fix error in spreadsheet, update DOI, JSON

README.md

@@ -1,12 +1,10 @@
 # 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 mechanism of action paths 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/3516335)
 <br><Small>Mayers, Michael; Steinecke, Dylan; Su, Andrew I.<small><br>
 
-
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3515518.svg)](https://doi.org/10.5281/zenodo.3515518)
-
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3516335.svg)](https://doi.org/10.5281/zenodo.3516335)
 
 ## Purpose
 
@@ -17,13 +15,13 @@ 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, 
+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. 
+to vary the targets and diseases treated.
 
-Paths were derived from free-text descriptions found on DrugBank, Wikipeida and within literature. Concepts within the 
+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 
+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|
@@ -38,7 +36,7 @@ the following table:
 |Drug         | MESH, DrugBank   |
 |Molecular Function | GO         |
 |Pathway      | REACT            |
-|Phenotype    | HP               | 
+|Phenotype    | HP               |
 |Protein      | UniProt          |
 |Protein Family | InterPro       |
 |Taxon        | NCBITaxon        |

indication_paths.json

@@ -3069,11 +3069,6 @@
         "id": "MESH:D010146",
         "name": "Pain",
         "label": "Disease"
-      },
-      {
-        "id": null,
-        "name": "Pain",
-        "label": null
       }
     ],
     "links": [
@@ -3091,11 +3086,6 @@
         "source": "GO:0019233 ",
         "target": "MESH:D010146",
         "key": "CAUSES"
-      },
-      {
-        "source": "MESH:D010146",
-        "target": null,
-        "key": null
       }
     ]
   },
@@ -6789,4 +6779,4 @@
       }
     ]
   }
-]
+]

xls_to_json.py

@@ -6,7 +6,7 @@
 from biothings_client import get_client
 mg = get_client('gene')
 
-file_location = "https://zenodo.org/record/3515518/files/indication_MOA_paths.xlsx?download=1"
+file_location = "https://zenodo.org/record/3516335/files/indication_MOA_paths.xlsx?download=1"
 all_sheets = pd.read_excel(file_location, None)
 
 # Dereference each sheet into an individual variable