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Renzo, can you add ELVIRA to the assembly methods?
(http://sourceforge.net/projects/elvira)
2009-02-16 11:53:33 UTC in The Genomics Standards Consortium (GSC)
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haploploid should be haploid. Also, diploid should be added. This is in cvTypes.xsd.
2009-02-14 14:55:59 UTC in The Genomics Standards Consortium (GSC)
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Perhaps we should have two top-level terms, autotroph and heterotroph (these terms describe the carbon source). Optionally, we can add an optional second level for the energy source: lithotroph, chemolithotroph, organotroph, phototroph. There are a number of other terms, that are combinations of the top level and 2nd level terms, e.g. mixotroph, photoautotroph, but we can avoid them by having...
2009-02-09 16:01:12 UTC in The Genomics Standards Consortium (GSC)
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I suggest to change the following terms:
'autotroph (producer)' to 'autotroph'
'heterotroph (consumer)' to 'heterotroph'
'saprotroph (decomposer)' to 'saprotroph'
I don't think a 'translation' of these terms is necessary.
2009-02-09 10:30:36 UTC in The Genomics Standards Consortium (GSC)
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Did we ever consider more trophic level terms apart from the 4 we have now. I have a chemo-organotrophic
organism. Heterotroph will cover it (and I am ok with this), but perhaps we should make a decision soon whether the current enumerations are adequate.
2009-02-06 15:50:24 UTC in The Genomics Standards Consortium (GSC)
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I have a suggestion to rename to
as the latest sequence platform do not always require traditonal subcloning of DNA fragments. Perhaps also of use is the ability to specify whether the reads are single-end or paired-end reads
(e.g. .
2009-02-06 15:45:16 UTC in The Genomics Standards Consortium (GSC)
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gcdml only allows one sequencing method. This problem was addresses by Tanya in GenCat by allowing terms like 'dideoxysequencing and pyrosequencing' or 'dideoxysequencing and solexa' etc. It gets even
messier when different DNA libraries for the different technologies, there is no way to specify which library was used for which technology.
2009-02-06 15:43:08 UTC in The Genomics Standards Consortium (GSC)
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For habitat, the current implementation is too restrictive as it does not allow host-associated habitats. This is solved in habitat-lite 0.3.
2009-02-06 15:39:13 UTC in The Genomics Standards Consortium (GSC)
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The data type for foldCoverage is currently positiveInteger. It would be better to change this to double.
2009-02-06 15:34:27 UTC in The Genomics Standards Consortium (GSC)
