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Update similarity and connectivity authored by Miquel Duran-Frigola's avatar Miquel Duran-Frigola
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similarity-and-connectivity.md
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......@@ -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)
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* Key-Drug: `drug` [Default] / vocabulary: DrugBank
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