Difference between revisions of "KB build process"
|Line 119:||Line 119:|
Revision as of 03:23, 25 February 2014
Still being fleshed out
The Phenoscape KB build process goes through several steps in converting input data sources to a queryable knowledgebase. This page provides some description for each of the steps, most or all of which are implemented in the phenoscape-owl-tools project.
The Phenoscape Knowledgebase works as a single unified OWL model. While some inputs (e.g. the shared ontologies such as Uberon and PATO) are natively distributed as OWL documents, others are converted to OWL from some other representation. In doing so the inputs are, as far as possible, converted to a shared data model. EQ annotations are converted to a specific semantic representation.
- ZFIN phenotype annotations are provided at their data download site. We translate each row into a phenotype instance: an individual instance of some PATO quality. Here is the column headers table from the ZFIN website, followed by representative OWL syntax (referencing column numbers where actual URI values would be):
|ID||Gene Symbol||Gene ID||Affected Structure or Process 1 subterm ID||Affected Structure or Process 1 subterm Name||Post-composed Relationship ID||Post-composed Relationship Name||Affected Structure or Process 1 superterm ID||Affected Structure or Process 1 superterm Name||Phenotype Keyword ID||Phenotype Keyword Name||Phenotype Tag||Affected Structure or Process 2 subterm ID||Affected Structure or Process 2 subterm name||Post-composed Relationship (rel) ID||Post-composed Relationship (rel) Name||Affected Structure or Process 2 superterm ID||Affected Structure or Process 2 superterm name||Genotype ID||Genotype Display Name||Knockdown Reagent ID||Start Stage ID||End Stage ID||Genotype Environment ID||Publication ID||Figure ID|
Individual: <uuid_1> Types: AnnotatedPhenotype, <uuid_2> Facts: ps:associated_with_gene: <col_3>, ps:associated_with_taxon: NCBITaxon:zebrafish, dc:source: <col_26> Class: <uuid_2>
Several standard OWL properties (part_of, has_part, develops_from, etc.) are conceptually shared across ontology and annotation resources, facilitating data integration. However, unlike class identifiers, identifiers for properties are often not standardized and they may not properly reference shared terms (usually because of poor tool support rather than user intent). We maintain a table of "alternative" URIs for common properties as we observe them in our data inputs. We could create equivalence axioms between these, but instead we just standardize all incoming content. This saves the reasoner some work and also makes it much easier to query across data using standard URIs, especially when not using a reasoner.
- "Absence" classes for OWL EL negation classification workaround
- General class axiom rules for presence–absence inference over part_of, develops_from
- SPARQL facilitation (e.g. materialized existential hierarchies such as part_of)
Materialization of inferred axioms
ELK reasoner using extracted tbox axioms only (not feasible with individuals included).
Assertion of absence hierarchy
Based on inverse of hierarchy of negated classes computed by ELK.