similarity-and-connectivity.md

@@ -81,122 +81,127 @@ The *mapping* (prediction) for new molecules/entities can be entered at one or m
 
 #### `A1.001` 2D fingerprints
 
-* Key-SMILES pairs: `smiles`
-* InChIKeys: `inchikey` [Default]
+* Key-raw molecule: `smiles` / vocabulary: SMILES
+* Key-standard molecule: `inchi` / vocabulary: InChI
+* InChIKeys: `inchikey` [Default] / vocabulary: InChIKey
 
 #### `A2.001` 3D fingerprints
 
-* Key-SMILES pairs: `smiles`
-* InChIKeys: `inchikey` [Default]
+* Key-raw molecule: `smiles` / vocabulary: SMILES
+* Key-standard molecule: `inchi` / vocabulary: InChI
+* InChIKeys: `inchikey` [Default] / vocabulary: InChIKey
 
 #### `A3.001` Scaffolds
 
-* Key-SMILES pairs: `smiles`
-* InChIKeys: `inchikey` [Default]
+* Key-raw molecule: `smiles` / vocabulary: SMILES
+* Key-standard molecule: `inchi` / vocabulary: InChI
+* InChIKeys: `inchikey` [Default] / vocabulary: InChIKey
 
 #### `A4.001` Structural keys
 
-* Key-SMILES pairs: `smiles`
-* InChIKeys: `inchikey` [Default]
+* Key-raw molecule: `smiles` / vocabulary: SMILES
+* Key-standard molecule: `inchi` / vocabulary: InChI
+* InChIKeys: `inchikey` [Default] / vocabulary: InChIKey
 
 #### `A5.001` Physicochemistry
 
-* Key-SMILES pairs: `smiles` [Default]
-* InChIKeys: `inchikey`
+* Key-raw molecule: `smiles` / vocabulary: SMILES
+* Key-standard molecule: `inchi` / vocabulary: InChI
+* InChIKeys: `inchikey` [Default] / vocabulary: InChIKey
 
 ### `B` Targets
 
 #### `B1.001` Mechanism of action
 
-* Key-Protein pairs (-1/+1; default = -1): `proteins` [Default]
-* Key-Class pairs (-1/+1; default = -1): `classes`
+* Key-Protein pairs (-1/+1; default = -1): `proteins` [Default] / vocabulary: UniProtAC
+* Key-Class pairs (-1/+1; default = -1): `classes` / vocabulary: ChEMBL target class
 
 #### `B2.001` Metabolic genes
 
-* Key-Protein pairs: `proteins` [Default]
-* Key-Class pairs: `classes`
+* Key-Protein pairs: `proteins` [Default] / vocabulary: UniProtAC
+* Key-Class pairs: `classes` / vocabulary: ChEMBL target class
 
 #### `B3.001` Crystals
 
-* Key-PDBs pairs: `pdbs` [Default]
-* Key-ECOD pairs: `domains`
+* Key-structure pairs: `structure` [Default] / vocabulary: PDB ID
+* Key-domain pairs: `domains` / vocabulary: ECOD
 
 #### `B4.001` Binding
 
-* Key-Protein pairs (2/1; default = 1): `proteins` [Default]
-* Key-Class pairs (2/1; default = 1): `classes`
+* Key-Protein pairs (2/1; default = 1): `proteins` [Default] / vocabulary: UniProtAC
+* Key-Class pairs (2/1; default = 1): `classes` / vocabulary: ChEMBL target class
 
 #### `B5.001` HTS bioassays
 
-* Key-Protein pairs: `proteins` [Default]
-* Key-Class pairs: `classes`
+* Key-Protein pairs: `proteins` [Default] / vocabulary: UniProtAC
+* Key-Class pairs: `classes` / vocabulary: ChEMBL target class
 
 ### `C` Networks
 
 #### `C1.001` Small molecule roles
 
-* Key-ChEBI pairs: `terms` [Default]
+* Key-ChEBI pairs: `terms` [Default] / vocabulary: ChEBI
 
 #### `C2.001` Small molecule pathways
 
-* Key-InChIKey pairs (exact nodes) (10-1; default = 5): `inchikeys` [Default]
-* Key-InChiKey pairs (neighbors) (10-1; default = 5): `inchikey_neighbors`
+* Key-metabolite pairs (exact nodes) (10-1; default = 5): `metabolites` [Default] / vocabulary: InChIKey
+* Key-metabolite pairs (neighbors) (10-1; default = 5): `metabolites_neighbors` / vocabulary: InChIKey
 
 #### `C3.001` Signaling pathways
 
-* Key-Protein pairs (2/1; default = 1): `proteins` [Default]
-* Key-Pathway pairs (2/1; default = 1): `pathways`
+* Key-Protein pairs (2/1; default = 1): `proteins` [Default] / vocabulary: UniprotAC
+* Key-Pathway pairs (2/1; default = 1): `pathways` / vocabulary: Reactome
 
 #### `C4.001` Biological processes
 
-* Key-Protein pairs (2/1; default = 1): `proteins` [Default]
-* Key-Process pairs (2/1; default = 1): `processes`
+* Key-Protein pairs (2/1; default = 1): `proteins` [Default] / vocabulary: UniprotAC
+* Key-Process pairs (2/1; default = 1): `processes` / vocabulary: Gene Ontology (Biological processes)
 
 #### `C5.001` Interactome
 
-* Key-Protein pairs (exact nodes) (2/1; default = 1): `proteins` [Default]
-* Key-Protein pairs (neighbors) (10-1; default = 5): `protein_neighbors`
+* Key-Protein pairs (exact nodes) (2/1; default = 1): `proteins` [Default] / vocabulary: UniprotAC
+* Key-Protein pairs (neighbors) (10-1; default = 5): `protein_neighbors` / vocabulary: UniprotAC
 
 ### `D` Cells
 
 #### `D1.001` Gene expression
 
-* Key-(perturbation)-Up&Down genes: `up_down` [Default]
+* Key-(perturbation)-Up&Down genes: `up_down` [Default] / vocabulary: Gene names/symbols
 
 #### `D2.001` Cancer cell lines
 
-* Key-Profile (score): `profile` [Default]
+* Key-Profile (score): `profile` [Default] / vocabulary: NCI-60 cancer cell lines
 
 #### `D3.001` Chemical genetics
 
-* Key-Strain (2/1; default = 1): `strain` [Default]
+* Key-Strain (2/1; default = 1): `strain` [Default] / vocabulary: Yeast mutants
 
 #### `D4.001` Morphology
 
-* Key-Measure (score): `measure` [Default]
+* Key-Measure (score): `measure` [Default] / vocabulary: 812 microscopy features
 
 #### `D5.001` Cell bioassays
 
-* Key-Cell: `cell` [Default]
+* Key-Cell: `cell` [Default] / vocabulary: Cellosaurus
 
 ### `E` Clinics
 
 #### `E1.001` Therapeutic areas
 
-* Key-ATC: `atc` [Default]
+* Key-ATC: `atc` [Default] / vocabulary: ATC codes
 
 #### `E2.001` Indications
 
-* Key-Disease (4/1; default = 2): `disease` [Default] (vocabulary: MEDIC/MeSH)
+* Key-Disease (4/1; default = 2): `disease` [Default] / vocabulary: MEDIC/MeSH
 
 #### `E3.001` Side effects
 
-* Key-Side effect: `side_effect` [Default] (vocabulary: UMLS)
+* Key-Side effect: `side_effect` [Default] / vocabulary: UMLS
 
 #### `E4.001` Diseases and Toxicology
 
-* Key-Disease (M/T; mandatory): `disease` [Default] (vocabulary: MEDIC/MeSH)
+* Key-Disease (M/T; mandatory): `disease` [Default] / vocabulary: MEDIC/MeSH
 
 #### `E5.001` Drug-drug interactions
 
-* Key-Drug: `drug` [Default] (vocabulary: DrugBank)
+* Key-Drug: `drug` [Default] / vocabulary: DrugBank
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