diff --git a/DESCRIPTION b/DESCRIPTION index 2f6b9de..57b4ab7 100644 --- 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 index 6e8698e..096ab62 100644 Binary files a/R/sysdata.rda and b/R/sysdata.rda differ diff --git a/README.md b/README.md index 06f4763..9302103 100644 --- 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 index 7d03e26..75bec53 100644 --- 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 index beff99c..fb567e1 100644 Binary files a/data-raw/metadata_phen_oncox.xlsx and b/data-raw/metadata_phen_oncox.xlsx differ diff --git a/pkgdown/index.md b/pkgdown/index.md index f608bdb..98a66ae 100644 --- 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