Sage-Bionetworks / annotator

A Synapse annotations automation tool.
MIT License
1 stars 2 forks source link

Add `schema` parameter to createFieView which accepts a path to json file #1

Closed philerooski closed 6 years ago

philerooski commented 6 years ago

Would the JSON essentially just be a string representation of a python dict? Something like:

{
"name":"John",
"age":30,
"car":"minivan"
}
philerooski commented 6 years ago

Like this: generated from https://shiny.synapse.org/users/nsanati/annotationUI/


  {
    "name": "genePerturbationTechnology",
    "description": "Technology used to perform gene perturbation",
    "columnType": "STRING",
    "maximumSize": "250",
    "enumValues": [
      {
        "value": "CRE Recombinase",
        "description": "CRE Recombinase catalyses site-specific recombination between two 34 base pair loxp sites and maintains the phage genome as a monomeric unit-copy plasmid in the lysogenic state.",
        "source": "http://purl.obolibrary.org/obo/NCIT_C17285"
      },
      {
        "value": "CRISPR",
        "description": "",
        "source": ""
      },
      {
        "value": "RNAi",
        "description": "High throughput sample analysis of RNAi molecules for potential application in gene knockdown or gene silencing of target genes",
        "source": "http://purl.obolibrary.org/obo/ERO_0001688"
      }
    ]
  },
  {
    "name": "genePerturbationType",
    "description": "Specific way in which a single gene was perturbed in a sample",
    "columnType": "STRING",
    "maximumSize": "250",
    "enumValues": [
      {
        "value": "knockdown",
        "description": "Gene knockdown refers to techniques by which the expression of one or more of an organism's genes is reduced, either through genetic modification (a change in the DNA of one of the organism's chromosomes) or by treatment with a reagent such as a short DNA or RNA oligonucleotide with a sequence complementary to either an mRNA transcript or a gene.",
        "source": "http://www.bioassayontology.org/bao#BAO_0002433"
      },
      {
        "value": "knockout",
        "description": "A gene knockout is a genetic technique in which an organism is engineered to carry genes that have been made inoperative (have been 'knocked out' of the organism).",
        "source": "http://www.bioassayontology.org/bao#BAO_0002441"
      },
      {
        "value": "overexpression",
        "description": "Gene overexpression refers to genetic techniques in which an organism or cell line is engineered to express increased levels of a gene.",
        "source": "http://www.bioassayontology.org/bao#BAO_0002442"
      }
    ]
  }
]
teslajoy commented 6 years ago

this issue will also close https://github.com/Sage-Bionetworks/synAnnotationUtils/issues/58

https://github.com/Sage-Bionetworks/synAnnotationUtils/issues/40