v0.4.0

sigven · Sep 21, 2022 · 9652efe · 9652efe
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: oncoPhenoMap
 Type: Package
 Title: A cross-referenced phenotype ontology map for the oncology domain
-Date: 2022-07-27
+Date: 2022-09-21
 Authors@R: 
     c(person(given = "Sigve",
              family = "Nakken",
@@ -11,7 +11,7 @@ Authors@R:
 Maintainer: Sigve Nakken <sigven@ifi.uio.no>
 URL: https://github.com/sigven/oncoPhenoMap
 BugReports: https://github.com/sigven/oncoPhenoMap/issues
-Version: 0.3.9
+Version: 0.4.0
 Description: A semi-manually curated resource that maps relevant phenotype terms for the oncology domain.
     Using OncoTree as the starting point, oncoPhenoMap gathers all key UMLS terms per main tumor type, 
     expands with all children in the UMLS tree, and maps these terms to cross-referenced terms in the 

diff --git a/README.md b/README.md
@@ -16,11 +16,11 @@ The mapping established within **oncoPhenoMap** is semi-manually curated, using
 
 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).
 
-Currently, the following ontology versions are used to create the mapping:
+As of v0.4.0, the following ontology versions are used to create the mapping:
 
 -   OncoTree (2021_11_02)
--   Experimental Factor Ontology v3.43.0 (2022-06-15)
--   Disease Ontology (v2022-06-07)
+-   Experimental Factor Ontology v3.46.0 (2022-09-15)
+-   Disease Ontology (v2022-08-29)
 
 **IMPORTANT NOTE**: The mapping established by **oncoPhenoMap** attempts to be comprehensive, but we acknowledge that the presence of missing or erroneous cross-references might still occur.
 

diff --git a/data-raw/data-raw.R b/data-raw/data-raw.R
@@ -1,13 +1,13 @@
 library(magrittr)
 source('data-raw/functions.R')
 
-disease_ontology_release <- 'v2022-06-07'
-efo_release <- 'v3.44.0'
+disease_ontology_release <- 'v2022-08-29'
+efo_release <- 'v3.46.0'
 oncotree_release <- '2021_11_02'
 
 ## Get UMLS / DiseaseOntology / EFO mappings
 umls_map <- map_umls(
-  update = F,
+  update = T,
   basedir = here::here())
 
 

diff --git a/data/auxiliary_maps.rda b/data/auxiliary_maps.rda
diff --git a/data/oncotree_basic.rda b/data/oncotree_basic.rda
diff --git a/data/oncotree_expanded_full.rda b/data/oncotree_expanded_full.rda
diff --git a/data/oncotree_expanded_slim.rda b/data/oncotree_expanded_slim.rda
diff --git a/renv.lock b/renv.lock
@@ -1,6 +1,6 @@
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@@ -19,10 +19,10 @@
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@@ -37,13 +37,11 @@
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@@ -93,10 +91,10 @@
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@@ -239,10 +237,10 @@
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@@ -297,10 +295,10 @@
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@@ -335,18 +333,18 @@
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@@ -447,10 +443,10 @@
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