Add pds tags and ManagedBy fields (awslabs#1400)

chueatwork · web-flow · commit b14cc29cf14b · 2022-06-15T17:26:43.000-04:00
* Update allenai-tqa.yaml

* Update gatk-sv-data.yaml

* Update ibl-brain-wide-map.yaml

* Update dandiarchive.yaml

* Update 3kricegenome.yaml

* Update aws-igenomes.yaml

* Update giab.yaml

* Update gmsdata.yaml

* Update hcp-openaccess.yaml

* Update hpgp-data.yaml

* Update human-microbiome-project.yaml

* Update ihart.yaml

* Update icgc.yaml

* Update mimiciii.yaml

* Update nanopore.yaml

* Update ucsc-genome-browser.yaml

* Update physionet.yaml

* Update openneuro.yaml

* Update 1000-genomes.yaml

* Update dandiarchive.yaml

* Update 3kricegenome.yaml

* Update cell-painting-image-collection.yaml

* Update physionet.yaml

* Update 3kricegenome.yaml

* Update aws-igenomes.yaml

* Update dandiarchive.yaml

* Update giab.yaml

* Update gmsdata.yaml

* Update hcp-openaccess.yaml

* Update hpgp-data.yaml

* Update human-microbiome-project.yaml

* Update icgc.yaml

* Update ihart.yaml

* Update mimiciii.yaml

* Update openneuro.yaml

* Update physionet.yaml
diff --git a/datasets/1000-genomes.yaml b/datasets/1000-genomes.yaml
@@ -2,12 +2,15 @@ Name: 1000 Genomes
 Description: The 1000 Genomes Project is an international collaboration which has established the most detailed catalogue of human genetic variation, including SNPs, structural variants, and their haplotype context. The final phase of the project sequenced more than 2500 individuals from 26 different populations around the world and produced an integrated set of phased haplotypes with more than 80 million variants for these individuals.
 Documentation: https://github.com/awslabs/open-data-docs/tree/main/docs/1000genomes
 Contact: http://www.internationalgenome.org/contact
+ManagedBy: National Institutes of Health
 UpdateFrequency: Not updated
 Tags:
   - aws-pds
   - genetic
   - genomic
   - life sciences
+  - whole genome sequencing
+  - fastq
 License: Data from the 1000 Genomes Project is now available without embargo, following the final publication from the project. Use of the data should be cited in the usual way, with current details available at http://www.internationalgenome.org/faq/how-do-i-cite-1000-genomes-project.
 Resources:
   - Description: http://www.internationalgenome.org/formats
diff --git a/datasets/3kricegenome.yaml b/datasets/3kricegenome.yaml
@@ -2,6 +2,7 @@ Name: 3000 Rice Genomes Project
 Description: The 3000 Rice Genome Project is an international effort to sequence the genomes of 3,024 rice varieties from 89 countries.
 Documentation: https://github.com/awslabs/open-data-docs/tree/main/docs/3kricegenome
 Contact: http://iric.irri.org/contact-us
+ManagedBy: '[International Rice Research Institute](https://www.irri.org/)'
 UpdateFrequency: Not updated
 Tags:
   - agriculture
diff --git a/datasets/allenai-tqa.yaml b/datasets/allenai-tqa.yaml
@@ -4,7 +4,9 @@ Documentation: https://allenai.org/data/tqa
 Contact: info@allenai.org
 ManagedBy: '[Allen Institute for AI](https://allenai.org)'
 UpdateFrequency: Not updated
-Tags: []
+Tags:
+ - aws-pds
+ - machine learning
 License: '[CC BY-SA](https://creativecommons.org/licenses/by-sa/4.0/)'
 Resources:
   - Description: Project data files in a public bucket
diff --git a/datasets/aws-igenomes.yaml b/datasets/aws-igenomes.yaml
@@ -2,6 +2,7 @@ Name: AWS iGenomes
 Description: Common reference genomes hosted on AWS S3. Can be used when aligning and analysing raw DNA sequencing data.
 Documentation: https://ewels.github.io/AWS-iGenomes/
 Contact: https://github.com/ewels/AWS-iGenomes/issues
+ManagedBy: '[SciLifeLab](https://opensource.scilifelab.se/)'
 UpdateFrequency: New data are added when available.
 Tags:
   - aws-pds
diff --git a/datasets/cell-painting-image-collection.yaml b/datasets/cell-painting-image-collection.yaml
@@ -14,6 +14,7 @@ Description: |
   applications.
 Documentation: https://github.com/cytodata/cytodata-hackathon-2018
 Contact:  Post on https://forum.image.sc/ and tag with "cellpainting"
+ManagedBy: The Broad Institute
 UpdateFrequency: irregularly
 Tags:
   - aws-pds
diff --git a/datasets/dandiarchive.yaml b/datasets/dandiarchive.yaml
@@ -9,7 +9,8 @@ Description: >
   [NIDM - Neuro Imaging Data Model](http://nidm.nidash.org/). Development of DANDI is 
   supported by the National Institute of Mental Health.
 Documentation: http://dandiarchive.org
-Contact: Support form at https://www.dandiarchive.org
+Contact: '[DANDI Archive Help Desk](https://github.com/dandi/helpdesk/issues/new/choose)'
+ManagedBy: '[DANDI Archive](https://www.dandiarchive.org/team)'
 UpdateFrequency: New datasets deposited every month
 Tags:
   - aws-pds
diff --git a/datasets/gatk-sv-data.yaml b/datasets/gatk-sv-data.yaml
@@ -7,6 +7,7 @@ Contact: awsdata@loka.com
 ManagedBy: "[Loka Inc.](https://loka.com/)"
 UpdateFrequency: Every 3 months
 Tags:
+  - aws-pds
   - biology
   - bioinformatics
   - genetic
diff --git a/datasets/giab.yaml b/datasets/giab.yaml
@@ -2,6 +2,7 @@ Name: Genome in a Bottle on AWS
 Description: "Several reference genomes to enable translation of whole human genome sequencing to clinical practice. On 11/12/2020 these data were updated to reflect the most [up to date GIAB release](https://www.nist.gov/programs-projects/genome-bottle)."
 Documentation: https://github.com/awslabs/open-data-docs/tree/main/docs/giab
 Contact: http://genomeinabottle.org/
+ManagedBy: '[National Institute of Standards and Technology](https://www.nist.gov/)'
 UpdateFrequency: New data are added as soon as they are available.
 Tags:
   - aws-pds
diff --git a/datasets/gmsdata.yaml b/datasets/gmsdata.yaml
@@ -2,13 +2,14 @@ Name: The Genome Modeling System
 Description: The Genome Institute at Washington University has developed a high-throughput, fault-tolerant analysis information management system called the Genome Modeling System (GMS), capable of executing complex, interdependent, and automated genome analysis pipelines at a massive scale. The GMS framework provides detailed tracking of samples and data coupled with reliable and repeatable analysis pipelines. GMS includes a full system image with software and services, expandable from one workstation to a large compute cluster.
 Documentation: https://github.com/genome/gms/wiki
 Contact: https://github.com/genome/gms/issues
+ManagedBy: Genome Institute at the Washington University School of Medicine in St. Louis
 UpdateFrequency: Not updated
 Tags:
   - aws-pds
   - genetic
   - genomic
   - life sciences
-License: GNU Lesser General Public License v3.0 https://github.com/genome/gms/blob/ubuntu-12.04/LICENSE
+License: '[GNU Lesser General Public License v3.0](https://github.com/genome/gms/blob/ubuntu-12.04/LICENSE)'
 Resources:
   - Description: https://gmsdata.s3.amazonaws.com/index.html
     ARN: arn:aws:s3:::gmsdata
diff --git a/datasets/hcp-openaccess.yaml b/datasets/hcp-openaccess.yaml
@@ -2,6 +2,7 @@ Name: "The Human Connectome Project"
 Description: The Human Connectome Project aims to provide an unparalleled compilation of neural data, an interface to graphically navigate this data and the opportunity to achieve never before realized conclusions about the living human brain.
 Documentation: http://www.humanconnectomeproject.org
 Contact: hcp-users@humanconnectome.org
+ManagedBy: '[Connectome Coordination Facility](https://www.humanconnectome.org/ccf-staff)'
 UpdateFrequency: Uncertain
 Tags:
   - aws-pds
diff --git a/datasets/hpgp-data.yaml b/datasets/hpgp-data.yaml
@@ -2,6 +2,7 @@ Name: Human PanGenomics Project
 Description: This dataset includes sequencing data, assemblies, and analyses for the offspring of ten parent-offspring trios.
 Documentation: https://github.com/human-pangenomics/hpgp-data
 Contact: https://github.com/human-pangenomics/hpgp-data/issues
+ManagedBy: '(Human Pangenome Reference Consortium)[https://humanpangenome.org/]'
 UpdateFrequency: Data will be added and updated as technologies improve or new data uses are encountered.
 Tags:
   - aws-pds
diff --git a/datasets/human-microbiome-project.yaml b/datasets/human-microbiome-project.yaml
@@ -2,6 +2,7 @@ Name: The Human Microbiome Project
 Description: The NIH-funded Human Microbiome Project (HMP) is a collaborative effort of over 300 scientists from more than 80 organizations to comprehensively characterize the microbial communities inhabiting the human body and elucidate their role in human health and disease. To accomplish this task, microbial community samples were isolated from a cohort of 300 healthy adult human subjects at 18 specific sites within five regions of the body (oral cavity, airways, urogenital track, skin, and gut). Targeted sequencing of the 16S bacterial marker gene and/or whole metagenome shotgun sequencing was performed for thousands of these samples. In addition, whole genome sequences were generated for isolate strains collected from human body sites to act as reference organisms for analysis. Finally, 16S marker and whole metagenome sequencing was also done on additional samples from people suffering from several disease conditions.
 Documentation: https://commonfund.nih.gov/hmp
 Contact: https://commonfund.nih.gov/hmp/related_activities
+ManagedBy: '[The National Institutes of Health Office of Strategic Coordination - The Common Fund](https://commonfund.nih.gov/hmp)'
 UpdateFrequency: Uncertain
 Tags:
   - aws-pds
diff --git a/datasets/ibl-brain-wide-map.yaml b/datasets/ibl-brain-wide-map.yaml
@@ -5,6 +5,8 @@ Contact: info@internationalbrainlab.org
 ManagedBy: "[IBL](https://www.internationalbrainlab.com)"
 UpdateFrequency: TBD
 Tags:
+  - aws-pds
+  - life sciences
   - neuroscience
   - neurophysiology
   - open source software
diff --git a/datasets/icgc.yaml b/datasets/icgc.yaml
@@ -2,12 +2,16 @@ Name: ICGC on AWS
 Description: The International Cancer Genome Consortium (ICGC) coordinates projects with the common aim of accelerating research into the causes and control of cancer. The PanCancer Analysis of Whole Genomes (PCAWG) study is an international collaboration to identify common patterns of mutation in whole genomes from ICGC. More than 2,400 consistently analyzed genomes corresponding to over 1,100 unique ICGC donors are now freely available on Amazon S3 to credentialed researchers subject to ICGC data sharing policies.
 Documentation: https://dcc.icgc.org/icgc-in-the-cloud/aws
 Contact: dcc-support@icgc.org
+ManagedBy: '[International Cancer Genome Collaboratory](https://dcc.icgc.org/)'
 UpdateFrequency: New data is added as soon as it is available.
 Tags:
   - aws-pds
   - cancer
+  - genetic
   - genomic
   - life sciences
+  - bam
+  - vcf
 License: Data use is subject to the access and publication polices of the source. Distribution of the data is subject to ICGC Trusted Partner Approval.  More information on terms of use is available at https://icgc.org/daco
 Resources:
   - Description: BAM and VCF files from the The PanCancer Analysis of Whole Genomes (PCAWG) study.
diff --git a/datasets/ihart.yaml b/datasets/ihart.yaml
@@ -2,13 +2,17 @@ Name: iHART Whole Genome Sequencing Data Set
 Description: iHART is the [Hartwell Foundation](http://www.thehartwellfoundation.org/)’s Autism Research and Technology Initiative. This release contains whole genome data from over 1000 families with 2 or more children with autism, of which biomaterials were provided by the Autism Genetic Resource Exchange ([AGRE](http://research.agre.org/)).
 Documentation: http://www.ihart.org/data
 Contact: ihart2-org@stanford.edu
+ManagedBy: '[Stanford University](https://wall-lab.stanford.edu/projects/ihart/)'
 UpdateFrequency: The dataset may be updated with additional or corrected data on a need-to-update basis.
 Tags:
  - aws-pds
  - autism spectrum disorder
+ - genetic
  - genomic
  - life sciences
  - whole genome sequencing
+ - bam
+ - vcf
 License: Data use is subject to the access and publication polices of the iHART. More information on terms of use is available at [iHART website](http://www.ihart.org/)
 Resources:
  - Description: BAM and VCF files from The iHART whole genome sequencing study.
diff --git a/datasets/mimiciii.yaml b/datasets/mimiciii.yaml
@@ -16,6 +16,7 @@ Description: |
   [request access to the MIMIC-III Clinical Database on AWS](https://physionet.org/projects/mimiciii/1.4/request_access/2).
 Documentation: https://mimic.physionet.org/
 Contact: https://mimic.physionet.org/help/
+ManagedBy: '[MIT Laboratory for Computational Physiology](https://lcp.mit.edu/)'
 UpdateFrequency: Not updated
 Tags:
   - aws-pds
diff --git a/datasets/nanopore.yaml b/datasets/nanopore.yaml
@@ -2,11 +2,14 @@ Name: Nanopore Reference Human Genome
 Description: This dataset includes the sequencing and assembly of a reference standard human genome (GM12878) using the MinION nanopore sequencing instrument with the R9.4 1D chemistry.
 Documentation: https://github.com/nanopore-wgs-consortium/NA12878
 Contact: https://github.com/nanopore-wgs-consortium/NA12878/issues
+ManagedBy: Nanopore Whole Genome Sequencing Consortium
 UpdateFrequency: Data will be added as methodology improves or new data uses are encountered.
 Tags:
   - aws-pds
+  - genetic
   - genomic
   - life sciences
+  - whole genome sequencing
 License: Nanopore Human Reference data is released under the Creative Commons CC-BY license and allows free, full and open access to all. For more details please refer to the data reuse and license section of the documentation.
 Resources:
   - Description: Nanopore Reference Human Genome
@@ -18,4 +21,4 @@ Resources:
 DataAtWork:
   Tutorials:
   Tools & Applications:
-  Publications:
+  Publications:
diff --git a/datasets/openneuro.yaml b/datasets/openneuro.yaml
@@ -2,6 +2,7 @@ Name: OpenNeuro
 Description: OpenNeuro is a database of openly-available brain imaging data. The data are shared according to a Creative Commons CC0 license, providing a broad range of brain imaging data to researchers and citizen scientists alike. The database primarily focuses on functional magnetic resonance imaging (fMRI) data, but also includes other imaging modalities including structural and diffusion MRI, electroencephalography (EEG), and magnetoencephalograpy (MEG). OpenfMRI is a project of the [Center for Reproducible Neuroscience at Stanford University](http://reproducibility.stanford.edu). Development of the OpenNeuro resource has been funded by the National Science Foundation, National Institute of Mental Health, National Institute on Drug Abuse, and the Laura and John Arnold Foundation.
 Documentation: http://openneuro.org
 Contact: Support form at https://openneuro.org
+ManagedBy: '[Stanford University Center for Reproducible Neuroscience](https://reproducibility.stanford.edu/)'
 UpdateFrequency: New datasets deposited every 4-6 days
 Tags:
   - aws-pds
diff --git a/datasets/physionet.yaml b/datasets/physionet.yaml
@@ -1,7 +1,8 @@
 Name: Physionet
 Description: PhysioNet offers free web access to large collections of recorded physiologic signals (PhysioBank) and related open-source software (PhysioToolkit).
 Documentation: https://physionet.org/
-Contact: https://physionet.org/faq.shtml
+Contact: contact@physionet.org
+ManagedBy: '[MIT Laboratory for Computational Physiology](https://lcp.mit.edu/)'
 UpdateFrequency: Not updated
 Tags:
   - aws-pds
@@ -16,4 +17,4 @@ Resources:
 DataAtWork:
   Tutorials:
   Tools & Applications:
-  Publications:
+  Publications:
diff --git a/datasets/ucsc-genome-browser.yaml b/datasets/ucsc-genome-browser.yaml
@@ -2,6 +2,7 @@ Name: UCSC Genome Browser Sequence and Annotations
 Description: "The UCSC Genome Browser is an online graphical viewer for genomes, a genome browser, hosted by the University of California, Santa Cruz (UCSC). The interactive website offers access to genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations. This dataset is a copy of the MySQL tables in MyISAM binary and tab-sep format and all binary files in custom formats, sometimes referred as 'gbdb'-files. Data from the UCSC Genome Browser is free and open for use by anyone. However, every genome annotation track has been created by an academic research group, or, in a few cases, by commercial companies. Please acknowledge them by citing them. The information can be found by going to https://genome.ucsc.edu, selecting the respective genome assembly and clicking on the data track. At the end of the documentation, we provide a list of references and acknowledgements."
 Documentation: https://hgdownload.soe.ucsc.edu/downloads.html
 Contact: https://genome.ucsc.edu/contacts.html
+ManagedBy:  University of California Santa Cruz Genome Institute
 UpdateFrequency: Monthly
 Tags:
   - aws-pds
