From 7719ed882dc84f7401b1802a60b68edd99831bab Mon Sep 17 00:00:00 2001 From: Heesu Kim Date: Thu, 30 Jan 2025 18:25:34 -0500 Subject: [PATCH 01/10] add news markdowns --- ...2024-05-15-CFDE-Monthly-Webinar-Series-Page.md | 12 ++++++++++++ ...ype-Added-to-the-CFDE-Workbench-Data-Matrix.md | 9 +++++++++ .../2024-06-21-Data-Assets-Accessible-via-DRS.md | 11 +++++++++++ ...Illuminating-the-Druggable-Genome-(IDG)-DCC.md | 12 ++++++++++++ .../2024-07-08-SenNet-Landmark-Publication.md | 11 +++++++++++ ...oth-at-the-Festival-of-Genomics-and-BioData.md | 11 +++++++++++ .../news/2024-07-09-FAIRshake-Integration.md | 9 +++++++++ ...0-Analyze-a-Gene-with-DD-Knowledge-Graph-UI.md | 10 ++++++++++ ...ent-Workshop-A-Discussion-of-Data-Resources.md | 11 +++++++++++ ...-12-Tutorial-Video-about-the-CFDE-Workbench.md | 11 +++++++++++ src/pages/news/2024-07-17-C2M2-Integration.md | 10 ++++++++++ .../2024-07-24-The-2024-HuBMAP-Fall-Hackathon.md | 10 ++++++++++ src/pages/news/2024-07-25-Keycloak-Upgrade.md | 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11 +++++++++++ ...elligent-Systems-for-Molecular-Biology-2025.md | 11 +++++++++++ src/pages/news/index.md | 6 ++++++ 45 files changed, 490 insertions(+) create mode 100644 src/pages/news/2024-05-15-CFDE-Monthly-Webinar-Series-Page.md create mode 100644 src/pages/news/2024-06-12-Apps-URLs-Metadata-Type-Added-to-the-CFDE-Workbench-Data-Matrix.md create mode 100644 src/pages/news/2024-06-21-Data-Assets-Accessible-via-DRS.md create mode 100644 src/pages/news/2024-07-02-June-2024-CFDE-Webinar-by-the-Illuminating-the-Druggable-Genome-(IDG)-DCC.md create mode 100644 src/pages/news/2024-07-08-SenNet-Landmark-Publication.md create mode 100644 src/pages/news/2024-07-08-The-CFDE-DRC-and-KC-booth-at-the-Festival-of-Genomics-and-BioData.md create mode 100644 src/pages/news/2024-07-09-FAIRshake-Integration.md create mode 100644 src/pages/news/2024-07-10-Analyze-a-Gene-with-DD-Knowledge-Graph-UI.md create mode 100644 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src/pages/news/2025-01-13-CFDE-Centers-Page-Added-to-the-Information-Portal.md create mode 100644 src/pages/news/2025-01-14-The-Multi-Omics-AI-Driven-Gene-Set-Analysis-with-GeneSetCart-Seminar-Added.md create mode 100644 src/pages/news/2025-01-17-CFDE-at-American-Society-of-Human-Genetics-2025.md create mode 100644 src/pages/news/2025-01-17-CFDE-at-Bio-IT-World-Boston-2025.md create mode 100644 src/pages/news/2025-01-17-CFDE-at-Intelligent-Systems-for-Molecular-Biology-2025.md create mode 100644 src/pages/news/index.md diff --git a/src/pages/news/2024-05-15-CFDE-Monthly-Webinar-Series-Page.md b/src/pages/news/2024-05-15-CFDE-Monthly-Webinar-Series-Page.md new file mode 100644 index 0000000..87da3d4 --- /dev/null +++ b/src/pages/news/2024-05-15-CFDE-Monthly-Webinar-Series-Page.md @@ -0,0 +1,12 @@ +--- +layout: '@/layouts/News.astro' +date: 2024-05-15 +portal: Information Portal +tags: + - Training & Outreach + - CFDE Webinar Series +title: CFDE Monthly Webinar Series Page +description: The CFDE Workbench now has a CFDE monthly webinar series page. This page provides information about webinars, including video recordings, summaries, presenters, and details about upcoming webinars. +img: https://cfde-drc.s3.us-east-2.amazonaws.com/assets/img/news-webinar.png +link: https://cfde-drc.s/info/training_and_outreach/cfde-webinar-series +--- diff --git a/src/pages/news/2024-06-12-Apps-URLs-Metadata-Type-Added-to-the-CFDE-Workbench-Data-Matrix.md b/src/pages/news/2024-06-12-Apps-URLs-Metadata-Type-Added-to-the-CFDE-Workbench-Data-Matrix.md new file mode 100644 index 0000000..c663adf --- /dev/null +++ b/src/pages/news/2024-06-12-Apps-URLs-Metadata-Type-Added-to-the-CFDE-Workbench-Data-Matrix.md @@ -0,0 +1,9 @@ +--- +layout: '@/layouts/News.astro' +date: 2024-06-12 +portal: Data Portal +title: Apps URLs Metadata Type Added to the CFDE Workbench Data Matrix +description: Apps URLs added to the CFDE Data Matrix providing URLs to apps developed by DCCs. +img: https://cfde-drc.s3.us-east-2.amazonaws.com/assets/img/news-apps-urls.png +link: https://cfde-drc.s/data/matrix +--- diff --git a/src/pages/news/2024-06-21-Data-Assets-Accessible-via-DRS.md b/src/pages/news/2024-06-21-Data-Assets-Accessible-via-DRS.md new file mode 100644 index 0000000..3aaa8fd --- /dev/null +++ b/src/pages/news/2024-06-21-Data-Assets-Accessible-via-DRS.md @@ -0,0 +1,11 @@ +--- +layout: '@/layouts/News.astro' +date: 2024-06-21 +portal: Data Portal +tags: + - Performance Improvement +title: Data Assets Accessible via DRS +description: All uploaded and approved assets digital objects on the CFDE Workbench are now accessible via DRS. +img: https://cfde-drc.s3.us-east-2.amazonaws.com/assets/img/news-drs.png +link: https://cfde-drc.s/info/documentation/C2M2#identifiers +--- diff --git a/src/pages/news/2024-07-02-June-2024-CFDE-Webinar-by-the-Illuminating-the-Druggable-Genome-(IDG)-DCC.md b/src/pages/news/2024-07-02-June-2024-CFDE-Webinar-by-the-Illuminating-the-Druggable-Genome-(IDG)-DCC.md new file mode 100644 index 0000000..bdb6f3d --- /dev/null +++ b/src/pages/news/2024-07-02-June-2024-CFDE-Webinar-by-the-Illuminating-the-Druggable-Genome-(IDG)-DCC.md @@ -0,0 +1,12 @@ +--- +layout: '@/layouts/News.astro' +date: 2024-07-02 +portal: Information Portal +tags: + - Training & Outreach + - CFDE Webinar Series +title: June 2024 CFDE Webinar by the Illuminating the Druggable Genome (IDG) DCC +description: CFDE webinar series video recordings, summaries, and presenter details delivered by Illuminating the Druggable Genome (IDG) Data Coordination Center were added to the Webinar section on the CFDE Workbench +img: https://cfde-drc.s3.us-east-2.amazonaws.com/assets/img/cfde-webinar-0624.jpg +link: https://cfde-drc.s/info/training_and_outreach/cfde-webinar-series +--- diff --git a/src/pages/news/2024-07-08-SenNet-Landmark-Publication.md b/src/pages/news/2024-07-08-SenNet-Landmark-Publication.md new file mode 100644 index 0000000..46d540e --- /dev/null +++ b/src/pages/news/2024-07-08-SenNet-Landmark-Publication.md @@ -0,0 +1,11 @@ +--- +layout: '@/layouts/News.astro' +date: 2024-07-08 +portal: Information Portal +tags: + - Publication +title: SenNet Landmark Publication +description: The SenNet DCC landmark publication recently appeared in Nature Reviews Molecular Cell Biology. It was added to the publication page of the CFDE Workbench. +img: https://cfde-drc.s3.us-east-2.amazonaws.com/assets/img/news-sennet-pub.png +link: https://cfde-drc.s/info/dcc/SenNet +--- diff --git a/src/pages/news/2024-07-08-The-CFDE-DRC-and-KC-booth-at-the-Festival-of-Genomics-and-BioData.md b/src/pages/news/2024-07-08-The-CFDE-DRC-and-KC-booth-at-the-Festival-of-Genomics-and-BioData.md new file mode 100644 index 0000000..f1785af --- /dev/null +++ b/src/pages/news/2024-07-08-The-CFDE-DRC-and-KC-booth-at-the-Festival-of-Genomics-and-BioData.md @@ -0,0 +1,11 @@ +--- +layout: '@/layouts/News.astro' +date: 2024-07-08 +portal: Information Portal +tags: + - Training & Outreach +title: The CFDE DRC and KC booth at the Festival of Genomics and BioData +description: The training and outreach event page was updated with an announcement about the CFDE participation in the Festival of Genomics and BioData scientific meeting. +img: https://cfde-drc.s3.amazonaws.com/assets/img/fog.png +link: https://cfde-drc.s/info/training_and_outreach/festival-of-genomics +--- diff --git a/src/pages/news/2024-07-09-FAIRshake-Integration.md b/src/pages/news/2024-07-09-FAIRshake-Integration.md new file mode 100644 index 0000000..588855f --- /dev/null +++ b/src/pages/news/2024-07-09-FAIRshake-Integration.md @@ -0,0 +1,9 @@ +--- +layout: '@/layouts/News.astro' +date: 2024-07-09 +portal: Data Portal +title: FAIRshake Integration +description: The data and metadata submission system was updated to support FAIR assessment of uploaded digital objects by the DCCs. The FAlRshake insignia is now displayed near each uploaded digital object. +img: https://cfde-drc.s3.us-east-2.amazonaws.com/assets/img/news-fairshake.png +link: https://cfde-drc.s/data/submit/uploaded +--- diff --git a/src/pages/news/2024-07-10-Analyze-a-Gene-with-DD-Knowledge-Graph-UI.md b/src/pages/news/2024-07-10-Analyze-a-Gene-with-DD-Knowledge-Graph-UI.md new file mode 100644 index 0000000..c2b6d12 --- /dev/null +++ b/src/pages/news/2024-07-10-Analyze-a-Gene-with-DD-Knowledge-Graph-UI.md @@ -0,0 +1,10 @@ +--- +layout: '@/layouts/News.astro' +date: 2024-07-10 +portal: Data Portal +tags: + - Data Query +title: Analyze a Gene with DD-Knowledge Graph UI +description: The Common Fund Data Ecosystem (CFDE) Data Distillery Knowledge Graph (DD-KG) partnership aims to establish a Knowledge Graph that integrates knowledge assertions from CFDE-affiliated Data Coordination Centers (DCCs). DD-KG-Ul is a web-based interface that enables users to efficiently query the DD-KG. Queries can range from simple single-term searches, revealing immediate neighboring terms, to more complex inquiries about two terms, showcasing the shortest paths between specified nodes or terms. CFDE DD-Knowledge Graph is now available from the gene page to query. +img: https://cfde-drc.s3.us-east-2.amazonaws.com/assets/img/news-ddkg.png +--- diff --git a/src/pages/news/2024-07-12-Community-Engagement-Workshop-A-Discussion-of-Data-Resources.md b/src/pages/news/2024-07-12-Community-Engagement-Workshop-A-Discussion-of-Data-Resources.md new file mode 100644 index 0000000..8cc7690 --- /dev/null +++ b/src/pages/news/2024-07-12-Community-Engagement-Workshop-A-Discussion-of-Data-Resources.md @@ -0,0 +1,11 @@ +--- +layout: '@/layouts/News.astro' +date: 2024-07-12 +portal: Information Portal +tags: + - Training & Outreach +title: 'Community Engagement Workshop: A Discussion of Data Resources' +description: 'A training and outreach event hosted by NIH Common Fund: Community Engagement Workshop: A Discussion of Data Resources (7/24/2024 - 7/25/2024) was added to the Training and Outreach page.' +img: https://cfde-drc.s3.us-east-2.amazonaws.com/assets/img/cfworkshop2024.jpg +link: https://cfde-drc.s/info/training_and_outreach +--- diff --git a/src/pages/news/2024-07-12-Tutorial-Video-about-the-CFDE-Workbench.md b/src/pages/news/2024-07-12-Tutorial-Video-about-the-CFDE-Workbench.md new file mode 100644 index 0000000..fdeacca --- /dev/null +++ b/src/pages/news/2024-07-12-Tutorial-Video-about-the-CFDE-Workbench.md @@ -0,0 +1,11 @@ +--- +layout: '@/layouts/News.astro' +date: 2024-07-12 +portal: Information Portal +tags: + - Training & Outreach +title: Tutorial Video about the CFDE Workbench +description: The tutorial video first travels through the Information Portal, covering participating programs, partnerships, training & outreach events, publications, and documentation. Next, the tutorial introduces how to query the Data Portal with examples of the search results and data types. The Data Portal also includes CFDE community-developed tools and workflows with use cases, a data and metadata submission system, and an LLM-powered chatbot. +img: https://cfde-drc.s3.us-east-2.amazonaws.com/assets/img/news-tutorial.png +link: https://www.youtube.com/watch?v=TAnKcNp2kdY +--- diff --git a/src/pages/news/2024-07-17-C2M2-Integration.md b/src/pages/news/2024-07-17-C2M2-Integration.md new file mode 100644 index 0000000..882ee02 --- /dev/null +++ b/src/pages/news/2024-07-17-C2M2-Integration.md @@ -0,0 +1,10 @@ +--- +layout: '@/layouts/News.astro' +date: 2024-07-17 +portal: Data Portal +tags: + - Data Ingestion +title: C2M2 Integration +description: C2M2 metadata search added to the search engine. +img: https://cfde-drc.s3.us-east-2.amazonaws.com/assets/img/news-c2m2-filter.png +--- diff --git a/src/pages/news/2024-07-24-The-2024-HuBMAP-Fall-Hackathon.md b/src/pages/news/2024-07-24-The-2024-HuBMAP-Fall-Hackathon.md new file mode 100644 index 0000000..4f03c54 --- /dev/null +++ b/src/pages/news/2024-07-24-The-2024-HuBMAP-Fall-Hackathon.md @@ -0,0 +1,10 @@ +--- +layout: '@/layouts/News.astro' +date: 2024-07-24 +portal: Information Portal +tags: + - Training & Outreach +title: The 2024 HuBMAP Fall Hackathon +description: A training and outreach event hosted by the HubMAP DCC was added to the event page. The 2024 HuBMAP Fall Hackathon will be held from September 20, 2024, to October 4, 2024. +img: https://cfde-drc.s3.us-east-2.amazonaws.com/assets/img/hubmap-fall2024.png +--- diff --git a/src/pages/news/2024-07-25-Keycloak-Upgrade.md b/src/pages/news/2024-07-25-Keycloak-Upgrade.md new file mode 100644 index 0000000..36a7349 --- /dev/null +++ b/src/pages/news/2024-07-25-Keycloak-Upgrade.md @@ -0,0 +1,15 @@ +--- +layout: '@/layouts/News.astro' +date: 2024-07-25 +portal: Cross Portal +tags: + - Account + - Security +title: Keycloak Upgrade +description: Keycloak is an open-source software for single sign-on with identity and access management. The CFDE Workbench portal login management was upgraded to support Keycloak integration. +supp_description: + - Sync user accounts across OAuth providers + - Support existing accounts + - Optimize existing user-related queries +img: https://cfde-drc.s3.us-east-2.amazonaws.com/assets/img/login.png +--- diff --git a/src/pages/news/2024-07-25-LINCS-Summer-Traniees-Virtual-Symposium-2024.md b/src/pages/news/2024-07-25-LINCS-Summer-Traniees-Virtual-Symposium-2024.md new file mode 100644 index 0000000..72d807e --- /dev/null +++ b/src/pages/news/2024-07-25-LINCS-Summer-Traniees-Virtual-Symposium-2024.md @@ -0,0 +1,10 @@ +--- +layout: '@/layouts/News.astro' +date: 2024-07-25 +portal: Information Portal +tags: + - Training & Outreach +title: LINCS Summer Traniees Virtual Symposium 2024 +description: A training and outreach event hosted by the LINCS DCC was added to the events page. The symposium is scheduled for August 8, 2024 at 10 AM ET. +img: https://cfde-drc.s3.us-east-2.amazonaws.com/assets/img/symposium-banner2024.png +--- diff --git a/src/pages/news/2024-08-09-CFDE-2024-Fall-Meeting.md b/src/pages/news/2024-08-09-CFDE-2024-Fall-Meeting.md new file mode 100644 index 0000000..4e97d84 --- /dev/null +++ b/src/pages/news/2024-08-09-CFDE-2024-Fall-Meeting.md @@ -0,0 +1,10 @@ +--- +layout: '@/layouts/News.astro' +date: 2024-08-09 +portal: Information Portal +tags: + - Training & Outreach +title: CFDE 2024 Fall Meeting +description: A training and outreach event hosted by the CFDE ICC was added to the event page. The 2024 CFDE Fall Meeting will be held from October 22, 2024, to October 23, 2024, at Bethesda, MD. +img: https://cfde-drc.s3.us-east-2.amazonaws.com/assets/img/cfde-fall-2024.png +--- diff --git a/src/pages/news/2024-08-09-CFDE-Webinar-Montlhy-Webinar-Series-by-the-A2CPS-DCC.md b/src/pages/news/2024-08-09-CFDE-Webinar-Montlhy-Webinar-Series-by-the-A2CPS-DCC.md new file mode 100644 index 0000000..dd642a0 --- /dev/null +++ b/src/pages/news/2024-08-09-CFDE-Webinar-Montlhy-Webinar-Series-by-the-A2CPS-DCC.md @@ -0,0 +1,12 @@ +--- +layout: '@/layouts/News.astro' +date: 2024-08-09 +portal: Information Portal +tags: + - Training & Outreach + - CFDE Webinar Series +title: CFDE Webinar Montlhy Webinar Series by the A2CPS DCC +description: A CFDE Monthly Webinar Series about Introduction to Acute to Chronic Pain Signatures (A2CPS) was added to the event page. The webinar is scheduled for August 30, 2024 at 1 PM ET. +img: https://cfde-drc.s3.us-east-2.amazonaws.com/assets/img/webinar-a2cps.png +link: https://cfde-drc.s/info/training_and_outreach/cfde-webinar-series +--- diff --git a/src/pages/news/2024-08-20-News-Page-Added-to-the-Information-Portal.md b/src/pages/news/2024-08-20-News-Page-Added-to-the-Information-Portal.md new file mode 100644 index 0000000..9232d30 --- /dev/null +++ b/src/pages/news/2024-08-20-News-Page-Added-to-the-Information-Portal.md @@ -0,0 +1,8 @@ +--- +layout: '@/layouts/News.astro' +date: 2024-08-20 +portal: Information Portal +title: News Page Added to the Information Portal +description: A news page was added to the CFDE Workbench information portal. The page will provide the latest updates on the Workbench, newly added metadata/processed data, and events. +img: https://cfde-drc.s3.us-east-2.amazonaws.com/assets/img/news.png +--- diff --git a/src/pages/news/2024-08-22-CFDE-2024-Fall-Meeting-Page-Added.md b/src/pages/news/2024-08-22-CFDE-2024-Fall-Meeting-Page-Added.md new file mode 100644 index 0000000..8d527c2 --- /dev/null +++ b/src/pages/news/2024-08-22-CFDE-2024-Fall-Meeting-Page-Added.md @@ -0,0 +1,11 @@ +--- +layout: '@/layouts/News.astro' +date: 2024-08-22 +portal: Information Portal +tags: + - Training & Outreach +title: CFDE 2024 Fall Meeting Page Added +description: A dedicated page about the 2024 CFDE F2F Fall Meeting was added to the information portal. The page provides the goal and agenda of the meeting. +img: https://cfde-drc.s3.amazonaws.com/assets/img/cfde-fall-2024.png +link: https://cfde-drc.s/info/training_and_outreach/cfde-fall-2024 +--- diff --git a/src/pages/news/2024-08-28-The-C2M2-Preparation-Script-and-Ontology-Terms-Updated.md b/src/pages/news/2024-08-28-The-C2M2-Preparation-Script-and-Ontology-Terms-Updated.md new file mode 100644 index 0000000..5bf4ef2 --- /dev/null +++ b/src/pages/news/2024-08-28-The-C2M2-Preparation-Script-and-Ontology-Terms-Updated.md @@ -0,0 +1,11 @@ +--- +layout: '@/layouts/News.astro' +date: 2024-08-28 +portal: Data Portal +tags: + - Data Ingestion +title: The C2M2 Preparation Script and Ontology Terms Updated +description: The CFDE Data Resource Center (DRC) team updated the C2M2 preparation script and ontology terms reflecting the properties of cross-DCC data types. +img: https://cfde-drc.s3.us-east-2.amazonaws.com/assets/img/c2m2-aug-2024.png +link: https://osf.io/bq6k9/ +--- diff --git a/src/pages/news/2024-09-03-CFDE-Webinar-Montlhy-Webinar-Series-by-the-exRNA-DCC.md b/src/pages/news/2024-09-03-CFDE-Webinar-Montlhy-Webinar-Series-by-the-exRNA-DCC.md new file mode 100644 index 0000000..f48d254 --- /dev/null +++ b/src/pages/news/2024-09-03-CFDE-Webinar-Montlhy-Webinar-Series-by-the-exRNA-DCC.md @@ -0,0 +1,12 @@ +--- +layout: '@/layouts/News.astro' +date: 2024-09-03 +portal: Information Portal +tags: + - Training & Outreach + - CFDE Webinar Series +title: CFDE Webinar Montlhy Webinar Series by the exRNA DCC +description: A CFDE Monthly Webinar Series event was added to the Webinars and Events pages. The webinar is an introduction to Extracellular RNA Communication (exRNA) DCC. The webinar is scheduled for September 27, 2024 at 1 PM ET. +img: https://cfde-drc.s3.us-east-2.amazonaws.com/assets/img/webinar-sep-2024.png +link: https://cfde-drc.s/info/training_and_outreach/cfde-webinar-series +--- diff --git a/src/pages/news/2024-09-03-Web-Design-Specifications-Page-Added-to-the-Information-Portal.md b/src/pages/news/2024-09-03-Web-Design-Specifications-Page-Added-to-the-Information-Portal.md new file mode 100644 index 0000000..2be0a15 --- /dev/null +++ b/src/pages/news/2024-09-03-Web-Design-Specifications-Page-Added-to-the-Information-Portal.md @@ -0,0 +1,9 @@ +--- +layout: '@/layouts/News.astro' +date: 2024-09-03 +portal: Information Portal +title: Web Design Specifications Page Added to the Information Portal +description: A web design specifications page was added to the CFDE Workbench information portal. The page provides typography specifications including colors, fonts, button examples, and instructions on how to incorporate images. +img: https://cfde-drc.s3.us-east-2.amazonaws.com/assets/img/web-spec.png +link: https://cfde-drc.s/info/specs +--- diff --git a/src/pages/news/2024-09-09-The-HuBMAP-JumpStart-Fellowship-2025-Added.md b/src/pages/news/2024-09-09-The-HuBMAP-JumpStart-Fellowship-2025-Added.md new file mode 100644 index 0000000..b977561 --- /dev/null +++ b/src/pages/news/2024-09-09-The-HuBMAP-JumpStart-Fellowship-2025-Added.md @@ -0,0 +1,11 @@ +--- +layout: '@/layouts/News.astro' +date: 2024-09-09 +portal: Information Portal +tags: + - Training & Outreach +title: The HuBMAP JumpStart Fellowship 2025 Added +description: A fellowship program hosted by the HuBMAP DCC was added to the Training & Outreach page. The fellowship accepts applications from October 14th, 2024 to November 14th, 2024. The project start date should be in the early summer of 2025, the earliest possible start date is June 2025 and the length can be up to 12 months. +img: https://cfde-drc.s3.us-east-2.amazonaws.com/assets/img/hubmap-2025-fellow.png +link: https://cfde-drc.s/info/training_and_outreach +--- diff --git a/src/pages/news/2024-09-17-Data,-Metadata,-and-Code-Assets-Added-to-the-CFDE-Workbench.md b/src/pages/news/2024-09-17-Data,-Metadata,-and-Code-Assets-Added-to-the-CFDE-Workbench.md new file mode 100644 index 0000000..7951d82 --- /dev/null +++ b/src/pages/news/2024-09-17-Data,-Metadata,-and-Code-Assets-Added-to-the-CFDE-Workbench.md @@ -0,0 +1,11 @@ +--- +layout: '@/layouts/News.astro' +date: 2024-09-17 +portal: Data Portal +tags: + - Data Ingestion +title: Data, Metadata, and Code Assets Added to the CFDE Workbench +description: New digital assets were recently added to the CFDE Workbench by the Common Fund DCCs. These include updated C2M2 metadata packages from GlyGen, IDG, HuBMAP, Metabolomics, SPARC, and Kids First; ETL and KG assertions from Bridge2AI; and an updated XMT file from LINCS. +img: https://cfde-drc.s3.us-east-2.amazonaws.com/assets/img/sep-2024-submission.png +link: https://cfde-drc.s/data/matrix +--- diff --git a/src/pages/news/2024-09-19-Automated-FAIR-Assessment-Performed-on-Newly-Added-Assets.md b/src/pages/news/2024-09-19-Automated-FAIR-Assessment-Performed-on-Newly-Added-Assets.md new file mode 100644 index 0000000..bcaa417 --- /dev/null +++ b/src/pages/news/2024-09-19-Automated-FAIR-Assessment-Performed-on-Newly-Added-Assets.md @@ -0,0 +1,9 @@ +--- +layout: '@/layouts/News.astro' +date: 2024-09-19 +portal: Data Portal +title: Automated FAIR Assessment Performed on Newly Added Assets +description: The CFDE DRC team performed a FAIR assessments on all newly added assets from the DCCs. These include FAIR assessments of C2M2, XMT, ETL, and KG assertions. These assessments were performed with FAIRshake. The FAIRshake insignia is now embedded near the listings of each asset to assist DCCs with improving the FAIRness of their data, metadata, and other digital assets. +img: https://cfde-drc.s3.us-east-2.amazonaws.com/assets/img/fair-fall-2024.png +link: https://fairshake.cloud/ +--- diff --git a/src/pages/news/2024-09-23-A-New-Dataset-Added-by-the-exRNA-DCC.md b/src/pages/news/2024-09-23-A-New-Dataset-Added-by-the-exRNA-DCC.md new file mode 100644 index 0000000..344767d --- /dev/null +++ b/src/pages/news/2024-09-23-A-New-Dataset-Added-by-the-exRNA-DCC.md @@ -0,0 +1,11 @@ +--- +layout: '@/layouts/News.astro' +date: 2024-09-23 +portal: Data Portal +tags: + - Data Ingestion +title: A New Dataset Added by the exRNA DCC +description: The new XMT data asset that was recently added to the CFDE Workbench by the exRNA DCC lists RNA binding proteins (RBPs) and the RNA fragments they bind to in different bodily fluids. +img: https://cfde-drc.s3.us-east-2.amazonaws.com/assets/img/exrna-fall-2024.png +link: https://cfde-drc.s/info/dcc/ExRNA#XMT +--- diff --git a/src/pages/news/2024-10-02-CFDE-Webinar-Monthly-Webinar-Series-by-the-MoTrPAC-DCC.md b/src/pages/news/2024-10-02-CFDE-Webinar-Monthly-Webinar-Series-by-the-MoTrPAC-DCC.md new file mode 100644 index 0000000..bd90811 --- /dev/null +++ b/src/pages/news/2024-10-02-CFDE-Webinar-Monthly-Webinar-Series-by-the-MoTrPAC-DCC.md @@ -0,0 +1,12 @@ +--- +layout: '@/layouts/News.astro' +date: 2024-10-02 +portal: Information Portal +tags: + - Training & Outreach + - CFDE Webinar Series +title: CFDE Webinar Monthly Webinar Series by the MoTrPAC DCC +description: A CFDE Monthly Webinar Series event was added to the Webinars and Events pages. The webinar is an introduction to Molecular Transducers of Physical Activity Consortium (MoTrPAC) DCC. The webinar is scheduled for October 25, 2024 at 1 PM ET. +img: https://cfde-drc.s3.us-east-2.amazonaws.com/assets/img/webinar-oct-2024.png +link: https://cfde-drc.s/info/training_and_outreach/cfde-webinar-series +--- diff --git a/src/pages/news/2024-10-02-DRC,-KC,-and-Kids-First-DCC-at-American-Society-of-Human-Genetics-.md b/src/pages/news/2024-10-02-DRC,-KC,-and-Kids-First-DCC-at-American-Society-of-Human-Genetics-.md new file mode 100644 index 0000000..2e693ba --- /dev/null +++ b/src/pages/news/2024-10-02-DRC,-KC,-and-Kids-First-DCC-at-American-Society-of-Human-Genetics-.md @@ -0,0 +1,11 @@ +--- +layout: '@/layouts/News.astro' +date: 2024-10-02 +portal: Information Portal +tags: + - Training & Outreach +title: DRC, KC, and Kids First DCC at American Society of Human Genetics +description: The CFDE Data Resource Center (DRC), Knowledge Center (KC), and Kids First DCC participate in the American Society of Human Genetics in Denver, representing the CFDE community. +img: https://cfde-drc.s3.us-east-2.amazonaws.com/assets/img/ASHG-2024.png +link: https://cfde-drc.s/info/training_and_outreach +--- diff --git a/src/pages/news/2024-10-02-SPARC-at-Society-for-Neuroscience-Annual-Meeting.md b/src/pages/news/2024-10-02-SPARC-at-Society-for-Neuroscience-Annual-Meeting.md new file mode 100644 index 0000000..9373a2b --- /dev/null +++ b/src/pages/news/2024-10-02-SPARC-at-Society-for-Neuroscience-Annual-Meeting.md @@ -0,0 +1,11 @@ +--- +layout: '@/layouts/News.astro' +date: 2024-10-02 +portal: Information Portal +tags: + - Training & Outreach +title: SPARC at Society for Neuroscience Annual Meeting +description: SPARC participates in the Society for Neuroscience (SfN) Annual Meeting where scientists worldwide meet to explore new ideas, exchange research findings, and immerse themselves in their field. Visit SPARC at Booth #1764. +img: https://cfde-drc.s3.us-east-2.amazonaws.com/assets/img/sparc-sfn-2024.png +link: https://cfde-drc.s/info/training_and_outreach +--- diff --git a/src/pages/news/2024-10-07-2025-LINCS-DCC-Summer-Research-Program-Announced.md b/src/pages/news/2024-10-07-2025-LINCS-DCC-Summer-Research-Program-Announced.md new file mode 100644 index 0000000..4114944 --- /dev/null +++ b/src/pages/news/2024-10-07-2025-LINCS-DCC-Summer-Research-Program-Announced.md @@ -0,0 +1,11 @@ +--- +layout: '@/layouts/News.astro' +date: 2024-10-07 +portal: Information Portal +tags: + - Training & Outreach +title: 2025 LINCS DCC Summer Research Program Announced +description: 'The LINCS DCC Summer Research Training Program in Biomedical Big Data Science, a research intensive ten-week training program for undergraduates interested in bioinformatics, was announced. In this program the summer fellows conduct faculty-mentored research in the areas: data harmonization, machine learning, cloud computing, and dynamic data visualization.' +img: https://cfde-drc.s3.us-east-2.amazonaws.com/assets/img/summer-2025-maayan.png +link: https://labs.icahn.mssm.edu/maayanlab/summer-research-program/ +--- diff --git a/src/pages/news/2024-10-10-CFDE-GSE-Added-as-a-Downstream-Analysis-Tool.md b/src/pages/news/2024-10-10-CFDE-GSE-Added-as-a-Downstream-Analysis-Tool.md new file mode 100644 index 0000000..f2c5f83 --- /dev/null +++ b/src/pages/news/2024-10-10-CFDE-GSE-Added-as-a-Downstream-Analysis-Tool.md @@ -0,0 +1,11 @@ +--- +layout: '@/layouts/News.astro' +date: 2024-10-10 +portal: Data Portal +tags: + - Performance Improvement +title: CFDE-GSE Added as a Downstream Analysis Tool +description: The CFDE-GSE app developed by the DRC is now available from the gene set entity pages on the CFDE Workbench. Users that search the data portal and find gene sets, can now analyze these gene sets in context of other gene sets from across eight Common Fund programs. +img: https://cfde-drc.s3.us-east-2.amazonaws.com/assets/img/gse-analysis.png +link: https://data.cfde.cloud/processed/gene_set/7f612259-8737-58c3-986b-821d95986a66 +--- diff --git a/src/pages/news/2024-10-15-Training-&-Outreach-Submission-Form-Added.md b/src/pages/news/2024-10-15-Training-&-Outreach-Submission-Form-Added.md new file mode 100644 index 0000000..b88919e --- /dev/null +++ b/src/pages/news/2024-10-15-Training-&-Outreach-Submission-Form-Added.md @@ -0,0 +1,11 @@ +--- +layout: '@/layouts/News.astro' +date: 2024-10-15 +portal: Information Portal +tags: + - Training & Outreach +title: Training & Outreach Submission Form Added +description: The members of the CFDE consortium can now use a training and outreach submission form to provide information about upcoming and past events. Once submitted, the Data Resource Center (DRC) team will review the submission and add it to the Training & Outreach page. +img: https://cfde-drc.s3.us-east-2.amazonaws.com/assets/img/event_submit.png +link: https://cfde-drc.s/info/training_and_outreach/submit +--- diff --git a/src/pages/news/2024-10-28-CFDE-Webinar-Monthly-Webinar-Series-by-the-COMPA-Partnership.md b/src/pages/news/2024-10-28-CFDE-Webinar-Monthly-Webinar-Series-by-the-COMPA-Partnership.md new file mode 100644 index 0000000..23455d2 --- /dev/null +++ b/src/pages/news/2024-10-28-CFDE-Webinar-Monthly-Webinar-Series-by-the-COMPA-Partnership.md @@ -0,0 +1,12 @@ +--- +layout: '@/layouts/News.astro' +date: 2024-10-28 +portal: Information Portal +tags: + - Training & Outreach + - CFDE Webinar Series +title: CFDE Webinar Monthly Webinar Series by the COMPA Partnership +description: A CFDE Monthly Webinar Series event was added to the Webinars and Events pages. The COMPA team will share an overview of the project followed by strategies to help the audience promote awareness and adoption of their products and tools from MetaCell (https://www.metacell.us/). They will discuss the cost-benefit of strategies such as interviews, workshops, and online presentations for targeted feedback and market validation and share methods to ensure data-driven outreach. The webinar is scheduled for November 22, 2024, at 1 PM ET. +img: https://cfde-drc.s3.us-east-2.amazonaws.com/assets/img/webinar-nov-2024.png +link: https://cfde-drc.s/info/training_and_outreach/cfde-webinar-series +--- diff --git a/src/pages/news/2024-11-01-Links-to-Tutorial-Videos-about-the-Use-Cases-and-Tools.md b/src/pages/news/2024-11-01-Links-to-Tutorial-Videos-about-the-Use-Cases-and-Tools.md new file mode 100644 index 0000000..e5c7bec --- /dev/null +++ b/src/pages/news/2024-11-01-Links-to-Tutorial-Videos-about-the-Use-Cases-and-Tools.md @@ -0,0 +1,9 @@ +--- +layout: '@/layouts/News.astro' +date: 2024-11-01 +portal: Data Portal +title: Links to Tutorial Videos about the Use Cases and Tools +description: Links to tutorial videos were added to the Tools and Workflow and Use Case pages. Four of these tutorials are about use cases created by the Playbook Workflow Builder, and six tutorials are about other CFDE-developed tools. +img: https://cfde-drc.s3.us-east-2.amazonaws.com/assets/img/tutorial.png +link: https://cfde-drc.s/data/usecases +--- diff --git a/src/pages/news/2024-11-04-New-CFDE-Partnerships.md b/src/pages/news/2024-11-04-New-CFDE-Partnerships.md new file mode 100644 index 0000000..32bf0b5 --- /dev/null +++ b/src/pages/news/2024-11-04-New-CFDE-Partnerships.md @@ -0,0 +1,15 @@ +--- +layout: '@/layouts/News.astro' +date: 2024-11-04 +portal: Information Portal +title: New CFDE Partnerships +description: Five new CFDE partnerships were established to further advance the reuse of Common Fund datasets by the broader scientific community. Details about each new partnership were added to the CFDE Workbench Partnership page. +supp_description: + - UniProt-CFDE Partnership + - Biomarker KB + - Metabotyping Humans + - Community Visualization Hub + - Genetic Basis of Birth Defects and Childhood Cancer +img: https://cfde-drc.s3.us-east-2.amazonaws.com/assets/img/partnership_fy25.png +link: https://cfde-drc.s/info/partnerships +--- diff --git a/src/pages/news/2024-11-11-The-IMPC-Webinar-Added.md b/src/pages/news/2024-11-11-The-IMPC-Webinar-Added.md new file mode 100644 index 0000000..9def2e9 --- /dev/null +++ b/src/pages/news/2024-11-11-The-IMPC-Webinar-Added.md @@ -0,0 +1,11 @@ +--- +layout: '@/layouts/News.astro' +date: 2024-11-11 +portal: Information Portal +tags: + - Training & Outreach +title: The IMPC Webinar Added +description: 'The IMPC Webinar: Investigating gene function and human disease through data on the IMPC portal will be held on November 20, 2024 at 10:30 AM EST. ' +img: https://cfde-drc.s3.us-east-2.amazonaws.com/assets/img/IMPC-webinar-2024.png +link: https://cfde-drc.s/info/training_and_outreach +--- diff --git a/src/pages/news/2024-12-02-Bridge2AI-Fall-2024-Leadership-Meeting-Added.md b/src/pages/news/2024-12-02-Bridge2AI-Fall-2024-Leadership-Meeting-Added.md new file mode 100644 index 0000000..8564227 --- /dev/null +++ b/src/pages/news/2024-12-02-Bridge2AI-Fall-2024-Leadership-Meeting-Added.md @@ -0,0 +1,11 @@ +--- +layout: '@/layouts/News.astro' +date: 2024-12-02 +portal: Information Portal +tags: + - Training & Outreach +title: Bridge2AI Fall 2024 Leadership Meeting Added +description: The Bridge2AI Fall 2024 Leadership Meeting will be held on December 5-6 in La Jolla, California. +img: https://cfde-drc.s3.us-east-2.amazonaws.com/assets/img/b2ai-fall-24.png +link: https://cfde-drc.s/info/training_and_outreach +--- diff --git a/src/pages/news/2024-12-02-CUSP-2025-Summer-Internship-Accepting-Applications.md b/src/pages/news/2024-12-02-CUSP-2025-Summer-Internship-Accepting-Applications.md new file mode 100644 index 0000000..d79eaed --- /dev/null +++ b/src/pages/news/2024-12-02-CUSP-2025-Summer-Internship-Accepting-Applications.md @@ -0,0 +1,11 @@ +--- +layout: '@/layouts/News.astro' +date: 2024-12-02 +portal: Information Portal +tags: + - Training & Outreach +title: CUSP 2025 Summer Internship Accepting Applications +description: The SenNet DCC summer internship program in 2025 was announced, and applications are accepted until January 15, 2025. The internship duration is 10 weeks between May and August 2025. +img: https://cfde-drc.s3.amazonaws.com/assets/img/SenNet_cusp_2024.png +link: https://cfde-drc.s/info/training_and_outreach +--- diff --git a/src/pages/news/2024-12-02-The-2025-Voice-AI-Symposium-and-Hackathon-Added.md b/src/pages/news/2024-12-02-The-2025-Voice-AI-Symposium-and-Hackathon-Added.md new file mode 100644 index 0000000..091250c --- /dev/null +++ b/src/pages/news/2024-12-02-The-2025-Voice-AI-Symposium-and-Hackathon-Added.md @@ -0,0 +1,11 @@ +--- +layout: '@/layouts/News.astro' +date: 2024-12-02 +portal: Information Portal +tags: + - Training & Outreach +title: The 2025 Voice AI Symposium and Hackathon Added +description: The 2025 Voice AI symposium will be held on April 22-23, followed by a hackathon on April 24th at the University of Florida in Tampa, FL. +img: https://cfde-drc.s3.us-east-2.amazonaws.com/assets/img/b2ai-summer-2024.png +link: https://cfde-drc.s/info/training_and_outreach +--- diff --git a/src/pages/news/2025-01-06-The-Virtual-CFDE-Workshop-Added.md b/src/pages/news/2025-01-06-The-Virtual-CFDE-Workshop-Added.md new file mode 100644 index 0000000..7463c08 --- /dev/null +++ b/src/pages/news/2025-01-06-The-Virtual-CFDE-Workshop-Added.md @@ -0,0 +1,11 @@ +--- +layout: '@/layouts/News.astro' +date: 2025-01-06 +portal: Information Portal +tags: + - Training & Outreach +title: The Virtual CFDE Workshop Added +description: The virtual CFDE workshop 'A Human Geneticists' Guide to the Common Fund Data Ecosystem' is added to the Event page. The workshop features the NIH perspective of the CFDE, gene set to human traits scientific presentation, introduction to CFDE centers, and NIH funding opportunities. It will be held on January 31st from 10 AM to 2 PM EST. +img: https://cfde-drc.s3.us-east-2.amazonaws.com/assets/img/workshop-2025.png +link: https://cfde-drc.s/info/training_and_outreach +--- diff --git a/src/pages/news/2025-01-13-CFDE-Centers-Page-Added-to-the-Information-Portal.md b/src/pages/news/2025-01-13-CFDE-Centers-Page-Added-to-the-Information-Portal.md new file mode 100644 index 0000000..d485e0b --- /dev/null +++ b/src/pages/news/2025-01-13-CFDE-Centers-Page-Added-to-the-Information-Portal.md @@ -0,0 +1,15 @@ +--- +layout: '@/layouts/News.astro' +date: 2025-01-13 +portal: Information Portal +title: CFDE Centers Page Added to the Information Portal +description: 'A centers page was added to the CFDE Workbench information portal. The page introduces the five CFDE centers:' +supp_description: + - The Integration and Coordination Center (ICC) + - The Data Resource Center (DRC) + - The Knowledge Center (KC) + - The Cloud Workspace Implementation Center (CWIC) + - The Training Center (TC) +img: https://cfde-drc.s3.us-east-2.amazonaws.com/assets/img/center-page.png +link: https://cfde-drc.s/info/centers +--- diff --git a/src/pages/news/2025-01-14-The-Multi-Omics-AI-Driven-Gene-Set-Analysis-with-GeneSetCart-Seminar-Added.md b/src/pages/news/2025-01-14-The-Multi-Omics-AI-Driven-Gene-Set-Analysis-with-GeneSetCart-Seminar-Added.md new file mode 100644 index 0000000..dcc8f49 --- /dev/null +++ b/src/pages/news/2025-01-14-The-Multi-Omics-AI-Driven-Gene-Set-Analysis-with-GeneSetCart-Seminar-Added.md @@ -0,0 +1,11 @@ +--- +layout: '@/layouts/News.astro' +date: 2025-01-14 +portal: Information Portal +tags: + - Training & Outreach +title: The Multi-Omics AI-Driven Gene Set Analysis with GeneSetCart Seminar Added +description: The virtual seminar 'Multi-Omics AI-Driven Gene Set Analysis with GeneSetCart' is added to the Event page. Members of the CFDE DRC will demonstrate GeneSetCart, a new CFDE platform geared for the analysis of gene sets created from various Common Fund programs data sources. It will be held on January 23rd from 2 PM to 3 PM EST. +img: https://cfde-drc.s3.us-east-2.amazonaws.com/assets/img/seminar-250123-1.png +link: https://cfde-drc.s/info/training_and_outreach +--- diff --git a/src/pages/news/2025-01-17-CFDE-at-American-Society-of-Human-Genetics-2025.md b/src/pages/news/2025-01-17-CFDE-at-American-Society-of-Human-Genetics-2025.md new file mode 100644 index 0000000..e7c9a66 --- /dev/null +++ b/src/pages/news/2025-01-17-CFDE-at-American-Society-of-Human-Genetics-2025.md @@ -0,0 +1,11 @@ +--- +layout: '@/layouts/News.astro' +date: 2025-01-17 +portal: Information Portal +tags: + - Training & Outreach +title: CFDE at American Society of Human Genetics 2025 +description: The CFDE will be showcased at the 2025 American Society of Human Genetics Annual (ASHG) meeting. An ancillary session and a CFDE booth are planned. The meeting will be held in Boston, MA. +img: https://cfde-drc.s3.us-east-2.amazonaws.com/assets/img/ashg-2025.png +link: https://cfde-drc.s/info/training_and_outreach +--- diff --git a/src/pages/news/2025-01-17-CFDE-at-Bio-IT-World-Boston-2025.md b/src/pages/news/2025-01-17-CFDE-at-Bio-IT-World-Boston-2025.md new file mode 100644 index 0000000..27a4aba --- /dev/null +++ b/src/pages/news/2025-01-17-CFDE-at-Bio-IT-World-Boston-2025.md @@ -0,0 +1,11 @@ +--- +layout: '@/layouts/News.astro' +date: 2025-01-17 +portal: Information Portal +tags: + - Training & Outreach +title: CFDE at Bio-IT World Boston 2025 +description: The CFDE will be showcased at the Bio-IT World 2025. The Bio-IT FAIR Data Hackathon will be facilitated by CFDE members led by the CFDE Training Center (TC) to promote the utilization and integration of CFDE tools and datasets. +img: https://cfde-drc.s3.us-east-2.amazonaws.com/assets/img/bioitexpo-2025.png +link: https://cfde-drc.s/info/training_and_outreach +--- diff --git a/src/pages/news/2025-01-17-CFDE-at-Intelligent-Systems-for-Molecular-Biology-2025.md b/src/pages/news/2025-01-17-CFDE-at-Intelligent-Systems-for-Molecular-Biology-2025.md new file mode 100644 index 0000000..6ab80b5 --- /dev/null +++ b/src/pages/news/2025-01-17-CFDE-at-Intelligent-Systems-for-Molecular-Biology-2025.md @@ -0,0 +1,11 @@ +--- +layout: '@/layouts/News.astro' +date: 2025-01-17 +portal: Information Portal +tags: + - Training & Outreach +title: CFDE at Intelligent Systems for Molecular Biology 2025 +description: Representative from several CFDE participating Common Fund programs’ DCCs plan to attend the Intelligent Systems for Molecular Biology (ISMB) 2025 in Liverpool, UK. +img: https://cfde-drc.s3.us-east-2.amazonaws.com/assets/img/ismb-2025.png +link: https://cfde-drc.s/info/training_and_outreach +--- diff --git a/src/pages/news/index.md b/src/pages/news/index.md new file mode 100644 index 0000000..6cb001f --- /dev/null +++ b/src/pages/news/index.md @@ -0,0 +1,6 @@ +--- +layout: '@/layouts/NewsMain.astro' +--- +### What's new on the CFDE Workbench? + +The latest updates of content added to the CFDE Workbench. From 41858a84e3e8264c7110d013d1f61caf0e8873a0 Mon Sep 17 00:00:00 2001 From: Heesu Kim Date: Thu, 30 Jan 2025 18:26:07 -0500 Subject: [PATCH 02/10] add documentation markdowns --- src/pages/documentation/C2M2.md | 297 ++++++++++++++ src/pages/documentation/FAIRshake.md | 80 ++++ src/pages/documentation/KGAssertions.md | 64 +++ src/pages/documentation/OpenAPI.md | 409 ++++++++++++++++++++ src/pages/documentation/PWBMetanodes.md | 108 ++++++ src/pages/documentation/RNA-seq.md | 5 + src/pages/documentation/SubmissionSystem.md | 5 + src/pages/documentation/WebSpecs.md | 84 ++++ src/pages/documentation/index.md | 10 + 9 files changed, 1062 insertions(+) create mode 100644 src/pages/documentation/C2M2.md create mode 100644 src/pages/documentation/FAIRshake.md create mode 100644 src/pages/documentation/KGAssertions.md create mode 100644 src/pages/documentation/OpenAPI.md create mode 100644 src/pages/documentation/PWBMetanodes.md create mode 100644 src/pages/documentation/RNA-seq.md create mode 100644 src/pages/documentation/SubmissionSystem.md create mode 100644 src/pages/documentation/WebSpecs.md create mode 100644 src/pages/documentation/index.md diff --git a/src/pages/documentation/C2M2.md b/src/pages/documentation/C2M2.md new file mode 100644 index 0000000..36afc15 --- /dev/null +++ b/src/pages/documentation/C2M2.md @@ -0,0 +1,297 @@ +--- +layout: '@/layouts/Documentation.astro' +title: C2M2 +label: C2M2 +--- + + +# C2M2 + + +## Table of Contents + +- [Introduction](#introduction) + - [Schematic of C2M2](#schematic-of-c2m2) +- [Resources](#resources) +- [Frictionless Data Packages](#frictionless-data-packages) +- [Identifiers](#identifiers) +- [C2M2 Tables](#c2m2-tables) + - [Entity relationship diagram of C2M2](#entity-relationship-diagram-of-c2m2) +- [Reference Tables](#reference-tables) +- [Submission Prep Script](#submission-prep-script) +- [Datapackage Submission](#datapackage-submission) +- [Tutorial](#tutorial) + + +## Introduction + +### Schematic of C2M2 +(please right-click on the image to see options to view a larger image in a different tab) + +
+ Graphical schematic of C2M2 +
+ +The Crosscut Metadata Model (C2M2) is a flexible metadata standard for describing experimental resources in biomedicine and related fields. A complete C2M2 submission, also called an "instance" or a "datapackage", is a zipped folder containing multiple tab-delimited files (TSVs) representing metadata records along with a JSON schema. To read more about datapackages, skip to the [Frictionless Data Packages](#frictionless-data-packages) section. + +Each TSV file is a **data table** containing various **data records** (rows) and their values for different **fields** (columns). **Entity tables** describe various types of data objects, while **association tables** describe the relationships between different entities. + +This page is adapted from the [original C2M2 documentation](https://github.com/nih-cfde/published-documentation) developed by the CFDE Coordination Center (CFDE-CC). + +## Resources +- The [c2m2-frictionless-dataclass](https://github.com/nih-cfde/c2m2-frictionless-dataclass/tree/main) + - This repository includes the `c2m2-frictionless` Python package, which contains specific helper functions for C2M2 datapackage building and validation. + - This package is not designed to generate a complete C2M2 datapackage from any given data, but should be used in collaboration with the provided schema and ontology preparation scripts, as well as with DCC-specific scripts. +- The most up-to-date [C2M2 JSON schema](https://osf.io/3sra4/) +- The most up-to-date [C2M2 ontology preparation script and files](https://osf.io/bq6k9/) +- The original [C2M2 documentation](https://github.com/nih-cfde/c2m2/blob/master/draft-C2M2_specification/README.md) from the CFDE Coordination Center contains more details on the concepts discussed here. + +## Frictionless Data Packages +C2M2 instances are also known as "datapackages" based on the [Data Package](http://frictionlessdata.io/docs/data-package/) meta-specification from [Frictionless Data](http://frictionlessdata.io/). + +From the original C2M2 documentation: +> The Data Package meta-specification is a platform-agnostic toolkit for defining format and content requirements for files so that automatic validation can be performed on those files, just as a database management system stores definitions for database tables and automatically validates incoming data based on those definitions. Using this toolkit, the C2M2 JSON Schema specification defines foreign-key relationships between metadata fields (TSV columns), rules governing missing data, required content types and formats for particular fields, and other similar database management constraints. These architectural rules help to guarantee the internal structural integrity of each C2M2 submission, while also serving as a baseline standard to create compatibility across multiple submissions received from different DCCs. + +## Identifiers +In order to standardize and integrate information across DCCs, there must be a system of assigning unambiguous identifiers to individual DCC concepts and resources. These are the "C2M2 IDs", consisting of a `id_namespace` prefix and `local_id` suffix. Additionally, the C2M2 also allows individual resources to be assigned a `persistent_id`. + +From the original C2M2 documentation: +> Optional `persistent_id` identifiers are meant to be stable enough to be scientifically cited, and to provide for further investigation by accessing related resolver services. To be used as a C2M2 `persistent_id`, an ID +> 1. will represent an explicit commitment by the managing DCC that the attachment of the ID to the resource it represents is permanent and final +> 2. must be a format-compliant URI or a compact identifier, where the protocol (the "scheme" or "prefix") specified in the ID is registered with at least one of the following (see the given lists for examples of URIs and compact identifiers) +> - the IANA (list of registered schemes) +> - scheme used must be assigned either "Permanent" or "Provisional" status +> - Identifiers.org (list of registered prefixes) +> - N2T (Name-To-Thing) (list of registered prefixes) +> - protocols not appearing in the above registries but explicitly approved by the CFDE-CC. Currently, this list is limited to one protocol, namely drs:// URIs identifying GA4GH Data Repository Service resources. +> 3. if representing a file, an ID used as a `persistent_id` cannot be a direct-download URL for that file: it must instead be an identifier permanently attached to the file and only indirectly resolvable (through the scheme or prefix specified within the ID) to the file itself + +## C2M2 Tables + +_Sourced from the [CFDE-CC Documentation Wiki](https://github.com/nih-cfde/published-documentation/wiki/C2M2-Table-Summary)_ + +All of the tables in a C2M2 datapackage are inter-linked via foreign key relationships, as shown in the following diagram of the complete C2M2 system. + +### Entity relationship diagram of C2M2 +(please right-click on the image to see options to view a larger image in a different tab) + +
+ [Entity relationship diagram of C2M2 +
+Crosscut Metadata Model (C2M2) Common Vocabulary (CV) Tables + +- All table files listed in this summary must be bundled together, along with the [C2M2 datapackage JSON Schema file](https://osf.io/3sra4/), to create a valid C2M2 datapackage for submission to CFDE +- TSV files for any empty (unused) tables must still be submitted, with only the (tab-separated) column-header row filled in +- Table (TSV) filenames must exactly match those listed in the JSON Schema file (and in these docs) +- Table column headers must exactly match those listed in the JSON Schema file (and in these docs) +- Table columns must appear in the order given in the JSON Schema file (and in these docs) +- Tables marked "CV term table" must be built using the CFDE submission prep script ([wiki](./submission-prep-script); [code](https://osf.io/bq6k9/)) +- Table (TSV) files must not contain any empty rows or extra lines +- Every TSV file must end with the final row of table data, terminated by a newline + +Table (click for detailed information)|Construction|Can be empty?|Notes +-----------|:-----------:|:-------------:|------------- +[analysis_type.tsv](./TableInfo:-analysis_type.tsv)|Built by script|Y|CV term table +[anatomy.tsv](./TableInfo:-anatomy.tsv)|Built by script|Y|CV term table +[assay_type.tsv](./TableInfo:-assay_type.tsv)|Built by script|Y|CV term table +[biofluid.tsv](./TableInfo:-biofluid.tsv)|Built by script|Y|CV term table +[biosample.tsv](./TableInfo:-biosample.tsv)|Prepared by submitter|Y|This table will have one row for each biosample +[biosample_disease.tsv](./TableInfo:-biosample_disease.tsv)|Prepared by submitter|Y|For biosamples with disease metadata, this table will have one row for each disease associated with each biosample, along with a field distinguishing "exemplar of disease" from "disease specifically ruled out" +[biosample_from_subject.tsv](./TableInfo:-biosample_from_subject.tsv)|Prepared by submitter|Y|This table will have one row for each attribution of a biosample to a subject +[biosample_gene.tsv](./TableInfo:-biosample_gene.tsv)|Prepared by submitter|Y|For each biosample with a small group of associated genes (e.g. knockdown targets), this table will have one row for each association of a gene with a biosample +[biosample_in_collection.tsv](./TableInfo:-biosample_in_collection.tsv)|Prepared by submitter|Y|This table will have one row for each assignment of a biosample as a member of a collection +[biosample_substance.tsv](./TableInfo:-biosample_substance.tsv)|Prepared by submitter|Y|For biosamples with substance metadata, this table will have one row for each association of a substance with a biosample +[collection.tsv](./TableInfo:-collection.tsv)|Prepared by submitter|Y|This table will have one row for each collection +[collection_anatomy.tsv](./TableInfo:-collection_anatomy.tsv)|Prepared by submitter|Y|Each row in this table is equivalent to the statement "the contents of collection X directly relate to the study of anatomy Y", for one particular (collection X, anatomy Y) pair +[collection_biofluid.tsv](./TableInfo:-collection_biofluid.tsv)|Prepared by submitter|Y|Each row in this table is equivalent to the statement "the contents of collection X directly relate to the study of biofluid Y", for one particular (collection X, biofluid Y) pair +[collection_compound.tsv](./TableInfo:-collection_compound.tsv)|Prepared by submitter|Y|Each row in this table is equivalent to the statement "the contents of collection X directly relate to the study of compound Y", for one particular (collection X, compound Y) pair +[collection_defined_by_project.tsv](./TableInfo:-collection_defined_by_project.tsv)|Prepared by submitter|Y|This table will have one row for each collection that was generated directly by a project listed in the [project.tsv](./TableInfo:-project.tsv) table +[collection_disease.tsv](./TableInfo:-collection_disease.tsv)|Prepared by submitter|Y|Each row in this table is equivalent to the statement "the contents of collection X directly relate to the study of disease Y", for one particular (collection X, disease Y) pair +[collection_gene.tsv](./TableInfo:-collection_gene.tsv)|Prepared by submitter|Y|Each row in this table is equivalent to the statement "the contents of collection X directly relate to the study of gene Y", for one particular (collection X, gene Y) pair +[collection_in_collection.tsv](./TableInfo:-collection_in_collection.tsv)|Prepared by submitter|Y|This table will have one row for each parent->child (collection->subcollection) relationship +[collection_phenotype.tsv](./TableInfo:-collection_phenotype.tsv)|Prepared by submitter|Y|Each row in this table is equivalent to the statement "the contents of collection X directly relate to the study of phenotype Y", for one particular (collection X, phenotype Y) pair +[collection_protein.tsv](./TableInfo:-collection_protein.tsv)|Prepared by submitter|Y|Each row in this table is equivalent to the statement "the contents of collection X directly relate to the study of protein Y", for one particular (collection X, protein Y) pair +[collection_substance.tsv](./TableInfo:-collection_substance.tsv)|Prepared by submitter|Y|Each row in this table is equivalent to the statement "the contents of collection X directly relate to the study of substance Y", for one particular (collection X, substance Y) pair +[collection_taxonomy.tsv](./TableInfo:-collection_taxonomy.tsv)|Prepared by submitter|Y|Each row in this table is equivalent to the statement "the contents of collection X directly relate to the study of taxonomy Y", for one particular (collection X, taxonomy Y) pair +[compound.tsv](./TableInfo:-compound.tsv)|Built by script|Y|CV term table +[data_type.tsv](./TableInfo:-data_type.tsv)|Built by script|Y|CV term table +[dcc.tsv (formerly `primary_dcc_contact.tsv`)](./TableInfo:-dcc.tsv)|Prepared by submitter|N|This table will have exactly one row +[disease.tsv](./TableInfo:-disease.tsv)|Built by script|Y|CV term table +[file.tsv](./TableInfo:-file.tsv)|Prepared by submitter|Y|This table will have one row for each file +[file_describes_biosample.tsv](./TableInfo:-file_describes_biosample.tsv)|Prepared by submitter|Y|This table will have one row for each association of a biosample with a describing file +[file_describes_collection.tsv](./TableInfo:-file_describes_collection.tsv)|Prepared by submitter|Y|This table will have one row for each association of a collection with a describing file +[file_describes_subject.tsv](./TableInfo:-file_describes_subject.tsv)|Prepared by submitter|Y|This table will have one row for each association of a subject with a describing file +[file_format.tsv](./TableInfo:-file_format.tsv)|Built by script|Y|CV term table +[file_in_collection.tsv](./TableInfo:-file_in_collection.tsv)|Prepared by submitter|Y|This table will have one row for each assignment of a file as a member of a collection +[gene.tsv](./TableInfo:-gene.tsv)|Built by script|Y|CV term table +[id_namespace.tsv](./TableInfo:-id_namespace.tsv)|Prepared by submitter|N|This table will have one row for each C2M2 identifier namespace registered with CFDE +[ncbi_taxonomy.tsv](./TableInfo:-ncbi_taxonomy.tsv)|Built by script|Y|CV term table +[phenotype.tsv](./TableInfo:-phenotype.tsv)|Built by script|Y|CV term table +[phenotype_disease.tsv](./TableInfo:-phenotype_disease.tsv)|Built by script|Y|Each row in this table is equivalent to the statement "phenotype X is known to be associated with disease Y", for one particular (phenotype X, disease Y) pair; contents are autoloaded from HPO by the submission prep script, which will add relevant rows for every phenotype term and every disease term used in submitter-prepared tables +[phenotype_gene.tsv](./TableInfo:-phenotype_gene.tsv)|Built by script|Y|Each row in this table is equivalent to the statement "phenotype X is known to be associated with gene Y", for one particular (phenotype X, gene Y) pair; contents are autoloaded from HPO by the submission prep script, which will add relevant rows for every phenotype term and every gene term used in submitter-prepared tables +[project.tsv](./TableInfo:-project.tsv)|Prepared by submitter|N|This table will have one row for each project +[project_in_project.tsv](./TableInfo:-project_in_project.tsv)|Prepared by submitter|Y*| This table will have one row for each parent->child (project->subproject) relationship.
---
*If you have more than one project in your [project.tsv](./TableInfo:-project.tsv) table, then you _must_ populate this table with all of your program's top-level projects, listed as children of your program's root project. +[protein.tsv](./TableInfo:-protein.tsv)|Built by script|Y|CV term table +[protein_gene.tsv](./TableInfo:-protein_gene.tsv)|Built by script|Y|Each row in this table is equivalent to the statement "protein X is known to be associated with gene Y", for one particular (protein X, gene Y) pair; contents are autoloaded from HPO by the submission prep script, which will add relevant rows for every protein term and every gene term used in submitter-prepared tables +[subject.tsv](./TableInfo:-subject.tsv)|Prepared by submitter|Y|This table will have one row for each subject +[subject_disease.tsv](./TableInfo:-subject_disease.tsv)|Prepared by submitter|Y|For subjects with disease metadata, this table will have one row for each disease associated with each subject, along with a field distinguishing "disease detected" from "disease specifically ruled out" +[subject_in_collection.tsv](./TableInfo:-subject_in_collection.tsv)|Prepared by submitter|Y|This table will have one row for each assignment of a subject as a member of a collection +[subject_phenotype.tsv](./TableInfo:-subject_phenotype.tsv)|Prepared by submitter|Y|For every subject with phenotype metadata, this table will have one row for each phenotype associated with each subject, along with a field distinguishing "exemplar of phenotype" from "phenotype specifically ruled out" +[subject_race.tsv](./TableInfo:-subject_race.tsv)|Prepared by submitter|Y|This table will have one row for each subject with a race assertion +[subject_role_taxonomy.tsv](./TableInfo:-subject_role_taxonomy.tsv)|Prepared by submitter|Y|This table will have one row for each taxon assigned to a subject +[subject_substance.tsv](./TableInfo:-subject_substance.tsv)|Prepared by submitter|Y|For subjects with substance metadata, this table will have one row for each substance associated with each subject +[substance.tsv](./TableInfo:-substance.tsv)|Built by script|Y|CV term table + +## Reference Tables + +Certain table fields within the C2M2 are restricted to only a few pre-defined values, such as `biosample_disease.association_type` or `subject.granularity`. Reference tables containing the allowed values for these fields, which were originally published on the [CFDE-CC Documentation Wiki](https://github.com/nih-cfde/published-documentation/wiki/C2M2-Table-Summary), are linked below: + +- [All reference tables](https://osf.io/m3a85/) + - [disease_association_type](https://osf.io/ap6gr/) + - [phenotype_association_type](https://osf.io/druqa/) + - [subject_ethnicity](https://osf.io/5gy7r/) + - [subject_granularity](https://osf.io/gpf3d/) + - [subject_race](https://osf.io/jp492/) + - [subject_role](https://osf.io/fapnr/) + - [subject_sex](https://osf.io/wepsz/) + +## Submission Prep Script + +_Sourced from the [CFDE-CC Documentation Wiki](https://github.com/nih-cfde/published-documentation/wiki/submission-prep-script)_ + + + +## Datapackage Submission + +As an optional but recommended step before submitting your data package, you may validate your pipeline using either the `c2m2-frictionless` Python package (see [Resources](#resources)) or by following the steps below for using the frictionless validator, from the [CFDE-CC Documentation Wiki Quickstart](https://github.com/nih-cfde/published-documentation/wiki/Quickstart#optional-frictionless): + +> `pip install frictionless` +If that command fails try: +`pip install frictionless-py` +Once it's installed, run it by doing: +`frictionless validate PATH/TO/JSON_FILE_IN_DIRECTORY` +This command takes several minutes to run, and dumps the results into your terminal by default. To make a nicer file to review do: +`frictionless validate PATH/TO/JSON_FILE_IN_DIRECTORY > report.txt` + +Currently, the CFDE Workbench Data Portal accepts complete datapackage submissions in ZIP file format (*.zip). + +For specific instructions on using the submission system, see the [Contribution Guide](https://data.cfde.cloud/submit). + +To submit a datapackage, navigate to the [Submission System](https://data.cfde.cloud/submit/form). + +## Tutorial +For the April 2022 CFDE Cross-Pollination meeting, the LINCS DCC demonstrated a Jupyter Notebook tutorial on building the `file`, `biosample`, and `subject` tables for LINCS L1000 signature data. The code and files can be found at the following link: + +[LINCS C2M2 Demo (04-05-2022 Cross-Pollination)](https://github.com/MaayanLab/lincs-data-manifests/tree/main/April-CrossPollination-Demo) + +Code snippets from this tutorial corresponding to each step are reproduced below. Note that the C2M2 datapackage building process will vary across DCCs, depending on the types of generated data, ontologies, and access standards in place. In general, the process will be as follows: +1. Become familiar with the current structure of the C2M2, including the required fields across the entity and association tables, and download the most recent version of the [JSON schema](https://osf.io/c63aw/). Gather any metadata mapping files you may need. +2. Identify the relevant namespace for all files, and build the `id_namespace` and `dcc` tables first. + + - For LINCS, the namespace "https://lincsproject.org" is used. The following code will generate the LINCS `id_namespace` table: + ``` + pd.DataFrame( + [ + [ + 'https://www.lincsproject.org', # id + 'LINCS', # abbreviation + 'Library of Integrated Network-Based Cellular Signatures', # name + 'A network-based understanding of biology' # description + ] + ], + columns=['id', 'abbreviation', 'name', 'description'] + ).to_csv('id_namespace.tsv', sep='\t', index=False) + ``` + +3. Identify all relevant projects and their associated files that will be included in the C2M2 datapackage. Generate container entity tables (`project`, `collection`) that describe logic, theme, or funding-based groups of the core entities. Note that projects and collections may be nested, in the `project_in_project` and `collection_in_collection` tables. + + - In the LINCS tutorial, the data comes from the 2021 release of the LINCS L1000 Connectivity Map dataset. In creating a project representing the files from this dataset, there must also be an overarching root project for all LINCS data. + ``` + pd.DataFrame( + [ + [ + 'https://www.lincsproject.org', # id_namespace + 'LINCS', # local_id + 'https://www.lincsproject.org', # persistent_id + date(2013, 1, 1), # creation_time + 'LINCS', # abbreviation + 'Library of Integrated Network-Based Cellular Signatures', # name + 'A network-based understanding of biology' # description + ], + [ + 'https://www.lincsproject.org', # id_namespace + 'LINCS-2021', # local_id + 'https://clue.io/data/CMap2020#LINCS2020', # persistent_id + date(2020, 11, 20), # creation_time + 'LINCS-2021', # abbreviation + 'LINCS 2021 Data Release', # name + 'The 2021 beta release of the CMap LINCS resource' # description + ] + ], + columns=[ + 'id_namespace', 'local_id', 'persistent_id', 'creation_time', + 'abbreviation', 'name', 'description' + ] + ).to_csv('project.tsv', sep='\t', index=False) + + pd.DataFrame( + [ + [ + 'https://www.lincsproject.org', # parent_project_id_namespace + 'LINCS', # parent_project_local_id + 'https://www.lincsproject.org/', # child_project_id_namespace + 'LINCS-2021' # child_project_local_id + ] + ], + columns=[ + 'parent_project_id_namespace', 'parent_project_local_id', + 'child_project_id_namespace', 'child_project_local_id' + ] + ).to_csv('project_in_project.tsv', sep='\t', index=False) + ``` + +4. Determine the relationships between files and their associated samples or biological subjects, as well as all relevant assay types, analysis methods, data types, file formats, etc. Also identify all appropriate ontological mappings, if any, corresponding to each value from above. + + - The LINCS DCC includes internal drug, gene, and cell line identifiers, which were mapped to PubChem, Ensembl, and Disease Ontology/UBERON manually ahead of time, but other DCCs may already make use of the CFDE-supported ontologies. + - For instance, the LINCS signature `L1000_LINCS_DCIC_ABY001_A375_XH_A16_lapatinib_10uM.tsv.gz` comes from the biosample `ABY001_A375_XH_A16_lapatinib_10uM` (in this case an experimental condition) and the subject cell line `A375`; has a data type of expression matrix (`data:0928`); is stored as a TSV file format (`format:3475`) with GZIP compression format (`format:3989`); and has a MIME type of `text/tab-separated-values`. + - The `ABY001_A375_XH_A16_lapatinib_10uM` biosample was obtained via the L1000 sequencing assay type (`OBI:0002965`); comes from a cell line derived from the skin (`UBERON:0002097`); and was treated with the compound lapatinib (`CID:208908`). + +5. Either manually or programmatically, generate each data table, starting with the core entity tables (`file`, `biosample`, `subject`). This step will depend entirely on the format of a DCC's existing metadata and ontology mapping tables. + +6. Generate the inter-entity linkage association tables (`file_describes_biosample`, `file_describes_subject`, `biosample_from_subject`). + + - In the LINCS tutorial, since the filenames come directly from the biosamples, once the `file` and `biosample` tables have both been built, `file_describes_biosample` can be generated. + ``` + fdb = file_df[['id_namespace', 'local_id']].copy() + fdb = fdb.rename( + columns={ + 'id_namespace': 'file_id_namespace', + 'local_id': 'file_local_id' + } + ) + fdb['biosample_id_namespace'] = fdb['file_id_namespace'] + fdb['biosample_local_id'] = fdb['file_local_id'].apply(file_2_biosample_map_function) + ``` + +7. Assign files, biosamples, and subjects to any collections, if applicable, using the `file_in_collection`, `subject_in_collection`, and `biosample_in_collection` tables. + + - Collections are optional, and can represent files from the same publications or other logical groupings outside of funding. + +8. Use provided [C2M2 submission preparation script and ontology support files](https://osf.io/bq6k9/) to automatically build term entity tables from your created files. + +9. Optionally validate the final datapackage containing all files and the schema using one of the following validator tools: + - [Frictionless validator](#datapackage-submission) + - [`c2m2-frictionless-datapackage` code package](#resources) + +10. Compress the entire directory into a *.zip file and upload to the [CFDE Workbench Metadata and Data Submission System](https://data.cfde.cloud/submit/form). + +### Return to [Documentation](./) +

diff --git a/src/pages/documentation/FAIRshake.md b/src/pages/documentation/FAIRshake.md new file mode 100644 index 0000000..6aa57ed --- /dev/null +++ b/src/pages/documentation/FAIRshake.md @@ -0,0 +1,80 @@ +--- +layout: '@/layouts/Documentation.astro' +title: FAIR Evaluations with FAIRshake +label: FAIRshake +short_description: The FAIRshake toolkit enables manual and automated assessments of the findability, accessibility, interoperability, and reusability (FAIRness) of digital resources. FAIRshake provides community-driven metrics and rubrics for evaluation, and visualizes the results with a characteristic embeddable insignia. The primary goal of FAIRshake is to enable researchers and developers to objectively measure and improve the FAIRness of their tools. +--- +# FAIRshake + +## Table of Contents + +- [Introduction](#introduction) +- [Resources](#resources) +- [General Steps](#general-steps) + - [Starting Projects](#starting-projects) + - [Registering Digital Objects](#registering-digital-objects) + - [Associating Rubrics](#associating-rubrics) + - [Performing Assessments](#performing-assessments) + +## Introduction + +The FAIR data principles -- findability, accessibility, interoperability, and resuability -- were first proposed by Wilkinson et al. (*Scientific Data*, 2016) to set guidelines for improving data reuse infrastructure in academia. In other words, the FAIR guidelines aim to facilitate continuous reuse of digital objects or re-analysis of data, improve automated knowledge integration, and simplify access to various tools and resources. + +Within the CFDE, the FAIR principles are a critical component of our goal to meaningfully synthesize information across Common Fund DCCs to maximize knowledge extraction and promote novel hypothesis generation. To learn more about how DCCs can improve the FAIRness of their digital objects, please see the example code and datasets available in the NIH-CFDE FAIR Cookbook. + +## Resources + +- FAIRshake +- FAIRshake User Guide V2 +- NIH-CFDE FAIR Cookbook + +## General Steps + +The steps below are adapted from the FAIRshake User Guide V2 and outline the basics of using FAIRshake, including creating a new project, registering digital objects and rubrics within the project, and running a FAIR assessment. + +### Starting Projects + +1. Navigate to the FAIRshake website and create a user account if you do not already have one. + ![Sign up for FAIRshake](https://github.com/MaayanLab/FAIRshake/blob/master/FAIRshakeHub/static/file/FAIRshakeUserGuide/files/image005.jpg?raw=true) + +1. Select the **Projects** page from the menu at the top of the page, then click on the **Create New Project** card in the bottom right corner. A project can be used to house a collection of related digital objects that are each associated with at least one FAIR rubric. + ![Create a new project](https://github.com/MaayanLab/FAIRshake/blob/master/FAIRshakeHub/static/file/FAIRshakeUserGuide/files/image009.jpg?raw=true) + +### Registering Digital Objects + +3. Navigate to an existing project or the project you just created, and fill in metadata for a digital object you would like to evaluate. Digital objects may be software, datasets, APIs, or workflows, among others. + ![Add a Digital Object](https://github.com/MaayanLab/FAIRshake/blob/master/FAIRshakeHub/static/file/FAIRshakeUserGuide/files/image011.jpg?raw=true) + +4. The **Rubrics** field will automatically present a list of potential rubrics that are appropriate for your digital object. If you would like to create your own rubric, see the following section on [Associating Rubrics](#associating-rubrics). +5. Submitting the form will take you to a new page for your now-registered digital object, which displays its metadata and associated projects and rubrics. + ![View a registered Digital Object](https://github.com/MaayanLab/FAIRshake/blob/master/FAIRshakeHub/static/file/FAIRshakeUserGuide/files/image013.jpg?raw=true) + +### Associating Rubrics + +6. To create a new rubric for evaluating your digital object, navigate to the **Rubrics** page via the menu bar, and select the **Create New Rubric** card in the bottom right. + ![Create a new rubric](https://github.com/MaayanLab/FAIRshake/blob/master/FAIRshakeHub/static/file/FAIRshakeUserGuide/files/image015.jpg?raw=true) +7. Use the autocomplete **Metrics** field to identify existing metrics, or specific assessment questions, that may be relevant for your rubric. Select as many metrics as you would like; these will be included in your FAIR assessment for the digital objects associated with your rubric. + ![Auto-complete FAIR metrics](https://github.com/MaayanLab/FAIRshake/blob/master/FAIRshakeHub/static/file/FAIRshakeUserGuide/files/image017.jpg?raw=true) + - A pre-existing rubric with list of universal FAIR metrics developed by Wilkinson et al. (*Scientific Data*, 2016) can be found here. + ![FAIR metrics rubric developed by fairmetrics.org](https://github.com/MaayanLab/FAIRshake/blob/master/FAIRshakeHub/static/file/FAIRshakeUserGuide/files/image019.jpg?raw=true) +1. Submit the form to finish building a rubric. Note that it is not necessary to meticulously cover all FAIR principles in your rubric, as long as they are broadly represented, and the metrics you choose can reasonably determine the FAIRness of your object within the broader community. + +### Performing Assessments + +9. Ensure that all digital objects in your project have been associated with a rubric. +10. Click on the **Assess** button in the top left corner of a registered digital object's icon, either from the project page or from the digital object page. +11. Select the rubric you would like to use to assess the tool -- it does *not* need to be the auto-selected rubric -- and confirm that the correct digital object and project (if applicable) are also selected. + ![Selecting a rubric for assessment](https://github.com/MaayanLab/FAIRshake/blob/master/FAIRshakeHub/static/file/FAIRshakeUserGuide/files/image027.jpg?raw=true) + ![Assigning the assessment to a project](https://github.com/MaayanLab/FAIRshake/blob/master/FAIRshakeHub/static/file/FAIRshakeUserGuide/files/image029.jpg?raw=true) +12. Begin the manual assessment of the digital object. For each metric, carefully read and consider the prompts, and then respond to the best of your knowledge. Add any comments or URLS as needed. + ![Example manual assessment page](https://github.com/MaayanLab/FAIRshake/blob/master/FAIRshakeHub/static/file/FAIRshakeUserGuide/files/image047.jpg?raw=true) + - Click on the metric card to the left of any prompt to see more detailed explanations about the metric. + ![Details about a single metric](https://github.com/MaayanLab/FAIRshake/blob/master/FAIRshakeHub/static/file/FAIRshakeUserGuide/files/image033.jpg?raw=true) + - For each metric, you can also examine how other digital objects have scored by clicking the **View Assessments** button from the metric page. + ![View other assessments associated with a rubric](https://github.com/MaayanLab/FAIRshake/blob/master/FAIRshakeHub/static/file/FAIRshakeUserGuide/files/image035.jpg?raw=true) +13. Once finished, you may save, publish, or delete the assessment. + - **Publishing** the assessment prevents any further changes, as each digital object in a project can be assessed only once with a given rubric. An insignia and analytics will be generated for the object. + - **Saving** the assessment means the responses, comments, and URLs will not be public, but will be visible to the creators of the tool, project, and assessment. + - **Deleting** the assessment will remove all data and responses from the assessment. + +#### Return to [Documentation](./) diff --git a/src/pages/documentation/KGAssertions.md b/src/pages/documentation/KGAssertions.md new file mode 100644 index 0000000..8bb5436 --- /dev/null +++ b/src/pages/documentation/KGAssertions.md @@ -0,0 +1,64 @@ +--- +layout: '@/layouts/Documentation.astro' +title: Knowledge Graph Assertions +label: KGAssertions +short_description: The CFDE Data Distillery Partnership aims to integrate data assertions + across DCCs into a functional knowledge graph for knowledge query + and discovery. The partnership has collected "distilled" data relationships + from each DCC to be unified in a knowledge graph model with controlled + ontology and vocabulary terms for exploring pre-defined, biologically + relevant use cases. +--- +# Data Distillery Knowledge Graph Assertions + +## Table of Contents + - [Introduction](#introduction) + - [Resources](#resources) + - [Generating Assertions](#generating-assertions) + +## Introduction + +**Knowledge graphs** are often used to represent and visualize the semantic relationships within an interconnected dataset. They are also helpful for querying and exploring those relationships between different data types, as well as for imputing knowledge through machine learning-based methods. + +The CFDE Data Distillery Partnership is building a **Data Distillery Knowledge Graph (DDKG)** that integrates data from each DCC into a unified knowledge graph. Each DCC provides standardized, machine-readable assertions generated from their datasets -- the "distilled" data" -- which follow a common schema. Specifically, the DDKG schema is based on the Unified Biomedical Knowledge Graph (UBKG) schema originating from the Unified Medical Language System (UMLS), and supports over 180 ontologies for representing Common Fund data. The goal of the project is to provide a single resource for querying and visualizing cross-DCC data relationships in order to further knowledge discovery and integration across the CFDE. + +## Resources +- CFDE Data Distillery Project Github Repository +- CFDE Data Distillery User Guide + +## Generating Assertions + +1. Before generating any assertions, identify the type of data and knowledge you want to capture -- what data sources are you using? What type of data does each source provide? What types of relationships exist between the different data types and data sources? + - These assertions will usually take the form of a **triple** consisting of a **subject**, **predicate**, and **object**. As an example, the Illuminating the Druggable Genome (IDG) DCC provides data on the relationships between compounds, diseases, and understudied proteins. An assertion that bipolar disorder is an indication for the drug aripiprazole may be represented as follows using PubChem and SNOMED ontology terms: + ``` + PUBCHEM 60795 indication SNOMED 13746004 + ``` + +2. Review the list of ontologies and vocabularies currently supported by the DDKG [here](https://github.com/TaylorResearchLab/CFDE_DataDistillery/blob/main/user_guide/ontology%20neo4j%20SABs%20and%20sample%20codes%20-%20ontology%20neo4j%20SABs%20and%20sample%20codes.csv), and make note of the overlap with your dataset. While edges/relationships can be described with a string, node identifiers should be an Internationalized Resource Identifier (IRI) or an ontology term from an integrated Source Abbreviation (SAB). + - For any unsupported terms or complicated situations in your data, check with the DDKG team on the best course of action. + +3. Review the current DDKG ingestion format, which can be found [here](https://github.com/TaylorResearchLab/CFDE_DataDistillery/blob/main/user_guide/Distillery_Ingest_format%20-%20Instructions.csv). Briefly, a complete set of assertions requires two tab-separated (TSV) text files, each with a set of unique columns: + + - **`nodes.tsv`**: A table containing metadata on entity nodes + - `node_id` **(Required)**: The unique identifier for the node; preferably a term in the format `{SAB}{Code}`, e.g. `PUBCHEM 60795` + - `node_namespace`: The source abbreviation (SAB) for the term, e.g. `PUBCHEM` + - `node_label` **(Required)**: The preferred term or human-readable label for the node, e.g. `aripiprazole` + - `node_definition`: A definition for the node + - `node_synonyms`: Text synonyms for the node, if any; these should be separated by vertical bars `|` + - `node_dbxrefs`: External database references for the node, preferably in `{SAB}{Code}` format + - `value`: A numeric decimal value, usually reserved for nodes representing some quantitative measurement + - `lowerbound`: A numeric decimal value representing the *minimum* allowed value for the node, if applicable + - `upperbound`: A numeric decimal value representing the *maximum* allowed value for the node, if applicable + - `units`: Units for the `value`, `lowerbound`, and `upperbound` field + - **`edges.tsv`**: A table describing relationships between entities defined in `nodes.tsv` + - `subject_id` **(Required)**: An existing `node_id` that is the subject of the assertion, e.g. `PUBCHEM 60795` + - `relationship` **(Required)**: A custom string or an IRI referencing a relational ontology relationship type, e.g. `indication` + - The DDKG recommends relationship IDs be obtained from the Relations Ontology (RO), but concise custom strings are allowed for relationships not covered within the RO. + - `object_id` **(Required)**: An existing `node_id` that is the object of the assertion, e.g. `SNOMED 13746004` + - `evidence_class`: Any evidence or value specific to the SAB and relevant to the relationship + +4. Begin generating assertions according to the required format. Although this process will vary depending on the dataset, one way to complete this task would be to first build `edges.tsv`, then fill in `nodes.tsv`. + a. First identify all relationships captured within a dataset, identify the ontologies/SABs involved, and build the `edges.tsv` table with just the triples. + b. Then extract all unique nodes represented within `edges.tsv`, identify the relevant SAB terms and metadata, and fill in `nodes.tsv`. + +#### Return to [Documentation](./) diff --git a/src/pages/documentation/OpenAPI.md b/src/pages/documentation/OpenAPI.md new file mode 100644 index 0000000..8ebbc0b --- /dev/null +++ b/src/pages/documentation/OpenAPI.md @@ -0,0 +1,409 @@ +--- +layout: '@/layouts/Documentation.astro' +title: OpenAPI & SmartAPI +label: OpenAPI +short_description: > + The OpenAPI specification allows for the standardization of + application programming interfaces (APIs), and facilitates + their interoperability. + + + The SmartAPI project builds on top of the OpenAPI specifications + to maximize the findability, accessibility, interoperability, + and reusability (FAIRness) of web-based tools, especially those + within the biomedical sphere. Through richer metadata descriptions, + SmartAPI enables users to search and use a connected network of tools. +--- +# OpenAPI and SmartAPI + +## Table of Contents + - [Introduction](#introduction) + - [Creating API Specifications](#creating-api-specifications) + - [Requests](#requests) + - [Responses](#responses) + - [Resources](#resources) + +## Introduction +Application programming interfaces (APIs) provide a set of protocols that broadly allow different software programs to communicate. In the biomedical sciences, many tools and resources have APIs that facilitate querying, downloading, or computing on the available data. For instance, the GTEx DCC provides APIs for programmatically retrieving RNA-seq data, while the GlyGen APIs return information related to different glycans, proteins, and motifs. + +The OpenAPI specification language, developed by the OpenAPI initiative, is a standardized language for succinctly describing an API’s functionality, including its inputs and outputs, without requiring users to have any prior knowledge of the backend. OpenAPI specifications are programming-language agnostic, and the standardized format is supported by resources such as Swagger, which allows for the efficient testing, development, and publishing of API specifications. Within the CFDE, the OpenAPI specification language has the potential to improve the interoperability of DCC APIs with each other and with tools external to the consortium. + +The SmartAPI specification language extends OpenAPI to capture more metadata to maximize the findability, accessibility, interoperability, and reusability (FAIRness) of web-based APIs, especially within the context of biomedical big data. Specifically, SmartAPIs allow for additional metadata fields, such as requiring an API version and a link to the original tool terms of service as well as including a space to list more contacts or external resources related to the API. In addition to the specifications, SmartAPI also provides an editor for writing and testing APIs as well as a registry of 200+ APIs that have already been deployed and published, including several DCC tools. Currently, SmartAPI is supported by the Biomedical Data Translator program from the National Center for Advancing Translational Sciences (NCATS). + +## Creating API Specifications + +As an example, the following tutorial will adapt two endpoints from the FAIRshake v2 API specifications. Note that this document is not meant to be a comprehensive manual for API development, but rather an introductory guide for writing OpenAPI/SmartAPI specifications. + +1. Initialize your root document with metadata and server information. OpenAPI/SmartAPI specifications can be written in either JSON or YAML, but the information contained should be generally the same regardless of format, and include the following required fields, as well as any relevant optional fields: + + - `openapi`: Semantic version number of OpenAPI specification + - `info`: API metadata + - `termsOfService`: URL to terms of service for API + - `version`: Semantic Version of the API definition + - `contact`: Name, email, and role of contact information + - `servers`: List of available servers called by API + - `paths`: List of endpoints/operations for the API + +

+ **JSON** + ``` + { + "openapi": "3.0", + "info": { + "title": "FAIRshake API", + "version": "1.0", + "description": "Web interface for scoring biomedical digital objects", + "termsOfService": "https://fairshake.cloud/", + "contact": { + "name": "John Doe", + "email": "johndoe@email.com", + "x-role": "responsible developer" + } + }, + "servers": [ + { + "url": "https://fairshake.cloud", + } + ], + "paths": { ... } + } + ``` + + **YAML** + ``` + openapi: 3.0 + info: + title: FAIRshake API + version: 1.0 + description: Web interface for scoring biomedical digital objects + termsOfService: https://fairshake.cloud/ + contact: + name: John Doe + email: johndoe@email.com + x-role: responsible developer + servers: + - url: https://fairshake.cloud + paths: + ... + ``` + +2. Identify the core functionality: What queries are available, and from which servers? What types of information can be extracted? Are any credentials needed to access certain data? + + - In our tutorial, we are concerned with two endpoints: a POST request which creates a new digital object from an integer `id`, a pre-defined `type`, a string `url`, and a list of `authors`; and a GET request to search through a list of existing digital objects using the `url` parameter. + +### Requests + +3. For each potential endpoint, determine the type of request method (POST, GET, DELETE, etc.) and the required input values and content type. Each of these should be listed under `paths` in the document. + + - For a POST method, the input will take the form of a Request Body Object, which also requires a media type. The most common media types are `text/plain` for plaintext inputs, `application/json` for JSON-formatted inputs, and `multipart/form-data` for single or multiple file upload inputs. Below, we define our example POST request. + +

+ **Example input** + ``` + { + "id": 1, + "type": "tool", + "title": "NewDigitalObject", + "url": "https://newdigitalobject.com", + "authors": [ + "John Doe", + "Jane Doe" + ] + } + ``` + + **JSON** + ``` + "paths": { + "/create_digital_object": { + "post": { + "operationId": "create_digital_object", + "description": "Create a digital object", + "requestBody": { + "required": true, + "content": { + "application/json": { + "schema": { + "type": "object", + "required": [ + "url", + "title" + ], + "properties": { + "id": { + "type": "integer" + }, + "type": { + "type": "string", + "enum": [ + "data", + "repo", + "test", + "tool" + ] + }, + "title": { + "type": "string" + }, + "url": { + "type": "string", + "maxLength": 255, + "minLength: 1 + }, + "authors": { + "type": "array", + "items": { + "type": "string", + }, + "uniqueItems": true + } + } + } + } + } + }, + "responses": { ... } + } + } + } + + ``` + + **YAML** + ``` + paths: + /create_digital_object: + post: + operationId: create_digital_object + description: Create a digital object + requestBody: + required: true + content: + application/json: + schema: + type: object + required: + - url + - title + properties: + id: + type: integer + type: + type: string + enum: + - data + - repo + - test + - tool + title: + type: string + url: + type: string + maxLength: 255 + minLength: 1 + authors: + type: array + items: + type: string + uniqueItems: true + ``` + + - For a GET method, the input may require defined parameters, which can usually be located within the path or the header of a request. In the example below, we search for our newly added digital object by its title. + +

+ **Example path** + ``` + https://fairshake.cloud/get_digital_object?title=NewDigitalObject" + ``` + + **JSON** + ``` + "paths": { + "/create_digital_object": { ... }, + "/get_digital_object": { + "get": { + "operationId": "get_digital_object", + "description": "Get a list of digital objects", + "parameters": [ + { + "name": "url", + "in": "query", + "description": "URL of digital object", + "required": false, + "type": "string" + }, + { + "name": "title", + "in": "query", + "description": "Title of digital object", + "required": true, + "type": "string" + } + ], + "responses": { ... } + } + } + } + ``` + + **YAML** + ``` + paths: + /create_digital_object: + ... + /get_digital_object: + get: + operationId: get_digital_object + description: Get a list of digital objects + parameters: + - name: url + in: query + description: URL of digital object + required: false + type: string + - name: title + in: query + description: Title of digital object + required: true + type: string + ``` + +### Responses + +4. For each potential endpoint, determine the type of response that should be returned for each status. The requested data should be returned only when the status code is 20X (200, 201, etc.). Defining the schema for a response will be similar to defining a schema for an input or request body. In our example GET request, a successful response is a list of digital objects that all must follow the same schema as the POST request defined earlier for submitting a digital object. + +

+ **Example response** + ``` + { + "count": 1 + "results": [ + { + "id": 1, + "type": "tool", + "title": "NewDigitalObject", + "url": "https://newdigitalobject.com", + "authors": [ + "John Doe", + "Jane Doe" + ] + } + ] + } + ``` + + **JSON** + ``` + "paths": { + "/get_digital_object": { + "get": { + "operationId": "get_digital_object", + "description": "Get a list of digital objects", + "parameters": { ... }, + "responses": { + "200": { + "description": "Successfully get a list of digital objects", + "content": { + "application/json": { + "schema": { + "type": "object", + "properties": { + "count": { + "type": "integer" + }, + "results": { + "type": "array", + "items": { + "type": "object", + "properties": { + "id": { + "type": "integer + }, + "type": { + "type": "string", + "enum": [ + "data", + "repo", + "test", + "tool" + ] + }, + "url": { + "type": "string", + }, + "authors": { + "type": "array", + "items": { + "type": "string", + } + } + } + } + } + } + } + } + } + } + } + } + } + } + ``` + + **YAML** + ``` + paths: + /get_digital_object: + get: + operationId: get_digital_object + description: Get a list of digital objects + parameters: + ... + responses: + 200: + description: Successfully get a list of digital objects + content: + application/json: + schema: + type: object + properties: + count: + type: integer + results: + type: array + items: + type: object + properties: + id: + type: integer + type: + type: string + enum: + - data + - repo + - test + - tool + url: + type: string + authors: + type: array + items: + type: string + ``` + Note that OpenAPI/SmartAPI allow for the definition of `Components`, which are reusable objects within a single API specification. These can be `schemas`, `parameters`, `requestBodies`, or other objects that may come up in multiple paths. In the examples above, the digital object schema could have been defined as a `schema` component, and the reference `#/components/schemas/DigitalObject` could have been used in place of its full definition under the `create_digital_object` `requestBody` and `responses` as well as the `get_digital_object` `responses`. + + - For error codes (4XX, 5XX), you may choose to “catch” these errors by defining some behavior that should occur if the error is triggered. + + 5. Fill in the rest of the path specifications according to the general steps above, based on your API. For more complicated requests or schemas that aren't covered here, refer to the full OpenAPI or SmartAPI documentation. + +## Resources + +- SmartAPI Registry +- Example SmartAPI v3.0 specifications +- Swagger Editor + +
+While not required, it is highly recommended to use a dedicated OpenAPI or SmartAPI editor, such as Swagger, to generate API specifications. Such tools designated for writing OpenAPIs/SmartAPIs can help with debugging and auto-formatting, as well as with testing and publishing API documentation. + +#### Return to [Documentation](./) diff --git a/src/pages/documentation/PWBMetanodes.md b/src/pages/documentation/PWBMetanodes.md new file mode 100644 index 0000000..be4520f --- /dev/null +++ b/src/pages/documentation/PWBMetanodes.md @@ -0,0 +1,108 @@ +--- +layout: '@/layouts/Documentation.astro' +title: Playbook Metanodes +label: PWBMetanodes +short_description: The Playbook Workflow Builder (PWB) is a web-based + knowledge resolution platform being developed by the CFDE Workflow + Playbook Partnership and consisting of a growing network of datasets, + semantically annotated API endpoints, and visualization tools + from across the CFDE. Users can construct workflows from the individual building blocks, + termed "metanodes", with little effort or technical expertise + required. +--- +# Playbook Workflow Metanodes + +## Table of Contents + - [Introduction](#introduction) + - [Resources](#resources) + - [Building Workflows](#building-workflows) + - [Developing Metanodes](#developing-metanodes) + - [Core Concepts](#core-concepts) + - [Contribution Guidelines](#contribution-guidelines) + +## Introduction + +The Playbook Workflow Builder (PWB) consists of a network of biomedical datasets, API endpoints, and other developed tools from both within and external to the CFDE. Users can traverse the graph database visually by selecting various options for some following data set or imputation task. Each meta node within the PWB can be independently constructed or used, preferably by someone already familiar with a given tool’s functionality. To use the PPWB, users start from a list of possible inputs, and then sequentially select the different transformations, queries, visualizations, or other computations they wish to add to the workflow. + +## Resources + +For more detailed tutorials on using or developing for the PPWB, please refer to the following guides: +- PWB User Guide +- PWB Developer Guide + +## Building Workflows + +The following tutorial, adapted from the PWB User Guide linked above, walks through how to build a workflow for investigating a specific gene. + +1. Navigate to the PPWB interface. You should see a display with multiple input "cards" to choose from, which can be filtered using the toggles on the left. + +2. Select the input card you would like and follow instructions for submitting or uploading the input. + - In our example, we will click the **Gene Input** card to enter the gene ACE2, and click the submit button when done. + - Note that the PPWB provides autocomplete suggestions for some entity input fields, such as genes. It is possible to move forward with a non-autocomplete suggested input in these cases, at risk of breaking the workflow in a future step. + +3. You should now see a new set of cards that all represent different operations available for your previously entered input. + - In our example, the new cards will all be gene-centric options such as identifying product records in GlyGen, finding regulatory elements from the Linked Data Hub, or querying LINCS L1000 signatures which reverse the effect of the gene's knockout. + +4. Select a new card to add to the workflow and wait for the operation to complete. Most operations should provide a new data view or visualization. + - As an example, we can select the **Query GTEx Median Tissue Expression** card, which displays a table of tissues from GTEx where the input gene is most significantly expressed. + - Some operations, including the example, rely on on-demand API calls, and can be re-computed or updated using the **Recompute** button at the bottom of the page. + +6. To continue the workflow, click the **+** breadcrumb at the top of the page to choose from a new set of option cards, and continue with the analysis. + +5. If you have reached the end of a workflow, you have two main options: + - You may return to any of the previous nodes by clicking on the corresponding "breadcrumb" graph at the top of the page, and select more operations from a previous node. All "branches" of the workflow, and their results, will be saved. + - You may move on to save or publish your workflow. + +6. You can view the full workflow, including all results and inputs, in **Report Mode** by clicking the **View Report** button at the top right corner of the screen. + - You can add a title and description of the overall workflow at the top of the page. + - Re-submitting or re-computing any of the steps will automatically update the following steps in the workflow. + - Playbook workflows can be saved to your account, shared via link, or published to the **Published Playbooks** section of the website. + +## Developing Metanodes + +### Core Concepts + +The PPWB is designed to allow for the independent and parallel development of individual components, known as **metanodes**. There are two main types of metanodes, `Data` and `Process`: +- **Data:** Entities that can be inputs/outputs of processes and have a designated "view" within the PPWB, e.g. a tabular view for gene count matrix data +- **Process:** Operations that act on an input data type to generate an output data type. Processes are divided into two subtypes: + - **Prompt:** A user-driven action, such as an input form or a selection interface where the user decides the operation + - **Resolver:** A programmatic action, such as an API call or a mathematical transformation, where the system automatically executes a pre-determined step + +### Contribution Guidelines + +1. Ensure that you have installed all system dependencies by following the Installation Guide. + +2. Clone the repository from Github and checkout a new branch. + +3. Install dependencies and initialize the development interface using the following commands: + ``` + npm i + npm run dev + ``` + +4. Create new component directories under the `components` directory. All components should contain at least the following files: + - `index.ts` or `index.tsx`: The file containing your exported meta node(s). For details on a specific meta node type, please refer to the full Developer Guide. + - `package.json`: Name and other metadata for the new meta node, as follows: + + ``` + { + "name": "mycomponent", + "version": "1.0.0", + "license": "CC-BY-NC-SA-4.0", + "author": "Your Name ", + "contributors": [], + "main": "index.tsx", + "private": true, + "dependencies": {}, + "devDependencies": {} + } + ``` + +5. Once your component is defined, run the following command to add the new meta node to the interface for development and testing on your local server: + ``` + npm run codegen:components + ``` + +6. Once the meta node is functional, submit a pull request to the remote main branch, and add any documentation as needed. + +#### Return to [Documentation](./) diff --git a/src/pages/documentation/RNA-seq.md b/src/pages/documentation/RNA-seq.md new file mode 100644 index 0000000..e715f7e --- /dev/null +++ b/src/pages/documentation/RNA-seq.md @@ -0,0 +1,5 @@ +--- +layout: '@/layouts/Documentation.astro' +title: RNA-seq Standard Pipeline +label: RNA-seq +--- diff --git a/src/pages/documentation/SubmissionSystem.md b/src/pages/documentation/SubmissionSystem.md new file mode 100644 index 0000000..9e445f8 --- /dev/null +++ b/src/pages/documentation/SubmissionSystem.md @@ -0,0 +1,5 @@ +--- +layout: '@/layouts/Documentation.astro' +title: CFDE Data and Metadata Submission System +label: SubmissionSystem +--- diff --git a/src/pages/documentation/WebSpecs.md b/src/pages/documentation/WebSpecs.md new file mode 100644 index 0000000..62346f3 --- /dev/null +++ b/src/pages/documentation/WebSpecs.md @@ -0,0 +1,84 @@ + +--- +layout: '@/layouts/Documentation.astro' +title: Web Specifications +label: WebSpecs +--- + +# Web Design Specifications + +The CFDE Workbench website is built using Next.js, Material UI, and Tailwind CSS. You can access the template of this website at drc-template. + +## Typography + +### Titles and Headers + +| Name | Font Family | Size | Weight | Transform | +|---------|-------------|------|---------|-----------| +| Title | Hanken Grotesk | 40px | 500 | Uppercase | +| Title (small) | Hanken Grotesk | 24px | 500 | Uppercase | +| h1 | Hanken Grotesk | 40px | 500 | - | +| h2 | Hanken Grotesk | 32px | 500 | - | +| h3 | Hanken Grotesk | 24px | 500 | - | +| h4 | Hanken Grotesk | 22px | 500 | - | +| h5 | Hanken Grotesk | 20px | 500 | - | + +### Body Text and Navigation + +| Name | Font Family | Size | Weight | Transform | Color | +|---------|-------------|------|---------|-----------|--------| +| subtitle1 | Hanken Grotesk | 16px | 500 | - | - | +| subtitle2 | Hanken Grotesk | 15px | 500 | - | - | +| body1 | DM Sans | 16px | 500 | - | - | +| body2 | DM Sans | 15px | 500 | - | - | +| caption | Hanken Grotesk | 14px | 500 | - | - | +| nav | Hanken Grotesk | 16px | 600 | Uppercase | #2D5986 | +| footer | DM Sans | 16px | 400 | - | - | + +### Data Portal Stats + +| Name | Font Family | Size | Weight | Color | +|---------|-------------|------|---------|--------| +| stats_h3 | Hanken Grotesk | 24px | 500 | #9E9E9E | +| stats_sub | Hanken Grotesk | 16px | 500 | #9E9E9E | +| stats_sub_small | Hanken Grotesk | 14px | 500 | #9E9E9E | +## Color Palette +### Primary Colors + +
+
+
+ Primary Main + #C3E1E6 +
+
+
+ Primary Light + #DBEDF0 +
+
+
+ Primary Dark + #84A9AE +
+
+ +### Secondary Colors + +
+
+
+ Secondary Main + #2D5986 +
+
+
+ Secondary Light + #9CBCDE +
+
+
+ Secondary Dark + #122436 +
+
diff --git a/src/pages/documentation/index.md b/src/pages/documentation/index.md new file mode 100644 index 0000000..e65853c --- /dev/null +++ b/src/pages/documentation/index.md @@ -0,0 +1,10 @@ +--- +layout: '@/layouts/Documentations.astro' +--- + +### Documentation + +This page contains descriptions of CFDE consortium standards, protocols, user guides, and other documents generated by the CFDE centers, partnerships, and Data Coordination Centers (DCCs). + +These documents are intended to provide CFDE-partnered DCCs, other Common Fund (CF) programs, and the broader research community with documentation about digital object products developed by the CFDE. While many of these documents were created within the context of the CFDE, they may be useful and generalizable for other researchers who are interested in using or interoperating with CF datasets, or who are interested in improving the FAIRness of their own resources. + From 52e2dfad2dbfad36987b38feb6676f28be7a2b19 Mon Sep 17 00:00:00 2001 From: Heesu Kim Date: Fri, 31 Jan 2025 13:50:36 -0500 Subject: [PATCH 03/10] fix tags format --- ...AP Undergraduate Student Internship Program 2024-08-16.md | 3 ++- src/pages/outreach/2024 SPARC FAIR Codeathon 2024-08-12.md | 3 ++- .../2025 Voice AI Symposium and Hackathon 2025-04-24.md | 4 +++- src/pages/outreach/4DN Hackathon 2024-03-21.md | 3 ++- src/pages/outreach/4DN Summer Internship Program.md | 3 ++- ...ts' Guide to the Common Fund Data Ecosystem 2024-11-06.md | 3 ++- ...ning Program in Biomedical Big Data Science 2025-02-01.md | 4 +++- ...tissue of origin from GTEx RNA-seq profiles 2024-09-12.md | 3 ++- .../Bridge2AI Fall 2024 Leadership Meeting 2024-12-06.md | 3 ++- src/pages/outreach/CFDE 2024 Fall Meeting 2024-10-23.md | 5 +++-- src/pages/outreach/CFDE Centers 2025-12-31.md | 3 ++- ...mics Workbench Virtual Summer Workshop 2024 2024-07-25.md | 3 ++- src/pages/outreach/CFDE Pediatric PowerUp I 2024-06-28.md | 3 ++- src/pages/outreach/CFDE Pediatric PowerUp II 2024-08-23.md | 3 ++- src/pages/outreach/CFDE Webinar Series 2024-04-26.md | 3 ++- src/pages/outreach/CFDE Webinar Series 2024-05-31.md | 3 ++- src/pages/outreach/CFDE Webinar Series 2024-06-28.md | 3 ++- src/pages/outreach/CFDE Webinar Series 2024-07-26.md | 3 ++- src/pages/outreach/CFDE Webinar Series 2024-08-30.md | 3 ++- src/pages/outreach/CFDE Webinar Series 2024-09-27.md | 3 ++- src/pages/outreach/CFDE Webinar Series 2024-10-25.md | 3 ++- src/pages/outreach/CFDE Webinar Series 2024-11-22.md | 3 ++- src/pages/outreach/CFDE Webinar Series 2025-01-31.md | 3 ++- .../outreach/CFDE at Bio-IT World Boston 2025 2025-04-04.md | 3 ++- ...elligent Systems for Molecular Biology 2025 2025-07-24.md | 3 ++- ...an Society of Human Genetics Annual Meeting 2024-11-09.md | 3 ++- ...an Society of Human Genetics Annual Meeting 2025-10-18.md | 3 ++- .../CFDE-GlyGen Summer Interns Symposium 2024 2024-07-25.md | 3 ++- ...nt Workshop: A Discussion of Data Resources 2024-07-25.md | 3 ++- ...he BD2K-LINCS Data Coordination and Integration Center.md | 3 ++- src/pages/outreach/From Atlas to Practice 2024-09-27.md | 3 ++- ...search Program\342\200\231s Spring Webinar 2024-05-29.md" | 3 ++- .../GlyGen & CFDE Workshop Summer 2023 2023-08-07.md | 3 ++- .../GlyGen-CFDE Summer Internship Program 2024-07-26.md | 3 ++- src/pages/outreach/HuBMAP Visible Human MOOC (VHMOOC).md | 3 ++- src/pages/outreach/IMPC Data API Workshop 2024-05-20.md | 3 ++- ...n disease through data on the IMPC portal 2024-11-20.md | 3 ++- ...cal Data Science, CFDE edition (ISBDS-CFDE) 2024-07-26.md | 3 ++- ...INCS Summer Trainees Virtual Symposium 2024 2024-08-08.md | 3 ++- src/pages/outreach/March All-Hands Meeting 2024-03-20.md | 3 ++- src/pages/outreach/MoTrPAC Office Hours.md | 3 ++- ...I-Driven Gene Set Analysis with GeneSetCart 2025-01-23.md | 3 ++- ...1s and Related Dementias (CARD) Fellowship 2026-05-12.md" | 3 ++- .../Playbook Workflow Builder USE-A-THON 2023-11-16.md | 5 +++-- ...book Workflow Builder Virtual Workshop 2024 2024-06-25.md | 3 ++- src/pages/outreach/SPARC Office Hours.md | 3 ++- .../outreach/SPARC at NANS Annual Meeting 2024 2024-01-21.md | 3 ++- src/pages/outreach/SPARC at SfN 2024 2024-10-09.md | 3 ++- ... Human Vasculature in 3D Kaggle Competition 2024-02-06.md | 3 ++- ...cations for the CUSP 2025 Summer Internship 2025-01-25.md | 4 +++- ...ortium Undergraduate Student Program (CUSP) 2024-08-31.md | 3 ++- ...arch Program in Biomedical Big Data Science 2024-08-09.md | 3 ++- .../outreach/The 2024 HuBMAP Fall Hackathon 2024-10-04.md | 3 ++- .../outreach/The HuBMAP JumpStart Fellowship 2026-06-01.md | 3 ++- ... Fund\342\200\231s Complement-ARIE program 2025-12-31.md" | 3 ++- src/pages/outreach/UDN Grand Rounds 2024-06-13.md | 3 ++- .../Voice AI Summer School Lecture Series 2024-07-19.md | 3 ++- ...kshop at the Festival of Genomics & Biodata 2024-06-13.md | 3 ++- 58 files changed, 121 insertions(+), 60 deletions(-) diff --git a/src/pages/outreach/2024 HuBMAP Undergraduate Student Internship Program 2024-08-16.md b/src/pages/outreach/2024 HuBMAP Undergraduate Student Internship Program 2024-08-16.md index a19b708..9c9874c 100644 --- a/src/pages/outreach/2024 HuBMAP Undergraduate Student Internship Program 2024-08-16.md +++ b/src/pages/outreach/2024 HuBMAP Undergraduate Student Internship Program 2024-08-16.md @@ -16,7 +16,8 @@ short_description: "The Undergraduate Student Internship Program provides the op \ and training from\_NIH Human Biomolecular Atlas Program (HuBMAP) labs over the\ \ summer." start_date: '2024-05-20T00:00:00-04:00' -tags: '["internship"]' +tags: +- internship title: 2024 HuBMAP Undergraduate Student Internship Program --- Applications will be accepted from November 27, 2023 until February 1, 2024.

Internship experiences can be computational or experimental. The lab descriptions below identify which experiences will be computational and which will be experimental.

Applicants can indicate their preference for computational or experimental internships on the application.

Questions? Email us at: internshipapply@hubmapconsortium.org \ No newline at end of file diff --git a/src/pages/outreach/2024 SPARC FAIR Codeathon 2024-08-12.md b/src/pages/outreach/2024 SPARC FAIR Codeathon 2024-08-12.md index 2aec663..cb7c82a 100644 --- a/src/pages/outreach/2024 SPARC FAIR Codeathon 2024-08-12.md +++ b/src/pages/outreach/2024 SPARC FAIR Codeathon 2024-08-12.md @@ -12,7 +12,8 @@ link: https://sparc.science/news-and-events/events/2024-sparc-fair-codeathon short_description: The SPARC Data and Resource Center (DRC), with funding from the National Institutes of Health, will host a cloud-based three-day codeathon. start_date: '2024-08-10T00:00:00-04:00' -tags: '["competition"]' +tags: +- competition title: 2024 SPARC FAIR Codeathon --- The SPARC Data and Resource Center (DRC), with funding from the National Institutes of Health, will host a cloud-based three-day codeathon. \ No newline at end of file diff --git a/src/pages/outreach/2025 Voice AI Symposium and Hackathon 2025-04-24.md b/src/pages/outreach/2025 Voice AI Symposium and Hackathon 2025-04-24.md index 5bd5c22..46108e9 100644 --- a/src/pages/outreach/2025 Voice AI Symposium and Hackathon 2025-04-24.md +++ b/src/pages/outreach/2025 Voice AI Symposium and Hackathon 2025-04-24.md @@ -14,7 +14,9 @@ short_description: "The 2025 Bridge2AI \u2013 Voice Symposium and Hackathon is a \ patients, clinicians, technology experts and students, all with a shared passion\ \ for the transformative potential of voice biomarkers in healthcare. " start_date: '2025-04-22T10:00:00-05:00' -tags: '["hackathon", "symposium"]' +tags: +- hackathon +- symposium title: 2025 Voice AI Symposium and Hackathon --- The 2025 Bridge2AI – Voice Symposium and Hackathon is an interactive conference that brings together scientists, ethicists, advocates, patients, clinicians, technology experts and students, all with a shared passion for the transformative potential of voice biomarkers in healthcare. \ No newline at end of file diff --git a/src/pages/outreach/4DN Hackathon 2024-03-21.md b/src/pages/outreach/4DN Hackathon 2024-03-21.md index 1760523..a3ce24b 100644 --- a/src/pages/outreach/4DN Hackathon 2024-03-21.md +++ b/src/pages/outreach/4DN Hackathon 2024-03-21.md @@ -15,7 +15,8 @@ short_description: "4DN Hackathon offers participants the chance to explore geno \ organization, build something novel, learn from peers, and get familiar with the\ \ 4DN program\u2019s data and research!" start_date: '2024-03-18T00:00:00-04:00' -tags: '["competition"]' +tags: +- competition title: 4DN Hackathon --- The 4D Nucleome program is accepting applications for the 2024 4DN Hackathon, which will be hosted at the University of Washington in Seattle, Washington from March 18-21st, 2024. The hackathon is open to all students, faculty, and staff from the general scientific community – no coding experience is required. This opportunity offers participants the chance to explore genome organization, build something novel, learn from peers, and get familiar with the 4DN program’s data and research! 40-50 applicants will be selected, and travel and accommodations will be completely supported. Please direct all questions to: hack4dnucleome@gmail.com. \ No newline at end of file diff --git a/src/pages/outreach/4DN Summer Internship Program.md b/src/pages/outreach/4DN Summer Internship Program.md index 60a48f8..bd75be6 100644 --- a/src/pages/outreach/4DN Summer Internship Program.md +++ b/src/pages/outreach/4DN Summer Internship Program.md @@ -14,7 +14,8 @@ short_description: The 4DN Summer Undergraduate Program for Excellence in Resear (SUPER) is seeking applications for a paid summer research internship for undergraduate students. Students will be hosted by labs participating in the 4DN program, studying the structure and function of the nucleus. -tags: '["internship"]' +tags: +- internship title: 4DN Summer Internship Program --- The 4DN Summer Undergraduate Program for Excellence in Research (SUPER) is seeking applications for a paid summer research internship for undergraduate students. Students will be hosted by labs participating in the 4DN program, studying the structure and function of the nucleus. The individual opportunities are experimental, computational or both in labs using genomics, imaging or both. The internship will provide an opportunity for students to build connections, gain scientific skills, and conduct research. NIH encourages the participation of individuals from populations that are underrepresented in the biomedical, clinical, behavioral and social sciences. \ No newline at end of file diff --git a/src/pages/outreach/A Human Geneticists' Guide to the Common Fund Data Ecosystem 2024-11-06.md b/src/pages/outreach/A Human Geneticists' Guide to the Common Fund Data Ecosystem 2024-11-06.md index 26086aa..d6fcfcf 100644 --- a/src/pages/outreach/A Human Geneticists' Guide to the Common Fund Data Ecosystem 2024-11-06.md +++ b/src/pages/outreach/A Human Geneticists' Guide to the Common Fund Data Ecosystem 2024-11-06.md @@ -13,7 +13,8 @@ short_description: An ancillary session at ASHG will be held to share the perspe Knowledge Center (KC), the Data Resource Center (DRC), and the MoTrPAC data coordination center (DCC). start_date: '2024-11-06T11:45:00-07:00' -tags: '["conference"]' +tags: +- conference title: A Human Geneticists' Guide to the Common Fund Data Ecosystem --- An ancillary session at ASHG will be held to share the perspectives about the the NIH Common Fund Data Ecosystem (CFDE) by NIH representatives, the Knowledge Center (KC), the Data Resource Center (DRC), and the MoTrPAC data coordination center (DCC). \ No newline at end of file diff --git a/src/pages/outreach/Accepting Application for the 2025 Summer Research Training Program in Biomedical Big Data Science 2025-02-01.md b/src/pages/outreach/Accepting Application for the 2025 Summer Research Training Program in Biomedical Big Data Science 2025-02-01.md index 099f015..9831107 100644 --- a/src/pages/outreach/Accepting Application for the 2025 Summer Research Training Program in Biomedical Big Data Science 2025-02-01.md +++ b/src/pages/outreach/Accepting Application for the 2025 Summer Research Training Program in Biomedical Big Data Science 2025-02-01.md @@ -18,7 +18,9 @@ short_description: "The LINCS DCC Summer Research Training Program in Biomedical \ data visualization.

Application Deadline: February 1, 2025
Program\ \ Dates: June 2, 2025 \u2013 August 8, 2025 " start_date: '2024-10-01T12:00:00-05:00' -tags: '["training program", "application deadline"]' +tags: +- training program +- application deadline title: Accepting Application for the 2025 Summer Research Training Program in Biomedical Big Data Science --- diff --git a/src/pages/outreach/Biomarker discovery from extracellular (cell-free) RNA-seq and tissue of origin from GTEx RNA-seq profiles 2024-09-12.md b/src/pages/outreach/Biomarker discovery from extracellular (cell-free) RNA-seq and tissue of origin from GTEx RNA-seq profiles 2024-09-12.md index 421f538..d023c89 100644 --- a/src/pages/outreach/Biomarker discovery from extracellular (cell-free) RNA-seq and tissue of origin from GTEx RNA-seq profiles 2024-09-12.md +++ b/src/pages/outreach/Biomarker discovery from extracellular (cell-free) RNA-seq and tissue of origin from GTEx RNA-seq profiles 2024-09-12.md @@ -17,7 +17,8 @@ short_description: Join us for an engaging hands-on workshop where Meenu Sriniva Ecosystem (CFDE) Data Coordinating Center portals followed by an interactive Q&A session. start_date: '2024-09-12T13:00:00-04:00' -tags: '["workshop"]' +tags: +- workshop title: Biomarker discovery from extracellular (cell-free) RNA-seq and tissue of origin from GTEx RNA-seq profiles --- diff --git a/src/pages/outreach/Bridge2AI Fall 2024 Leadership Meeting 2024-12-06.md b/src/pages/outreach/Bridge2AI Fall 2024 Leadership Meeting 2024-12-06.md index 3f68721..f78e3e3 100644 --- a/src/pages/outreach/Bridge2AI Fall 2024 Leadership Meeting 2024-12-06.md +++ b/src/pages/outreach/Bridge2AI Fall 2024 Leadership Meeting 2024-12-06.md @@ -15,7 +15,8 @@ short_description: 'The meeating will be an opportunity for researchers and expe Bridge Center (BC) will present highlights of their research and facilitate discussions aligned with the theme of the meeting.' start_date: '2024-12-05T12:00:00-05:00' -tags: '["symposium"]' +tags: +- symposium title: Bridge2AI Fall 2024 Leadership Meeting --- The meeating will be an opportunity for researchers and experts to engage in vibrant discussions. The theme of the Fall Leadership Meeting is: Cross Consortium Synergies. Representatives from all the Grand Challenges (GC) and the Bridge Center (BC) will present highlights of their research and facilitate discussions aligned with the theme of the meeting. \ No newline at end of file diff --git a/src/pages/outreach/CFDE 2024 Fall Meeting 2024-10-23.md b/src/pages/outreach/CFDE 2024 Fall Meeting 2024-10-23.md index c130cb9..bf3b855 100644 --- a/src/pages/outreach/CFDE 2024 Fall Meeting 2024-10-23.md +++ b/src/pages/outreach/CFDE 2024 Fall Meeting 2024-10-23.md @@ -18,7 +18,8 @@ short_description: The CFDE Fall face-to-face (F2F) meeting will feature announc topics will include building methods for sustainability and harmonizing CFDE data to answer integrative questions. start_date: '2024-10-22T00:00:00-04:00' -tags: '["face to face meeting"]' +tags: +- face to face meeting title: CFDE 2024 Fall Meeting --- -The CFDE Fall face-to-face (F2F) meeting will feature announcements about upcoming data from ([Bridge2AI](https://info.cfde.cloud/dcc/Bridge2AI)), ([SenNet](https://info.cfde.cloud/dcc/SenNet), ([HubMAP](https://info.cfde.cloud/dcc/HuBMAP)), and ([MoTrPAC](https://info.cfde.cloud/dcc/MoTrPAC)), along with multiple brainstorming sessions discussing the future of CFDE. Special topics will include building methods for sustainability and harmonizing CFDE data to answer integrative questions. \ No newline at end of file +The CFDE Fall face-to-face (F2F) meeting will feature announcements about upcoming data from ([Bridge2AI](https://info.cfde.cloud/dcc/Bridge2AI)), ([SenNet](https://info.cfde.cloud/dcc/SenNet)), ([HubMAP](https://info.cfde.cloud/dcc/HuBMAP)), and ([MoTrPAC](https://info.cfde.cloud/dcc/MoTrPAC)), along with multiple brainstorming sessions discussing the future of CFDE. Special topics will include building methods for sustainability and harmonizing CFDE data to answer integrative questions. \ No newline at end of file diff --git a/src/pages/outreach/CFDE Centers 2025-12-31.md b/src/pages/outreach/CFDE Centers 2025-12-31.md index 71887d5..eacd6b1 100644 --- a/src/pages/outreach/CFDE Centers 2025-12-31.md +++ b/src/pages/outreach/CFDE Centers 2025-12-31.md @@ -8,7 +8,8 @@ image: https://cfde-drc.s3.us-east-2.amazonaws.com/assets/img/cfde-centers.png layout: '@/layouts/Outreach.astro' link: /info/centers short_description: '-' -tags: '["none"]' +tags: +- none title: CFDE Centers --- - \ No newline at end of file diff --git a/src/pages/outreach/CFDE Metabolomics Workbench Virtual Summer Workshop 2024 2024-07-25.md b/src/pages/outreach/CFDE Metabolomics Workbench Virtual Summer Workshop 2024 2024-07-25.md index 7e6200b..ef16373 100644 --- a/src/pages/outreach/CFDE Metabolomics Workbench Virtual Summer Workshop 2024 2024-07-25.md +++ b/src/pages/outreach/CFDE Metabolomics Workbench Virtual Summer Workshop 2024 2024-07-25.md @@ -16,7 +16,8 @@ short_description: UCSD Metabolomics Workbench ([MW](https://www.metabolomicswor [here](https://sc-cfdewebdev.sdsc.edu/MW/mwsw24.html) for additional information and registration. start_date: '2024-07-22T08:00:00-07:00' -tags: '["workshop"]' +tags: +- workshop title: CFDE Metabolomics Workbench Virtual Summer Workshop 2024 --- UCSD Metabolomics Workbench ([MW](https://www.metabolomicsworkbench.org/)), as part of the NIH Common Fund Data Ecosystem ([CFDE](https://commonfund.nih.gov/dataecosystem)) is pleased to announce a 4-day virtual Summer Workshop on July 22-25, 2024. Click [here](https://sc-cfdewebdev.sdsc.edu/MW/mwsw24.html) for additional information and registration. \ No newline at end of file diff --git a/src/pages/outreach/CFDE Pediatric PowerUp I 2024-06-28.md b/src/pages/outreach/CFDE Pediatric PowerUp I 2024-06-28.md index 16663e4..215c747 100644 --- a/src/pages/outreach/CFDE Pediatric PowerUp I 2024-06-28.md +++ b/src/pages/outreach/CFDE Pediatric PowerUp I 2024-06-28.md @@ -15,7 +15,8 @@ short_description: This summer, join the Pediatric PowerUp training program unde that equip you with the skills to find answers faster. This free, week-long program is designed to supercharge your research like a pro in just two hours a day. start_date: '2024-06-24T00:00:00-04:00' -tags: '["workshop"]' +tags: +- workshop title: CFDE Pediatric PowerUp I --- This summer, join the Pediatric PowerUp training program underwritten by the NIH Common Fund Data Ecosystem (CFDE) and featuring the Gabriella Miller Kids First Data Resource Center (Kids First). Dive into powerful cloud-based platforms that equip you with the skills to find answers faster. This free, week-long program is designed to supercharge your research like a pro in just two hours a day. \ No newline at end of file diff --git a/src/pages/outreach/CFDE Pediatric PowerUp II 2024-08-23.md b/src/pages/outreach/CFDE Pediatric PowerUp II 2024-08-23.md index 2fc9c55..42ce1a8 100644 --- a/src/pages/outreach/CFDE Pediatric PowerUp II 2024-08-23.md +++ b/src/pages/outreach/CFDE Pediatric PowerUp II 2024-08-23.md @@ -15,7 +15,8 @@ short_description: This summer, join the Pediatric PowerUp training program unde that equip you with the skills to find answers faster. This free, week-long program is designed to supercharge your research like a pro in just two hours a day. start_date: '2024-08-19T00:00:00-04:00' -tags: '["workshop"]' +tags: +- workshop title: CFDE Pediatric PowerUp II --- This summer, join the Pediatric PowerUp training program underwritten by the NIH Common Fund Data Ecosystem (CFDE) and featuring the Gabriella Miller Kids First Data Resource Center (Kids First). Dive into powerful cloud-based platforms that equip you with the skills to find answers faster. This free, week-long program is designed to supercharge your research like a pro in just two hours a day. \ No newline at end of file diff --git a/src/pages/outreach/CFDE Webinar Series 2024-04-26.md b/src/pages/outreach/CFDE Webinar Series 2024-04-26.md index ecb5391..4d3e080 100644 --- a/src/pages/outreach/CFDE Webinar Series 2024-04-26.md +++ b/src/pages/outreach/CFDE Webinar Series 2024-04-26.md @@ -39,7 +39,8 @@ short_description: The NIH Common Fund Data Ecosystem (CFDE) is a network of pr behind the research programs that comprise CFDE, as well as about the CFDE as a whole and its coordination Centers. start_date: '2024-04-26T13:00:00-04:00' -tags: '["webinar"]' +tags: +- webinar title: CFDE Webinar Series --- The NIH Common Fund Data Ecosystem (CFDE) is a network of programs conducting innovative, cross-domain research to benefit human health. This CFDE Webinar Series brings the varied programs of the CFDE to the broad biomedical research community. Join us on the last Friday of each month at 1-2 PM ET to learn the science behind the research programs that comprise CFDE, as well as about the CFDE as a whole and its coordination Centers. \ No newline at end of file diff --git a/src/pages/outreach/CFDE Webinar Series 2024-05-31.md b/src/pages/outreach/CFDE Webinar Series 2024-05-31.md index d8cddcc..185720c 100644 --- a/src/pages/outreach/CFDE Webinar Series 2024-05-31.md +++ b/src/pages/outreach/CFDE Webinar Series 2024-05-31.md @@ -16,7 +16,8 @@ short_description: The CFDE Webinar Series brings the varied programs of the CFD at 1-2 PM ET to learn the science behind the research programs that comprise CFDE, as well as about the CFDE as a whole and its coordination Centers. start_date: '2024-05-31T13:00:00-04:00' -tags: '["webinar"]' +tags: +- webinar title: CFDE Webinar Series --- The NIH Common Fund Data Ecosystem (CFDE) is a network of programs conducting innovative, cross-domain research to benefit human health. This CFDE Webinar Series brings the varied programs of the CFDE to the broad biomedical research community. Join us on the last Friday of each month at 1-2 PM ET to learn the science behind the research programs that comprise CFDE, as well as about the CFDE as a whole and its coordination Centers. \ No newline at end of file diff --git a/src/pages/outreach/CFDE Webinar Series 2024-06-28.md b/src/pages/outreach/CFDE Webinar Series 2024-06-28.md index f5ed849..9b67a9a 100644 --- a/src/pages/outreach/CFDE Webinar Series 2024-06-28.md +++ b/src/pages/outreach/CFDE Webinar Series 2024-06-28.md @@ -23,7 +23,8 @@ short_description: The CFDE Webinar Series brings the varied programs of the CFD Yang, Ph.D, Anna Waller, Ph.D, Jayme Holmes from IDG, and Timothy Sheils from NIH NCATS. start_date: '2024-06-28T13:00:00-04:00' -tags: '["webinar"]' +tags: +- webinar title: CFDE Webinar Series --- The CFDE Webinar Series brings the varied programs of the CFDE to the broad biomedical research community. The title for the month is Illuminating the Druggable Genome (IDG) Overview and Highlights and will be presented by Jeremy Yang, Ph.D, Anna Waller, Ph.D, Jayme Holmes from IDG, and Timothy Sheils from NIH NCATS. \ No newline at end of file diff --git a/src/pages/outreach/CFDE Webinar Series 2024-07-26.md b/src/pages/outreach/CFDE Webinar Series 2024-07-26.md index 4b131c9..e3d4a88 100644 --- a/src/pages/outreach/CFDE Webinar Series 2024-07-26.md +++ b/src/pages/outreach/CFDE Webinar Series 2024-07-26.md @@ -16,7 +16,8 @@ short_description: "The CFDE Webinar Series features HuBMAP and SenNet DCCs abou \ Director for CNS provide a tour of the Human Reference Atlas (HRA) while highlighting\ \ their work mapping data from the heart, kidney, and lung. " start_date: '2024-07-26T13:00:00-04:00' -tags: '["webinar"]' +tags: +- webinar title: CFDE Webinar Series --- The CFDE Webinar Series features HuBMAP and SenNet DCCs about A Tour of the Human Reference Atlas v2.1. Katy Börner, Center Director for the Cyberinfrastructure for Network Science Center (CNS), and Bruce Herr, Technical Director for CNS provide a tour of the Human Reference Atlas (HRA) while highlighting their work mapping data from the heart, kidney, and lung. \ No newline at end of file diff --git a/src/pages/outreach/CFDE Webinar Series 2024-08-30.md b/src/pages/outreach/CFDE Webinar Series 2024-08-30.md index 473259d..cb2c87c 100644 --- a/src/pages/outreach/CFDE Webinar Series 2024-08-30.md +++ b/src/pages/outreach/CFDE Webinar Series 2024-08-30.md @@ -14,7 +14,8 @@ short_description: The CFDE Webinar Series was established to share with the com as about the CFDE as a whole and its DCCs. This month we will feature the Acute to Chronic Pain Signatures (A2CPS) DCC. start_date: '2024-08-30T13:00:00-04:00' -tags: '["webinar"]' +tags: +- webinar title: CFDE Webinar Series --- The CFDE Webinar Series was established to share with the community information about the Common Fund programs that participate in the CFDE, as well as about the CFDE as a whole and its DCCs. This month we will feature the Acute to Chronic Pain Signatures (A2CPS) DCC. \ No newline at end of file diff --git a/src/pages/outreach/CFDE Webinar Series 2024-09-27.md b/src/pages/outreach/CFDE Webinar Series 2024-09-27.md index 88c1bda..9bcf34e 100644 --- a/src/pages/outreach/CFDE Webinar Series 2024-09-27.md +++ b/src/pages/outreach/CFDE Webinar Series 2024-09-27.md @@ -14,7 +14,8 @@ short_description: "The CFDE Webinar Series will feature the exRNA DCC. The semi \ variants from WGS data with application to Congenital Heart Disease\u2019 presented\ \ by Keyang Yu, a Genboree Research Assistant." start_date: '2024-09-27T13:00:00-04:00' -tags: '["webinar"]' +tags: +- webinar title: CFDE Webinar Series --- The CFDE Webinar Series will feature the exRNA DCC. The seminar will be about ‘Tools and methods for discovering disease-causing gene regulatory variants from WGS data with application to Congenital Heart Disease’ presented by Keyang Yu, a Genboree Research Assistant. \ No newline at end of file diff --git a/src/pages/outreach/CFDE Webinar Series 2024-10-25.md b/src/pages/outreach/CFDE Webinar Series 2024-10-25.md index fedf7f7..321d1f9 100644 --- a/src/pages/outreach/CFDE Webinar Series 2024-10-25.md +++ b/src/pages/outreach/CFDE Webinar Series 2024-10-25.md @@ -14,7 +14,8 @@ short_description: The CFDE Webinar Series will feature the MoTrPAC DCC. The sem (MoTrPAC)', which will cover MoTrPAC Data Hub, recent updates, upcoming data releases, pipelines, and data structures. start_date: '2024-10-25T13:00:00-04:00' -tags: '["webinar"]' +tags: +- webinar title: CFDE Webinar Series --- The CFDE Webinar Series will feature the MoTrPAC DCC. The seminar will be about Introduction to The Molecular Transducers of Physical Activity Consortium (MoTrPAC), which will cover MoTrPAC Data Hub, recent updates, upcoming data releases, pipelines, and data structures. \ No newline at end of file diff --git a/src/pages/outreach/CFDE Webinar Series 2024-11-22.md b/src/pages/outreach/CFDE Webinar Series 2024-11-22.md index 2cb0c86..01f2ef6 100644 --- a/src/pages/outreach/CFDE Webinar Series 2024-11-22.md +++ b/src/pages/outreach/CFDE Webinar Series 2024-11-22.md @@ -13,7 +13,8 @@ short_description: The COMPA team will share an overview of the project followed interviews, workshops, and online presentations for targeted feedback and market validation and share methods to ensure data-driven outreach. start_date: '2024-11-22T13:00:00-05:00' -tags: '["webinar"]' +tags: +- webinar title: CFDE Webinar Series --- The COMPA team will share an overview of the project followed by strategies to help the audience promote awareness and adoption of their products and tools from MetaCell. We will discuss the cost-benefit of strategies such as interviews, workshops, and online presentations for targeted feedback and market validation and share methods to ensure data-driven outreach. \ No newline at end of file diff --git a/src/pages/outreach/CFDE Webinar Series 2025-01-31.md b/src/pages/outreach/CFDE Webinar Series 2025-01-31.md index dcb8c98..5c772fe 100644 --- a/src/pages/outreach/CFDE Webinar Series 2025-01-31.md +++ b/src/pages/outreach/CFDE Webinar Series 2025-01-31.md @@ -11,7 +11,8 @@ short_description: The virtual CFDE workshop 'A Human Geneticists' Guide to the Fund Data Ecosystem' will feature the NIH perspective of the CFDE, gene set to human traits scientific presentation, introduction to CFDE centers, and NIH funding opportunities. start_date: '2025-01-31T10:00:00-05:00' -tags: '["webinar"]' +tags: +- webinar title: CFDE Webinar Series --- This CFDE workshop will feature the NIH perspective of the CFDE, gene set to human traits scientific presentation, introduction to CFDE centers, and NIH funding opportunities. \ No newline at end of file diff --git a/src/pages/outreach/CFDE at Bio-IT World Boston 2025 2025-04-04.md b/src/pages/outreach/CFDE at Bio-IT World Boston 2025 2025-04-04.md index 4666163..90cbac0 100644 --- a/src/pages/outreach/CFDE at Bio-IT World Boston 2025 2025-04-04.md +++ b/src/pages/outreach/CFDE at Bio-IT World Boston 2025 2025-04-04.md @@ -11,7 +11,8 @@ short_description: The CFDE will be showcased at the Bio-IT World 2025. The Bio- FAIR Data Hackathon will be facilitated by CFDE members led by the CFDE Training Center (TC) to promote the utilization and integration of CFDE tools and datasets. start_date: '2025-04-02T12:00:00-05:00' -tags: '["conference"]' +tags: +- conference title: CFDE at Bio-IT World Boston 2025 --- The CFDE will be showcased at the Bio-IT World 2025. The Bio-IT FAIR Data Hackathon will be facilitated by CFDE members led by the CFDE Training Center (TC) to promote the utilization and integration of CFDE tools and datasets. \ No newline at end of file diff --git a/src/pages/outreach/CFDE at Intelligent Systems for Molecular Biology 2025 2025-07-24.md b/src/pages/outreach/CFDE at Intelligent Systems for Molecular Biology 2025 2025-07-24.md index 4577870..2e7c392 100644 --- a/src/pages/outreach/CFDE at Intelligent Systems for Molecular Biology 2025 2025-07-24.md +++ b/src/pages/outreach/CFDE at Intelligent Systems for Molecular Biology 2025 2025-07-24.md @@ -11,7 +11,8 @@ short_description: "Representative from several CFDE participating Common Fund p \ DCCs plan to attend the Intelligent Systems for Molecular Biology (ISMB) 2025\ \ in Liverpool, UK." start_date: '2025-07-20T12:00:00-01:00' -tags: '["conference"]' +tags: +- conference title: CFDE at Intelligent Systems for Molecular Biology 2025 --- Representative from several CFDE participating Common Fund programs’ DCCs plan to attend the Intelligent Systems for Molecular Biology (ISMB) 2025 in Liverpool, UK. \ No newline at end of file diff --git a/src/pages/outreach/CFDE at the American Society of Human Genetics Annual Meeting 2024-11-09.md b/src/pages/outreach/CFDE at the American Society of Human Genetics Annual Meeting 2024-11-09.md index e279c9a..41a5610 100644 --- a/src/pages/outreach/CFDE at the American Society of Human Genetics Annual Meeting 2024-11-09.md +++ b/src/pages/outreach/CFDE at the American Society of Human Genetics Annual Meeting 2024-11-09.md @@ -12,7 +12,8 @@ short_description: "The CFDE will be showcased at the American Society of Human \ Center (DRC), Kids First DCC, MoTrPAC DCC, and other CFDE representatives.\_To\ \ learn more, visit us at booths #571 and #1120!" start_date: '2024-11-05T12:00:00-04:00' -tags: '["conference"]' +tags: +- conference title: CFDE at the American Society of Human Genetics Annual Meeting --- The CFDE Knowledge Center (KC), the CFDE Data Resource Center (DRC), and the Kids First DCC plan to participate in the American Society of Human Genetics Annual Meeting in Denver, Colorado. \ No newline at end of file diff --git a/src/pages/outreach/CFDE at the American Society of Human Genetics Annual Meeting 2025-10-18.md b/src/pages/outreach/CFDE at the American Society of Human Genetics Annual Meeting 2025-10-18.md index 4ec5877..ebbcc64 100644 --- a/src/pages/outreach/CFDE at the American Society of Human Genetics Annual Meeting 2025-10-18.md +++ b/src/pages/outreach/CFDE at the American Society of Human Genetics Annual Meeting 2025-10-18.md @@ -11,7 +11,8 @@ short_description: The CFDE will be showcased at the 2025 American Society of Hu Genetics Annual (ASHG) meeting. An ancillary session and a CFDE booth are planned. The meeting will be held in Boston, MA. start_date: '2025-10-14T12:00:00-05:00' -tags: '["conference"]' +tags: +- conference title: CFDE at the American Society of Human Genetics Annual Meeting --- The CFDE will be showcased at the 2025 American Society of Human Genetics Annual (ASHG) meeting. An ancillary session and a CFDE booth are planned. The meeting will be held in Boston, MA. \ No newline at end of file diff --git a/src/pages/outreach/CFDE-GlyGen Summer Interns Symposium 2024 2024-07-25.md b/src/pages/outreach/CFDE-GlyGen Summer Interns Symposium 2024 2024-07-25.md index 4f4aec0..9a6d4a5 100644 --- a/src/pages/outreach/CFDE-GlyGen Summer Interns Symposium 2024 2024-07-25.md +++ b/src/pages/outreach/CFDE-GlyGen Summer Interns Symposium 2024 2024-07-25.md @@ -14,7 +14,8 @@ short_description: "Join us at the Virtual CFDE-GlyGen Summer Interns Symposium \ to share our discoveries, learnings, and experiences from this internship. Click\ \ the visit page below for more information and the Zoom link." start_date: '2024-07-25T13:00:00-04:00' -tags: '["training program"]' +tags: +- training program title: 'CFDE-GlyGen Summer Interns Symposium 2024 ' --- Join us at the Virtual CFDE-GlyGen Summer Interns Symposium as we present the projects we’ve been working on this summer. We’re excited to share our discoveries, learnings, and experiences from this internship. Scan the QR code below for more information and the Zoom link. \ No newline at end of file diff --git a/src/pages/outreach/Community Engagement Workshop: A Discussion of Data Resources 2024-07-25.md b/src/pages/outreach/Community Engagement Workshop: A Discussion of Data Resources 2024-07-25.md index f315dc2..7e3c98a 100644 --- a/src/pages/outreach/Community Engagement Workshop: A Discussion of Data Resources 2024-07-25.md +++ b/src/pages/outreach/Community Engagement Workshop: A Discussion of Data Resources 2024-07-25.md @@ -12,7 +12,8 @@ short_description: "Join the NIH Common Fund\u2019s collaborative discussion at \ culturally relevant data can shape future outreach, training, and support the\ \ biomedical and behavioral research community." start_date: '2024-07-24T00:00:00-04:00' -tags: '["workshop"]' +tags: +- workshop title: 'Community Engagement Workshop: A Discussion of Data Resources' --- Join the NIH Common Fund’s collaborative discussion at the Community Engagement Workshop! Learn how data accessibility, inclusivity, and culturally relevant data can shape future outreach, training, and support the biomedical and behavioral research community. \ No newline at end of file diff --git a/src/pages/outreach/Coursera Course: Big Data Science with the BD2K-LINCS Data Coordination and Integration Center.md b/src/pages/outreach/Coursera Course: Big Data Science with the BD2K-LINCS Data Coordination and Integration Center.md index 3165bce..eecfaa5 100644 --- a/src/pages/outreach/Coursera Course: Big Data Science with the BD2K-LINCS Data Coordination and Integration Center.md +++ b/src/pages/outreach/Coursera Course: Big Data Science with the BD2K-LINCS Data Coordination and Integration Center.md @@ -11,7 +11,8 @@ link: https://www.coursera.org/learn/bd2k-lincs short_description: 'In this course the LINCS DCC covers computational methods including: clustering, gene-set enrichment analysis, interactive data visualization, and supervised learning applied to the LINCS program datasets.' -tags: '["course"]' +tags: +- course title: 'Coursera Course: Big Data Science with the BD2K-LINCS Data Coordination and Integration Center' --- diff --git a/src/pages/outreach/From Atlas to Practice 2024-09-27.md b/src/pages/outreach/From Atlas to Practice 2024-09-27.md index 815eb68..c4d68a8 100644 --- a/src/pages/outreach/From Atlas to Practice 2024-09-27.md +++ b/src/pages/outreach/From Atlas to Practice 2024-09-27.md @@ -16,7 +16,8 @@ short_description: Accelerating the Convergence of Spatial Biology and Pathology and pathology. You can help shape how large-scale spatial atlas research can be used to directly impact patient care. start_date: '2024-09-23T00:00:00-04:00' -tags: '["workshop"]' +tags: +- workshop title: From Atlas to Practice --- Accelerating the Convergence of Spatial Biology and Pathology! Join the NIH Innovation Lab "FROM ATLAS TO PRACTICE" where you can help shape how large-scale spatial atlas research can be used to directly impact patient care. \ No newline at end of file diff --git "a/src/pages/outreach/Gabriella Miller Kids First Pediatric Research Program\342\200\231s Spring Webinar 2024-05-29.md" "b/src/pages/outreach/Gabriella Miller Kids First Pediatric Research Program\342\200\231s Spring Webinar 2024-05-29.md" index d757f3f..69a55fb 100644 --- "a/src/pages/outreach/Gabriella Miller Kids First Pediatric Research Program\342\200\231s Spring Webinar 2024-05-29.md" +++ "b/src/pages/outreach/Gabriella Miller Kids First Pediatric Research Program\342\200\231s Spring Webinar 2024-05-29.md" @@ -10,7 +10,8 @@ short_description: 'The Kids First program team, experts and families will take deep dive into pediatric research advancement through big data and its implications for discovering new cures in rare diseases. ' start_date: '2024-05-29T11:00:00-04:00' -tags: '["webinar"]' +tags: +- webinar title: "Gabriella Miller Kids First Pediatric Research Program\u2019s Spring Webinar" --- Join us for the Gabriella Miller Kids First Pediatric Research Program’s Spring Webinar, “Big Data Dialogue, The Next Catalyst for Cures.” On May 29 at 11 a.m. EDT, the Kids First program team, experts and families will take a deep dive into pediatric research advancement through big data and its implications for discovering new cures in rare diseases. Learn about Kids First’s role in the big data landscape, how it impacts research, new analysis tools and implications for identifying and implementing patient- and family-level change. Bring your questions: We want to hear from you. Start brainstorming your questions now to dive into a dynamic live discussion. This event is open to everyone in our community. Seize the opportunity to be part of a united community propelling pediatric research forward. Register now and contribute to the transformative power of collective impact. \ No newline at end of file diff --git a/src/pages/outreach/GlyGen & CFDE Workshop Summer 2023 2023-08-07.md b/src/pages/outreach/GlyGen & CFDE Workshop Summer 2023 2023-08-07.md index 2cc9fd8..66cdea5 100644 --- a/src/pages/outreach/GlyGen & CFDE Workshop Summer 2023 2023-08-07.md +++ b/src/pages/outreach/GlyGen & CFDE Workshop Summer 2023 2023-08-07.md @@ -11,7 +11,8 @@ link: https://wiki.glygen.org/GlyGen_CFDE_Workshop_Summer_2023 short_description: This workshop provides an opportunity to learn about glycobiology and introduce bioinformatics resources to answer a biological questions. start_date: '2023-08-07T00:00:00-04:00' -tags: '["workshop"]' +tags: +- workshop title: GlyGen & CFDE Workshop Summer 2023 --- The purpose of this workshop is to bring together high school students who are interested in developing early-on research knowledge and skills in biochemistry, glycobiology, computer science, and bioinformatics. Each presenter will demonstrate glycan and protein analysis using GlyGen and CFDE tools described above, followed by a Q&A session at the end of the workshop. The attendees will gain basic knowledge on how to efficiently use bioinformatics resources to answer biological questions and provide valuable feedback on the user experience perspective which aids in the continuous development of GlyGen. \ No newline at end of file diff --git a/src/pages/outreach/GlyGen-CFDE Summer Internship Program 2024-07-26.md b/src/pages/outreach/GlyGen-CFDE Summer Internship Program 2024-07-26.md index 2b1a28b..24702b9 100644 --- a/src/pages/outreach/GlyGen-CFDE Summer Internship Program 2024-07-26.md +++ b/src/pages/outreach/GlyGen-CFDE Summer Internship Program 2024-07-26.md @@ -18,7 +18,8 @@ short_description: The GlyGen-CFDE project is seeking applications for a paid 8- in biomedical research through Common Fund Data Ecosystem (CFDE) and GlyGen tools and data. start_date: '2024-06-03T00:00:00-04:00' -tags: '["internship"]' +tags: +- internship title: GlyGen-CFDE Summer Internship Program --- The GlyGen-CFDE project is seeking applications for a paid 8-week summer research in-person internship in 2024 for undergraduate and graduate students in Washington DC at George Washington University. This 8-week internship program is tailored to provide hands-on experience in bioinformatics and biology applications in biomedical research through Common Fund Data Ecosystem (CFDE) and GlyGen tools and data. Interns will have the opportunity to expand their understanding of biology, biochemistry, and bioinformatics concepts, including exploration and analysis of glycans, proteins, and biomarkers while working on tasks and projects, enabling them to find answers to specific biological questions. The internship will provide benefits such as professional networking, soft skills development, hands-on experience in bioinformatics programming, data wrangling, and exploration of biomedical web resources and tools. \ No newline at end of file diff --git a/src/pages/outreach/HuBMAP Visible Human MOOC (VHMOOC).md b/src/pages/outreach/HuBMAP Visible Human MOOC (VHMOOC).md index aa3f54d..6834a01 100644 --- a/src/pages/outreach/HuBMAP Visible Human MOOC (VHMOOC).md +++ b/src/pages/outreach/HuBMAP Visible Human MOOC (VHMOOC).md @@ -10,7 +10,8 @@ layout: '@/layouts/Outreach.astro' link: https://expand.iu.edu/browse/sice/cns/courses/hubmap-visible-human-mooc short_description: This 10h course introduces the HuBMAP project which aims to create an open, global reference atlas of the human body at the cellular level. -tags: '["course"]' +tags: +- course title: HuBMAP Visible Human MOOC (VHMOOC) --- This 10h course introduces the HuBMAP project which aims to create an open, global reference atlas of the human body at the cellular level. Among others, the course describes the compilation and coverage of HuBMAP data, demonstrates new single-cell analysis and mapping techniques, and introduces major features of the HuBMAP portal. \ No newline at end of file diff --git a/src/pages/outreach/IMPC Data API Workshop 2024-05-20.md b/src/pages/outreach/IMPC Data API Workshop 2024-05-20.md index 6d10786..91b6c5e 100644 --- a/src/pages/outreach/IMPC Data API Workshop 2024-05-20.md +++ b/src/pages/outreach/IMPC Data API Workshop 2024-05-20.md @@ -11,7 +11,8 @@ short_description: The objective of the course is to enable researchers to const Solr API queries to obtain IMPC data based on an understanding of how knowledge of IMPReSS can be used together with the Solr API. start_date: '2024-05-20T10:00:00-04:00' -tags: '["workshop"]' +tags: +- workshop title: IMPC Data API Workshop --- Due to high demand the registration for the Data API workshop has been closed. But if you’re interested, please register interest to be added to the waiting list and to scope for interest for another session.Please save the date for the 2nd virtual IMPC workshop in the 2024 series, titled ‘IMPC Data API Workshop‘ organised by the IMPC Data Analysis WG/MPI team.The target audience for the workshop would be people familiar with mouse biology and IMPC data to some extent, with some basic knowledge of programming and data transformation, but not necessarily knowledge of using an Apache Solr API. The objective of the course would be to enable people to construct simple Solr API queries to obtain IMPC data based on an understanding of the structure of IMPC data, specifically how knowledge of IMPReSS can be used together with the Solr API to extract datasets from IMPC. \ No newline at end of file diff --git a/src/pages/outreach/IMPC Webinar: Investigating gene function and human disease through data on the IMPC portal 2024-11-20.md b/src/pages/outreach/IMPC Webinar: Investigating gene function and human disease through data on the IMPC portal 2024-11-20.md index 1a726ae..1e4672b 100644 --- a/src/pages/outreach/IMPC Webinar: Investigating gene function and human disease through data on the IMPC portal 2024-11-20.md +++ b/src/pages/outreach/IMPC Webinar: Investigating gene function and human disease through data on the IMPC portal 2024-11-20.md @@ -13,7 +13,8 @@ short_description: The webinar will offer an overview of how IMPC data is genera and how the PhenoDigm algorithm can be applied to identify new models of human disease-gene associations. start_date: '2024-11-20T10:30:00-05:00' -tags: '["webinar"]' +tags: +- webinar title: 'IMPC Webinar: Investigating gene function and human disease through data on the IMPC portal ' --- diff --git a/src/pages/outreach/Independent Study in Biomedical Data Science, CFDE edition (ISBDS-CFDE) 2024-07-26.md b/src/pages/outreach/Independent Study in Biomedical Data Science, CFDE edition (ISBDS-CFDE) 2024-07-26.md index cf55332..c60ece4 100644 --- a/src/pages/outreach/Independent Study in Biomedical Data Science, CFDE edition (ISBDS-CFDE) 2024-07-26.md +++ b/src/pages/outreach/Independent Study in Biomedical Data Science, CFDE edition (ISBDS-CFDE) 2024-07-26.md @@ -13,7 +13,8 @@ short_description: The CFDE Edition of ISBDS is an NIH CFDE sponsored training c focused on effective use and integration of Common Fund (CF) datasets for biomedical discovery. start_date: '2024-06-03T00:00:00-06:00' -tags: '["course"]' +tags: +- course title: Independent Study in Biomedical Data Science, CFDE edition (ISBDS-CFDE) --- The Illuminating the Druggable Genome (IDG) Data Coordinating Center (DCC), led by the University of New Mexico, is offering an online summer training course featuring CFDE resources. The course is suitable for beginners to advanced learners, who select from a menu of research plan templates to customize according to their interests, utilize CFDE resources, and produce a scholarly final report and poster with support and advisement from the course developers and administrators. Featured research plan templates will be derived from IDG use cases. \ No newline at end of file diff --git a/src/pages/outreach/LINCS Summer Trainees Virtual Symposium 2024 2024-08-08.md b/src/pages/outreach/LINCS Summer Trainees Virtual Symposium 2024 2024-08-08.md index f6f1b88..ed2651b 100644 --- a/src/pages/outreach/LINCS Summer Trainees Virtual Symposium 2024 2024-08-08.md +++ b/src/pages/outreach/LINCS Summer Trainees Virtual Symposium 2024 2024-08-08.md @@ -16,7 +16,8 @@ short_description: "This virtual symposium hosted by the Ma\u2019ayan Lab and th \ and knowledge graphs in the field of biomedical data science and bioinformatics,\ \ leveraging the power of AI and other computational tools and methods." start_date: '2024-08-08T10:00:00-04:00' -tags: '["symposium"]' +tags: +- symposium title: LINCS Summer Trainees Virtual Symposium 2024 --- A virtual symposium hosted by the Ma’ayan Lab and the Mount Sinai Center for Bioinformatics will feature the accomplishments made by 10 summer trainees during a 10-week research-intensive full-time training program. The projects cover topics such as data integration, data visualization, LLM integration, and Knowledge Graphs in the field of biomedical data science and bioinformatics, leveraging the power of AI and other computational tools and methods. \ No newline at end of file diff --git a/src/pages/outreach/March All-Hands Meeting 2024-03-20.md b/src/pages/outreach/March All-Hands Meeting 2024-03-20.md index 3c1edf1..ca3e984 100644 --- a/src/pages/outreach/March All-Hands Meeting 2024-03-20.md +++ b/src/pages/outreach/March All-Hands Meeting 2024-03-20.md @@ -12,7 +12,8 @@ short_description: The CFDE Program Team is pleased to announce we will be holdi will be coming soon including registration links for the meeting and hotel booking links. start_date: '2024-03-19T00:00:00-04:00' -tags: '["face to face meeting"]' +tags: +- face to face meeting title: March All-Hands Meeting --- The CFDE Program Team is pleased to announce we will be holding the annual CFDE Program Meeting on March 19-20, 2024 in Bethesda, MD. More details will be coming soon including registration links for the meeting and hotel booking links. \ No newline at end of file diff --git a/src/pages/outreach/MoTrPAC Office Hours.md b/src/pages/outreach/MoTrPAC Office Hours.md index 5585334..12f5252 100644 --- a/src/pages/outreach/MoTrPAC Office Hours.md +++ b/src/pages/outreach/MoTrPAC Office Hours.md @@ -12,7 +12,8 @@ short_description: The MoTrPAC Bioinformatics Center (BIC) hosts monthly open of hours to support the scientific community. Each session is hosted by one member from our infrastructure team and one from our bioinformatics team with a focus on the discussions of MoTrPAC data. -tags: '["office hours"]' +tags: +- office hours title: MoTrPAC Office Hours --- The MoTrPAC Bioinformatics Center (BIC) hosts monthly open office hours to support the scientific community. Each session is hosted by one member from our infrastructure team and one from our bioinformatics team with a focus on the discussions of MoTrPAC data. \ No newline at end of file diff --git a/src/pages/outreach/Multi-Omics AI-Driven Gene Set Analysis with GeneSetCart 2025-01-23.md b/src/pages/outreach/Multi-Omics AI-Driven Gene Set Analysis with GeneSetCart 2025-01-23.md index 29dd0a1..79a2291 100644 --- a/src/pages/outreach/Multi-Omics AI-Driven Gene Set Analysis with GeneSetCart 2025-01-23.md +++ b/src/pages/outreach/Multi-Omics AI-Driven Gene Set Analysis with GeneSetCart 2025-01-23.md @@ -11,7 +11,8 @@ short_description: Members of the CFDE DRC will present a seminar that will demo GeneSetCart, a new CFDE platform geared for the analysis of gene sets created from various Common Fund programs data sources. start_date: '2025-01-23T14:00:00-05:00' -tags: '["workshop"]' +tags: +- workshop title: Multi-Omics AI-Driven Gene Set Analysis with GeneSetCart --- The CFDE Workbench Tool Festival is a monthly workshop that features CFDE-developed tools. To start, it will showcase the GeneSetCart, which enables gene sets to be retrieved from various Common Fund program data sources and offers CFDE GMT crossings and other gene set operations. \ No newline at end of file diff --git "a/src/pages/outreach/NIH Center for Alzheimer\342\200\231s and Related Dementias (CARD) Fellowship 2026-05-12.md" "b/src/pages/outreach/NIH Center for Alzheimer\342\200\231s and Related Dementias (CARD) Fellowship 2026-05-12.md" index fdca783..63fc21b 100644 --- "a/src/pages/outreach/NIH Center for Alzheimer\342\200\231s and Related Dementias (CARD) Fellowship 2026-05-12.md" +++ "b/src/pages/outreach/NIH Center for Alzheimer\342\200\231s and Related Dementias (CARD) Fellowship 2026-05-12.md" @@ -13,7 +13,8 @@ short_description: "The Master\u2019s in Data Science Fellowship allows students \ with real-world data in the dementia space, working to explore the genetic architecture\ \ of disease from a data science perspective." start_date: '2024-08-28T00:00:00-04:00' -tags: '["fellowship"]' +tags: +- fellowship title: "NIH Center for Alzheimer\u2019s and Related Dementias (CARD) Fellowship" --- We are currently recruiting for a fully paid Master’s in Data Science Fellowship. The application deadline is the end of the day on April 22, 2024. This opportunity allows students to earn an MPS degree in data science while earning a full stipend to work at CARD with real-world data in the dementia space, working to explore the genetic architecture of disease from a data science perspective. This program is a collaboration with NIH FAES and UMBC. We are particularly passionate about recruiting diverse fellows. We have a blog post featuring interviews with current MPS in Data Science Fellows at CARD – students can learn what it’s like to be in the program: https://card.nih.gov/news-events/card-news/what-its-be-masters-data-science-student-nih-card. Prospective fellows can learn more about this opportunity and apply here: https://faes.org/CARD-FAES-UMBC_Fellowship. \ No newline at end of file diff --git a/src/pages/outreach/Playbook Workflow Builder USE-A-THON 2023-11-16.md b/src/pages/outreach/Playbook Workflow Builder USE-A-THON 2023-11-16.md index fe33633..a5cf7f3 100644 --- a/src/pages/outreach/Playbook Workflow Builder USE-A-THON 2023-11-16.md +++ b/src/pages/outreach/Playbook Workflow Builder USE-A-THON 2023-11-16.md @@ -15,7 +15,8 @@ link: https://playbook-workflow-builder.cloud/playbooks short_description: The first Use-A-Thon of Playbook Partnership to test platform and public use cases start_date: '2023-11-16T11:00:00-04:00' -tags: '["use-a-thon"]' +tags: +- use-a-thon title: Playbook Workflow Builder USE-A-THON --- -The first Use-A-Thon of Playbook Partnershi[ to test platform and public use cases \ No newline at end of file +The first Use-A-Thon of Playbook Partnership to test platform and public use cases \ No newline at end of file diff --git a/src/pages/outreach/Playbook Workflow Builder Virtual Workshop 2024 2024-06-25.md b/src/pages/outreach/Playbook Workflow Builder Virtual Workshop 2024 2024-06-25.md index 2557d56..97432a0 100644 --- a/src/pages/outreach/Playbook Workflow Builder Virtual Workshop 2024 2024-06-25.md +++ b/src/pages/outreach/Playbook Workflow Builder Virtual Workshop 2024 2024-06-25.md @@ -16,7 +16,8 @@ short_description: The Playbook Workflow Builder (PWB) is a web-based platform t The workshop will demonstrate how to use the platform via interactive sessions, as well as, introduce ways the community can contribute to the project. start_date: 2024-06-25T013:00:00-04:00 -tags: '["workshop"]' +tags: +- workshop title: Playbook Workflow Builder Virtual Workshop 2024 --- The Playbook Workflow Builder (PWB) is a web-based platform that facilitates the interactive construction of workflows by enabling users to utilize an ever-growing network of input datasets, semantically annotated API endpoints, and data visualization tools contributed by an ecosystem. Via a user-friendly web-based user interface (UI), workflows can be constructed from contributed building blocks without technical expertise. The workshop will demonstrate how to use the platform via interactive sessions, as well as, introduce ways the community can contribute to the project. \ No newline at end of file diff --git a/src/pages/outreach/SPARC Office Hours.md b/src/pages/outreach/SPARC Office Hours.md index de9d972..b2d5446 100644 --- a/src/pages/outreach/SPARC Office Hours.md +++ b/src/pages/outreach/SPARC Office Hours.md @@ -12,7 +12,8 @@ short_description: The SPARC Data and Resource Center (DRC) hosts regular open o hours to support the scientific community. Each session is hosted by experts with a focus on a specific SPARC resource; however, we welcome all attendees to any open office hours. -tags: '["office hours"]' +tags: +- office hours title: SPARC Office Hours --- The SPARC Data and Resource Center (DRC) hosts regular open office hours to support the scientific community. Each session is hosted by experts with a focus on a specific SPARC resource; however, we welcome all attendees to any open office hours. We will strive to answer your questions and point you to the appropriate resource. \ No newline at end of file diff --git a/src/pages/outreach/SPARC at NANS Annual Meeting 2024 2024-01-21.md b/src/pages/outreach/SPARC at NANS Annual Meeting 2024 2024-01-21.md index f3ceac1..af352c4 100644 --- a/src/pages/outreach/SPARC at NANS Annual Meeting 2024 2024-01-21.md +++ b/src/pages/outreach/SPARC at NANS Annual Meeting 2024 2024-01-21.md @@ -14,7 +14,8 @@ short_description: SPARC is joining the 2024 North American Neuromodulation Soci Portal and discuss collaboration opportunities, learn about current research projects, and get a demo of the research portal. start_date: '2024-01-18T00:00:00-04:00' -tags: '["conference"]' +tags: +- conference title: SPARC at NANS Annual Meeting 2024 --- Save the date for the most exciting event in neuromodulation innovation! Join the 2024 North American Neuromodulation Society (NANS) conference Jan 18-21 in Las Vegas for cutting-edge research, speakers, networking and innovations. NANS links patients, physicians and health care professionals, scientists, engineers, and industry to advance neuromodulation, drive multidisciplinary collaboration, enhance therapy awareness and inspire innovation to transform patients’ lives. What can you do when you visit booth 412? View published neuromodulation datasets on the SPARC Portal. Discuss collaboration opportunities, Learn about current research projects and get a demo of the research portal that bridges the body and the brain. Also, plan to congratulate SPARC Researcher Dr. Pelot, who has been named a 2024 NANS Rising Star! See the research she has published on the SPARC Portal. \ No newline at end of file diff --git a/src/pages/outreach/SPARC at SfN 2024 2024-10-09.md b/src/pages/outreach/SPARC at SfN 2024 2024-10-09.md index 3759566..91a5c5c 100644 --- a/src/pages/outreach/SPARC at SfN 2024 2024-10-09.md +++ b/src/pages/outreach/SPARC at SfN 2024 2024-10-09.md @@ -13,7 +13,8 @@ short_description: 'The SPARC DCC will participate in the Society for Neuroscien (SfN) Annual Meeting. The SPARC team will have booth to promote the program (Booth #1764).' start_date: '2024-10-05T00:00:00-04:00' -tags: '["conference"]' +tags: +- conference title: SPARC at SfN 2024 --- The SPARC DCC will participate in the Society for Neuroscience (SfN) Annual Meeting. The SPARC team will have booth to promote the program (Booth #1764). \ No newline at end of file diff --git a/src/pages/outreach/SenNet + HOA - Hacking the Human Vasculature in 3D Kaggle Competition 2024-02-06.md b/src/pages/outreach/SenNet + HOA - Hacking the Human Vasculature in 3D Kaggle Competition 2024-02-06.md index e67a41f..faa1d97 100644 --- a/src/pages/outreach/SenNet + HOA - Hacking the Human Vasculature in 3D Kaggle Competition 2024-02-06.md +++ b/src/pages/outreach/SenNet + HOA - Hacking the Human Vasculature in 3D Kaggle Competition 2024-02-06.md @@ -14,7 +14,8 @@ short_description: The goal of this competition is to segment blood vessels. You create a model trained on 3D Hierarchical Phase-Contrast Tomography (HiP-CT) data from human kidneys to help complete a picture of vasculature throughout a body. start_date: '2023-11-07T00:00:00-05:00' -tags: '["competition"]' +tags: +- competition title: SenNet + HOA - Hacking the Human Vasculature in 3D Kaggle Competition --- The “SenNet + HOA - Hacking the Human Vasculature in 3D” Kaggle competition is now LIVE at https://www.kaggle.com/competitions/blood-vessel-segmentation. The Cellular Senescence Program (SenNet) and the Human Organ Atlas (HOA) teams welcome contributions that help ​​​​improve 3D segmentation of vasculature. With better data on the healthy human vasculature, researchers will be able to simulate the flow of blood, oxygen, or even drugs through the vessel network. The 3D segmentation data will also be valuable for understanding how blood vasculature changes for different sex, age, and BMI. Ultimately, 3D vessel segmentation data will help pave the way towards a more complete Vascular Common Coordinate Framework (VCCF) and Human Reference Atlas (HRA) for the healthy human body. \ No newline at end of file diff --git a/src/pages/outreach/SenNet Accepting Applications for the CUSP 2025 Summer Internship 2025-01-25.md b/src/pages/outreach/SenNet Accepting Applications for the CUSP 2025 Summer Internship 2025-01-25.md index 2f842e7..0ade080 100644 --- a/src/pages/outreach/SenNet Accepting Applications for the CUSP 2025 Summer Internship 2025-01-25.md +++ b/src/pages/outreach/SenNet Accepting Applications for the CUSP 2025 Summer Internship 2025-01-25.md @@ -13,7 +13,9 @@ short_description: "The Consortium Undergraduate Student Program (CUSP) is a sum \ research internship program for undergraduate students hosted by laboratories\ \ participating in the NIH Common Fund\u2019s Cellular Senescence Network (SenNet)." start_date: '2024-11-15T00:00:00-05:00' -tags: '["internship", "application deadline"]' +tags: +- internship +- application deadline title: SenNet Accepting Applications for the CUSP 2025 Summer Internship --- SenNet is actively recruiting students for the May-August 2024 cohort of the Consortium Undergraduate Student Program (CUSP). CUSP is a summer research internship program for undergraduate students hosted by laboratories participating in the NIH Common Fund’s Cellular Senescence Network (SenNet). The application deadline is January 25. Interested students can always reach out to [cusp@sennetconsortium.org] or visit https://sennetconsortium.org/internship/ for application information and eligibility requirements. We're looking forward to an excellent summer with the 2024 CUSP interns! \ No newline at end of file diff --git a/src/pages/outreach/SenNet Consortium Undergraduate Student Program (CUSP) 2024-08-31.md b/src/pages/outreach/SenNet Consortium Undergraduate Student Program (CUSP) 2024-08-31.md index a86498d..c1a2e01 100644 --- a/src/pages/outreach/SenNet Consortium Undergraduate Student Program (CUSP) 2024-08-31.md +++ b/src/pages/outreach/SenNet Consortium Undergraduate Student Program (CUSP) 2024-08-31.md @@ -15,7 +15,8 @@ short_description: "CUSP is a summer research internship program for undergradua \ students hosted by laboratories participating in the NIH Common Fund\u2019s Cellular\ \ Senescence Network (SenNet)." start_date: '2024-05-01T00:00:00-04:00' -tags: '["internship"]' +tags: +- internship title: SenNet Consortium Undergraduate Student Program (CUSP) --- SenNet is actively recruiting students for the May-August 2024 cohort of the Consortium Undergraduate Student Program (CUSP). CUSP is a summer research internship program for undergraduate students hosted by laboratories participating in the NIH Common Fund’s Cellular Senescence Network (SenNet). The application deadline is January 25. Interested students can always reach out to [cusp@sennetconsortium.org] or visit https://sennetconsortium.org/internship/ for application information and eligibility requirements. We're looking forward to an excellent summer with the 2024 CUSP interns! \ No newline at end of file diff --git a/src/pages/outreach/Summer Research Program in Biomedical Big Data Science 2024-08-09.md b/src/pages/outreach/Summer Research Program in Biomedical Big Data Science 2024-08-09.md index d84bdc0..67ab553 100644 --- a/src/pages/outreach/Summer Research Program in Biomedical Big Data Science 2024-08-09.md +++ b/src/pages/outreach/Summer Research Program in Biomedical Big Data Science 2024-08-09.md @@ -20,7 +20,8 @@ short_description: "This virtual symposium was hosted by the Ma\u2019ayan Lab an \ here." start_date: '2024-06-03T00:00:00-04:00' -tags: '["training program"]' +tags: +- training program title: Summer Research Program in Biomedical Big Data Science --- LINCS’ Summer Research Training Program in Biomedical Big Data Science is a research intensive ten-week training program for undergraduate and master’s students interested in participating in cutting edge research projects aimed at solving data-intensive biomedical problems. Summer fellows training conduct faculty-mentored independent research projects in the following areas: data harmonization, machine learning, cloud computing and dynamic data visualization. \ No newline at end of file diff --git a/src/pages/outreach/The 2024 HuBMAP Fall Hackathon 2024-10-04.md b/src/pages/outreach/The 2024 HuBMAP Fall Hackathon 2024-10-04.md index b1b83dc..25d6f64 100644 --- a/src/pages/outreach/The 2024 HuBMAP Fall Hackathon 2024-10-04.md +++ b/src/pages/outreach/The 2024 HuBMAP Fall Hackathon 2024-10-04.md @@ -14,7 +14,8 @@ short_description: The 2024 HuBMAP Fall Hackathon will be held virtually with a Data Portal that enable lightweight exploration of public HuBMAP data and user-provided data using Python and R in a Jupyter Lab environment hosted by HuBMAP at no cost. start_date: '2024-09-20T00:00:00-04:00' -tags: '["hackathon"]' +tags: +- hackathon title: 'The 2024 HuBMAP Fall Hackathon ' --- The 2024 HuBMAP Fall Hackathon will be held virtually with synchronous meetings on September 20th and October 4th, and asynchronous hackathon activities during the two weeks between, with a focus on the HuBMAP Data Portal Workspaces. \ No newline at end of file diff --git a/src/pages/outreach/The HuBMAP JumpStart Fellowship 2026-06-01.md b/src/pages/outreach/The HuBMAP JumpStart Fellowship 2026-06-01.md index 3cfd0cd..8138c2f 100644 --- a/src/pages/outreach/The HuBMAP JumpStart Fellowship 2026-06-01.md +++ b/src/pages/outreach/The HuBMAP JumpStart Fellowship 2026-06-01.md @@ -18,7 +18,8 @@ short_description: The HuBMAP JumpStart fellowship offers junior investigators w junior researchers, and to promote collaboration among HuBMAP and the atlas-building community. start_date: '2025-06-01T00:00:00-04:00' -tags: '["fellowship"]' +tags: +- fellowship title: The HuBMAP JumpStart Fellowship --- The HuBMAP JumpStart fellowship offers junior investigators working on human atlasing projects the opportunity to take a leadership role in conducting synergistic, collaborative research projects within the HuBMAP consortium. These projects will build on work that already exists in HuBMAP by either extending aims of current awards or as a new but related research project. The goal of this program is two-fold: 1) create a mentored, career development opportunity for promising junior researchers, and 2) promote collaboration among HuBMAP and the atlas-building community. \ No newline at end of file diff --git "a/src/pages/outreach/The NIH Common Fund\342\200\231s Complement-ARIE program 2025-12-31.md" "b/src/pages/outreach/The NIH Common Fund\342\200\231s Complement-ARIE program 2025-12-31.md" index 843d607..aae80b8 100644 --- "a/src/pages/outreach/The NIH Common Fund\342\200\231s Complement-ARIE program 2025-12-31.md" +++ "b/src/pages/outreach/The NIH Common Fund\342\200\231s Complement-ARIE program 2025-12-31.md" @@ -8,7 +8,8 @@ image: https://cfde-drc.s3.us-east-2.amazonaws.com/assets/img/AIRE-nofo.png layout: '@/layouts/Outreach.astro' link: https://commonfund.nih.gov/complementarie short_description: '-' -tags: '["none"]' +tags: +- none title: "The NIH Common Fund\u2019s Complement-ARIE program" --- - \ No newline at end of file diff --git a/src/pages/outreach/UDN Grand Rounds 2024-06-13.md b/src/pages/outreach/UDN Grand Rounds 2024-06-13.md index 189fbd8..bd3e0b1 100644 --- a/src/pages/outreach/UDN Grand Rounds 2024-06-13.md +++ b/src/pages/outreach/UDN Grand Rounds 2024-06-13.md @@ -10,7 +10,8 @@ short_description: Presentations from UDN sites and cores typically describe the phenotype and multidisciplinary, personalized diagnostic evaluation of one or more UDN participants. start_date: '2024-06-13T13:00:00-04:00' -tags: '["webinar"]' +tags: +- webinar title: UDN Grand Rounds --- UDN Grand Rounds are open to the public. Presentations from UDN sites and cores typically describe the clinical phenotype and multidisciplinary, personalized diagnostic evaluation of one or more UDN participants. Students, trainees, advocates, and others are welcome to attend, ask questions, and offer insights on cases. One hour of CME credit is available at no charge for attendees. \ No newline at end of file diff --git a/src/pages/outreach/Voice AI Summer School Lecture Series 2024-07-19.md b/src/pages/outreach/Voice AI Summer School Lecture Series 2024-07-19.md index 5d02c6f..1a7c972 100644 --- a/src/pages/outreach/Voice AI Summer School Lecture Series 2024-07-19.md +++ b/src/pages/outreach/Voice AI Summer School Lecture Series 2024-07-19.md @@ -15,7 +15,8 @@ short_description: The Voice AI summer school is the first specialized training and analysis, and were presented by Satrajit Ghosh, PhD, Alistair Johnson, DPhil, and Alexandros Sigaras. start_date: '2024-07-19T15:00:00-04:00' -tags: '["training program"]' +tags: +- training program title: Voice AI Summer School Lecture Series --- The Voice AI Summer school is the first specialized training program in utilizing voice data for the development of AI models. The lecture covered the Bridge2AI Voice dataset, including voice data collection, storage, access, and analysis, and was presented by Satrajit Ghosh, PhD, Alistair Johnson, DPhil, and Alexandros Sigaras. \ No newline at end of file diff --git a/src/pages/outreach/Workshop at the Festival of Genomics & Biodata 2024-06-13.md b/src/pages/outreach/Workshop at the Festival of Genomics & Biodata 2024-06-13.md index 0cea698..6744345 100644 --- a/src/pages/outreach/Workshop at the Festival of Genomics & Biodata 2024-06-13.md +++ b/src/pages/outreach/Workshop at the Festival of Genomics & Biodata 2024-06-13.md @@ -12,7 +12,8 @@ short_description: "At the Festival of Genomics & Biodata, we will hold a worksh \ NIH Common Fund Data Ecosystem (CFDE). The theme of the workshop is \u2018Catalyzing\ \ Discovery by Integrating Data Across Biomedical Research Domains\u2019" start_date: '2024-06-13T11:30:00-04:00' -tags: '["workshop"]' +tags: +- workshop title: Workshop at the Festival of Genomics & Biodata --- At the Festival of Genomics & Biodata, we will hold a workshop to introduce the wide range of biomedical data and knowledge available via the NIH Common Fund Data Ecosystem (CFDE). The theme of the workshop is ‘Catalyzing Discovery by Integrating Data Across Biomedical Research Domains’ \ No newline at end of file From 041a390e4677cdad395f4c1ad4abd53d452103c8 Mon Sep 17 00:00:00 2001 From: Heesu Kim Date: Mon, 3 Feb 2025 18:44:37 -0500 Subject: [PATCH 04/10] update package --- package-lock.json | 371 ++++++++++++++-------------------------------- package.json | 2 + 2 files changed, 114 insertions(+), 259 deletions(-) diff --git a/package-lock.json b/package-lock.json index eba8f4e..6bd4117 100644 --- a/package-lock.json +++ b/package-lock.json @@ -8,6 +8,7 @@ "name": "drc-static", "version": "0.0.1", "dependencies": { + "@astrojs/markdown-remark": "^6.0.2", "@astrojs/mdx": "^4.0.5", "@astrojs/react": "^4.1.4", "@astrojs/tailwind": "^5.1.5", @@ -16,6 +17,7 @@ "@types/react": "^18.3.12", "@types/react-dom": "^18.3.1", "astro": "^5.1.6", + "astro-remote": "^0.3.3", "react": "^18.3.1", "react-dom": "^18.3.1", "tailwindcss": "^3.4.17" @@ -55,9 +57,9 @@ "integrity": "sha512-EdDWkC3JJVcpGpqJAU/5hSk2LKXyG3mNGkzGoAuyK+xoPHbaVdSuIWoN1QTnmK3N/gGfaaAfM8gO2KDCAW7S3w==" }, "node_modules/@astrojs/markdown-remark": { - "version": "6.0.1", - "resolved": "https://registry.npmjs.org/@astrojs/markdown-remark/-/markdown-remark-6.0.1.tgz", - "integrity": "sha512-CTSYijj25NfxgZi15TU3CwPwgyD1/7yA3FcdcNmB9p94nydupiUbrIiq3IqeTp2m5kCVzxbPZeC7fTwEOaNyGw==", + "version": "6.0.2", + "resolved": "https://registry.npmjs.org/@astrojs/markdown-remark/-/markdown-remark-6.0.2.tgz", + "integrity": "sha512-aAoHGVRK3rebCYbaLjyyR+3VeAuTz4q49syUxJP29Oo5yZHdy4cCAXRqLBdr9mJVlxCUUjZiF0Dau6YBf65SGg==", "dependencies": { "@astrojs/prism": "3.2.0", "github-slugger": "^2.0.0", @@ -72,7 +74,7 @@ "remark-parse": "^11.0.0", "remark-rehype": "^11.1.1", "remark-smartypants": "^3.0.2", - "shiki": "^1.23.1", + "shiki": "^1.26.2", "unified": "^11.0.5", "unist-util-remove-position": "^5.0.0", "unist-util-visit": "^5.0.0", @@ -106,6 +108,32 @@ "astro": "^5.0.0" } }, + "node_modules/@astrojs/mdx/node_modules/@astrojs/markdown-remark": { + "version": "6.0.1", + "resolved": "https://registry.npmjs.org/@astrojs/markdown-remark/-/markdown-remark-6.0.1.tgz", + "integrity": "sha512-CTSYijj25NfxgZi15TU3CwPwgyD1/7yA3FcdcNmB9p94nydupiUbrIiq3IqeTp2m5kCVzxbPZeC7fTwEOaNyGw==", + "dependencies": { + "@astrojs/prism": "3.2.0", + "github-slugger": "^2.0.0", + "hast-util-from-html": "^2.0.3", + "hast-util-to-text": "^4.0.2", + "import-meta-resolve": "^4.1.0", + "js-yaml": "^4.1.0", + "mdast-util-definitions": "^6.0.0", + "rehype-raw": "^7.0.0", + "rehype-stringify": "^10.0.1", + "remark-gfm": "^4.0.0", + "remark-parse": "^11.0.0", + "remark-rehype": "^11.1.1", + "remark-smartypants": "^3.0.2", + "shiki": "^1.23.1", + "unified": "^11.0.5", + "unist-util-remove-position": "^5.0.0", + "unist-util-visit": "^5.0.0", + "unist-util-visit-parents": "^6.0.1", + "vfile": "^6.0.3" + } + }, "node_modules/@astrojs/prism": { "version": "3.2.0", "resolved": "https://registry.npmjs.org/@astrojs/prism/-/prism-3.2.0.tgz", @@ -2090,6 +2118,47 @@ "sharp": "^0.33.3" } }, + "node_modules/astro-remote": { + "version": "0.3.3", + "resolved": "https://registry.npmjs.org/astro-remote/-/astro-remote-0.3.3.tgz", + "integrity": "sha512-ufS/aOBXQKAe6hZ5NbiHUsC01o0ZcEwS+nNhd/mr1avLV+NbgYJEbwY8VRorzLs/GH5COOTaxl2795DkGIUTcw==", + "dependencies": { + "entities": "^4.5.0", + "marked": "^12.0.0", + "marked-footnote": "^1.2.2", + "marked-smartypants": "^1.1.6", + "ultrahtml": "^1.5.3" + }, + "engines": { + "node": ">=18.14.1" + } + }, + "node_modules/astro/node_modules/@astrojs/markdown-remark": { + "version": "6.0.1", + "resolved": "https://registry.npmjs.org/@astrojs/markdown-remark/-/markdown-remark-6.0.1.tgz", + "integrity": "sha512-CTSYijj25NfxgZi15TU3CwPwgyD1/7yA3FcdcNmB9p94nydupiUbrIiq3IqeTp2m5kCVzxbPZeC7fTwEOaNyGw==", + "dependencies": { + "@astrojs/prism": "3.2.0", + "github-slugger": "^2.0.0", + "hast-util-from-html": "^2.0.3", + "hast-util-to-text": "^4.0.2", + "import-meta-resolve": "^4.1.0", + "js-yaml": "^4.1.0", + "mdast-util-definitions": "^6.0.0", + "rehype-raw": "^7.0.0", + "rehype-stringify": "^10.0.1", + "remark-gfm": "^4.0.0", + "remark-parse": "^11.0.0", + "remark-rehype": "^11.1.1", + "remark-smartypants": "^3.0.2", + "shiki": "^1.23.1", + "unified": "^11.0.5", + "unist-util-remove-position": "^5.0.0", + "unist-util-visit": "^5.0.0", + "unist-util-visit-parents": "^6.0.1", + "vfile": "^6.0.3" + } + }, "node_modules/astro/node_modules/semver": { "version": "7.6.3", "resolved": "https://registry.npmjs.org/semver/-/semver-7.6.3.tgz", @@ -3579,248 +3648,6 @@ "node": ">=6" } }, - 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"node": ">= 12.0.0" - }, - "funding": { - "type": "opencollective", - "url": "https://opencollective.com/parcel" - } - }, - "node_modules/lightningcss/node_modules/detect-libc": { - "version": "1.0.3", - "resolved": "https://registry.npmjs.org/detect-libc/-/detect-libc-1.0.3.tgz", - "integrity": "sha512-pGjwhsmsp4kL2RTz08wcOlGN83otlqHeD/Z5T8GXZB+/YcpQ/dgo+lbU8ZsGxV0HIvqqxo9l7mqYwyYMD9bKDg==", - "optional": true, - "peer": true, - "bin": { - "detect-libc": "bin/detect-libc.js" - }, - "engines": { - "node": ">=0.10" - } - }, "node_modules/lilconfig": { "version": "3.1.3", "resolved": "https://registry.npmjs.org/lilconfig/-/lilconfig-3.1.3.tgz", @@ -3963,6 +3790,36 @@ "url": "https://github.com/sponsors/wooorm" } }, + "node_modules/marked": { + "version": "12.0.2", + "resolved": "https://registry.npmjs.org/marked/-/marked-12.0.2.tgz", + "integrity": "sha512-qXUm7e/YKFoqFPYPa3Ukg9xlI5cyAtGmyEIzMfW//m6kXwCy2Ps9DYf5ioijFKQ8qyuscrHoY04iJGctu2Kg0Q==", + "bin": { + "marked": "bin/marked.js" + }, + "engines": { + "node": ">= 18" + } + }, + "node_modules/marked-footnote": { + "version": "1.2.4", + "resolved": "https://registry.npmjs.org/marked-footnote/-/marked-footnote-1.2.4.tgz", + "integrity": "sha512-DB2Kl+wFh6YwZd70qABMY6WUkG1UuyqoNTFoDfGyG79Pz24neYtLBkB+45a7o72V7gkfvbC3CGzIYFobxfMT1Q==", + "peerDependencies": { + "marked": ">=7.0.0" + } + }, + "node_modules/marked-smartypants": { + "version": "1.1.9", + "resolved": "https://registry.npmjs.org/marked-smartypants/-/marked-smartypants-1.1.9.tgz", + "integrity": "sha512-VPeuaUr5IWptI7nJdgQ9ugrLWYGv13NdzEXTtKY3cmB4aRWOI2RzhLlf+xQp6Wnob9SAPO2sNVlfSJr+nflk/A==", + "dependencies": { + "smartypants": "^0.2.2" + }, + "peerDependencies": { + "marked": ">=4 <16" + } + }, "node_modules/mdast-util-definitions": { "version": "6.0.0", "resolved": "https://registry.npmjs.org/mdast-util-definitions/-/mdast-util-definitions-6.0.0.tgz", @@ -6137,6 +5994,15 @@ "resolved": "https://registry.npmjs.org/sisteransi/-/sisteransi-1.0.5.tgz", "integrity": "sha512-bLGGlR1QxBcynn2d5YmDX4MGjlZvy2MRBDRNHLJ8VI6l6+9FUiyTFNJ0IveOSP0bcXgVDPRcfGqA0pjaqUpfVg==" }, + "node_modules/smartypants": { + "version": "0.2.2", + "resolved": "https://registry.npmjs.org/smartypants/-/smartypants-0.2.2.tgz", + "integrity": "sha512-TzobUYoEft/xBtb2voRPryAUIvYguG0V7Tt3de79I1WfXgCwelqVsGuZSnu3GFGRZhXR90AeEYIM+icuB/S06Q==", + "bin": { + "smartypants": "bin/smartypants.js", + "smartypantsu": "bin/smartypantsu.js" + } + }, "node_modules/source-map": { "version": "0.7.4", "resolved": "https://registry.npmjs.org/source-map/-/source-map-0.7.4.tgz", @@ -6457,19 +6323,6 @@ "url": "https://github.com/sponsors/sindresorhus" } }, - "node_modules/typescript": { - "version": "5.7.3", - "resolved": "https://registry.npmjs.org/typescript/-/typescript-5.7.3.tgz", - "integrity": "sha512-84MVSjMEHP+FQRPy3pX9sTVV/INIex71s9TL2Gm5FG/WG1SqXeKyZ0k7/blY/4FdOzI12CBy1vGc4og/eus0fw==", - "peer": true, - "bin": { - "tsc": "bin/tsc", - "tsserver": "bin/tsserver" - }, - "engines": { - "node": ">=14.17" - } - }, "node_modules/ufo": { "version": "1.5.4", "resolved": "https://registry.npmjs.org/ufo/-/ufo-1.5.4.tgz", diff --git a/package.json b/package.json index 98f6882..c9b42e7 100644 --- a/package.json +++ b/package.json @@ -9,6 +9,7 @@ "astro": "astro" }, "dependencies": { + "@astrojs/markdown-remark": "^6.0.2", "@astrojs/mdx": "^4.0.5", "@astrojs/react": "^4.1.4", "@astrojs/tailwind": "^5.1.5", @@ -17,6 +18,7 @@ "@types/react": "^18.3.12", "@types/react-dom": "^18.3.1", "astro": "^5.1.6", + "astro-remote": "^0.3.3", "react": "^18.3.1", "react-dom": "^18.3.1", "tailwindcss": "^3.4.17" From a3b2f8817ce6226851289d95c6db9f701f72620c Mon Sep 17 00:00:00 2001 From: Heesu Kim Date: Mon, 3 Feb 2025 18:46:07 -0500 Subject: [PATCH 05/10] add styling --- src/components/Prose.astro | 43 ++++++++--- src/styles/base.css | 148 +++++++++++++++++++++++++++++++++++++ tailwind.config.mjs | 141 +++++++++++++++++++++++++++++++++-- 3 files changed, 316 insertions(+), 16 deletions(-) diff --git a/src/components/Prose.astro b/src/components/Prose.astro index 6e1823a..819ef31 100644 --- a/src/components/Prose.astro +++ b/src/components/Prose.astro @@ -3,14 +3,39 @@
+ font-dm-sans + text-secondary-main + + /* Headings */ + prose-h1:font-hanken + prose-h1:text-[40px] + prose-h1:font-medium + prose-h1:text-secondary-main + + prose-h2:font-hanken + prose-h2:text-[32px] + prose-h2:font-medium + + prose-h3:font-hanken + prose-h3:text-[24px] + prose-h3:font-medium + prose-h3:text-secondary-main + + prose-h4:font-hanken + prose-h4:text-[22px] + prose-h4:font-medium + prose-h4:text-secondary-main + + prose-h5:font-hanken + prose-h5:text-[20px] + prose-h5:font-medium + prose-h5:text-secondary-main + + + prose-a:no-underline + + /* Spacing */ + px-10 +">
diff --git a/src/styles/base.css b/src/styles/base.css index c8ba827..441be04 100644 --- a/src/styles/base.css +++ b/src/styles/base.css @@ -13,6 +13,15 @@ -webkit-box-orient: vertical; } } +:root { + --primary-main: #C3E1E6; + --primary-light: #DBEDF0; + --primary-dark: #84A9AE; + + --secondary-main: #2D5986; + --secondary-light: #9CBCDE; + --secondary-dark: #122436; +} .hanken-grotesk-500 { font-family: "Hanken Grotesk", serif; @@ -27,3 +36,142 @@ font-weight: 500; font-style: normal; } + +.title { + font-family: "Hanken Grotesk", sans-serif; + font-weight: 500; + font-size: 40px; + text-transform: uppercase; +} + +.title-small { + font-family: "Hanken Grotesk", sans-serif; + font-weight: 500; + font-size: 24px; + text-transform: uppercase; +} + +.h1 { + font-family: "Hanken Grotesk", sans-serif; + font-weight: 500; + font-size: 40px; + color: var(--secondary-main); +} + +.h2 { + font-family: "Hanken Grotesk", sans-serif; + font-weight: 500; + font-size: 32px; + color: var(--secondary-main); +} + +.h3 { + font-family: "Hanken Grotesk", sans-serif; + font-weight: 500; + font-size: 24px; + color: var(--secondary-main); +} + +.h4 { + font-family: "Hanken Grotesk", sans-serif; + font-weight: 500; + font-size: 22px; + color: var(--secondary-main); +} + +.h5 { + font-family: "Hanken Grotesk", sans-serif; + font-weight: 500; + font-size: 20px; + color: var(--secondary-main); +} + +.subtitle1 { + font-family: "Hanken Grotesk", sans-serif; + font-weight: 500; + font-size: 16px; +} + +.subtitle2 { + font-family: "Hanken Grotesk", sans-serif; + font-weight: 500; + font-size: 15px; +} + +.dm-sans-500 { + font-family: "DM Sans", sans-serif; + font-weight: 500; + font-size: 16px; +} + +.body1 { + font-family: "DM Sans", sans-serif; + font-weight: 500; + font-size: 16px; +} + +.body2 { + font-family: "DM Sans", sans-serif; + font-weight: 500; + font-size: 15px; +} + +.caption { + font-family: "Hanken Grotesk", sans-serif; + font-weight: 400; + font-size: 14px; +} + +.caption-sm { + font-family: "Hanken Grotesk", sans-serif; + font-weight: 500; + font-size: 12px; +} + +.nav { + font-family: "Hanken Grotesk", sans-serif; + font-weight: 600; + font-size: 16px; + text-transform: uppercase; + color: #2D5986; + padding: 0.25rem; + transition: background-color 0.2s; +} + +.nav:hover { + background-color: #f3f4f6; + } + +.footer { + font-family: "DM Sans", sans-serif; + font-weight: 400; + font-size: 16px; +} + + + .chip { + border-radius: 0.5rem; + padding: 0.3rem 0.7rem; + display: inline-flex; + align-items: center; + } + + .chip-main { + background-color: var(--primary-main); + color: var(--secondary-main); + } + + .chip-secondary { + background-color: var(--secondary-main); + color: white; + } + +.hanken-grotesk { + font-family: "Hanken Grotesk", sans-serif; + font-optical-sizing: auto; +} + +.dm-sans { + font-family: "DM Sans", sans-serif; + font-optical-sizing: auto; +} diff --git a/tailwind.config.mjs b/tailwind.config.mjs index 8dfe645..a0189ac 100644 --- a/tailwind.config.mjs +++ b/tailwind.config.mjs @@ -1,15 +1,142 @@ /** @type {import('tailwindcss').Config} */ export default { content: ['./src/**/*.{astro,html,js,jsx,md,mdx,svelte,ts,tsx,vue}'], + // theme: { + // extend: { + // colors: { + // 'primary': 'rgb(45, 89, 134)', # secondary-main + // 'secondary': 'rgb(219, 237, 240)', # primary light + // } + // }, + // }, theme: { - extend: { - colors: { - 'primary': 'rgb(45, 89, 134)', - 'secondary': 'rgb(219, 237, 240)', - } + extend: { + colors: { + primary: { + main: '#C3E1E6', + light: '#DBEDF0', + dark: '#84A9AE' + }, + secondary: { + main: '#2D5986', + light: '#9cbcde', + dark: '#122436' + }, + tertiary: { + main: '#2D5986', + light: '#9cbcde', + dark: '#122436' + }, + paperGray: { + main: '#FAFAFA', + light: '#fdfdfd', + dark: '#afafaf' + }, }, - }, + fontSize: { + 'h1': '40px', + 'h2': '32px', + 'h3': '24px', + 'h4': '22px', + 'h5': '20px', + 'cfde': '40px', + 'cfde-small': '24px', + 'subtitle1': '16px', + 'subtitle2': '15px', + 'body1': '16px', + 'body2': '15px', + 'caption': '14px', + 'nav': '16px', + 'footer': '16px', + 'stats-h3': '24px', + 'stats-sub': '16px', + 'stats-sub-small': '14px' + }, + fontWeight: { + normal: 400, + medium: 500, + semibold: 600, + bold: 700 + }, + fontFamily: { + 'hanken': ['Hanken Grotesk', 'serif'], + 'dm-sans': ['DM Sans', 'serif'] + }, + borderRadius: { + 'chip': '120px' + }, + padding: { + 'btn': '8px 16px', + 'chip': '10px 16px' + }, + backgroundColor: { + 'app-bar': '#FFF' + }, + boxShadow: { + 'app-bar': 'none' + }, + textColor: { + 'nav': '#2D5986', + 'stats': '#9E9E9E' + } + } + }, plugins: [ require('@tailwindcss/typography'), + ], -} + // plugins: [ + // plugin(function({ addComponents }) { + // addComponents({ + // // Titles and Headers + // '.title': { + // fontFamily: 'Hanken Grotesk, sans-serif', + // fontSize: '40px', + // fontWeight: '500', + // textTransform: 'uppercase', + // }, + // '.title-small': { + // fontFamily: 'Hanken Grotesk, sans-serif', + // fontSize: '24px', + // fontWeight: '500', + // textTransform: 'uppercase', + // }, + // 'h1': { + // fontFamily: 'Hanken Grotesk, sans-serif', + // fontSize: '40px', + // fontWeight: '500', + // }, + // 'h2': { + // fontFamily: 'Hanken Grotesk, sans-serif', + // fontSize: '32px', + // fontWeight: '500', + // }, + // 'h3': { + // fontFamily: 'Hanken Grotesk, sans-serif', + // fontSize: '24px', + // fontWeight: '500', + // }, + // // Body text + // '.body1': { + // fontFamily: 'DM Sans, sans-serif', + // fontSize: '16px', + // fontWeight: '500', + // }, + // '.nav': { + // fontFamily: 'Hanken Grotesk, sans-serif', + // fontSize: '16px', + // fontWeight: '600', + // textTransform: 'uppercase', + // color: '#2D5986', + // }, + // // Stats + // '.stats-h3': { + // fontFamily: 'Hanken Grotesk, sans-serif', + // fontSize: '24px', + // fontWeight: '500', + // color: '#9E9E9E', + // } + // }) + // }) + // ], + } From 506ebd18d57e51372cecc6a423fc19815d39c7c6 Mon Sep 17 00:00:00 2001 From: Heesu Kim Date: Mon, 3 Feb 2025 18:46:36 -0500 Subject: [PATCH 06/10] add layouts --- src/layouts/Centers.astro | 17 ++- src/layouts/DCCs.astro | 8 +- src/layouts/Documentation.astro | 11 ++ src/layouts/Documentations.astro | 205 +++++++++++++++++++++++++++++++ src/layouts/News.astro | 12 ++ src/layouts/NewsMain.astro | 124 +++++++++++++++++++ src/layouts/Outreachs.astro | 119 +++++++++++++----- src/layouts/Publications.astro | 20 +-- 8 files changed, 469 insertions(+), 47 deletions(-) create mode 100644 src/layouts/Documentation.astro create mode 100644 src/layouts/Documentations.astro create mode 100644 src/layouts/News.astro create mode 100644 src/layouts/NewsMain.astro diff --git a/src/layouts/Centers.astro b/src/layouts/Centers.astro index 27ccc46..84ff38c 100644 --- a/src/layouts/Centers.astro +++ b/src/layouts/Centers.astro @@ -10,13 +10,20 @@ const centers = Object.values(import.meta.glob('@/pages/centers/*.md', { eager: {centers.map(center =>
-
- {center.frontmatter.short_label} +
+ +
+ {center.frontmatter.label} ({center.frontmatter.short_label}) +
+
+

{center.frontmatter.short_description}

+
+
+

{center.rawContent()}

-

{center.rawContent()}

- Expand - Go to DCC portal + Expand + Go to DCC portal
)} diff --git a/src/layouts/DCCs.astro b/src/layouts/DCCs.astro index fb05ef5..769ba19 100644 --- a/src/layouts/DCCs.astro +++ b/src/layouts/DCCs.astro @@ -11,12 +11,12 @@ const dccs = Object.values(import.meta.glob('@/pages/dccs/*.md', { eager: true }
- {dcc.frontmatter.short_label} + {dcc.frontmatter.short_label}
-

{dcc.rawContent()}

+

{dcc.rawContent()}

- Expand - Go to DCC portal + Expand + Go to DCC portal
)} diff --git a/src/layouts/Documentation.astro b/src/layouts/Documentation.astro new file mode 100644 index 0000000..041a5a3 --- /dev/null +++ b/src/layouts/Documentation.astro @@ -0,0 +1,11 @@ +--- +import '@/styles/base.css' +import Layout from '@/components/Layout.astro' + +--- + + +
+ +
+ diff --git a/src/layouts/Documentations.astro b/src/layouts/Documentations.astro new file mode 100644 index 0000000..703e673 --- /dev/null +++ b/src/layouts/Documentations.astro @@ -0,0 +1,205 @@ +--- +import '@/styles/base.css' +import Layout from '@/components/Layout.astro' +const documentations = Object.values(import.meta.glob('@/pages/documentation/*.md', { eager: true })) + .filter(documentation => documentation.frontmatter.layout === '@/layouts/Documentation.astro') + .sort((a, b) => (a.frontmatter.title || '').localeCompare(b.frontmatter.title || '')) + +// Define descriptions object +const descriptions = { + 'SubmissionSystem': { + content: `The CFDE Workbench Data Resource Portal allows users to download + DCC datasets, files, and interoperability assets via + the Data Matrix. + Representatives from each DCC are encouraged to contribute assets + from their CF programs by creating an account for submitting and + approving uploads to the CFDE Workbench. Currently, the submission + system accepts C2M2 metadata packages, entity matrix transpose (XMT) + files, knowledge graph assertions, attribute tables, SmartAPI and + OpenAPI specifications, extract-transform-load (ETL) scripts, + entity pages, PWB metanodes, and chatbot specifications. +

+ Learn more about submitting to the Data Resource Portal in the Contribution Guide.` + }, + 'C2M2': { + content: ` The Crosscut Metadata Model (C2M2) was designed to standardize + metadata annotations across Common Fund DCCs by the original CFDE + Coordination Center. C2M2 datapackage files are usually a zipfile + containing a set of TSV files already standardized to a set of known + ontologies, along with a single JSON schema. +

+ Learn more about generating a C2M2 datapackage here.` + }, + 'C2M2Table': { + content: ` Preview of imported C2M2 table.` + }, + 'OpenAPI': { + content: ` The OpenAPI specification allows for the standardization of + application programming interfaces (APIs), and facilitates + their interoperability. +

+ The SmartAPI project builds on top of the OpenAPI specifications + to maximize the findability, accessibility, interoperability, + and reusability (FAIRness) of web-based tools, especially those + within the biomedical sphere. Through richer metadata descriptions, + SmartAPI enables users to search and use a connected network of tools. +

+ Learn more about generating an OpenAPI or SmartAPI specification here.` + }, + 'RNA-seq': { + content: ` The CFDE RNA-seq Partnership aims to harmonize diverse RNA-seq + datasets across the CFDE to improve their interoperability and + reusability for the broader scientific research community. To this + end, the partnership is developing common pipelines for both bulk + and single cell RNA-seq data analysis, with the end goal of building + a large, readily accessible, and harmonized resource of RNA-seq + datasets and processing tools from various DCCs and CFDE projects. +

+ More information about the standardized bulk and single cell RNA-seq + pipelines will be available soon.` + }, + 'FAIRshake': { + content: ` The FAIRshake toolkit enables manual and automated assessments of + the findability, accessibility, interoperability, and reusability + (FAIRness) of digital resources. FAIRshake provides community-driven + metrics and rubrics for evaluation, and visualizes the results with + a characteristic embeddable insignia. The primary goal of FAIRshake + is to enable researchers and developers to objectively measure and + improve the FAIRness of their tools. +

+ Learn more about performing FAIR assessments with FAIRshake here. ` + }, + 'KGAssertions': { + content: ` The CFDE Data Distillery Partnership aims to integrate data assertions + across DCCs into a functional knowledge graph for knowledge query + and discovery. The partnership has collected "distilled" data relationships + from each DCC to be unified in a knowledge graph model with controlled + ontology and vocabulary terms for exploring pre-defined, biologically + relevant use cases. +

+ Learn more about generating Data Distillery Knowledge Graph Assertions here.` + }, + 'PWBMetanodes': { + content: ` The Playbook Workflow Builder (PWB) is a web-based + knowledge resolution platform being developed by the CFDE Workflow + Playbook Partnership and consisting of a growing network of datasets, + semantically annotated API endpoints, and visualization tools + from across the CFDE. Users can construct workflows from the individual building blocks, + termed "metanodes", with little effort or technical expertise + required. +

+ Learn more about building PWB metanodes here.` + }, + 'WebSpecs': { + content: ` The CFDE Workbench is built using Next.js, Material UI, and Tailwind CSS. Design Specifications for this site's user interface can be found here.` + } +} +--- + + + + + + +
+ {documentations.map((doc) => ( +
+ + + + ))} +
+ + + + + + + + + \ No newline at end of file diff --git a/src/layouts/News.astro b/src/layouts/News.astro new file mode 100644 index 0000000..c9aaf15 --- /dev/null +++ b/src/layouts/News.astro @@ -0,0 +1,12 @@ +--- +import '@/styles/base.css' +import Layout from '@/components/Layout.astro' +const { frontmatter } = Astro.props +--- + + + +

{frontmatter.title}

+

{frontmatter.date}

+ + diff --git a/src/layouts/NewsMain.astro b/src/layouts/NewsMain.astro new file mode 100644 index 0000000..6c542ea --- /dev/null +++ b/src/layouts/NewsMain.astro @@ -0,0 +1,124 @@ +--- +import "@/styles/base.css"; +import Layout from "@/components/Layout.astro"; +const news = Object.values( + import.meta.glob("@/pages/news/*.md", { eager: true }), +) + .filter((news) => news.frontmatter.layout === "@/layouts/News.astro") + .sort((b, a) => + (a.frontmatter.date || "").localeCompare(b.frontmatter.date || ""), + ); + +const formatDate = (date: string) => { + return new Date(date).toLocaleDateString(undefined, { + year: "numeric", + month: "long", + day: "numeric", + }); +}; +--- + + + + + + +
+ { + news.map((item, i) => ( + +
+
+ {/* Title and date */} +
+
+

{item.frontmatter.title}

+
+
+ {formatDate(item.frontmatter.date)} +
+
+ +
+ {/* Content section */} +
+ {/* Version */} + {item.frontmatter.version && ( +

+ Version {item.frontmatter.version} +

+ )} + + {/* Description */} + {item.frontmatter.description && ( +
+

{item.frontmatter.description}

+ + {/* Supplementary lists */} + {item.frontmatter.supp_description && ( +
    + {item.frontmatter.supp_description.map((desc: string) => ( +
  • {desc}
    • + ))} +
+ )} +
+ )} + + {/* Learn more link */} + {item.frontmatter.link && ( +
+ + Learn more → + +
+ )} + + {/* Tags */} +
+ {item.frontmatter.portal && ( + // + + {item.frontmatter.portal} + + )} + {item.frontmatter.tags && + item.frontmatter.tags.map((tag: string) => ( + + {tag} + + ))} +
+
+ + {/* Image section */} + {item.frontmatter.img && ( +
+ {item.frontmatter.title} +
+ )} +
+
+ + )) + } +
+ + diff --git a/src/layouts/Outreachs.astro b/src/layouts/Outreachs.astro index e80b332..44a7e89 100644 --- a/src/layouts/Outreachs.astro +++ b/src/layouts/Outreachs.astro @@ -1,36 +1,99 @@ --- -import '@/styles/base.css' -import Layout from '@/components/Layout.astro' -const outreach = Object.values(import.meta.glob('@/pages/outreach/*.md', { eager: true })).filter(outreach => outreach.frontmatter.layout === '@/layouts/Outreach.astro') -const dccs = Object.fromEntries(Object.values(import.meta.glob('@/pages/dccs/*.md', { eager: true })).filter(dcc => dcc.frontmatter.layout === '@/layouts/DCC.astro').map(dcc => [dcc.frontmatter.short_label, dcc])) +import "@/styles/base.css"; +import Layout from "@/components/Layout.astro"; +const outreach = Object.values( + import.meta.glob("@/pages/outreach/*.md", { eager: true }), +).filter( + (outreach) => outreach.frontmatter.layout === "@/layouts/Outreach.astro", +); +const dccs = Object.fromEntries( + Object.values(import.meta.glob("@/pages/dccs/*.md", { eager: true })) + .filter((dcc) => dcc.frontmatter.layout === "@/layouts/DCC.astro") + .map((dcc) => [dcc.frontmatter.short_label, dcc]), +); + +const parseDate = (dateStr: string | null): Date | null => { + if (!dateStr) return null; + return new Date(dateStr); +}; + +const isActive = (event: any): boolean => { + const now = new Date(); + const appEnd = parseDate(event.frontmatter.application_end); + const appStart = parseDate(event.frontmatter.application_start); + const endDate = parseDate(event.frontmatter.end_date); + const startDate = parseDate(event.frontmatter.start_date); + + return ( + (appEnd && appEnd >= now) || + (appStart && !appEnd && appStart >= now) || + (endDate && !appEnd && endDate >= now) || + (!endDate && startDate && startDate >= now) + ); +}; --- - -
- {outreach.map(event => -
-
-

{event.frontmatter.title}

-
- -
- {event.frontmatter.dcc && event.frontmatter.dcc.length > 0 && -
- Hosted by: - {event.frontmatter.dcc.map(dcc => dccs[dcc]).map(dcc => - -
- {dcc.frontmatter.short_label} -
+ +
+ { outreach.filter(event => event.frontmatter.tags && !event.frontmatter.tags.includes('none')).map((event) => ( + +
+
+ +
+
+ {event.frontmatter.tags.map((tag) => ( + {tag} + ))} +
+
{event.frontmatter.title}
+
+ +
+ {event.frontmatter.dcc && event.frontmatter.dcc.length > 0 && ( +
+ Hosted by: + {event.frontmatter.dcc + .map((dcc) => dccs[dcc]) + .map((dcc) => ( + +
+ {dcc.frontmatter.short_label} +
+ + ))} +
+ )} +
+ +
+ {event.frontmatter.link && ( + + Event Details -> )} +
- } -
- {event.frontmatter.link && Visit Page} -
-
- )} -
+
+ )) + } +
diff --git a/src/layouts/Publications.astro b/src/layouts/Publications.astro index b60a2ff..b34ff60 100644 --- a/src/layouts/Publications.astro +++ b/src/layouts/Publications.astro @@ -18,42 +18,42 @@ const toCamelCase = (str: String) => {
{ publication.frontmatter.pmid && - + PubMed } { publication.frontmatter.pmcid && - + PMC } { publication.frontmatter.doi && - + DOI } { publication.frontmatter.pmcid && - Export citation {publication.frontmatter.pmcid} + Export citation } {publication.frontmatter.landmark && -
+
Landmark
} {publication.frontmatter.centers && publication.frontmatter.centers.length > 0 && <> -
Center
+
Center
{publication.frontmatter.centers.map((c) => ( -
{c.center.short_label}
+
{c.center.short_label}
))} } {publication.frontmatter.dccs && publication.frontmatter.dccs.map(dcc => dccs[dcc]).map((dcc) => - dcc &&
{dcc.frontmatter.short_label}
+ dcc &&
{dcc.frontmatter.short_label}
)} {publication.frontmatter.r03s && publication.frontmatter.r03s.length > 0 && ( publication.frontmatter.r03s.map((r03, index) => ( -
R03
+
R03
)) )} @@ -62,7 +62,7 @@ const toCamelCase = (str: String) => {
{publication.frontmatter.keywords && ( JSON.parse(publication.frontmatter.keywords).map((keyword, idx) => ( -
{toCamelCase(keyword)}
+
{toCamelCase(keyword)}
)) )}
From 989e4577d293fcddc85e6261346506a71811c892 Mon Sep 17 00:00:00 2001 From: Heesu Kim Date: Mon, 3 Feb 2025 18:46:52 -0500 Subject: [PATCH 07/10] add components --- src/components/Breadcrumbs.astro | 78 ++++++++++++++ src/components/C2M2Table.astro | 36 +++++++ src/components/Footer.astro | 7 ++ src/components/Layout.astro | 67 +++--------- src/components/Nav.astro | 149 +++++++++++++++++++++++++++ src/components/PartnershipCard.astro | 15 ++- 6 files changed, 293 insertions(+), 59 deletions(-) create mode 100644 src/components/Breadcrumbs.astro create mode 100644 src/components/C2M2Table.astro create mode 100644 src/components/Footer.astro create mode 100644 src/components/Nav.astro diff --git a/src/components/Breadcrumbs.astro b/src/components/Breadcrumbs.astro new file mode 100644 index 0000000..cbc537f --- /dev/null +++ b/src/components/Breadcrumbs.astro @@ -0,0 +1,78 @@ +--- +// NavBreadcrumbs.astro +const { pathname } = Astro.url; + +// Utility function to format path segments +function formatPathSegment(segment: string, index: number) { + // Decode and basic formatting + let formatted = decodeURIComponent(segment).replace('_', ' '); + + // Replace drc-static with INFO + if (segment === 'drc-static') { + return 'INFO'; + } + + // Handle special cases + if (segment === 'processed') return 'Processed Data'; + if (segment === 'entity') return 'Entity'; + if (segment === 'form') return 'Data and Metadata Form'; + if (segment === 'urlform') return 'Code Assets Form'; + if (segment === 'uploaded') return 'Uploaded Assets'; + + return formatted; +} + +// Process the path +const pathSegments = pathname.split('/').filter(Boolean); +const formattedSegments = pathSegments.map((segment, index) => { + let formatted = formatPathSegment(segment, index); + + // Special case handling + if (pathSegments[0] === 'data' && pathSegments[1] === 'processed') { + if (index === 2 && pathSegments[2] === 'entity') formatted = 'Entity'; + } + if (pathSegments[0] === 'data' && pathSegments[1] === 'search') { + if (index === 3 && pathSegments[3] === 'entity') formatted = 'Entity'; + } + if (pathSegments[0] === 'search') { + if (index === 2 && pathSegments[2] === 'entity') formatted = 'Entity'; + } + + return { + segment: segment === 'drc-static' ? 'INFO' : segment, // Use INFO in the path + formatted: formatted.toUpperCase(), + path: '/' + pathSegments.slice(0, index + 1).join('/') + }; +}); + +// Don't render if we're at the root +if (pathSegments.length < 2) return null; +--- + + + + \ No newline at end of file diff --git a/src/components/C2M2Table.astro b/src/components/C2M2Table.astro new file mode 100644 index 0000000..4b4f626 --- /dev/null +++ b/src/components/C2M2Table.astro @@ -0,0 +1,36 @@ +--- +import { Markdown } from 'astro-remote'; + +interface Props { + content: string; +} + +const { content } = Astro.props; +--- + +
+ +
+ + \ No newline at end of file diff --git a/src/components/Footer.astro b/src/components/Footer.astro new file mode 100644 index 0000000..99a36ed --- /dev/null +++ b/src/components/Footer.astro @@ -0,0 +1,7 @@ +--- +import "@/styles/base.css"; +--- +
+ +
+ diff --git a/src/components/Layout.astro b/src/components/Layout.astro index da4ba63..fb046fb 100644 --- a/src/components/Layout.astro +++ b/src/components/Layout.astro @@ -1,6 +1,8 @@ --- -import '@/styles/base.css' -import Prose from '@/components/Prose.astro' +import "@/styles/base.css"; +import Prose from "@/components/Prose.astro"; +import Nav from "./Nav.astro"; +import Footer from "./Footer.astro"; --- @@ -8,57 +10,20 @@ import Prose from '@/components/Prose.astro' - + + CFDE Information Portal -
-
- - Home - - - CF Programs - - - CFDE Centers - - - Partnerships - - - Outreach - - - Publications - - - Webinars - -
- - - +
+
+