Update DOI and download location to version 1.0.1

SuLab · Oct 22, 2019 · 8e95687 · 8e95687
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diff --git a/README.md b/README.md
@@ -1,8 +1,45 @@
 # Indication Mechanism of Action Database
 A database of paths that represent the mechanism of action from a drug to a disease in an indication.
 
-> [**Database of paths of mechanism of action for selected drug-disease indications**](https://zenodo.org/record/3515487)
+> [**Database of mechanism of action paths for selected drug-disease indications**](https://zenodo.org/record/3515487)
 <br><Small>Mayers, Michael; Steinecke, Dylan; Su, Andrew I.<small><br>
 
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3515487.svg)](https://doi.org/10.5281/zenodo.3515487)
+
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3515518.svg)](https://doi.org/10.5281/zenodo.3515518)
+
+
+## Purpose
+
+Most drug mechanisms are described simply as a protein target, or sometimes a pathway, that then treats the disease.
+However, there are usually more steps across a biological knowledge graph required to traverse from the target through
+its mechanism to the reduction of a disease.  This database attempts to catalog a subset of known drug-disease indications
+as a path through a network of biomedical entities.
+
+## Curation
+
+Indications were selected at random from the set contained within DrugCentral. Half were taken from the full set, 
+representing a set of common drug disease pairs, and the other half were selected from a pool of less-common diseases
+to vary the targets and diseases treated. 
+
+Paths were derived from free-text descriptions found on DrugBank, Wikipeida and within literature. Concepts within the 
+text were then normalized to a concept type (Drug, Protein, Pathway, etc) and relationships between the concepts were
+determined from the source. Finally concepts were mapped to an identifier depending on the concept type according to 
+the following table:
+
+|Concept Type | Identifier Source|
+|-------------|------------------|
+|Anatomy      | UBERON           |
+|BiologicalProcess | GO, (MESH)  |
+|Cell Type    | CL               |
+|Cellular Component | GO         |
+|Compound     | MESH, CHEBI      |
+|Compound Class | MESH, CHEBI    |
+|Disease      | MESH             |
+|Drug         | MESH, DrugBank   |
+|Molecular Function | GO         |
+|Pathway      | REACT            |
+|Phenotype    | HP               | 
+|Protein      | UniProt          |
+|Protein Family | InterPro       |
+|Taxon        | NCBITaxon        |
 
diff --git a/indication_paths.json b/indication_paths.json
@@ -883,7 +883,7 @@
       {
         "id": "GO:0050900",
         "name": "Immune Cell Funciton",
-        "label": "Pathway"
+        "label": "Biological Process"
       },
       {
         "id": "GO:0006954",
@@ -3748,7 +3748,7 @@
       {
         "id": "UniProt:P0AD65",
         "name": "Penicillin-binding proteins",
-        "label": "Protein Family"
+        "label": "Protein"
       },
       {
         "id": "GO:0009252",
@@ -3988,7 +3988,7 @@
       {
         "id": "UniProt:P44469",
         "name": "Penicillin-binding proteins",
-        "label": "Protein Family"
+        "label": "Protein"
       },
       {
         "id": "GO:0009252",
@@ -4236,7 +4236,7 @@
         "label": "Drug"
       },
       {
-        "id": "MESH:Q14145",
+        "id": "UniProt:Q14145",
         "name": "Kelch-like ECH-associated protein 1",
         "label": "Protein"
       },
@@ -4259,11 +4259,11 @@
     "links": [
       {
         "source": "MESH:D000069462",
-        "target": "MESH:Q14145",
+        "target": "UniProt:Q14145",
         "key": "INHIBITS"
       },
       {
-        "source": "MESH:Q14145",
+        "source": "UniProt:Q14145",
         "target": "UniProt:Q16236",
         "key": "DOWN_REGULATES"
       },
@@ -4548,7 +4548,7 @@
       {
         "id": "MESH:D012338",
         "name": "23S Ribosomal RNA",
-        "label": "Protein"
+        "label": "Compound Class"
       },
       {
         "id": "GO:0006412",
@@ -6618,12 +6618,12 @@
       {
         "id": "NCBITaxon:6282",
         "name": "Onchocerca volvulus",
-        "label": "Disease"
+        "label": "Taxon"
       },
       {
         "id": "MESH:D009855",
         "name": "Onchocerciasis",
-        "label": null
+        "label": "Disease"
       }
     ],
     "links": [

diff --git a/xls_to_json.py b/xls_to_json.py
@@ -4,10 +4,16 @@
 import networkx as nx
 
 from biothings_client import get_client
-
 mg = get_client('gene')
 
-file_location = "https://zenodo.org/record/3515487/files/indication_MOA_paths.xlsx?download=1"
+file_location = "https://zenodo.org/record/3515518/files/indication_MOA_paths.xlsx?download=1"
+all_sheets = pd.read_excel(file_location, None)
+
+# Dereference each sheet into an individual variable
+moa_inds = all_sheets['sample_indications']
+moa_paths = all_sheets['paths']
+moa_metapaths = all_sheets['metapaths']
+moa_ids = all_sheets['node_ids']
 
 def uniprot_to_entrez(uniprot):
     """Converts a Uniprot ID to an Entrez Gene ID"""
@@ -72,10 +78,6 @@ def j_to_n(j):
 
 
 if __name__ == "__main__":
-    moa_inds = pd.read_excel(file_location, 'sample_indications')
-    moa_paths = pd.read_excel(file_location, 'paths')
-    moa_metapaths = pd.read_excel(file_location, 'metapaths')
-    moa_ids = pd.read_excel(file_location, 'node_ids')
 
     n_cols = [c for c in moa_ids.columns if c.startswith('n')]
     e_cols = [c for c in moa_paths.columns if c.startswith('e')]