Difference between revisions of "OBD:Similarity Statistics"
(New page: See the javadoc for [http://www.berkeleybop.org/obd/docs/org/obd/model/stats/SimilarityPair.html SimilarityPair] Category:OBD) |
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| + | OBD has various capabilities for computing the similarity between entities based on ontology annotations. | ||
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| + | OBD is flexible with respect to what kind of annotations and ontologies are used. For example: | ||
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| + | * Based on phenotypes annotations, what mouse genes (or genotypes) are similar to the human gene EPB41? | ||
| + | * Based on GO annotations, what is the correlation between similarity between functional annotations and sequence similarity? | ||
| + | * Based on annotations of microbes to environmental habitats, what organisms have similar profiles to a particular microbe? | ||
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| + | Here we will use annotations of genes, alleles and genotypes to phenotypes for illustrative purposes, but the methods are generic. | ||
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| + | == Use of reasoner == | ||
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| + | All similarity statistics are run using the pre-reasoned database. If a gene affects the hippocampus it also affects the brain. If a mutation affects the permeability of a mitochondrial membrane, it also affects the permeability of a membrane. This ensure that annotations are different levels of granularity and specificity are compared, commonalities are found. | ||
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| + | == Inter-species comparisons == | ||
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| + | In cases where we want to compare anatomical terms across species we reason using [[UBERON:Main_Page|Uberon]] | ||
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| + | == Statistics == | ||
See the javadoc for [http://www.berkeleybop.org/obd/docs/org/obd/model/stats/SimilarityPair.html SimilarityPair] | See the javadoc for [http://www.berkeleybop.org/obd/docs/org/obd/model/stats/SimilarityPair.html SimilarityPair] | ||
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[[Category:OBD]] | [[Category:OBD]] | ||
Latest revision as of 12:00, 9 October 2008
OBD has various capabilities for computing the similarity between entities based on ontology annotations.
OBD is flexible with respect to what kind of annotations and ontologies are used. For example:
- Based on phenotypes annotations, what mouse genes (or genotypes) are similar to the human gene EPB41?
- Based on GO annotations, what is the correlation between similarity between functional annotations and sequence similarity?
- Based on annotations of microbes to environmental habitats, what organisms have similar profiles to a particular microbe?
Here we will use annotations of genes, alleles and genotypes to phenotypes for illustrative purposes, but the methods are generic.
Use of reasoner
All similarity statistics are run using the pre-reasoned database. If a gene affects the hippocampus it also affects the brain. If a mutation affects the permeability of a mitochondrial membrane, it also affects the permeability of a membrane. This ensure that annotations are different levels of granularity and specificity are compared, commonalities are found.
Inter-species comparisons
In cases where we want to compare anatomical terms across species we reason using Uberon
Statistics
See the javadoc for SimilarityPair