Karen Eilbeck 7/22/08 Ontological relations and computable definitions for sequences at DNA, RNA and...
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Transcript of Karen Eilbeck 7/22/08 Ontological relations and computable definitions for sequences at DNA, RNA and...
Karen Eilbeck 7/22/08
Ontological relations and computable definitions for sequences at DNA, RNA
and protein levels
Karen Eilbeck
Neocles Leontis
Thomas Bittner
Colin Batchelor
Karen Eilbeck 7/22/08
Two sections
1. A report on the joint RNAO and SO meeting held in SLC in April 2008 (Eilbeck, Leontis and Bittner)
2. Computable definitions for 1D and 2D structures (Batchelor)
Karen Eilbeck 7/22/08
Ontological Relations for Sequences at DNA, RNA, and protein levels
A report on the joint RNAO and SO meeting held in SLC in April 2008.
Karen Eilbeck
Neocles Leontis
Thomas Bittner
Karen Eilbeck 7/22/08
Aim of meeting
• Coordinate the development of relationships between SO and RNAO
Karen Eilbeck 7/22/08
Universals and instances
• Universal: repeatable or recurrent entities that can be instantiated or exemplified by many particular things.
• Instance: A universal may have instances, known as its particulars. They identify single objects such as “that chromosome under that microscope”.
Karen Eilbeck 7/22/08
What is a sequence?
• Sequence is a universal. A sequence can be located in places at the same time.
• Manifestation of the sequence happens at the molecular level.
Karen Eilbeck 7/22/08
Same sequence different molecule.
Karen Eilbeck 7/22/08
Identifying regions and relations between regions
• Category theory.– Morphism: relationship between some posited
domain and codomain.– Isomorphism between dna and RNA (both
directions)– Morphism between rna and protein (information
loss from protein to rna.)– Morphism between DNA and protein.
Karen Eilbeck 7/22/08
Next step 1: core terms and relations
http://song.cvs.sourceforge.net/*checkout*/song/ontology/working_draft.obo
Karen Eilbeck 7/22/08
Next step 2: even more relationships
• Homology and similarity relationships
• Topological relationships• Supportive evidence relationships
Karen Eilbeck 7/22/08
Next step 3: Description logic
• Conversion of core types and relations to formal logic.
• A sound foundation to build upon for the features and other types in RNAO and SO
Karen Eilbeck 7/22/08
People:Karen Eilbeck - SO
University of [email protected]
Neocles Leontis - RNAOBGSU
Thomas Bittner - OBOBuffalo
Colin Batchelor - relations in SORSC
Karen Eilbeck 7/22/08
Computable definitions
Colin Batchelor
Karen Eilbeck 7/22/08
Computable definitionsThese consist of necessary and sufficient conditions. Generally
written in OBO or OWL format.
Example from SO: any primary transcript that is adjacent to a cap must be a capped_primary_transcript, and conversely all capped_primary_transcripts are primary transcripts that are adjacent to caps.
id: SO:0000861name: capped_primary_transcriptdef: "A primary transcript that is capped." [SO:xp]intersection_of: SO:0000185 ! primary_transcriptintersection_of: adjacent_to SO:0000581 ! cap
Karen Eilbeck 7/22/08
What does this buy us?
It makes ontology maintenance easier for the curators.
But most importantly:
With computable definitions, reasoners can in principle annotate automatically…
Karen Eilbeck 7/22/08
Loops (1)Consider an example 1D sequence:
……(((((….((….))..))).))…
The definition of a tetraloop could look like this:
tetraloop =”.…” that (adjacent_to “(“) and (adjacent to “)”)
Much like the capture group in the regex \((\.{4})\)
Karen Eilbeck 7/22/08
Loops (2):(includes cardinality)
loop = “.+” that adjacent_to “(“ and adjacent_to “)”
diloop = loop that has_part “.” cardinality exactly 2
triloop = loop that has_part “.” cardinality exactly 3
Karen Eilbeck 7/22/08
Loops (3): stem-loopsAssume no kinks or bulges or pseudoknots. Take a simple
example: ((((..))))
“424 stemloop” = sequence that has_part (“(“ cardinality exactly 4 that adjacent_to diloop) and has_part (diloop adjacent_to “(“) and has_part (diloop adjacent_to “)”) and has_part (“)” cardinality exactly 4 that adjacent_to diloop)
But what about the general case?
Karen Eilbeck 7/22/08
Loops (4): stem-loops and formal grammar
This:\({n}\.+\){n}
is not a valid regular expression. It reduces to anbn, which is well-known to be non-regular.
Likewise in OWL you cannot say cardinality exactly n. So what do we do?
Karen Eilbeck 7/22/08
A way out
Write the necessary and sufficient conditions in terms of the 2D structure.
Hence:stem-loop = structure thathas_part (base-pair that bound_to base-pair)
and has_part (base-pair that bound_to loop) and has_part loop
Karen Eilbeck 7/22/08
What next?
Write necessary and sufficient conditions for some example motifs.
Take 2D structures in RNAML that contain known example motifs.
Convert RNAML to OWL.Run reasoner.