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pantherdb / pango

BSD 3-Clause "New" or "Revised" License
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Adding enrichment analysis: Complete Data Compilation in structured format #46

Open tmushayahama opened 5 months ago

tmushayahama commented 5 months ago

Can you provide me with complete structured data so we have it in one place. It's hard to scrap and compile the list from website or html

example dropdown list

[
  {
    "value": "biological_process",
    "label": "biological process"
  },
  {
    "value": "molecular_function",
    "label": "molecular function"
  },
  {
    "value": "cellular_component",
    "label": "cellular component"
  }
]

List Of Genes

[
"abca1",
"air-2"
]

tagging @mugitty @thomaspd

mugitty commented 5 months ago

@tmushayahama please expand the JSON definition to include hidden and default selections

mugitty commented 5 months ago

@tmushayahama, you need to update as necessary to feed this into Angular IFormStructure. Note, I have added action and method to indicate URL and request type POST; these have to be removed. 'controls' should make up the bulk of the form. There is no automated way to go from html form to JSON. You have to look at each field in the form and create a control field in JSON. I had to go through emails from @thomaspd to determine the genes and labels for the ontology drop down list. It is not specified in any API. Note, each gene in the text box should be delimited by newline.

{
    "form": {
        "action": "https://pantree-dev.usc.edu//webservices/go/overrep.jsp?",
        "method": "POST",
        "controls": [
            {"type": "textarea",   
             "name": "input",
             "value": "AKT1
BDNF
CCKAR
CHI3L1
CHRNA7
CLDN5
CNR1
COMT
DPYSL2
DTNBP1
EGF
GABRA1
GABRB2
GAD1
GRIK3
GRM3
IL10
MCHR1
MLC1
NEUROG1
NOS1
NOS1AP
NOTCH4
NPY
NRG1
OLIG2
PDE4B
PLA2G4A
PLXNA2
PPP3CC
PRODH
RELN
RGS4
RTN4
SNAP25
SRR
SYN2
TNF
TP53
UFD1L
XBP1
YWHAE"
            },
            {"type": "select",
             "name": "ontology",
             "value": "biological_process_IBA",
             "options": [{"label": "biological process PAN-GO", "value": "biological_process_IBA"},
                         {"label": "molecular function PAN-GO", "value": "molecular_function_IBA"},
                         {"label": "cellular component PAN-GO", "value": "cellular_component_IBA"}]
            },
            {"type": "hidden",
             "name": "species",
             "value": "HUMAN"},
            {"type": "hidden",
             "name": "test_type",
             "value": "FISHER"}
        ]
    }
}