EFO 3.67, DO May 2024

sigven · Jun 18, 2024 · dac942b · dac942b
1 parent 61bcb42
commit dac942b
Show file tree

Hide file tree

Showing 7 changed files with 10 additions and 11 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,6 @@
 Package: phenOncoX
 Type: Package
 Title: A phenotype ontology map for cancer
-Date: 2024-05-21
 Version: 0.7.5
 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 mid May 2024, the following ontology versions are used to create the mapping:
+As of mid June 2024, the following ontology versions are used to create the mapping:
 
 -   OncoTree (2021_11_02)
--   Experimental Factor Ontology v3.66.0 (2024-05-15)
--   Disease Ontology (v2024-04-30)
+-   Experimental Factor Ontology v3.67.0 (2024-06-15)
+-   Disease Ontology (v2024-05-29)
 
 **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(
@@ -73,7 +73,7 @@ db[['oncotree_core']] <- oncotree_core
 db[['oncotree_expanded']] <- oncotree_expanded
 db[['auxiliary_maps']] <- auxiliary_maps
 
-version_bumped <- "0.7.5"
+version_bumped <- "0.7.6"
 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/data-raw/phen_oncox_utilities.R b/data-raw/phen_oncox_utilities.R
@@ -1183,7 +1183,7 @@ onco_pheno_map <- function(
     dplyr::distinct()
 
   ot_tumor_types_tree <-
-    jsonlite::fromJSON("http://oncotree.mskcc.org/api/tumorTypes/tree")
+    jsonlite::fromJSON("http://oncotree.info/api/tumorTypes/tree")
 
 
   oncotree_entries <- data.frame()
@@ -1902,7 +1902,7 @@ onco_pheno_map <- function(
     "affecting|complicating|configuration|involving|involves|confined|",
     "number of|percent of|cancer diagnosis|therapy|assessed|surgery|",
     "surgical|( in (remission|relapse))|cancer-(related|associated)| the rat |",
-    "benign |uncertain behavior|surgery|mouse|invades|",
+    "uncertain behavior|surgery|mouse|invades|",
     "finding|^t[0-9]|^p(t|m|(x|[0-9]{1,}))")
 
   cancer_terms <- cui_name_map_lower |>

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 mid May 2024, the following ontology versions are used to create the mapping:
+As of mid June 2024, the following ontology versions are used to create the mapping:
 
 -   OncoTree (2021_11_02)
--   Experimental Factor Ontology v3.66.0 (2024-05-15)
--   Disease Ontology (v2024-04-30)
+-   Experimental Factor Ontology v3.67.0 (2024-06-15)
+-   Disease Ontology (v2024-05-29)
 
 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