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| − | ==Goal and motivation==
| + | #REDIRECT [[Ontology Data Service API]] |
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| − | A common API implemented by ontology data services enables clients such as EQ editors that heavily rely on such a service to plug into different data providers, local or remote, at their choice.
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| − | ==Service definitions==
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| − | # Ontology listing lookup | |
| − | #* Function: lookup the ontologies being served by the data service
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| − | #* Input: none, or a particular name, and/or the name of the ontology category
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| − | #* Output: a record of name, version, identifier, meta-data (e.g., retired? in production? purpose?) for each ontology being served
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| − | # Look up term
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| − | #* Function: Obtain the full term information for a given ID
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| − | #* Input: a term ID, or the combination of a term name and ontology ID
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| − | #* Output: the matching term in OBO or RDF/OWL format
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| − | #* Notes: do we need neighborhood here too (e.g., with IDs only); OBO only has parents, not children.
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| − | # Completion list
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| − | #* Function: Obtain matching term names for a partial term name string
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| − | #* Input: partial term name string, a list of ontology IDs, search parameters (search names only or synonyms only or both, search obsoletes or not, search definition or not)
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| − | #* Output: matches as records of term name, term ID, ontology ID, synonym that was hit, how the term was hit (name, synonym, or definition)
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| − | # Neighborhood graph
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| − | #* Function: Obtain parents, children, descendants, or ancestors for a given term
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| − | #* Input: term ID, list of relationships to include or exclude, number of levels (path length) up and down to include
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| − | #* Output: list of terms in OBO or RDF format
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| − | #* Note: Is it sensible to return a graph as OBO format? Do we need to mandate the semantics of matching mixed-type paths (e.g., is-a and part-of)?
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| − | # Downloading ontology
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| − | #* Function: Obtain all terms and relationships comprising an ontology
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| − | #* Input: ontology ID, optionally name of the slim
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| − | #* Output: the ontology as an OBO or OWL stream of text
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| − | #* Notes: do we need a parameter for specifying the desired format? do we need parameter for including obsoletes or not
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| − | # Login
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| − | #* Function: Given a username and secret, obtain an authentication token
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| − | #* Input:
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| − | #* Output:
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| − | # Save EQ statements
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| − | #* Function: Save an array of EQ statements to the data store
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| − | #* Input: a list of EQ statements on OBD-xml or pheno-xml format
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| − | #* Output: success/failure indicator
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| − | # Load EQ statements
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| − | #* Function: Load an array of EQ statements from the data store
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| − | #* Input: author, or list of taxa,
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| − | #* Output: matching EQ statements in pheno-xml or pheno-syntax format
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| − | #* Notes: do we need parameter of list of entities to obtain EQs for?
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| − | # SPARQL endpoint
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| − | #* Function: Issue SPARQL queries and obtain the results in RDF
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| − | #* Input:
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| − | #* Output:
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| − | ; Notes :
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| − | ;*
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| − | ==Query languages==
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| − | * SPARQL
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| − | ==Data exchange formats==
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| − | * Text over HTTP:
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| − | ** OBO format
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| − | ** OBO-XML format
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| − | ** OBD-XML format
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| − | ** RDF
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