EFO/DO Feb 2024 update

sigven · Mar 8, 2024 · 5ba95de · 5ba95de
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Showing 6 changed files with 10 additions and 10 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: phenOncoX
 Type: Package
 Title: A phenotype ontology map for cancer
-Date: 2024-02-08
+Date: 2024-03-08
 Version: 0.7.1
 Authors@R: 
     c(person(given = "Sigve",

diff --git a/R/sysdata.rda b/R/sysdata.rda
diff --git a/README.md b/README.md
@@ -40,11 +40,11 @@ For each entry in the final list of phenotype terms, we make cross-mappings
 with phenotype terms from [EFO](https://github.com/EBISPOT/efo), 
 [DO](https://disease-ontology.org/), and the [ICD10 classification](https://www.who.int/standards/classifications/classification-of-diseases).
 
-As of early February 2024, the following ontology versions are used to create the mapping:
+As of early March 2024, the following ontology versions are used to create the mapping:
 
 -   OncoTree (2021_11_02)
--   Experimental Factor Ontology v3.62.0 (2024-01-15)
--   Disease Ontology (v2024-01-31)
+-   Experimental Factor Ontology v3.63.0 (2024-02-15)
+-   Disease Ontology (v2024-02-28)
 
 **IMPORTANT NOTE**: The mapping established by **phenOncoX** attempts 
 to be comprehensive, but we acknowledge that the presence of missing or 

diff --git a/data-raw/data-raw.R b/data-raw/data-raw.R
@@ -21,7 +21,7 @@ lgr::lgr$appenders$console$set_layout(
 )
 ## Get UMLS / DiseaseOntology / EFO mappings
 umls_map <- map_umls(
-  update = T,
+  update = F,
   basedir = here::here())
 
 icd10_map <- map_icd10(
@@ -40,7 +40,7 @@ efo_map <- map_efo(
   umls_map = umls_map,
   efo_release = metadata$phen_oncox[
     metadata$phen_oncox$source == "Experimental Factor Ontology",]$source_version,
-  update = F,
+  update = T,
   basedir = here::here())
 
 ## Use OncoTree as starting point for phenotype cross-map
@@ -73,7 +73,7 @@ db[['oncotree_core']] <- oncotree_core
 db[['oncotree_expanded']] <- oncotree_expanded
 db[['auxiliary_maps']] <- auxiliary_maps
 
-version_bumped <- "0.7.1"
+version_bumped <- "0.7.2"
 gd_records <- list()
 db_id_ref <- data.frame()
 

diff --git a/data-raw/metadata_phen_oncox.xlsx b/data-raw/metadata_phen_oncox.xlsx
diff --git a/pkgdown/index.md b/pkgdown/index.md
@@ -40,11 +40,11 @@ For each entry in the final list of phenotype terms, we make cross-mappings
 with phenotype terms from [EFO](https://github.com/EBISPOT/efo), 
 [DO](https://disease-ontology.org/), and the [ICD10 classification](https://www.who.int/standards/classifications/classification-of-diseases).
 
-As of early February 2024, the following ontology versions are used to create the mapping:
+As of early March 2024, the following ontology versions are used to create the mapping:
 
 -   OncoTree (2021_11_02)
--   Experimental Factor Ontology v3.62.0 (2024-01-15)
--   Disease Ontology (v2024-01-31)
+-   Experimental Factor Ontology v3.63.0 (2024-02-15)
+-   Disease Ontology (v2024-02-28)
 
 The package offers a few pre-processed datasets, along with metadata, that 
 the user can retrieve and use for their own projects or set-ups. The package