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nlw added pmabee to the Open Biomedical Ontologies project.
2009-06-18 21:21:21 UTC in Open Biomedical Ontologies
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whatever works best... I trust you. :)
2009-05-27 19:28:26 UTC in Sequence Ontology
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perhaps as a child of RNA_sequence_secondary_structure?.
2009-05-27 17:59:19 UTC in Sequence Ontology
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need a term for the antisense part of a miRNA. mature strand is the side that represents the functional miRNA, the * strand is the other side (opposite strand in miRNA hairpin).
2009-05-27 17:57:49 UTC in Sequence Ontology
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Name: primer_match
Definition: A nucleotide match to a primer sequence.
is_a: SO:0000347 !nucleotide_match.
2009-04-21 16:44:58 UTC in Sequence Ontology
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name: UST
definition: An EST spanning part or all of the untranslated regions of a protein-coding transcript
is_a: SO:0000345 ! EST
name: three_prime_UST
definition: An UST located in the 3'UTR of a protein-coding transcript.
is_a: SO:0000xxx ! UST
name: five_prime_UST
definition: An UST located in the 5'UTR of a protein-coding transcript.
is_a: SO:0000xxx ! UST
then, a flavor of...
2009-04-14 16:31:55 UTC in Sequence Ontology
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i was looking at whatever was in miso. maybe its an old version.
2009-02-05 22:37:27 UTC in Sequence Ontology
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i think it is an incorrect relationship to say that a noncoding_exon is part_of ncRNA. you can have an exon in a 3' UTR, which is clearly noncoding.
so, i think a noncoding_exon should be part_of a mature_transcript (ncRNA's parent).
2009-02-05 00:24:48 UTC in Sequence Ontology
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How about something like this:
[Term]
id: SO:xxxxxxxx
name: three_prime_RACE_clone
def: "Three prime RACE (Rapid Amplification of cDNA Ends) clone; A piece of DNA copied from the 3' end of an mRNA (using a poly-dT primer to capture the polyA tail and a gene-specific or randomly primed 5' primer), and spliced into a vector for propagation in a suitable host."
is_a: SO:0000317 ! cDNA_clone.
2009-02-02 23:18:17 UTC in Sequence Ontology
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Here's another example.
We have a group that performs an analysis basically calculating how strongly an exon is included in a particular transcript. This analysis takes into account the particular transcript that it is being measured for. The resulting GFF then has an exon feature, that should then have two child analyses features with different scores. This is similar to a blast analysis...
2009-01-23 18:13:53 UTC in Sequence Ontology
