External datasets for other curation arm

[anngvu]

We have two arms of dataset curation. One is to use existing Synapse resources like manifest.csv and/or Wikis and/or tables to create dataset metadata; let's call this the internal arm. The other is to curate external datasets (see Robert's idea that we should enable thangs.com-like discovery). Here are some identified, actually-interesting datasets for the external arm.

• The Lipid Asset Is Unbalanced in Peripheral Nerve Sheath Tumors: https://zenodo.org/records/5883313
• Spatial transcriptomic analysis of a pre-clinical NF1 pseudarthrosis fracture model: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE218046
• NF1 Schwann Cell Genotype Cell Painting images: https://figshare.com/projects/NF1_Schwann_Cell_Genotype_Cell_Painting_Assay/161620
• Data used for training glioblastoma NF1 classifier: https://zenodo.org/records/56735

Note: These would have to go into separate view than the current dataset collections (which requires Synapse Datasets), so ultimately we use another table to union the two.

[cconrad8]

Random thoughts

1. We can pull out the schema.org metadata (particularly in the zenodo datasets) to base our structure off theirs.
2. potentially use the embedded metadata as a mechanism for importing details

examples:

      <script type='application/ld+json'>{
            "@context": "http://schema.org",
            "@id": "https://doi.org/10.5281/zenodo.5883313",
            "@type": "https://schema.org/Dataset",
            "author": [
                  {
                        "@id": "https://orcid.org/0000-0003-0664-9700",
                        "@type": "Person",
                        "affiliation": [
                              {
                                    "@type": "Organization",
                                    "name": "Fondazione IRCCS Istituto Neurologico Carlo Besta"
                              }
                        ],
                        "familyName": "Vetrano",
                        "givenName": "Ignazio Gaspare",
                        "name": "Vetrano, Ignazio Gaspare"
                  },
                  {
                        "@id": "https://orcid.org/0000-0001-7359-8558",
                        "@type": "Person",
                        "affiliation": [
                              {
                                    "@type": "Organization",
                                    "name": "Universit\u00e0 degli Studi di Milano"
                              }
                        ],
                        "familyName": "Dei Cas",
                        "givenName": "Michele",
                        "name": "Dei Cas, Michele"
                  },
                  {
                        "@id": "https://orcid.org/0000-0003-4744-9377",
                        "@type": "Person",
                        "affiliation": [
                              {
                                    "@type": "Organization",
                                    "name": "Fondazione IRCCS Istituto Neurologico Carlo Besta"
                              }
                        ],
                        "familyName": "Eoli",
                        "givenName": "Marica",
                        "name": "Eoli, Marica"
                  },
                  {
                        "@id": "https://orcid.org/0000-0001-6811-6112",
                        "@type": "Person",
                        "affiliation": [
                              {
                                    "@type": "Organization",
                                    "name": "Fondazione IRCCS Istituto Neurologico Carlo Besta"
                              }
                        ],
                        "familyName": "Potenza",
                        "givenName": "Antonella",
                        "name": "Potenza, Antonella"
                  },
                  {
                        "@id": "https://orcid.org/0000-0001-5752-1374",
                        "@type": "Person",
                        "affiliation": [
                              {
                                    "@type": "Organization",
                                    "name": "Fondazione IRCCS Istituto Neurologico Carlo Besta"
                              }
                        ],
                        "familyName": "Carrozzini",
                        "givenName": "Tatiana",
                        "name": "Carrozzini, Tatiana"
                  },
                  {
                        "@id": "https://orcid.org/0000-0001-8483-3509",
                        "@type": "Person",
                        "affiliation": [
                              {
                                    "@type": "Organization",
                                    "name": "Fondazione IRCCS Istituto Neurologico Carlo Besta"
                              }
                        ],
                        "familyName": "Gorla",
                        "givenName": "Gemma",
                        "name": "Gorla, Gemma"
                  },
                  {
                        "@id": "https://orcid.org/0000-0002-3186-8860",
                        "@type": "Person",
                        "affiliation": [
                              {
                                    "@type": "Organization",
                                    "name": "Universit\u00e0 degli Studi di Milano"
                              }
                        ],
                        "familyName": "Paroni",
                        "givenName": "Rita",
                        "name": "Paroni, Rita"
                  },
                  {
                        "@id": "https://orcid.org/0000-0002-6300-5867",
                        "@type": "Person",
                        "affiliation": [
                              {
                                    "@type": "Organization",
                                    "name": "Universit\u00e0 degli Studi di Milano"
                              }
                        ],
                        "familyName": "Ghidoni",
                        "givenName": "Riccardo",
                        "name": "Ghidoni, Riccardo"
                  },
                  {
                        "@id": "https://orcid.org/0000-0001-6751-5031",
                        "@type": "Person",
                        "affiliation": [
                              {
                                    "@type": "Organization",
                                    "name": "Fondazione IRCCS Istituto Neurologico Carlo Besta"
                              }
                        ],
                        "familyName": "Gatti",
                        "givenName": "Laura",
                        "name": "Gatti, Laura"
                  }
            ],
            "creator": [
                  {
                        "@id": "https://orcid.org/0000-0003-0664-9700",
                        "@type": "Person",
                        "affiliation": [
                              {
                                    "@type": "Organization",
                                    "name": "Fondazione IRCCS Istituto Neurologico Carlo Besta"
                              }
                        ],
                        "familyName": "Vetrano",
                        "givenName": "Ignazio Gaspare",
                        "name": "Vetrano, Ignazio Gaspare"
                  },
                  {
                        "@id": "https://orcid.org/0000-0001-7359-8558",
                        "@type": "Person",
                        "affiliation": [
                              {
                                    "@type": "Organization",
                                    "name": "Universit\u00e0 degli Studi di Milano"
                              }
                        ],
                        "familyName": "Dei Cas",
                        "givenName": "Michele",
                        "name": "Dei Cas, Michele"
                  },
                  {
                        "@id": "https://orcid.org/0000-0003-4744-9377",
                        "@type": "Person",
                        "affiliation": [
                              {
                                    "@type": "Organization",
                                    "name": "Fondazione IRCCS Istituto Neurologico Carlo Besta"
                              }
                        ],
                        "familyName": "Eoli",
                        "givenName": "Marica",
                        "name": "Eoli, Marica"
                  },
                  {
                        "@id": "https://orcid.org/0000-0001-6811-6112",
                        "@type": "Person",
                        "affiliation": [
                              {
                                    "@type": "Organization",
                                    "name": "Fondazione IRCCS Istituto Neurologico Carlo Besta"
                              }
                        ],
                        "familyName": "Potenza",
                        "givenName": "Antonella",
                        "name": "Potenza, Antonella"
                  },
                  {
                        "@id": "https://orcid.org/0000-0001-5752-1374",
                        "@type": "Person",
                        "affiliation": [
                              {
                                    "@type": "Organization",
                                    "name": "Fondazione IRCCS Istituto Neurologico Carlo Besta"
                              }
                        ],
                        "familyName": "Carrozzini",
                        "givenName": "Tatiana",
                        "name": "Carrozzini, Tatiana"
                  },
                  {
                        "@id": "https://orcid.org/0000-0001-8483-3509",
                        "@type": "Person",
                        "affiliation": [
                              {
                                    "@type": "Organization",
                                    "name": "Fondazione IRCCS Istituto Neurologico Carlo Besta"
                              }
                        ],
                        "familyName": "Gorla",
                        "givenName": "Gemma",
                        "name": "Gorla, Gemma"
                  },
                  {
                        "@id": "https://orcid.org/0000-0002-3186-8860",
                        "@type": "Person",
                        "affiliation": [
                              {
                                    "@type": "Organization",
                                    "name": "Universit\u00e0 degli Studi di Milano"
                              }
                        ],
                        "familyName": "Paroni",
                        "givenName": "Rita",
                        "name": "Paroni, Rita"
                  },
                  {
                        "@id": "https://orcid.org/0000-0002-6300-5867",
                        "@type": "Person",
                        "affiliation": [
                              {
                                    "@type": "Organization",
                                    "name": "Universit\u00e0 degli Studi di Milano"
                              }
                        ],
                        "familyName": "Ghidoni",
                        "givenName": "Riccardo",
                        "name": "Ghidoni, Riccardo"
                  },
                  {
                        "@id": "https://orcid.org/0000-0001-6751-5031",
                        "@type": "Person",
                        "affiliation": [
                              {
                                    "@type": "Organization",
                                    "name": "Fondazione IRCCS Istituto Neurologico Carlo Besta"
                              }
                        ],
                        "familyName": "Gatti",
                        "givenName": "Laura",
                        "name": "Gatti, Laura"
                  }
            ],
            "dateCreated": "2022-01-20T12:45:56.958153+00:00",
            "dateModified": "2022-01-20T13:48:56.704381+00:00",
            "datePublished": "2022-01-20",
            "description": "\u003cp\u003e\u003cstrong\u003eLipid species derived from analyses, anonymized sample series\u003c/strong\u003e\u003c/p\u003e",
            "identifier": "https://doi.org/10.5281/zenodo.5883313",
            "keywords": "ceramide, phospholipids, lipidomic, neurofibroma, plexiform neurofibroma, PNST, schwannoma, sphingolipids",
            "name": "dataset related to article \"The Lipid Asset Is Unbalanced in Peripheral Nerve Sheath Tumors\"",
            "publisher": {
                  "@type": "Organization",
                  "name": "Zenodo"
            },
            "url": "https://zenodo.org/records/5883313"
      }</script>

example 2:

<script type='application/ld+json'>{
      "@context": "http://schema.org",
      "@id": "https://doi.org/10.5281/zenodo.56735",
      "@type": "https://schema.org/Dataset",
      "author": [
            {
                  "@type": "Person",
                  "affiliation": [
                        {
                              "@type": "Organization",
                              "name": "University of Pennsylvania"
                        }
                  ],
                  "familyName": "Way",
                  "givenName": "Gregory",
                  "name": "Way, Gregory"
            }
      ],
      "contentSize": "531.82 MB",
      "creator": [
            {
                  "@type": "Person",
                  "affiliation": [
                        {
                              "@type": "Organization",
                              "name": "University of Pennsylvania"
                        }
                  ],
                  "familyName": "Way",
                  "givenName": "Gregory",
                  "name": "Way, Gregory"
            }
      ],
      "dateCreated": "2016-06-30T16:38:24+00:00",
      "dateModified": "2020-01-24T19:24:03.056777+00:00",
      "datePublished": "2016-06-30",
      "description": "\u003cp\u003eAll data is publicly available and downloaded from UCSC Xena\u003cbr /\u003e\nhttps://genome-cancer.ucsc.edu/proj/site/xena/datapages/?cohort=TCGA%20Pan-Cancer\u003c/p\u003e\n\n\u003cp\u003eBecause the database is continously updated and to ensure reproducibility,\u0026nbsp;access data from this cached download.\u003c/p\u003e\n\n\u003cp\u003eRNAseq and Clincal data were downloaded on 8 March 2016\u003cbr /\u003e\nMutation data was downloaded on 12 June 2015\u003c/p\u003e",
      "distribution": [
            {
                  "@type": "DataDownload",
                  "contentUrl": "https://zenodo.org/api/records/56735/files/gbm_classifier_data.tar.gz/content",
                  "encodingFormat": "application/gzip"
            }
      ],
      "identifier": "https://doi.org/10.5281/zenodo.56735",
      "license": "https://creativecommons.org/publicdomain/zero/1.0/legalcode",
      "name": "Data used for training glioblastoma NF1 classifier",
      "publisher": {
            "@type": "Organization",
            "name": "Zenodo"
      },
      "size": "531.82 MB",
      "url": "https://zenodo.org/records/56735"
}</script>