updates to landing page

Author: nsheff

docs/README.md

@@ -1,27 +1,32 @@
-# Refget specifications
 
-## What is refget?
+![GA4GH logo](img/ga4gh-logo.png){ width="300" align=right }
 
-Refget is a protocol for identifying and distributing reference biological sequences.
-It currently consists of 2 standards:
 
-1. [Refget sequences](sequences.md): a GA4GH-approved standard for individual sequences
-2. [Refget sequence collections](seqcol.md): a standard for collections of sequences, under review 
+# Refget specifications
 
-<img src="img/seqcol_abstract_simple.svg" alt="Refget abstract" class="img-responsive">
+## What is refget?
 
+Refget is a set of GA4GH standards for identifying and distributing reference biological sequences.
+It consists of these standards:
 
-## What is the refget sequences standard?
 
-The original refget standard, now called *Refget sequences*, handles sequences only.
-Refget sequences enables access to reference sequences using an identifier derived from the sequence itself.
+| Standard      | Description                          | Status |
+| ----------- | ------------------------------------ | |
+| [Refget sequences](sequences.md)      | For individual sequences  | :white_check_mark: v1.0 Approved in 2021 <br>:white_check_mark:&nbsp;v2.0&nbsp;Approved in 2024 |
+| [Refget sequence collections](seqcol.md)      | For collections of sequences | :white_check_mark: v1.0 Approved in 2025 |
+| Refget pangenomes  | For collections of sequence collections | :fontawesome-solid-gears: Currently in process |
 
+## What is the main purpose of the refget project?
 
-## What is the refget sequence collections standard?
+Refget standards help to **identify**, **retrieve**, and **compare** reference sequences, like a reference genome. Key principles include:
 
-*Refget sequence collections*, or `seqcol` for short, standardizes unique identifiers for collections of sequences. Seqcol identifiers can be used to identify genomes, transcriptomes, or proteomes -- anything that can be represented as a collection of sequences. The seqcol protocol provides:
+- Reference data, including sequences and collections of sequences, are identified using cryptographic digest-based identifiers that are **derived from the data itself**. This allows reference data to be identified without requiring a centralized accessioning authority.
+- Refget standards can be used for any type of sequences: DNA, RNA, protein, etc -- anything that can be represented as a string of characters.
+- Refget standards also specify **retrieval APIs**, providing a mechanism for retrieving a sequence or collection if you have its identifier.
+- Refget sequence collections also provides a programmatic approach to assessing compatibility among sequence collections.
 
-- implementations of an algorithm for computing sequence identifiers;
-- a lookup service to retrieve sequences given a seqcol identifier
-- programmatic approach to assessing compatibility among sequence collections.
+This image shows how the Refget Sequences standard is used by the Sequence Collections standard. First, sequences are digested to yield a deterministic identifier. These sequence identifiers are then used, together with their names, to create an identifier for a collection.
 
+<figure>
+<img src="img/seqcol_abstract_simple.svg" alt="Refget abstract" class="img-responsive">
+</figure>

docs/img/GA-logo.png renamed to docs/img/ga4gh-logo-dark-bg.png

@@ -1,29 +1,14 @@
 ---
-title: Seqcol specification version 0.1.0
+title: Refget Sequence Collections v1.0.0
 ---
 
-<!-- Table of contents: 
-* The generated Toc will be an unordered list
-{:toc} -->
-
-# Seqcol specification version 0.1.0
-
-<!-- Table of contents:
-
-[TOC] -->
-
-## Specification version
-
-This specification is in **DRAFT** form. This is **NOT YET AN APPROVED GA4GH specification**. This document is **formal technical explanation for implementers**. See also:
-
-- [Architectural decision record](decision_record.md), a chronological record of spec decisions.
-- [Sequence collection rationale](seqcol_rationale.md), motivation for our major design decisions.
+# Refget Sequence Collections v1.0.0
 
 ## Introduction
 
 Reference sequences are fundamental to genomic analysis.
 To make their analysis reproducible and efficient, we require tools that can identify, store, retrieve, and compare reference sequences.
-The primary goal of the *Sequence Collections* (seqcol) project is **to standardize identifiers for collections of sequences**.
+The primary goal of the *Refget Sequence Collections* (seqcol) project is **to standardize identifiers for collections of sequences**.
 Seqcol can be used to identify genomes, transcriptomes, or proteomes -- anything that can be represented as a collection of sequences.
 A common example and primary use case of sequence collections is for a reference genome, so this documentation sometimes refers to reference genomes for convenience; really, it can be applied to any collection of sequences.
 
@@ -66,6 +51,10 @@ Building on refget, the sequence collections specification introduces foundation
 - **Genome browser integration**:  *As a genome browser, I use one sequence collection for the displayed coordinate system and want to check if a digest representing a given BED file's coordinate system is compatible with it.*  
 - **Annotating unknown references**:  *As a data processor, I encounter input data without reference genome information and want to generate a sequence collection digest to attach, enabling further processing with seqcol features.*  
 
+## Architectural decision record
+
+For a chronological record of decisions related to this specification, see the [Architectural decision record](decision_record.md).
+
 ## Definitions of key terms
 
 ### General terms

docs/img/ga4gh-logo.png

@@ -4,7 +4,7 @@ title: refget protocol
 suppress_footer: true
 ---
 
-# Refget API Specification v2.0.0
+# Refget Sequences v2.0.0
 
 ## Introduction
 

docs/seqcol.md

@@ -34,7 +34,7 @@ navbar:
     href: contributing
 
 theme:
-  logo: img/seqcol_logo.svg
+  logo: img/ga4gh-logo-dark-bg.png
   favicon: img/seqcol_logo.svg
   name: material
 
@@ -54,9 +54,14 @@ extra_css:
   - stylesheets/extra.css
 
 markdown_extensions:
+  - attr_list
+  - md_in_html
   - admonition
   - pymdownx.highlight:
       use_pygments: true
+  - pymdownx.emoji:
+      emoji_index: !!python/name:material.extensions.emoji.twemoji
+      emoji_generator: !!python/name:material.extensions.emoji.to_svg
   - pymdownx.superfences:
       custom_fences:
         - name: mermaid