Hello, Thanks for all the links, has been very helpful!
Take care Oliver On Fri, Jul 26, 2013 at 7:17 AM, Phillip Lord <phillip.l...@newcastle.ac.uk>wrote: > > In what sense? See if we can generate the description of the karyotype > from a genome sequence? Or at least compare the two? > > I agree that this would be interesting. At the moment, the problem that > we have is the ISCN string is computationally relatively intractable. In > most cases, though, the ISCN is all we have: there is no sequence, and > no biological material. > > Phil > > > Karen Eilbeck <keilb...@genetics.utah.edu> writes: > > > Hi Phil > > Nice model of ISCN. We currently allow ISCN strings to be annotated in > GVF to > > describe a genome structure. It may be interesting to validate against > whole > > genome sequence. > > --K > > > > On Jul 23, 2013, at 5:24 AM, Phillip Lord wrote: > > > > > > To the extent that it helps to answer our use case, co-ordination might > > be useful; our work on the karyotype is reasonably tightly scoped, and I > > wish to maintain this. > > > > Phil > > > > > > Melissa Haendel <haen...@ohsu.edu<mailto:haen...@ohsu.edu>> writes: > > Hi all, It would be great if we could coordinate these efforts - The > > genotype work we are doing that Chris Baker mentioned earlier on this > > thread (see > > > http://www.unbsj.ca/sase/csas/data/ws/icbo2013/papers/ec/icbo2013_submission_60.pdf > > ) > > is already being integrated into the sequence ontology. > > > > Cheers, > > Melissa > > > > On Jul 22, 2013, at 10:22 AM, Suzanna Lewis <s...@berkeleybop.org > <mailto:s...@berkeleybop.org><mailto:s...@berkeleybop.org>> wrote: > > > > Check out the Sequence Ontology. It is well-established in the genomics > community. > > http://sequenceontology.org/ > > > > On Jul 22, 2013, at 4:53 PM, Phillip Lord > > <phillip.l...@newcastle.ac.uk<mailto:phillip.l...@newcastle.ac.uk > ><mailto:phillip.l...@newcastle.ac.uk>> > > wrote: > > > > > > We are working on a karyotype ontology which describes chromosome > abnormalities. > > > > The first paper is available here which also includes links to the > ontology. > > > > http://arxiv.org/abs/1305.3758 > > > > > > > > > > Oliver Ruebenacker <cur...@gmail.com<mailto:cur...@gmail.com><mailto: > cur...@gmail.com>> writes: > > > > Hello, > > > > Does any one know of an ontology for somatic mutations (including SNPs, > > chromosomal abnormalities, etc.)? > > > > Take care > > Oliver > > > > -- > > Phillip Lord, Phone: +44 (0) 191 222 7827 > > Lecturer in Bioinformatics, Email: > > phillip.l...@newcastle.ac.uk<mailto:phillip.l...@newcastle.ac.uk > ><mailto:phillip.l...@newcastle.ac.uk> > > School of Computing Science, > http://homepages.cs.ncl.ac.uk/phillip.lord > > Room 914 Claremont Tower, skype: russet_apples > > Newcastle University, twitter: phillord > > NE1 7RU > > > > > > > > Dr. Melissa Haendel > > > > Assistant Professor > > Ontology Development Group, OHSU Library > > http://www.ohsu.edu/library/ > > Department of Medical Informatics and Epidemiology > > Oregon Health & Science University > > haen...@ohsu.edu<mailto:haen...@ohsu.edu><mailto:haen...@ohsu.edu> > > skype: melissa.haendel > > 503-407-5970 > > > > > > > > > > -- > > Phillip Lord, Phone: +44 (0) 191 222 7827 > > Lecturer in Bioinformatics, Email: > phillip.l...@newcastle.ac.uk<mailto:phillip.l...@newcastle.ac.uk> > > School of Computing Science, > http://homepages.cs.ncl.ac.uk/phillip.lord > > Room 914 Claremont Tower, skype: russet_apples > > Newcastle University, twitter: phillord > > NE1 7RU > > > > Karen Eilbeck > > Associate Professor > > Department of Biomedical Informatics, University of Utah > > > > -- > Phillip Lord, Phone: +44 (0) 191 222 7827 > Lecturer in Bioinformatics, Email: > phillip.l...@newcastle.ac.uk > School of Computing Science, > http://homepages.cs.ncl.ac.uk/phillip.lord > Room 914 Claremont Tower, skype: russet_apples > Newcastle University, twitter: phillord > NE1 7RU > -- Oliver Ruebenacker IT Project Lead at PanGenX (http://www.pangenx.com) Be always grateful, but never satisfied.