Merge pull request #32 from EBISPOT/dev

sprintell · web-flow · commit 65270d4bb5eb · 2025-11-10T13:49:19.000Z
Dev
diff --git a/assets/images/nar-resource-paper-2024/Fig1.png b/assets/images/nar-resource-paper-2024/Fig1.png
diff --git a/assets/images/nar-resource-paper-2024/Fig2.png b/assets/images/nar-resource-paper-2024/Fig2.png
diff --git a/assets/images/nar-resource-paper-2024/Fig3.png b/assets/images/nar-resource-paper-2024/Fig3.png
diff --git a/assets/images/nar-resource-paper-2024/core-resources.png b/assets/images/nar-resource-paper-2024/core-resources.png
diff --git a/content/blog/association-file-update.md b/content/blog/association-file-update.md
@@ -0,0 +1,32 @@
+---
+title: Changes to associations tsv download file 
+author: GWAS Catalog
+description: If you use the GWAS Catalog “All associations” tsv download file, you may have noticed we’ve made some changes.The GWAS Catalog recently passed an incredible milestone of >1m curated associations! This is a huge achievement for the genomics community. However, it presents challenges for some users in analysing the data, since the “All associations” file now has more
+slug: association-file-update
+img:
+date: 2025-11-10
+displayDate: Nov 10, 2025
+---
+
+If you use the GWAS Catalog “All associations” tsv download file, you may have noticed we’ve made some changes.
+
+The GWAS Catalog recently passed an incredible milestone of >1m curated associations! This is a huge achievement for the genomics community. However, it presents challenges for some users in analysing the data, since the “All associations” file now has more than 1m rows. 
+
+You now have a choice of two formats for the v1 and v2 “all associations” files:
+
+1. File now provided as a compressed .zip; data format unchanged.
+2. Data split into multiple smaller files, and compressed together. This split file is divided by publication year, with a separate file for each year from 2023 onwards, and pre-2023 data in a single file.
+
+The split file (2) facilitates analysis for users of Excel or other software which cannot handle >1m rows. Please note that data may continue to be added for previous years - you are advised to always work with the latest version of the complete file set. 
+
+The files can be downloaded from the ftp links listed on the [file downloads page](https://www.ebi.ac.uk/gwas/docs/file-downloads). 
+
+If you’re trying to download the file programmatically for processing, we advise you do so from our [public FTP](https://ftp.ebi.ac.uk/pub/databases/gwas/releases/latest/). The previously available endpoint 
+ebi.ac.uk/gwas/api/search/downloads/full was intended for manual access and has been deprecated. 
+
+To access subsets of the data, e.g. all associations for a given trait (e.g. “cancer”), you’re advised to either:
+- Use the website to navigate to your data type of interest and then click “download Catalog data” to download relevant associations
+- Use our recently updated [REST API](https://www.ebi.ac.uk/gwas/rest/api/v2/docs) for programmatic access
+
+*Want to receive updates like this directly to your inbox? Sign up for our low-volume mailing list by sending an e-mail to **gwas-announce-join@ebi.ac.uk** with subject heading "subscribe"*
+
diff --git a/content/blog/background-trait-update.md b/content/blog/background-trait-update.md
@@ -1,10 +1,11 @@
 ---
 title: Trait annotation in the GWAS Catalog
 author: Elliot Sollis
-date: August 3, 2021
 description: Each study in the GWAS Catalog investigates the association between variants in the human genome and a particular trait or phenotypic characteristic. For each study, we annotate the trait in two ways, a reported trait that reflects the author’s description of the disease or phenotypic characteristic under investigation. This is a free text description and sometimes. 
 slug: background-trait-update
 img: blog-1.jpg
+date: 2021-08-03
+displayDate: Aug 3, 2021
 ---
 
 Each study in the GWAS Catalog investigates the association between variants in the human genome and a particular trait or phenotypic characteristic.
@@ -151,4 +152,4 @@ The changes affect some trait terms more than others. Here are some of the terms
 
 ## Questions and feedback
 
-If you have any questions or comments about this change, please contact us as gwas-info@ebi.ac.uk.
+If you have any questions or comments about this change, please contact us as gwas-info@ebi.ac.uk.
diff --git a/content/blog/cohorts-now-available.md b/content/blog/cohorts-now-available.md
@@ -1,10 +1,11 @@
 ---
 title: Cohorts now available in the GWAS Catalog
 author: GWAS Catalog team
-date: Nov 14, 2023
 description: We are pleased to announce our latest data release includes a new version of the Catalog studies downloads containing additional fields describing the discovery stage (genome-wide) cohorts used in each study (see below for more details), and clearer information on the availability of full genomewide summary statistics. 
 slug: cohorts-now-available
 img: blog-1.img
+date: 2023-11-14
+displayDate: Nov 14, 2023
 ---
 We are pleased to announce our latest data release includes a new version of the Catalog studies downloads containing additional fields describing the discovery stage (genome-wide) cohorts used in each study (see below for more details), and clearer information on the availability of full genomewide summary statistics. 
 
diff --git a/content/blog/everything-you-need-to-know-about-the-new-gwas-catalog.md b/content/blog/everything-you-need-to-know-about-the-new-gwas-catalog.md
@@ -1,10 +1,11 @@
 ---
 title: Everything you need to know about the new GWAS Catalog
 author: Annalisa Buniello
-date: Jun 13, 2018
 description: Genetic evidence could double the rate of success in drug targets identification - so the scientific community predicts. With this in mind, it is crucial for Open Targets to be able to feed as many SNP-trait associations as possible into its pipeline for systematic target identification and validation.
 slug: everything-you-need-to-know-about-the-new-gwas-catalog
 img: blog-1.jpg
+date: 2018-03-13
+displayDate: Jun 13, 2018
 ---
 
 Genetic evidence could double the rate of success in drug targets identification - so the scientific community predicts. With this in mind, it is crucial for Open Targets to be able to feed as many SNP-trait associations as possible into its pipeline for systematic target identification and validation.
diff --git a/content/blog/gwas-ssf-release.md b/content/blog/gwas-ssf-release.md
@@ -1,11 +1,11 @@
 ---
 title: New submissions standard - release date
 author: GWAS Catalog team
-date: 22 March 2023
 description: Next month the GWAS Catalog is switching to a NEW summary statistics format. Find out more about what this means for submitters and consumers of summary statistics
 slug: gwas-ssf-release
 img: blog-1.jpg
-
+date: 2023-03-22
+displayDate: March 22, 2023
 ---
 
 ## The new summary statistics format is coming - what you need to know
diff --git a/content/blog/gwas-ui-labs-release.md b/content/blog/gwas-ui-labs-release.md
@@ -1,10 +1,11 @@
 ---
 title: GWAS Catalog web search updates - help us with testing
 author: GWAS Catalog team
-date: 5 May 2023
 description: We are pleased to announce the release of a new version of the GWAS Catalog web search interface, which is available for testing at www.ebi.ac.uk/gwas/labs. Here is a guide to the main differences you will see.
 slug: gwas-ui-labs-release
 img: blog-1.jpg
+date: 2023-05-05
+displayDate: 5 May 2023
 ---
 
 # New GWAS web search interface ready for testing
diff --git a/content/blog/gwas-ui-production-release-2023.md b/content/blog/gwas-ui-production-release-2023.md
@@ -1,10 +1,11 @@
 ---
 title: GWAS Catalog web search - new release!
 author: GWAS Catalog team
-date: 12 July 2023
 description: We are pleased to announce the release of a new version of the GWAS Catalog web search interface, which is now in production. Here is a guide to the main differences you will see.
 slug: gwas-ui-production-release-2023
 img: blog-1.jpg
+date: 2023-07-12
+displayDate: 12 July 2023
 ---
 
 # New GWAS web search interface
diff --git a/content/blog/nar-resource-paper-2024.md b/content/blog/nar-resource-paper-2024.md
@@ -0,0 +1,40 @@
+---
+title: Our new resource update paper is out in Nucleic Acids Research!
+author: GWAS Catalog team
+description: We are very happy to announce the GWAS Catalog’s latest resource update paper in Nucleic Acids Research! We discuss standards for reusability, sustainability and diversity, new software features, and more.... 
+slug: nar-resource-paper-2024
+img: ...
+date: 2024-11-20
+displayDate: Nov 20, 2024
+---
+**We're happy to announce the GWAS Catalog’s [latest resource update paper](https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkae1070/7893318) in Nucleic Acids Research!**
+
+<article-image src="nar-resource-paper-2024/graphical-abstract.png" alt="gwas-catalog"></article-image>
+
+Here’s a hint of what you can find inside:
+
+The **GWAS-SSF standard** for full genome-wide summary statistics data and metadata has been fully implemented in our submission pipeline. More than 30k files have been submitted containing ALL mandatory data & metadata fields, on top of 50k files in the previous format.  We’ve also scaled our **harmonisation pipeline** to keep up with the increased rate of data submission - now 92% of all summary statistics with the necessary data content have a [harmonised version](https://www.ebi.ac.uk/gwas/docs/methods/summary-statistics#_directories)  available. 
+
+We have seen a huge growth in **molecular quantitative trait GWAS** (proteomic, lipidomic & metabolomic measurements) and are working with our colleagues at the Experimental Factor Ontology to improve mapping to chemical entities. 
+<article-image src="nar-resource-paper-2024/Fig1.png" alt="molecular-gwas"></article-image>
+
+New features enable faster page loading and allow you to easily find **GxE studies** in our website and download files, preparing the way for anticipated growth in GxE data is anticipated to grow as the scale of exposome data expands. Thanks to funding from the [Human Ecosystems Transversal Theme](https://www.embl.org/about/info/human-ecosystems/) at EMBL-EBI to enable this new feature!
+<article-image src="nar-resource-paper-2024/Fig2.png" alt="gwas-catalog-new-software"></article-image>
+
+
+The **lack of diversity** in genomics data continues to be an issue. We share our thoughts on how to enable monitoring of diversity and inclusion in GWAS studies while taking care that the **language** we use to describe populations does not lead to misuse. [New documentation and terminology](https://www.ebi.ac.uk/gwas/population-descriptors) (labels instead of categories) guide our users towards correct interpretation.
+Our analysis found that only around 50% of GWAS samples reported in the literature are being defined by genetic similarity measures, of those less than half clearly described a reference panel.  
+<article-image src="nar-resource-paper-2024/SupFig3.png" alt="gwas-catalog"></article-image>
+
+UKB is still the most used cohort in GWAS, accounting for around 30% of all studies in the Catalog! Unfortunately 70% of these restrict analysis to samples with the European population label, losing a significant amount of diversity. New inclusion of **cohort** names in Catalog data now enables this analysis, and in future linking out to rich cohort metadata. 
+<article-image src="nar-resource-paper-2024/Fig3.png" alt="gwas-catalog-diversity"></article-image>
+
+
+Finally, we are now recognised as a [Global Biodata Core Resource](https://globalbiodata.org/what-we-do/global-core-biodata-resources/list-of-current-global-core-biodata-resources/) and [Elixir Core Data resource](https://elixir-europe.org/platforms/data/core-data-resources)!
+<article-image src="nar-resource-paper-2024/core-resources.png" alt="gwas-catalog-diversity"></article-image>
+
+
+Read the full article, *[Cerezo et al 2024](https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkae1070/7893318)*, open access at NAR.
+
+
+Comments, feedback…? Contact us via gwas-info@ebi.ac.uk
diff --git a/content/blog/new-standard-for-gwas-summary-statistics.md b/content/blog/new-standard-for-gwas-summary-statistics.md
@@ -1,10 +1,11 @@
 ---
 title: A new standard for GWAS summary statistics
 author: Laura Harris
-date: July 20, 2022
 description: Today we are very pleased to share our manuscript describing a new standard format for GWAS summary statistics, GWAS-SSF. The work towards this goal began in 2017 when we began to host summary statistics in the GWAS Catalog. It rapidly became apparent that summary statistics were formatted in a whole host of different ways, with only a few features in common between them, and little has changed since, with a recent analysis of 327 summary statistics
 slug: new-standard-for-gwas-summary-statistics
 img: blog-1.jpg
+date: 2022-07-20
+displayDate: July 20, 2022
 ---
 
 Today we are very pleased to share our manuscript describing a new standard format for GWAS summary statistics, [GWAS-SSF](https://www.biorxiv.org/content/10.1101/2022.07.15.500230v1). The work towards this goal began in 2017 when we began to host summary statistics in the GWAS Catalog. It rapidly became apparent that summary statistics were formatted in a whole host of different ways, with only a few features in common between them, and little has changed since, with a [recent analysis](https://academic.oup.com/bioinformatics/article/37/23/4593/6380562) of 327 summary statistics files finding over 100 unique formats. We were about to launch the GWAS Catalog author submission system and needed to enforce a standard format as QC on submissions, and to ensure that submitted data could be passed through our harmonisation pipeline. So we quickly developed a [minimal standard format](https://pubmed.ncbi.nlm.nih.gov/30445434/) based on the most commonly included fields, with variant ID/genomic location and p-value as mandatory fields, and standard headers for other fields such as beta and CI. This was enough for our goal of getting data into the GWAS Catalog. But we heard many consumers of the data complain that datasets with the minimum mandatory fields did not meet their requirements, for example to use the data for Mendelian randomisation or to generate polygenic scores. We needed to encourage our submitters to share their data more fully. A second issue is that while the GWAS Catalog curates metadata from the literature, there is no standard for GWAS metadata reporting, resulting in missing data that limits re-use of the summary statistics.
diff --git a/content/blog/open-sharing-of-cancer-summary-statistics.md b/content/blog/open-sharing-of-cancer-summary-statistics.md
@@ -1,10 +1,11 @@
 ---
 title: Sharing is caring, why we need more freely available cancer GWAS summary statistics
 author: Annalisa Buniello
-date: March 11, 2021
 description: The NHGRI-EBI GWAS Catalog is a central resource for the Genome Wide Association Study (GWAS) community, demonstrating the benefit of expert data curation and integration of full p-value GWAS summary statistics into a central repository for variant-trait associations. For more than 10 years, the Catalog has aimed to make GWAS data FAIR (Findable, Accessible, Interoperable and Re-usable)
 slug: open-sharing-of-cancer-summary-statistics
 img: blog-1.jpg
+date: 2021-03-11
+displayDate: March 11, 2021
 ---
 
 The [NHGRI-EBI GWAS Catalog](https://www.ebi.ac.uk/gwas/) is a central resource for the Genome Wides Association Study (GWAS) community, demonstrating the benefit of expert data curation and integration of full p-value GWAS summary statistics into a central repository for variant-trait associations.
diff --git a/content/blog/rest-api-v2-release.md b/content/blog/rest-api-v2-release.md
@@ -0,0 +1,23 @@
+---
+title: The GWAS Catalog REST API Version 2.0 is here!
+author: Laura Harris
+description: The GWAS Catalog has released a completely redesigned REST API, supporting programmatic access to the curated data. Find out more about the new features and timeline for switching over.  
+slug: rest-api-v2-release
+img: blog-1.jpg
+date: 2025-08-11
+displayDate: 11 August 2025
+---
+
+We’re pleased to announce the release of the GWAS Catalog REST API, Version 2.0!
+
+Supporting programmatic access to the GWAS Catalog’s curated dataset, the REST API has been completely redesigned based on user feedback, to facilitate a robust and resilient mechanism for delivering the growing volume of data. The new design aims to provide all the tools you need to perform complex queries and effectively integrate GWAS Catalog data services into your scientific pipelines, scripts, and web applications. 
+
+New endpoints (including publications, genes, genomic context, and ancestries), allow users to create previously complex queries in a dynamic and simple manner. More data is exposed such as cohorts, background traits, full free text sample description, terms/license and other fields, which were previously accessible only in the GUI and downloads. Ontology powered search functionality, more search and filtering features, and additional integrated data from other sources such as Ensembl help to provide a richer user experience. 
+
+We’ve also made technical improvements to increase resiliency and scaling, applying industry standard architectural standards. 
+
+Extensive documentation is available, including a detailed reference manual containing endpoints, schemas, parameters, syntax and more, and including a visual, interactive interface for exploring and testing the endpoints. If you’re new to programmatic analysis, you might like to check out our Jupyter notebook tutorial. To get started, please go to our [documentation page](https://www.ebi.ac.uk/gwas/docs/api) where you’ll find links to all of these.  The previous API version will be available alongside v2 until May 2026, so you’ll need to switch over your pipelines before then.  
+
+Thanks to all our testers and survey respondents, and a special thank you to our super-user Ramiro Magno, developer of the gwasrapidd package, for making this work possible! 
+
+As always, if you have any questions, please reach out to our helpdesk gwas-info@ebi.ac.uk.
diff --git a/content/blog/ten-years-of-the-gwas-catalog-past-present-and-future.md b/content/blog/ten-years-of-the-gwas-catalog-past-present-and-future.md
@@ -1,7 +1,8 @@
 ---
 title: Ten years of the GWAS Catalog – Past, present and future
 author:  Laura Harris (GWAS Catalog) and Astrid Gall (Ensembl Outreach)
-date: Jun 28, 2018
+date: 2018-06-28
+displayDate: Jun 28, 2018
 description: This year marks a special anniversary for the GWAS Catalog, as we have reached ten years since our launch in 2008. The GWAS Catalog is a widely used publicly available resource of all published human genome wide association studies (GWAS) and association results. Each GWAS study contains a wealth of information which is effectively inaccessible to researchers 
 slug: ten-years-of-the-gwas-catalog-past-present-and-future
 img: blog-1.jpg
diff --git a/pages/index.vue b/pages/index.vue
@@ -18,7 +18,7 @@
                                 <div class="column large-12 medium-12" style="padding: 0 5px; margin-bottom: 10px;">
                                     <div class="card-2 card-body card-3b my-card">
                                         <h3 class="gwas-card-head">{{ article.title }}
-                                            <em style="float:right; font-size:11px; color:#347883;"> {{article.date}} By {{ article.author }} </em>
+                                            <em style="float:right; font-size:11px; color:#347883;"> {{article.displayDate}} By {{ article.author }} </em>
                                         </h3>
                                         <div class="gwas-card-body-one" style="margin-top:-15px;">
                                             <p class="mg-t-0">{{ article.description }} ... </p>
@@ -51,8 +51,8 @@ export default {
 
   async asyncData({ $content, params }) {
     const articles = await $content("blog", params.slug)
-      .only(["title", "author", "date", "description", "img", "slug"])
-      .sortBy("createdAt", "desc")
+      .only(["title", "author", "description", "img", "slug", "date", "displayDate"])
+      .sortBy("date", "desc")
       .fetch();
 
     return {
