tawny.obo
Support for numeric, incrementing identifiers, OBO style.
Support for numeric, incrementing identifiers, OBO style.
extract-obsoleteclj
(extract-obsolete remembered current)Extract identifiers for which there are mapping to a full IRI, but which no longer exist in the ontology. There are, effectively, obsolete terms.
Extract identifiers for which there are mapping to a full IRI, but which no longer exist in the ontology. There are, effectively, obsolete terms.
obo-generate-permanent-iriclj
(obo-generate-permanent-iri file prefix)Given a file, replace all the preiris with permanent, incrementing, numeric IDs.
Given a file, replace all the preiris with permanent, incrementing, numeric IDs.
obo-iri-generateclj
(obo-iri-generate o name)Generator function for numeric style IRIs. New OWLEntities will be given an temporary ID, while existing OWLEntities will reuse a numeric, incrementing ID. For full usage details see numeric.md documentation.
Implemented using ontology-options functionality. Newly created IDs are stored in :name-to-iri-current, while IDs loaded from file are stored in :name-to-iri-remembered.
Generator function for numeric style IRIs. New OWLEntities will be given an temporary ID, while existing OWLEntities will reuse a numeric, incrementing ID. For full usage details see numeric.md documentation. Implemented using ontology-options functionality. Newly created IDs are stored in :name-to-iri-current, while IDs loaded from file are stored in :name-to-iri-remembered.
obo-iri-generate-or-retrieveclj
(obo-iri-generate-or-retrieve name remembered current)Given an OWLEntity name return either the remembered name if there is one, or the current, or generate a new temporary name
Given an OWLEntity name return either the remembered name if there is one, or the current, or generate a new temporary name
obo-pre-iriclj
Root of IRI that is used for temporary IRIs
Root of IRI that is used for temporary IRIs
obo-read-mapclj
(obo-read-map file)Read a properties file, and return a hashmap of Clojure identifier to IRI.
Read a properties file, and return a hashmap of Clojure identifier to IRI.
obo-report-obsoleteclj
(obo-report-obsolete o)Print a list of obsolete terms
Print a list of obsolete terms
obo-restore-iriclj
(obo-restore-iri o file)Read an existing properties file containing identifier to IRI data.
Read an existing properties file containing identifier to IRI data.
obo-save-mapclj
(obo-save-map file map)Save a map into a properties file. Assumes entities are easily stringifiable.
Save a map into a properties file. Assumes entities are easily stringifiable.
obo-sortclj
(obo-sort map)Sort identifiers. This is just to give a defined and repeatable order to the save file, and is not functionality important for other reasons. Final IRIs are placed before pre-IRIs, and both are organised alphabetically.
Sort identifiers. This is just to give a defined and repeatable order to the save file, and is not functionality important for other reasons. Final IRIs are placed before pre-IRIs, and both are organised alphabetically.
obo-store-iriclj
(obo-store-iri o file)Save both existing and new identifier to IRI mappings into the given file.
Save both existing and new identifier to IRI mappings into the given file.
preiri?clj
(preiri? iri)Return true if the (string) IRI is a auto-generated 'pre' IRI.
Return true if the (string) IRI is a auto-generated 'pre' IRI.
update-map-with-new-iriclj
(update-map-with-new-iri name-to-iri prefix)Assigns new permanent identifiers to map. In detail, this expects an map between identifiers and IRI. For all those IRIs which return true for preiri?, a new numeric identifier is created, incrementing from the current largest.
Assigns new permanent identifiers to map. In detail, this expects an map between identifiers and IRI. For all those IRIs which return true for preiri?, a new numeric identifier is created, incrementing from the current largest.
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