EFO 3.69.0

DESCRIPTION

@@ -9,7 +9,7 @@ Authors@R:
              email = "[email protected]",
              comment = c(ORCID = "0000-0001-8468-2050")))
 Maintainer: Sigve Nakken <[email protected]>
-URL: https://github.com/sigven/phenOncoX
+URL: https://sigven.github.io/phenOncoX
 BugReports: https://github.com/sigven/phenOncoX/issues
 Description: A semi-manually curated resource that maps relevant phenotype 
     terms for the oncology domain. Using OncoTree as the starting point, 

README.md

@@ -40,10 +40,10 @@ 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 August 2024, the following ontology versions are used to create the mapping:
+As of mid August 2024, the following ontology versions are used to create the mapping:
 
 -   OncoTree (2021_11_02)
--   Experimental Factor Ontology v3.68.0 (2024-07-15)
+-   Experimental Factor Ontology v3.69.0 (2024-08-15)
 -   Disease Ontology (v2024-07-31)
 
 **IMPORTANT NOTE**: The mapping established by **phenOncoX** attempts 

data-raw/data-raw.R

@@ -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 = T,
+  update = F,
   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 <- "0.7.7"
+version_bumped <- "0.7.8"
 gd_records <- list()
 db_id_ref <- data.frame()
 

data-raw/phen_oncox_utilities.R

@@ -807,6 +807,11 @@ map_disease_ontology <- function(
 
   ## manual correction of erroneous or missing UMLS cross-references
   do_map <- do_map |>
+    dplyr::filter(!(
+      !is.na(cui) & 
+        cui == "C0206687" &
+        do_id == "DOID:2871"
+    )) |>
     # dplyr::mutate(do_name =
     #                 stringi::stri_enc_toascii(do_name)) |>
     ## sarcoma (non-existent UMLS_CUI = C0153519)
@@ -1324,6 +1329,11 @@ onco_pheno_map <- function(
       !is.na(nci_t) & nci_t == "C9305",
       "C1334557",
       as.character(cui)
+    )) |>
+    dplyr::mutate(cui = dplyr::if_else(
+      !is.na(cui) & cui == "C0206687",
+      "C1332913",
+      as.character(cui)
     ))
 
   cui_name_map_lower <- cui_name_map |>
@@ -2248,6 +2258,22 @@ onco_pheno_map <- function(
       "Blood_Cancer_NOS",
       as.character(ot_main_type)
     )) |>
+    dplyr::mutate(primary_site = dplyr::if_else(
+      stringr::str_detect(tolower(cui_name),"ewing sarcoma") &
+        stringr::str_detect(tolower(cui_name),"bone") &
+        !is.na(primary_site) &
+        primary_site != "Bone",
+      "Bone",
+      as.character(primary_site)
+    )) |>
+    dplyr::mutate(ot_main_type = dplyr::if_else(
+      stringr::str_detect(tolower(cui_name),"ewing sarcoma") &
+        stringr::str_detect(tolower(cui_name),"bone") &
+        !is.na(primary_site) &
+        primary_site != "Bone",
+      "Bone_Cancer_NOS",
+      as.character(ot_main_type)
+    )) |>
     dplyr::distinct() 
 
   missing_hereditary <- dplyr::bind_rows(
@@ -2431,6 +2457,17 @@ onco_pheno_map <- function(
                  primary_site, "CNS/Brain|Peripheral Nervous System"
                ))
         )) |>
+      dplyr::filter(
+        !(!is.na(cui_name) & 
+            stringr::str_detect(
+              tolower(cui_name),"ewing sarcoma") &
+            stringr::str_detect(
+              tolower(cui_name),"bone") &
+            (!is.na(primary_site) & 
+               stringr::str_detect(
+                 primary_site, "Soft Tissue|Peripheral Nervous System"
+               ))
+        )) |>
       dplyr::filter(
         !(!is.na(efo_name) & 
             stringr::str_detect(
@@ -2575,6 +2612,21 @@ onco_pheno_map <- function(
         stringr::str_detect(tolower(cui_name), "heart") &
           (!is.na(ot_main_type) & ot_main_type == "Lung_Cancer_NOS"))
       ) |>
+      dplyr::filter(!(
+        stringr::str_detect(tolower(cui_name), "desmoid") &
+          (!is.na(ot_main_type) & ot_main_type == "Bone_Cancer_NOS"))
+      ) |>
+      dplyr::filter(!(
+        stringr::str_detect(tolower(cui_name), 
+                            "malignant peripheral nerve sheath") &
+          (!is.na(primary_site) & 
+             !(primary_site == "Soft Tissue" | 
+                 primary_site == "Peripheral Nervous System"))
+      )) |>
+      dplyr::filter(!(
+        cui == "C0019562" & 
+          !is.na(primary_site) & primary_site == "Soft Tissue"
+      )) |>
       dplyr::filter(
         !(stringr::str_detect(tolower(cui_name), "cardiac"))) |>
       dplyr::filter(

pkgdown/_pkgdown.yml

@@ -2,12 +2,30 @@ url: https://sigven.github.io/phenOncoX/
 title: phenOncoX
 template:
   bootstrap: 5
+  bslib:
+    info: "#00483A"
+    dropdown-link-hover-bg: "#00483A"
+    dropdown-link-hover-color: "white"
+    dropdown-link-active-color: "white"
+    navbar-light-color: "white"
+    navbar-light-brand-color: "white"
+    navbar-link-hover-color: "white !important"
+    nav-link-hover-color: "white !important"
+    navbar-light-brand-hover-color: "white !important"
+    navbar-link-color: "white"
+
 toc:
   depth: 3
 authors:
   Sigve Nakken:
     href: "https://github.com/sigven"
 navbar:
+  link-color: "white"
+  light-color: "white"
+  light-brand-color: "white"
+  light-hover-color: "white !important"
+  type: light
+  bg: info
   structure:
     left: [home, get_started, reference, news]
     right: [search, github]

pkgdown/index.md

@@ -40,10 +40,10 @@ 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 August 2024, the following ontology versions are used to create the mapping:
+As of mid August 2024, the following ontology versions are used to create the mapping:
 
 -   OncoTree (2021_11_02)
--   Experimental Factor Ontology v3.68.0 (2024-07-15)
+-   Experimental Factor Ontology v3.69.0 (2024-08-15)
 -   Disease Ontology (v2024-07-31)
 
 The package offers a few pre-processed datasets, along with metadata, that