Merge branch 'add-depmap-omics-ccle' of https://github.com/dpmccabe/open-data-registry into add-depmap-omics-ccle

Author: dpmccabe

datasets/aws-public-blockchain.yaml

@@ -13,6 +13,7 @@ Description: >
   - XRP Ledger              - SonarX  - <code>s3://aws-public-blockchain/v1.1/sonarx/xrp/</code><br>
   - Stellar(<a href="https://developers.stellar.org/docs/learn/fundamentals/data-format/xdr" rel="noopener noreferrer">XDR files</a>)              - Stellar - <code>s3://aws-public-blockchain/v1.1/stellar/</code><br>
   - The Open Network (TON)  - TON - <code>s3://aws-public-blockchain/v1.1/ton/</code><br>
+  - Cronos                  - Cronos - <code>s3://aws-public-blockchain/v1.1/cronos/</code><br>
   </br> 
 
   <h4>Become a Data Provider</h4>
@@ -24,6 +25,7 @@ Contact: [email protected]
 ManagedBy: "[Amazon Web Services](https://aws.amazon.com/)"
 UpdateFrequency: New data is delivered daily to the current date folders Parquet files.
 Tags:
+  - aws-pds
   - blockchain
   - web3
 License: https://github.com/aws-samples/digital-assets-examples/blob/main/LICENSE

datasets/colorado-elevation-data.yaml

@@ -2,7 +2,7 @@ Name: State of Colorado Elevation Data
 Description: The State of Colorado has gathered public historical elevation data.
 Documentation: https://docs.google.com/document/d/1HMO-d4cCrBvFa2F6-N3lhP6rkezlvBmSUFA5S8t_ekQ/edit?usp=sharing
 Contact: [email protected]
-ManagedBy: State of Colorado Governor's Office of Information Technology (OIT) GIS team
+ManagedBy: State of Colorado Governors Office of Information Technology OIT GIS team
 UpdateFrequency: Periodically
 Tags:
   - aws-pds

datasets/colorado-imagery.yaml

@@ -2,7 +2,7 @@ Name: State of Colorado Imagery
 Description: The State of Colorado has gathered public historical imagery ranging from 2005 to 2021.
 Documentation: https://docs.google.com/document/d/1YDHignUj9lQTMw2J-SqA96MTP8KmJYtk2ZKKC2ZYuPE/edit?usp=sharing
 Contact: [email protected]
-ManagedBy: State of Colorado Governor's Office of Information Technology (OIT) GIS team
+ManagedBy: State of Colorado Governors Office of Information Technology OIT GIS team
 UpdateFrequency: Periodically
 Collabs:
   ASDI:

datasets/deepdrug-dpeb.yaml

@@ -0,0 +1,38 @@
+Name: DeepDrug Protein Embeddings Bank (DPEB)
+Description: DPEB is a multimodal database of human protein embeddings integrating four biologically complementary representations—AlphaFold2, BioEmbeddings, ESM-2, and ProtVec—designed for enhanced protein-protein interaction prediction and functional classification.
+Documentation: https://github.com/deepdrugai/DPEB
+Contact: https://github.com/deepdrugai/DPEB/issues
+ManagedBy: "Louisiana State University"
+UpdateFrequency: Initial release; maintained for at least 2 years with updates planned based on new embedding models and protein coverage.
+Tags:
+  - bioinformatics
+  - protein
+  - structural biology
+  - machine learning
+  - life sciences
+  - aws-pds
+License: MIT
+Citation: "Sajol MSI et al. DeepDrug Protein Embeddings Bank (DPEB) was accessed on [DATE] at https://registry.opendata.aws/dpeb"
+Resources:
+  - Description: Multimodal human protein embeddings (AlphaFold2, BioEmbeddings, ESM-2, ProtVec) with JSONL-formatted metadata containing FASTA, UniProt IDs, and embeddings.
+    ARN: arn:aws:s3:::deepdrug-dpeb
+    Region: us-west-2
+    Type: S3 Bucket
+DataAtWork:
+  Tutorials:
+    - Title: Aggregating and Clustering AlphaFold2 Embeddings from DPEB
+      URL: https://github.com/deepdrugai/DPEB/tree/main
+      AuthorName: Md. Saiful Islam Sajol
+      AuthorURL: https://github.com/deepdrugai
+  Tools & Applications:
+    - Title: DPEB Explorer Tool
+      URL: https://github.com/deepdrugai/DPEB
+      AuthorName: DeepDrug Lab
+      AuthorURL: https://github.com/deepdrugai
+  Publications:
+    - Title: A Multimodal Human Protein Embeddings Database - DeepDrug Protein Embeddings Bank (DPEB)
+      URL: https://doi.org/10.XXXX/nar.dpeb2025
+      AuthorName: Sajol MSI, Rajasekaran M, Bess A, Alvin C, Mukhopadhyay S
+      AuthorURL: https://github.com/deepdrugai/DPEB
+ADXCategories:
+  - Healthcare & Life Sciences Data

datasets/e11bio-prism.yaml

@@ -0,0 +1,62 @@
+Name: E11bio PRISM
+Description: |
+  This dataset was generated using E11.bio's PRISM technology (Protein Reconstruction and Identification through Multiplexing),
+  a platform that combines viral barcoding, expansion microscopy, and iterative immunolabeling for large-scale neuronal reconstruction.
+
+  Neurons in the mouse hippocampal CA3 were transduced with a library of adeno-associated viruses (AAVs)
+  encoding diverse “protein bits”—small epitope tags that act as combinatorial barcodes. 
+  Tissue was then processed with an expansion microscopy protocol, physically enlarging the sample ~5×
+  to achieve an effective voxel size of ~35 × 35 × 80 nm.
+  Across multiple cycles of staining, imaging, and antibody stripping, the same expanded tissue was repeatedly labeled,
+  enabling iterative immunostaining for dozens of molecular targets.
+
+  The dataset includes:
+  1) Light microscopy data of multiplexed brain tissue
+  2) Segmentations of cell morphology and protein expression in the tissue
+  3) Files for faster visualization of the data (e.g. precomputed format)
+  4) Additional supporting files (e.g. model predictions, manual annotations etc.)
+Documentation: https://github.com/e11bio/e11-open-data
+Contact: [email protected]
+ManagedBy: "[E11.bio](https://e11.bio)"
+UpdateFrequency: As required
+Tags:
+  - bioinformatics
+  - biology
+  - brain images
+  - cell imaging
+  - computer vision
+  - fluorescence imaging
+  - high-throughput imaging
+  - image processing
+  - imaging
+  - ion channels
+  - life sciences
+  - machine learning
+  - microscopy
+  - morphological reconstructions
+  - Mus musculus
+  - neurobiology
+  - neuroimaging
+  - neuroscience
+  - protein
+  - segmentation
+  - zarr
+  - aws-pds
+License: https://e11.bio/terms-of-use
+Resources:
+  - Description: Data files in a public bucket
+    ARN: arn:aws:s3:::e11bio-prism
+    Region: us-east-1
+    Type: S3 Bucket
+DataAtWork:
+  Tutorials:
+    - Title: E11.Bio PRISM OpenData
+      URL: https://github.com/e11bio/e11-open-data
+      NotebookURL:
+      AuthorName: Arlo Sheridan & Johan Winnubst
+      AuthorURL: https://e11.bio/team
+  Tools & Applications:
+    - Title: Volara 
+      URL: https://github.com/e11bio/volara
+      AuthorName: Arlo Sheridan & Will Patton
+      AuthorURL: https://e11.bio/team

datasets/ecmwf-era5.yaml

@@ -1,5 +1,6 @@
 Deprecated: True
-DeprecatedNotice: The provider of this dataset will no longer maintain this dataset.  We are open to talking with anyone else who might be willing to provide this dataset to the community.  Contact <a href="mailto:[email protected]">[email protected]</a>.
+DeprecatedNotice: |
+  <h3>The provider of this dataset will no longer maintain it, but has instead worked with NSF NCAR to rehost the dataset here: <a href=https://registry.opendata.aws/nsf-ncar-era5/>https://registry.opendata.aws/nsf-ncar-era5/</a> </h3>
 Name: ECMWF ERA5 Reanalysis
 Description: |
   ERA5 is the fifth generation of ECMWF atmospheric reanalyses of the global climate, and the first reanalysis produced as an operational service. It utilizes the best available observation data from satellites and in-situ stations, which are assimilated and processed using ECMWF's Integrated Forecast System (IFS) Cycle 41r2.

datasets/humancellatlas.yaml

@@ -12,7 +12,7 @@ Documentation: https://data.humancellatlas.org/
 
 Contact: https://data.humancellatlas.org/contact
 
-ManagedBy: UC Santa Cruz Genomics Institute, University of California, Santa Cruz (UCSC)
+ManagedBy: UC Santa Cruz Genomics Institute, University of California, Santa Cruz, UCSC
 
 UpdateFrequency: Monthly
 
@@ -95,4 +95,4 @@ DataAtWork:
       AuthorName: "Various authors"
 
 ADXCategories:
-  - Healthcare & Life Sciences Data
+  - Healthcare & Life Sciences Data

datasets/ideam-radares.yaml

@@ -29,9 +29,9 @@ DataAtWork:
     - Title: Read and plot Sigmet files available on AWS using Xradar
       URL: https://docs.openradarscience.org/projects/xradar/en/stable/notebooks/Read-plot-Sigmet-data-from-AWS.html
       AuthorName: Alfonso Ladino
-    - Title: Taller de datos científicos con Python y R - AtmosCol 2023
-      URL: https://projectpythia.org/AtmosCol-2023/notebooks/2.acceso-datos/2.2.Radares.html
+    - Title: Ciencia de Datos Hidrometeorológicos con Python
+      URL: https://projectpythia.org/AtmosCol-2023/radares
       AuthorName: Alfonso Ladino, Nicole Rivera, Max Grover
     - Title: Specific Differential Phase (KDP) retrieval methods comparison
-      URL: https://projectpythia.org/radar-cookbook/notebooks/example-workflows/kdp-comparison.html
+      URL: https://projectpythia.org/radar-cookbook/notebooks/example-workflows/kdp-comparison/
       AuthorName: Alfonso Ladino, Max Grover

datasets/oceanomics.yaml

@@ -2,7 +2,7 @@ Name: OceanOmics
 Description: "Minderoo Foundation OceanOmics aims to establish environmental DNA (eDNA) as a tool to measure, understand, and protect oceans. OceanOmics mainly generates two types of data: eDNA sequencing data (metabarcoding, metagenomics), and genome assembly data (marine vertebrates)."
 Documentation: https://edna.minderoo.org
 Contact: [email protected]
-ManagedBy: Minderoo Foundation OceanOmics (Dr Shannon Corrigan, Dr Philipp Bayer)
+ManagedBy: Minderoo Foundation OceanOmics, Dr Shannon Corrigan, Dr Philipp Bayer
 UpdateFrequency: Data will be continually updated as it is generated.
 Collabs:
   ASDI:

datasets/proteingym.yaml

@@ -3,7 +3,7 @@ Description: |
   ProteinGym is a benchmark suite for assessing the performance of protein fitness prediction and design models. It comprises a large curated collection of 200+ high-throughput experimental assays (~3M mutated sequences), as well as clinical annotations from experts about the pathogenicity of mutants in over 3k human genes.
 Documentation: https://github.com/OATML-Markslab/ProteinGym/blob/main/README.md
 Contact: [email protected]
-ManagedBy: "Harvard Medical School; University of Oxford"
+ManagedBy: "Harvard Medical School, University of Oxford"
 UpdateFrequency: Quarterly
 Tags:
   - aws-pds