From dac942bedb8ff085f31fbec6afaefeb3d83483b7 Mon Sep 17 00:00:00 2001 From: Sigve Nakken Date: Wed, 19 Jun 2024 00:09:36 +0200 Subject: [PATCH] EFO 3.67, DO May 2024 --- DESCRIPTION | 1 - R/sysdata.rda | Bin 509 -> 508 bytes README.md | 6 +++--- data-raw/data-raw.R | 4 ++-- data-raw/metadata_phen_oncox.xlsx | Bin 10568 -> 10565 bytes data-raw/phen_oncox_utilities.R | 4 ++-- pkgdown/index.md | 6 +++--- 7 files changed, 10 insertions(+), 11 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 55c689d..f2ee3eb 100644 --- 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 index dc1f74ca6babde8f965d9e5ed508d9d932a8779a..a0da56e05d37aeb85482af1568ed894c5a27ce60 100644 GIT binary patch literal 508 zcmVQ6}8CYUuc2AXXqnlx=jnLRN=y+q1r^qLxI&;V!v000Jn27pNvPenGT 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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 index aec3469..af1e347 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( - 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a/data-raw/phen_oncox_utilities.R b/data-raw/phen_oncox_utilities.R index c738c40..05ba7a0 100644 --- 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 index 0551d63..906d93d 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 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