-
Notifications
You must be signed in to change notification settings - Fork 3
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Additional EFO xref context from axioms #19
Merged
Merged
Changes from all commits
Commits
Show all changes
4 commits
Select commit
Hold shift + click to select a range
File filter
Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
@@ -0,0 +1,17 @@ | ||||||||||||||||||||||||||||||||||||||
PREFIX mondo: <http://purl.obolibrary.org/obo/mondo#> | ||||||||||||||||||||||||||||||||||||||
PREFIX efo: <http://www.ebi.ac.uk/efo/> | ||||||||||||||||||||||||||||||||||||||
PREFIX skos: <http://www.w3.org/2004/02/skos/core#> | ||||||||||||||||||||||||||||||||||||||
|
||||||||||||||||||||||||||||||||||||||
SELECT ?efo_id (?xref_uri as ?xref_id) ?mapping_property_id ?efo_uri ?xref_uri ?mapping_property_uri | ||||||||||||||||||||||||||||||||||||||
WHERE { | ||||||||||||||||||||||||||||||||||||||
VALUES ?mapping_property_uri {mondo:closeMatch mondo:exactMatch skos:mappingRelation skos:closeMatch skos:exactMatch skos:broadMatch skos:narrowMatch skos:relatedMatch} | ||||||||||||||||||||||||||||||||||||||
|
||||||||||||||||||||||||||||||||||||||
?efo_uri rdf:type owl:Class . | ||||||||||||||||||||||||||||||||||||||
?efo_uri ?mapping_property_uri ?xref_uri | ||||||||||||||||||||||||||||||||||||||
|
||||||||||||||||||||||||||||||||||||||
|
||||||||||||||||||||||||||||||||||||||
BIND( REPLACE( STR(?efo_uri), "^http.+/([^:]+)_(.+)$", "$1:$2" ) AS ?efo_id ) | ||||||||||||||||||||||||||||||||||||||
BIND( REPLACE( STR(?mapping_property_uri), "^http://purl\\.obolibrary\\.org/obo/mondo#(.+)$", "mondo:$1" ) AS ?mapping_property_id ) | ||||||||||||||||||||||||||||||||||||||
BIND( REPLACE( STR(?mapping_property_id), "^http://www\\.w3\\.org/2004/02/skos/core#(.+)$", "skos:$1" ) AS ?mapping_property_id ) | ||||||||||||||||||||||||||||||||||||||
} | ||||||||||||||||||||||||||||||||||||||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. Can you reply to this comment with the head of the output table? There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more.
|
||||||||||||||||||||||||||||||||||||||
ORDER BY ?efo_id ?xref_id ?mapping_property_id |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,18 @@ | ||
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> | ||
PREFIX owl: <http://www.w3.org/2002/07/owl#> | ||
PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#> | ||
|
||
SELECT ?efo_id ?xref ?axiom_source | ||
WHERE { | ||
?axiom rdf:type owl:Axiom. | ||
?axiom owl:annotatedSource ?source. | ||
?axiom owl:annotatedProperty oboInOwl:hasDbXref. | ||
?axiom owl:annotatedTarget ?xref. | ||
|
||
OPTIONAL { ?axiom oboInOwl:source ?axiom_source }. | ||
|
||
BIND( REPLACE( STR(?source), "^http.+/([^:]+)_(.+)$", "$1:$2" ) AS ?efo_id ) | ||
} | ||
|
||
GROUP BY ?efo_id ?xref ?axiom_source | ||
ORDER BY ?efo_id ?xref ?axiom_source |
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
We can save the tables as output and/or we can include in the nxontology. We'll have to decide how we want to represent this information as node data in networkx. Doing so is tricky because we have to decide to what extent users will want access to rawer forms versus a more consolidated but opinionated format.
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
@dhimmel How about saving the table in the output for now, so that users can access this data? We could create a follow up issue to discuss how we can represent this information as node data in networkx.
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Sounds good.