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Rebuild with updated data

Updated indications, stargeo, LINCS L1000, Gene Ontology Annotations.

Collapse LINCS L1000 genetic perturbations to a single edge type.

Rerun `evaluate-permutations.ipynb`.
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dhimmel committed Mar 11, 2016
1 parent 537610a commit d68b823bf2167e7ab7f0e784d1280200c33fb3bf
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@@ -1,124 +1,118 @@
{
"metanode_kinds": [
"anatomy",
"disease",
"biological process",
"gene",
"cellular component",
"symptom",
"molecular function",
"pathway",
"cellular component",
"perturbation",
"side effect",
"symptom",
"compound"
"gene",
"perturbation",
"compound",
"biological process",
"anatomy"
],
"metaedge_tuples": [
[
"compound",
"gene",
"upregulates",
"binds",
"both"
],
[
"gene",
"gene",
"overexpression upregulates",
"forward"
],
[
"anatomy",
"gene",
"expresses",
"covaries",
"both"
],
[
"compound",
"disease",
"palliates",
"gene",
"upregulates",
"both"
],
[
"anatomy",
"gene",
"downregulates",
"biological process",
"participates",
"both"
],
[
"disease",
"gene",
"cellular component",
"participates",
"upregulates",
"both"
],
[
"perturbation",
"gene",
"regulates",
"compound",
"disease",
"palliates",
"both"
],
[
"disease",
"gene",
"gene",
"evolves",
"associates",
"both"
],
[
"compound",
"compound",
"resembles",
"gene",
"molecular function",
"participates",
"both"
],
[
"disease",
"disease",
"resembles",
"symptom",
"presents",
"both"
],
[
"disease",
"gene",
"upregulates",
"downregulates",
"both"
],
[
"compound",
"gene",
"binds",
"cellular component",
"participates",
"both"
],
[
"gene",
"gene",
"knockdown upregulates",
"forward"
"interacts",
"both"
],
[
"compound",
"disease",
"treats",
"disease",
"resembles",
"both"
],
[
"gene",
"gene",
"interacts",
"compound",
"compound",
"resembles",
"both"
],
[
"gene",
"biological process",
"participates",
"compound",
"side effect",
"causes",
"both"
],
[
"perturbation",
"gene",
"gene",
"knockdown downregulates",
"forward"
"regulates",
"both"
],
[
"disease",
"gene",
"downregulates",
"pathway",
"participates",
"both"
],
[
@@ -129,21 +123,9 @@
],
[
"gene",
"molecular function",
"participates",
"both"
],
[
"disease",
"symptom",
"presents",
"both"
],
[
"compound",
"side effect",
"causes",
"both"
"gene",
"regulates",
"forward"
],
[
"anatomy",
@@ -158,54 +140,50 @@
"both"
],
[
"anatomy",
"gene",
"gene",
"overexpression downregulates",
"forward"
"expresses",
"both"
],
[
"compound",
"disease",
"gene",
"associates",
"treats",
"both"
],
[
"anatomy",
"gene",
"pathway",
"participates",
"downregulates",
"both"
]
],
"kind_to_abbrev": {
"expresses": "e",
"knockdown downregulates": "kd",
"participates": "p",
"knockdown upregulates": "ku",
"treats": "t",
"compound": "C",
"overexpression downregulates": "od",
"upregulates": "u",
"causes": "c",
"disease": "D",
"symptom": "S",
"localizes": "l",
"associates": "a",
"covaries": "c",
"presents": "p",
"cellular component": "CC",
"perturbation": "PB",
"anatomy": "A",
"biological process": "BP",
"evolves": "e",
"palliates": "p",
"molecular function": "MF",
"regulates": "r",
"associates": "a",
"participates": "p",
"binds": "b",
"side effect": "SE",
"symptom": "S",
"downregulates": "d",
"interacts": "i",
"perturbation": "PB",
"side effect": "SE",
"treats": "t",
"resembles": "r",
"presents": "p",
"overexpression upregulates": "ou",
"gene": "G",
"palliates": "p",
"localizes": "l",
"causes": "c",
"regulates": "r",
"pathway": "PW",
"disease": "D"
"anatomy": "A",
"upregulates": "u",
"gene": "G",
"expresses": "e",
"compound": "C",
"biological process": "BP"
}
}

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