[Go] MT attachment to chromosome
Midori Harris
midori at ebi.ac.uk
Mon Nov 24 02:16:54 PST 2008
Hi Lisa,
Although I added the terms, I don't have any specialist knowledge about
these complexes, so most likely I put them under the more generic parent
because I wasn't completely confident that the more specific parent would
always be correct.
Maybe it would be good to put the question to Iain along with the rest --
unless the SGD curators or Val know of anything more specific. In any
case, if the verdict is that the terms should be moved down to part_of
condensed chromosome kinetochore, that'll be easy to do.
Midori
On Fri, 21 Nov 2008, Lisa Matthews wrote:
> Hi Midori,
> I know, it's good to be back in touch! I'm back in the USA now.
> , I just had one question before popping the question over to Iain. Based on
> the definition of Ndc80 complex and NMS Complex (and the fact that Ndc80
> associates with the kinetochore only during mitosis), I would have thought
> that these terms would be "part of" condensed chromosome kinetochore rather
> that the more generic kinetochore or am I missing something(?)
>
> * part_of relationship GO:0000776 : kinetochore [234 gene products]
> <http://amigo.geneontology.org/cgi-bin/amigo/term-assoc.cgi?term=GO:0000776&session_id=7795amigo1227278122>
>
> *
> o close
> <http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?action=minus_node&target=GO:0000777&term=GO:0000776&open_1=GO:0000777,GO:0000776&session_id=7795amigo1227278122#lineage>
> is_a relationship GO:0000777 : condensed chromosome
> kinetochore
> <http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0000777&session_id=7795amigo1227278122>
> [134 gene products]
> <http://amigo.geneontology.org/cgi-bin/amigo/term-assoc.cgi?term=GO:0000777&session_id=7795amigo1227278122>
>
> o
> + open
> <http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?action=plus_node&target=GO:0000778&term=GO:0000776&open_1=GO:0000777,GO:0000776&session_id=7795amigo1227278122#lineage>
> is_a relationship GO:0000778 : condensed nuclear
> chromosome kinetochore
> <http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0000778&session_id=7795amigo1227278122>
> [69 gene products]
> <http://amigo.geneontology.org/cgi-bin/amigo/term-assoc.cgi?term=GO:0000778&session_id=7795amigo1227278122>
>
> + open
> <http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?action=plus_node&target=GO:0000939&term=GO:0000776&open_1=GO:0000777,GO:0000776&session_id=7795amigo1227278122#lineage>
> part_of relationship GO:0000939 : inner kinetochore of
> condensed chromosome
> <http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0000939&session_id=7795amigo1227278122>
> [34 gene products]
> <http://amigo.geneontology.org/cgi-bin/amigo/term-assoc.cgi?term=GO:0000939&session_id=7795amigo1227278122>
>
> + open
> <http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?action=plus_node&target=GO:0000444&term=GO:0000776&open_1=GO:0000777,GO:0000776&session_id=7795amigo1227278122#lineage>
> part_of relationship GO:0000444 : MIS12/MIND type
> complex
> <http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0000444&session_id=7795amigo1227278122>
> [18 gene products]
> <http://amigo.geneontology.org/cgi-bin/amigo/term-assoc.cgi?term=GO:0000444&session_id=7795amigo1227278122>
>
> + leaf node part_of relationship GO:0033551 : monopolin
> complex
> <http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0033551&session_id=7795amigo1227278122>
> [8 gene products]
> <http://amigo.geneontology.org/cgi-bin/amigo/term-assoc.cgi?term=GO:0033551&session_id=7795amigo1227278122>
>
> + open
> <http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?action=plus_node&target=GO:0000940&term=GO:0000776&open_1=GO:0000777,GO:0000776&session_id=7795amigo1227278122#lineage>
> part_of relationship GO:0000940 : outer kinetochore of
> condensed chromosome
> <http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0000940&session_id=7795amigo1227278122>
> [17 gene products]
> <http://amigo.geneontology.org/cgi-bin/amigo/term-assoc.cgi?term=GO:0000940&session_id=7795amigo1227278122>
>
> o leaf node part_of relationship GO:0031262 : Ndc80 complex
> <http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0031262&session_id=7795amigo1227278122>
> [16 gene products]
> <http://amigo.geneontology.org/cgi-bin/amigo/term-assoc.cgi?term=GO:0031262&session_id=7795amigo1227278122>
>
> o leaf node part_of relationship GO:0031617 : NMS complex
> <http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0031617&session_id=7795amigo1227278122>
> [13 gene products]
> <http://amigo.geneontology.org/cgi-bin/amigo/term-assoc.cgi?term=GO:0031617&session_id=7795amigo1227278122>
>
> :
> Ndc80 Complex
> A supercomplex formed by the association of two subcomplexes (known as MIND
> and Ndc80 in Schizosaccharomyces) with additional proteins at the
> kinetochores of condensed nuclear chromosomes. [source: PMID:16079914
> <http://www.ncbi.nlm.nih.gov/pubmed/16079914>]
>
> NMS Complex:
> A supercomplex formed by the association of two subcomplexes (known
> as MIND and Ndc80 in Schizosaccharomyces) with additional proteins
> at the kinetochores of condensed nuclear chromosomes. [source:
> PMID:16079914 <http://www.ncbi.nlm.nih.gov/pubmed/16079914>]
>
> Thanks,
> Lisa
>
>
> Midori Harris wrote:
>> Hi Lisa,
>>
>> It would be great if you could ask Iain Cheeseman what he thinks. We seem
>> to be converging on agreeing that kinetochore-port_of-chromosome is the
>> best we can do for now, until we implement more relationship types, but it
>> can't hurt to get an expert's view.
>>
>> (Great to hear fraom you again, too -- it's been a while!)
>>
>> Midori
>>
>> On Fri, 21 Nov 2008, Lisa Matthews wrote:
>>
>>> Hi all,
>>> There is a really good review that just came out on this written by the
>>> Cheeseman group (they've done a lot on defining the highly conserved
>>> kinetochore DNA to microtubule molecular connectivity PMID: 19000831. I
>>> can run this question by Iain Cheeseman who has recently helped Reactome
>>> out with some annotations on centrosome function.
>>> Lisa
>>>
>>> Valerie Wood wrote:
>>>> Currently a placement of kinetochore under chromosome would be correct
>>>> based on how condensed nuclear centromeric region is defined
>>>>
>>>> def
>>>> condensed nuclear chromosome, centromeric region
>>>> The region of a condensed chromosome in the nucleus that includes the
>>>> centromere and associated proteins, including the kinetochore. In
>>>> monocentric chromosomes, this region corresponds to a single area of the
>>>> chromosome, whereas in holocentric chromosomes, it is evenly distributed
>>>> along the chromosome.
>>>>
>>>> which is a child of chromosome
>>>> although at present kinetochore is not a child of this term
>>>>
>>>> I don't know what is right though.
>>>>
>>>> VAl
>>>>
>>>> Midori Harris <midori at ebi.ac.uk> wrote:
>>>>> I think what would really help are those spatial relationship types that
>>>>> we've talked about with Chris. Kinetochore-chromosome is one of many
>>>>> cases where I suspect that biologists would expect to see some
>>>>> connection (tho I'm sure Rex or Val can correct me if I'm wrong), so
>>>>> we've used part_of even though it's far from ideal.
>>>>>
>>>>> m
>>>>>
>>>>> On Fri, 21 Nov 2008, David Hill wrote:
>>>>>
>>>>>
>>>>>> I'm not sure the kinetochore should be a part_of the chromosome. It
>>>>>> attaches to the centromere, which is part of the chromosome. I think
>>>>>> we might want to have Rex weigh in on this too. He's a cell biologist.
>>>>>>
>>>>>> David
>>>>>>
>>>>>> Midori Harris wrote:
>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> Working on some cross-product definitions, I came up with a question
>>>>>>> about whether two terms that are currently siblings should have an
>>>>>>> is_a link. The terms are:
>>>>>>>
>>>>>>> attachment of spindle microtubules to chromosome GO:0051313
>>>>>>> attachment of spindle microtubules to kinetochore GO:0008608
>>>>>>>
>>>>>>> and I think we shoud have GO:0008608 is_a GO:0051313 because
>>>>>>> kinetochore is part_of chromosome in the component ontology.
>>>>>>>
>>>>>>> I've opened a SourceForge item, and I'd appreciate any comments.
>>>>>>>
>>>>>>> https://sourceforge.net/tracker/?func=detail&atid=440764&aid=2320413&group_id=36855
>>>>>>> thanks,
>>>>>>> midori
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Go mailing list
>>>>>>> Go at geneontology.org
>>>>>>> http://fafner.stanford.edu/mailman/listinfo/go
>>>>>>>
>>>>>>
>>>>> _______________________________________________
>>>>> Go mailing list
>>>>> Go at geneontology.org
>>>>> http://fafner.stanford.edu/mailman/listinfo/go
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------
>>>>
>>>> _______________________________________________
>>>> Go mailing list
>>>> Go at geneontology.org
>>>> http://fafner.stanford.edu/mailman/listinfo/go
>>>>
>
More information about the Go
mailing list