 

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