From e7ffaead76181f5f45ce95c7fd8dd1f8541f594d Mon Sep 17 00:00:00 2001 From: Chris Hunter Date: Thu, 21 Sep 2023 15:23:30 +0100 Subject: [PATCH] Update README.md replaced "environmental package" with the newly agreed terminology "extension", but only in the main part of the document. The general background section lower down still contains the old terminology. I think we should consider removing that section entirely in favour of a link pointing to the gensc.org website. --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 7955e1a4eb..5b85e74c09 100644 --- a/README.md +++ b/README.md @@ -14,13 +14,13 @@ The current standards can be browsed at https://genomicsstandardsconsortium.gith To support existing implementers who have been using previous Excel-based versions of MIxS, we have provided a manually created [Excel workbook](mixs/excel) with the same format as MIxS 5. However, we highly recommend using one of the machine-readable artifacts available in the [mixs](mixs) folder. -MIxS is divided into checklists and packages. +MIxS is divided into checklists and extensions (previously known as environmental packages). **[Checklists](https://genomicsstandardsconsortium.github.io/mixs/#checklists)** include the required, recommended, and optional metadata fields for a specific type of sequence: genome, metagenome, marker gene, or xxx. For genomic sequences (MIGS), there are specific checklists for different taxa groups (Eukaryotes, Bacteria, Viruses, and Plants as hosts). -**[Packages](https://genomicsstandardsconsortium.github.io/mixs/#packages)** supplement checklists by providing additional terms to describe specific environments from which a sample was collected. For example, the Agriculture package has a number of terms to record attributes specific to agricultural environments. +**[Extensions](https://genomicsstandardsconsortium.github.io/mixs/#packages)** supplement checklists by providing additional terms to describe specific environments from which a sample was collected. For example, the Agriculture extension has a number of terms to record attributes specific to agricultural environments. -Packages can be used in conjunction with any checklist, so, for example, if you generate metagenomic sequences from an agricultural environment, you would use MIMS + the Agriculture package. All possible [combinations](https://genomicsstandardsconsortium.github.io/mixs/#combinations) of checklists and packages are available on the web browser. +Extensions can be used in conjunction with any checklist, so, for example, if you generate metagenomic sequences from an agricultural environment, you would use MIMS + the Agriculture extension. All possible [combinations](https://genomicsstandardsconsortium.github.io/mixs/#combinations) of checklists with extensions are available on the web browser. **To request changes to the MIxS standards, please use the [issue tracker](https://github.com/GenomicsStandardsConsortium/mixs/issues) in this repo.**