From a1a89a0b8ab22491e88b9155c51ca45923dd21e0 Mon Sep 17 00:00:00 2001 From: Bl4ckH4wkGER <25514600+Bl4ckH4wkGER@users.noreply.github.com> Date: Mon, 11 Aug 2025 11:33:42 -0700 Subject: [PATCH 1/6] Add allen-hmba-releases.yaml to datasets folder --- datasets/allen-hmba-releases.yaml | 50 +++++++++++++++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 datasets/allen-hmba-releases.yaml diff --git a/datasets/allen-hmba-releases.yaml b/datasets/allen-hmba-releases.yaml new file mode 100644 index 000000000..1c63d3b3a --- /dev/null +++ b/datasets/allen-hmba-releases.yaml @@ -0,0 +1,50 @@ +Name: Human and Mammalian Brain Atlas +Description: + Human and Mammalian Brain Atlas (HMBA) is a major atlas of the BRAIN Initiative Cell Atlas Network (BICAN) that proposes to establish a comprehensive, + highly granular cell atlas in complete adult human, macaque, and marmoset brains that links brain structure, function and cellular architecture. + Release artifacts have been made available in this OpenData bucket to enable utilization along with their paper publications by the neuroscience community. +Documentation: https://portal.brain-map.org/explore/hmba +Contact: awspds@alleninstitute.org +ManagedBy: "[Allen Institute](http://www.alleninstitute.org/)" +UpdateFrequency: Never +Tags: + - aws-pds + - biology + - gene expression + - neurobiology + - life sciences + - transcriptomics + - basal ganglia + - Mus musculus + - Macaca mulatta + - Callithrix jacchus + - Homo sapiens +License: http://www.alleninstitute.org/legal/terms-use/ +Citation: +Resources: + - Description: project data files in a public bucket + ARN: arn:aws:s3:::allen-hmba-releases + Region: us-west-2 + Type: S3 bucket + Explore: +DataAtWork: + Tutorials: + - Title: + URL: + NotebookURL: + AuthorName: + AuthorURL: + Services: + Tools & Applications: + - Title: + URL: + AuthorName: + AuthorURL: + Publications: + - Title: + URL: + AuthorName: + AuthorURL: +DeprecatedNotice: +ADXCategories: + - \ No newline at end of file From 08810bff102df752f4d12140532855a59325713d Mon Sep 17 00:00:00 2001 From: Bl4ckH4wkGER <25514600+Bl4ckH4wkGER@users.noreply.github.com> Date: Tue, 28 Oct 2025 10:31:39 -0700 Subject: [PATCH 2/6] Update allen-hmba-releases.yaml Update tags, add citation, application, and publication. --- datasets/allen-hmba-releases.yaml | 40 ++++++++++++++----------------- 1 file changed, 18 insertions(+), 22 deletions(-) diff --git a/datasets/allen-hmba-releases.yaml b/datasets/allen-hmba-releases.yaml index 1c63d3b3a..d45699fce 100644 --- a/datasets/allen-hmba-releases.yaml +++ b/datasets/allen-hmba-releases.yaml @@ -13,12 +13,10 @@ Tags: - gene expression - neurobiology - life sciences - - transcriptomics - - basal ganglia + - single cell transcriptomics - Mus musculus - - Macaca mulatta - - Callithrix jacchus - Homo sapiens + - non-human primate License: http://www.alleninstitute.org/legal/terms-use/ Citation: Resources: @@ -26,25 +24,23 @@ Resources: ARN: arn:aws:s3:::allen-hmba-releases Region: us-west-2 Type: S3 bucket - Explore: DataAtWork: Tutorials: - - Title: - URL: - NotebookURL: - AuthorName: - AuthorURL: - Services: + - Title: Human-Mammalian Brain - Basal Ganglia - Data + URL: https://alleninstitute.github.io/abc_atlas_access/descriptions/HMBA-BG_dataset.html + AuthorName: Allen Institute for Brain Science + AuthorURL: www.alleninstitute.org + - Title: Human-Mammalian Brain - CCF Book + URL: https://alleninstitute.github.io/CCF-MAP/ + AuthorName: Allen Institute for Brain Science + AuthorURL: www.alleninstitute.org Tools & Applications: - - Title: - URL: - AuthorName: - AuthorURL: + - Title: HMBA Basal Ganglia resources in Brain Knowledge Platform's Data Catalog + URL: https://knowledge.brain-map.org/data/POZ2HCPBT60DSDJ8UA7 + AuthorName: Allen Institute for Brain Science + AuthorURL: www.alleninstitute.org Publications: - - Title: - URL: - AuthorName: - AuthorURL: -DeprecatedNotice: -ADXCategories: - - \ No newline at end of file + - Title: Cross-species consensus atlas of primate basal ganglia + URL: Preprint in preparation. + AuthorName: Johansen N.J., Fu Y., Schmitz M., et al. + AuthorURL: https://alleninstitute.org/person/nelson-johansen/ From 3af85ddda716836cd32f9c25fb0c5a112503c2b9 Mon Sep 17 00:00:00 2001 From: Beryl Rabindran Date: Thu, 30 Oct 2025 09:23:38 -0400 Subject: [PATCH 3/6] ok: Update allen-hmba-releases.yaml --- datasets/allen-hmba-releases.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/datasets/allen-hmba-releases.yaml b/datasets/allen-hmba-releases.yaml index d45699fce..67f606184 100644 --- a/datasets/allen-hmba-releases.yaml +++ b/datasets/allen-hmba-releases.yaml @@ -20,7 +20,7 @@ Tags: License: http://www.alleninstitute.org/legal/terms-use/ Citation: Resources: - - Description: project data files in a public bucket + - Description: Project data files in a public bucket ARN: arn:aws:s3:::allen-hmba-releases Region: us-west-2 Type: S3 bucket @@ -44,3 +44,4 @@ DataAtWork: URL: Preprint in preparation. AuthorName: Johansen N.J., Fu Y., Schmitz M., et al. AuthorURL: https://alleninstitute.org/person/nelson-johansen/ + From 4776fc546062e8995456d20f3e52011825a48ab2 Mon Sep 17 00:00:00 2001 From: Beryl Rabindran Date: Thu, 30 Oct 2025 09:30:42 -0400 Subject: [PATCH 4/6] ok: Update allen-hmba-releases.yaml updated tag --- datasets/allen-hmba-releases.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/datasets/allen-hmba-releases.yaml b/datasets/allen-hmba-releases.yaml index 67f606184..b9547631b 100644 --- a/datasets/allen-hmba-releases.yaml +++ b/datasets/allen-hmba-releases.yaml @@ -13,7 +13,7 @@ Tags: - gene expression - neurobiology - life sciences - - single cell transcriptomics + - single-cell transcriptomics - Mus musculus - Homo sapiens - non-human primate @@ -45,3 +45,4 @@ DataAtWork: AuthorName: Johansen N.J., Fu Y., Schmitz M., et al. AuthorURL: https://alleninstitute.org/person/nelson-johansen/ + From 95db693c3e91a2c829c70ceaae88d214387a438c Mon Sep 17 00:00:00 2001 From: Beryl Rabindran Date: Thu, 30 Oct 2025 09:34:49 -0400 Subject: [PATCH 5/6] ok: Update allen-hmba-releases.yaml --- datasets/allen-hmba-releases.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/datasets/allen-hmba-releases.yaml b/datasets/allen-hmba-releases.yaml index b9547631b..7e07d440e 100644 --- a/datasets/allen-hmba-releases.yaml +++ b/datasets/allen-hmba-releases.yaml @@ -23,7 +23,7 @@ Resources: - Description: Project data files in a public bucket ARN: arn:aws:s3:::allen-hmba-releases Region: us-west-2 - Type: S3 bucket + Type: S3 Bucket DataAtWork: Tutorials: - Title: Human-Mammalian Brain - Basal Ganglia - Data @@ -46,3 +46,4 @@ DataAtWork: AuthorURL: https://alleninstitute.org/person/nelson-johansen/ + From 4db9f81782d543c5f747b75eb8ee75df9c77448c Mon Sep 17 00:00:00 2001 From: Beryl Rabindran Date: Thu, 30 Oct 2025 09:40:14 -0400 Subject: [PATCH 6/6] ok: Update allen-hmba-releases.yaml Removing publication info as it expects a link. Please add the link when it is ready. --- datasets/allen-hmba-releases.yaml | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/datasets/allen-hmba-releases.yaml b/datasets/allen-hmba-releases.yaml index 7e07d440e..b7275588d 100644 --- a/datasets/allen-hmba-releases.yaml +++ b/datasets/allen-hmba-releases.yaml @@ -39,11 +39,8 @@ DataAtWork: URL: https://knowledge.brain-map.org/data/POZ2HCPBT60DSDJ8UA7 AuthorName: Allen Institute for Brain Science AuthorURL: www.alleninstitute.org - Publications: - - Title: Cross-species consensus atlas of primate basal ganglia - URL: Preprint in preparation. - AuthorName: Johansen N.J., Fu Y., Schmitz M., et al. - AuthorURL: https://alleninstitute.org/person/nelson-johansen/ + +