Restructure repository

- moved each spec into a subfolder
- removed old no longer used files for previous setup
- updated some examples

Author: nsheff

.readthedocs.yaml

@@ -1,11 +1,23 @@
 # Refget Docs
 
-This is the repository for documentation of the GA4GH Refget specifications, which includes both Refget Sequences and Refget Sequence Collections. These docs are written using `mkdocs` using Material for Mkdocs and hosted using GitHub Pages.
+This is the repository for documentation of the GA4GH Refget specifications, which includes both Refget Sequences and Refget Sequence Collections.
+These docs are written using `mkdocs`, themed with Material for Mkdocs, and hosted using GitHub Pages.
 
-## Building locally
+View the rendered documentation at <https://ga4gh.github.io/refget/>.
 
-Switch to the branch you want to build and use either `mkdocs build` or `mkdocs serve` to render the docs.
+## Navigating this repository
+
+The documentation is stored in the `/docs` folder, with a subfolder corresponding to each of the 3 refget standards.
+The main text content for each specifation can be found in these files:
+
+- Sequences: [/docs/sequences/README.md](/docs/sequences/README.md)
+- Sequence collections: [/docs/seqcols/README.md](/docs/seqcols/README.md)
+- Pangenomes: [/docs/pangenomes/README.md](/docs/pangenomes/README.md)
 
 ## Contributing
 
-Edit the files in the `docs` subdirectory. Please submit a PR to the appropriate branch for the version you are editing.
+To contribute, edit the files in the `docs` subdirectory. Please submit any changes for review via PR.
+
+## Building locally
+
+Switch to the branch you want to build and use either `mkdocs build` or `mkdocs serve` to render the docs.

README.md

@@ -1,27 +1,4 @@
-
-<style>
-img.title {
-  float: right;
-  max-width: 50%; /* Adjust as needed */
-  height: auto;
-  margin-left: 20px; /* Space between text and image */
-}
-
-.container {
-  overflow: hidden; /* Ensures the float does not affect the container height */
-}
-
-@media (max-width: 768px) {
-  img.title {
-    float: none; /* Removes float on small screens */
-    display: block;
-    margin: 10px auto; /* Centers the image */
-    max-width: 80%; /* Prevents it from being too large */
-  }
-}
-</style>
-
-<div class="container">
+<div class="title container">
 <img src="img/ga4gh-logo.png" class="title" width="300">
 <h1>Refget specifications</h1>
 </div>

docs/README.md

@@ -1,9 +1,17 @@
 # Citation information
 
+If you use any of the refget standards or software in your work, please cite us.
 
-Refget sequences was described in:
+## Refget sequences
 
-Yates AD; Adams J; Chaturvedi S; Davies RM; Laird M; Leinonen R; Nag R; Sheffield N.; Hofmann O & Keane TM.
+Please cite:
+
+Yates AD; Adams J; Chaturvedi S; Davies RM; Laird M; Leinonen R; Nag R; Sheffield NC; Hofmann O & Keane TM.
 **Refget: standardized access to reference sequences**. *Bioinformatics*, 2022, 38, 299-300. DOI: [10.1093/bioinformatics/btab524](https://dx.doi.org/10.1093/bioinformatics/btab524)
 
-Sequence collections has not been published.
+## Sequence collections
+
+Sequence collections publication is pending. An initial implementation that formed the groundwork for the current standard was described in:
+
+Stolarczyk M; Xue B; Sheffield NC.
+**Identity and compatibility of reference genome resources**. *NAR Genomics and Bioinformatics*, Volume 3, Issue 2, June 2021, lqab036. DOI: <https://doi.org/10.1093/nargab/lqab036>

docs/citation.md

@@ -1,5 +1,6 @@
 
 # Seqcol API service
 
-You can find a semi-functional draft implementation of the API available at: [https://seqcolapi.databio.org](https://seqcolapi.databio.org)
+You can find a demo implementation at [https://refget.databio.org](https://refget.databio.org).
 
+As of 2025, additional implementations are planned or under development at ENA and Ensembl.

theme_dir/seqcol_abstract.svg renamed to docs/img/seqcol_abstract.svg

@@ -0,0 +1,3 @@
+# Refget pangenomes
+
+TBD

docs/implementation_api.md

@@ -0,0 +1,35 @@
+{
+    "description": "A collection of biological sequences.",
+    "type": "object",
+    "properties": {
+      "lengths": {
+        "type": "array",
+        "collated": true,
+        "description": "Number of elements, such as nucleotides or amino acids, in each sequence.",
+        "items": {
+          "type": "integer"
+        }
+      },
+      "names": {
+        "type": "array",
+        "collated": true,
+        "description": "Human-readable labels of each sequence (chromosome names).",
+        "items": {
+          "type": "string"
+        }
+      },
+      "sequences": {
+        "type": "array",
+        "collated": true,
+        "items": {
+          "type": "string",
+          "description": "Refget sequences v2 identifiers for sequences."
+        }
+      }
+    },
+    "required": ["names", "lengths", "sequences"],
+    "ga4gh": {
+      "inherent": ["names", "sequences"]
+    }
+  }
+