Merge branch 'main' into main

Author: rsignell

datasets/1kg-ont-vienna.yaml

@@ -0,0 +1,27 @@
+Name: 1KG-ONT-VIENNA panel
+Description: The 1KG-ONT-VIENNA panel comprises medium coverage ONT sequencing data for 1.019 samples from the 1000 Genomes Project collection, structural variants, and their haplotype context. 
+Documentation: https://github.com/1kg-ont-vienna/sv-analysis
+Contact: [email protected]
+ManagedBy: Institute of Molecular Pathology
+UpdateFrequency: Irregular
+Tags:
+  - genetic
+  - genomic
+  - life sciences
+  - whole genome sequencing
+  - fastq
+  - fast5
+License: There are no restrictions on the use of this data. Use of the data should be cited in the usual way, with current details available at https://github.com/1kg-ont-vienna/sv-analysis/
+Resources:
+  - Description: Primary and derived data
+    ARN: arn:aws:s3:::1kg-ont-vienna
+    Region: eu-west-1
+    Type: S3 Bucket
+DataAtWork:
+    Tutorials:
+    Tools & Applications:
+    Publications:
+    - Title: Long-read sequencing and structural variant characterization in 1,019 samples from the 1000 Genomes Project
+      URL: https://doi.org/10.1101/2024.04.18.590093 
+      AuthorName: Siegfried Schloissnig, Samarendra Pani, Bernardo Rodriguez-Martin, Jana Ebler, Carsten Hain, Vasiliki Tsapalou, Arda Söylev, Patrick Hüther, Hufsah Ashraf, Timofey Prodanov, Mila Asparuhova, Sarah Hunt, Tobias Rausch, Tobias Marschall, Jan O Korbel
+

datasets/3kricegenome.yaml

@@ -4,6 +4,10 @@ Documentation: https://github.com/awslabs/open-data-docs/tree/main/docs/3kricege
 Contact: http://iric.irri.org/contact-us
 ManagedBy: '[International Rice Research Institute](https://www.irri.org/)'
 UpdateFrequency: Not updated
+Collabs:
+  ASDI:
+    Tags:
+      - agriculture
 Tags:
   - agriculture
   - food security

datasets/africa-field-boundary-labels.yaml

@@ -1,15 +1,22 @@
 Name: A region-wide, multi-year set of crop field boundary labels for Africa
 Description: >
   Crop field boundaries digitized in Planet imagery collected across Africa
-  between 2017 and 2023, developed by [Farmerline](https://farmerline.co/),
-  [Spatial Collective](https://spatialcollective.com/), and the
-  [Agricultural Impacts Research Group](https://agroimpacts.info/) at
-  [Clark University](https://www.clarku.edu/), with support from the
-  [Lacuna Fund](https://lacunafund.org/)
-Documentation: "https://github.com/agroimpacts/lacunalabels/"
+  between 2017 and 2023, developed by [Farmerline](https://farmerline.co/), [Spatial Collective](https://spatialcollective.com/), 
+  and the [Agricultural Impacts Research Group](https://agroimpacts.info/) at [Clark University](https://www.clarku.edu/), with support from the
+  [Lacuna Fund](https://lacunafund.org/) ([Estes et al, 2024](https://arxiv.org/abs/2412.18483); [Wussah et al. (2023)](https://zenodo.org/records/11060871)). This dataset has been 
+  further supplemented by additional labels collected primarily for 
+  for 2018 over a subset of countries, which provide an example of their
+  application in training and validating a CNN-based cropland mapping model 
+  [(Khallaghi et al. 2025)](https://www.mdpi.com/2072-4292/17/3/474).
+Documentation: Information on the primary dataset can be found [here](https://github.com/agroimpacts/lacunalabels/).
+  Documentation for added labels is available [here](https://github.com/agroimpacts/cnn-generalization-enhancement).
 Contact: [email protected]
 ManagedBy: "[The Agricultural Impacts Research Group](https://agroimpacts.info/)"
 UpdateFrequency: "Updated versions of the dataset are added as they are developed"
+Collabs:
+  ASDI:
+    Tags:
+      - agriculture
 Tags:
   - agriculture
   - machine learning
@@ -19,10 +26,14 @@ Tags:
   - labeled
 License: "[Planet NICFI participant license agreement](https://assets.planet.com/docs/Planet_ParticipantLicenseAgreement_NICFI.pdf)"
 Resources:
-  - Description: Field boundary labels and corresponding Planet images
+  - Description: Field boundaries and corresponding Planet images
     ARN: arn:aws:s3:::africa-field-boundary-labels
     Region: us-west-2
     Type: S3 Bucket
+  - Description: '[Additional rasterized field labels and corresponding Planet images](https://www.mdpi.com/2072-4292/17/3/474)'
+    ARN: arn:aws:s3:::africa-field-boundary-labels/extra
+    Region: us-west-2
+    Type: S3 Bucket
 DataAtWork:
   Tutorials:
     - Title: Instructions on data access and label-making demonstration notebook
@@ -31,6 +42,12 @@ DataAtWork:
       AuthorName: Lyndon Estes
       AuthorURL: https://github.com/ldemaz
   Publications:
+    - Title: Generalization enhancement strategies to enable cross-year cropland mapping with convolutional neural networks trained using historical samples
+      URL: https://www.mdpi.com/2072-4292/17/3/474 
+      AuthorName: Khallaghi et al. (2025)
+    - Title: A region-wide, multi-year set of crop field boundary labels for Africa
+      URL: https://arxiv.org/abs/2412.18483
+      AuthorName: Estes et al. (2024)
     - Title: A region-wide, multi-year set of crop field boundary labels for Africa
       URL: https://zenodo.org/records/11060871
       AuthorName: Wussah et al. (2023)
@@ -43,3 +60,6 @@ DataAtWork:
     - Title: A platform for crowdsourcing the creation of representative, accurate landcover maps
       URL: http://www.sciencedirect.com/science/article/pii/S136481521630010X
       AuthorName: Estes et al. (2016)
+Citation: >
+  Primary dataset: Estes et al. (2024). A region-wide, multi-year set of crop field boundary labels for Africa. arXiv:2412.18483.
+  Additional labels: Khallaghi et al. (2025). Generalization enhancement strategies to enable cross-year cropland mapping with convolutional neural networks trained using historical samples. Remote Sensing, 17(3), 474.

datasets/ag-loam.yaml

@@ -9,6 +9,10 @@ Documentation: https://github.com/UCR-Robotics/AG-LOAM
 Contact: Hanzhe Teng ([email protected]), Konstantinos Karydis ([email protected])
 ManagedBy: "[Autonomous Robots and Control Systems Lab](https://sites.google.com/view/arcs-lab)"
 UpdateFrequency: NA
+Collabs:
+  ASDI:
+    Tags:
+      - agriculture
 Tags:
   - aws-pds
   - robotics

datasets/allen-sea-ad-atlas.yaml

@@ -30,18 +30,30 @@ Resources:
     Type: S3 Bucket
     Explore:
     - '[Browse Bucket](https://sea-ad-single-cell-profiling.s3.amazonaws.com/index.html)'
+  - Description: "Update notifications for s3://sea-ad-single-cell-profiling. Users can subscribe to this SNS topic with [AWS Lambda](https://aws.amazon.com/lambda/) or [AWS Simple Queue Service](https://aws.amazon.com/sqs/)."
+    ARN: arn:aws:sns:us-west-2:208217671510:sea-ad-single-cell-profiling-object_created
+    Region: us-west-2
+    Type: SNS Topic
   - Description: Quantitative neuropathology (full resolution images, processed images, and quantifications) in a public bucket
     ARN: arn:aws:s3:::sea-ad-quantitative-neuropathology
     Region: us-west-2
     Type: S3 Bucket
     Explore:
     - '[Browse Bucket](https://sea-ad-quantitative-neuropathology.s3.amazonaws.com/index.html)'
+  - Description: "Update notifications for s3://sea-ad-quantitative-neuropathology. Users can subscribe to this SNS topic with [AWS Lambda](https://aws.amazon.com/lambda/) or [AWS Simple Queue Service](https://aws.amazon.com/sqs/)."
+    ARN: arn:aws:sns:us-west-2:208217671510:sea-ad-quantitative-neuropathology-object_created
+    Region: us-west-2
+    Type: SNS Topic
   - Description: Spatial transcriptomics data files in a public bucket
     ARN: arn:aws:s3:::sea-ad-spatial-transcriptomics
     Region: us-west-2
     Type: S3 Bucket
     Explore:
     - '[Browse Bucket](https://sea-ad-spatial-transcriptomics.s3.amazonaws.com/index.html)'
+  - Description: "Update notifications for s3://sea-ad-spatial-transcriptomics. Users can subscribe to this SNS topic with [AWS Lambda](https://aws.amazon.com/lambda/) or [AWS Simple Queue Service](https://aws.amazon.com/sqs/)."
+    ARN: arn:aws:sns:us-west-2:208217671510:sea-ad-spatial-transcriptomics-object_created
+    Region: us-west-2
+    Type: SNS Topic
 DataAtWork:
   Tools & Applications:
     - Title: Seattle Alzheimer’s Disease Brain Cell Atlas

datasets/allthebacteria.yaml

@@ -0,0 +1,48 @@
+Name: AllTheBacteria
+Description: All bacterial isolate whole-genome sequencing data from INSDC, uniformly assembled, quality-controlled, annotated, and searchable.
+Documentation: https://allthebacteria.org
+Contact: https://github.com/AllTheBacteria/AllTheBacteria/issues
+ManagedBy: "[European Bioinformatics Institute](https://www.ebi.ac.uk/)"
+UpdateFrequency: |
+  The current release is for all SRA bacterial isolate data up to August 2024. The 
+  colllection will be updated occasionally, with no fixed schedule.
+Tags:
+  - assembly
+  - bacteria
+  - bioinformatics
+  - fasta
+  - genomic
+  - life sciences
+  - microbial genomics
+  - short read sequencing
+  - whole genome sequencing
+License: "[MIT License](https://opensource.org/license/mit)"
+Resources:
+  - Description: Individual, compressed genome assemblies in .fasta format in a public S3 bucket.
+    ARN: arn:aws:s3:::allthebacteria-assemblies
+    Region: eu-west-2
+    Type: S3 Bucket
+    Explore:
+  - Description: Phylogenetically-compressed, batched xz archives of all genome assemblies in .fasta format in a public S3 bucket.
+    ARN: arn:aws:s3:::allthebacteria-phylogeneticbatches
+    Region: eu-west-2
+    Type: S3 Bucket
+    Explore:
+  - Description: Metadata for each genome assembly, including taxonomic information, in a public S3 bucket.
+    ARN: arn:aws:s3:::allthebacteria-metadata
+    Region: eu-west-2
+    Type: S3 Bucket
+    Explore:
+  - Description: "A [LexicMap](https://github.com/shenwei356/LexicMap) index of all genome assemblies. This can be used for efficient sequence alignment against all genomes."
+    ARN: arn:aws:s3:::allthebacteria-lexicmap
+    Region: eu-west-2
+    Type: S3 Bucket
+    Explore:
+DataAtWork:
+  Publications:
+    - Title: AllTheBacteria - all bacterial genomes assembled, available and searchable
+      URL: https://doi.org/10.1101/2024.03.08.584059
+      AuthorName: Hunt M, Lima L, Anderson D, Hawkey J, Shen W, Lees J, Iqbal I
+      AuthorURL: https://researchportal.bath.ac.uk/en/persons/zamin-iqbal
+ADXCategories:
+  - Healthcare & Life Sciences Data

datasets/amazon-last-mile-challenges.yaml

@@ -7,6 +7,10 @@ Contact: [email protected]
 ManagedBy: "[Amazon](https://www.amazon.com/)"
 UpdateFrequency: None
 
+Collabs:
+  ASDI:
+    Tags:
+      - infrastructure
 Tags:
   - transportation
   - machine learning

datasets/aodn_animal_acoustic_tracking_delayed_qc.yaml

@@ -23,6 +23,10 @@ Documentation: https://catalogue-imos.aodn.org.au/geonetwork/srv/eng/catalog.sea
 Contact: [email protected]
 ManagedBy: AODN
 UpdateFrequency: As Needed
+Collabs:
+  ASDI:
+    Tags:
+      - biodiversity
 Tags:
 - oceans
 - marine mammals

datasets/aodn_animal_ctd_satellite_relay_tagging_delayed_qc.yaml

@@ -23,6 +23,10 @@ Documentation: https://catalogue-imos.aodn.org.au/geonetwork/srv/eng/catalog.sea
 Contact: [email protected]
 ManagedBy: AODN
 UpdateFrequency: As Needed
+Collabs:
+  ASDI:
+    Tags:
+      - biodiversity
 Tags:
 - oceans
 - marine mammals

datasets/aodn_model_sea_level_anomaly_gridded_realtime.yaml

@@ -37,6 +37,10 @@ Resources:
     anomaly - Near real time
   Region: ap-southeast-2
   Type: S3 Bucket
+Collabs:
+  ASDI:
+    Tags:
+      - oceans
 Tags:
 - oceans
 - ocean velocity