From 3c296c6b48622fc42d2eca1a58f5bf3a425dd414 Mon Sep 17 00:00:00 2001 From: Vedanth Date: Wed, 21 Aug 2024 10:16:47 +0530 Subject: [PATCH] DOC add argnorm overview figure to supplement argnorm workflow figure --- README.md | 6 + docs/images/argnorm_overview.svg | 738 +++++++++++++++++++++++++++++++ docs/index.md | 5 + 3 files changed, 749 insertions(+) create mode 100644 docs/images/argnorm_overview.svg diff --git a/README.md b/README.md index c5b73bd..7c513c0 100644 --- a/README.md +++ b/README.md @@ -30,6 +30,12 @@ The `confers_resistance_to` column will contain ARO numbers of all the drug clas The `resistance_to_drug_classes` column will contain ARO numbers of the broader categories of the drug classes in the `confers_resistance_to` column (`ARO:3000007` for `beta lactam antibiotic` in the previous example). +### argNorm Overview +![argNorm Overview](./docs/images/argnorm_overview.svg) + +*General overview of argNorm. (a) Genomes and metagenomes can be annotated using ARG annotation tools. argNorm accepts the outputs of these ARG annotation tools directly or after the outputs are processed by hAMRonization to perform ARO normalization and drug categorization. (b) The argNorm workflow includes: mapping gene names in the ARG annotation outputs to ARO accessions from ARO annotation tables constructed using RGI and manual curation; and mapping gene ARO accessions to drugs and drugs classes. (c) In categorizing drugs, agrNorm reports the immediate child of the ‘antibiotic molecule’ node in the ARO* + + ## argNorm workflow *Schematic illustration of argNorm workflow through a Resfinder output example: mapping gene names in the ARG annotation outputs to gene names from the ARO mapped ARG databases and adding corresponding drug categorization, namely “confers resistance to immediate drug class” and “overall category of drug class”, from the ARO ontology file.* diff --git a/docs/images/argnorm_overview.svg b/docs/images/argnorm_overview.svg new file mode 100644 index 0000000..c8cf90b --- /dev/null +++ b/docs/images/argnorm_overview.svg @@ -0,0 +1,738 @@ + + + + + + + + + + + + + + Genomes and + + + + + + + + + + + + + ARG annotation + hAMRonization + ResFinder + DeepARG + ARGs-OAP + ABRicate + AMRFinderPlus + + + + + + + + argNorm: normalization + + + + a + b + c + Inconsistent gene + + Mapping gene ARO + Mapping drugs to + accession to drugs + ARO:3000230 + ARO:3000230 + + + + drug classes + + + + metagenomes + and drug categorization + + + + + + + naming (argNorm input) + Mapping gene names + to ARO + ANT(2")-Ia + ant(2")-Ia + ant(2")-I + (AGly)aadB + ANT2-DPRIME + 2"-aminoglycoside + nucleotidyltransferase + aminoglycoside antibiotic + antibiotic molecule + tobramycin + confers_resistance_to_antibiotic + is_a + is_a + + + + + + + + + + + + + + + diff --git a/docs/index.md b/docs/index.md index 7058399..5a4e419 100644 --- a/docs/index.md +++ b/docs/index.md @@ -30,6 +30,11 @@ The `confers_resistance_to` column will contain ARO numbers of all the drug clas The `resistance_to_drug_classes` column will contain ARO numbers of the broader categories of the drug classes in the `confers_resistance_to` column (`ARO:3000007` for `beta lactam antibiotic` in the previous example). +### argNorm Overview +![argNorm Overview](./images//argnorm_overview.svg) + +*General overview of argNorm. (a) Genomes and metagenomes can be annotated using ARG annotation tools. argNorm accepts the outputs of these ARG annotation tools directly or after the outputs are processed by hAMRonization to perform ARO normalization and drug categorization. (b) The argNorm workflow includes: mapping gene names in the ARG annotation outputs to ARO accessions from ARO annotation tables constructed using RGI and manual curation; and mapping gene ARO accessions to drugs and drugs classes. (c) In categorizing drugs, agrNorm reports the immediate child of the ‘antibiotic molecule’ node in the ARO* + ## argNorm workflow *Schematic illustration of argNorm workflow through a Resfinder output example: mapping gene names in the ARG annotation outputs to gene names from the ARO mapped ARG databases and adding corresponding drug categorization, namely “confers resistance to immediate drug class” and “overall category of drug class”, from the ARO ontology file.*