diff --git a/DESCRIPTION b/DESCRIPTION index e01c0e6..e7d57e3 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: phenOncoX Type: Package Title: A phenotype ontology map for cancer -Date: 2024-01-26 +Date: 2024-02-08 Version: 0.7.0 Authors@R: c(person(given = "Sigve", diff --git a/R/sysdata.rda b/R/sysdata.rda index c03d05b..6e8698e 100644 Binary files a/R/sysdata.rda and b/R/sysdata.rda differ diff --git a/README.md b/README.md index f66b42a..06f4763 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 January 2024, the following ontology versions are used to create the mapping: +As of early February 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 (v2023-12-20) +- Disease Ontology (v2024-01-31) **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 81df551..7d03e26 100644 --- a/data-raw/data-raw.R +++ b/data-raw/data-raw.R @@ -21,7 +21,7 @@ lgr::lgr$appenders$console$set_layout( ) ## Get UMLS / DiseaseOntology / EFO mappings umls_map <- map_umls( - update = F, + update = T, basedir = here::here()) icd10_map <- map_icd10( @@ -40,7 +40,7 @@ efo_map <- map_efo( umls_map = umls_map, efo_release = metadata$phen_oncox[ metadata$phen_oncox$source == "Experimental Factor Ontology",]$source_version, - update = 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 <- "0.6.8" +version_bumped <- "0.7.1" 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 6709ce7..beff99c 100644 Binary files a/data-raw/metadata_phen_oncox.xlsx and b/data-raw/metadata_phen_oncox.xlsx differ diff --git a/data-raw/phen_oncox_utilities.R b/data-raw/phen_oncox_utilities.R index aacceec..e17be61 100644 --- a/data-raw/phen_oncox_utilities.R +++ b/data-raw/phen_oncox_utilities.R @@ -171,12 +171,15 @@ map_efo <- function(umls_map, } if (stringr::str_detect( line, - "property_value: exactMatch NCIT:")) { + "^xref: NCIt:")) { nci_t <- stringr::str_replace_all( line, - "property_value: exactMatch NCIT:","") + "xref: NCIt:","") nci_all <- c(nci_all, nci_t) } + if(i %% 10000 == 0){ + cat(paste0("Processing line: ", i), sep="",'\n') + } i <- i + 1 } diff --git a/pkgdown/index.md b/pkgdown/index.md index 9e3dc02..f608bdb 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 January 2014, the following ontology versions are used to create the mapping: +As of early February 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 (v2023-12-20) +- Disease Ontology (v2024-01-31) 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