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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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......@@ -88,7 +88,8 @@ Vocabularies are specified below. Terms in these vocabularies should look like:
|UniProtAC|Q9H3N8|
|ChEMBL target class|Class:1033|
|PDB ID|1f3v|
|ECOD|E:e1m48A1 X:150 H:3 T:1 F:13|
|ECOD domain ID|e1m48A1|
|ECOD hierarchy ID|E:e1m48A1 X:150 H:3 T:1 F:13|
|ChEBI|CHEBI:52206|
|Reactome|R-HSA-6804756|
|Gene Ontology|GO:0023051|
......@@ -154,8 +155,9 @@ Accordingly, some input files are specified below:
#### `B3.001` Crystals
* Key-structure pairs: `structure` [Default] / vocabulary: PDB ID
* Key-domain pairs: `domains` / vocabulary: ECOD
* Key-structure pairs: `structures` / vocabulary: PDB ID
* Key-domain pairs: `domains` [Default] / vocabulary: ECOD domain ID
* Key-domain pairs: `domain_hierarchies` / vocabulary: ECOD hierarchy ID
#### `B4.001` Binding
......@@ -175,7 +177,7 @@ Accordingly, some input files are specified below:
#### `C2.001` Small molecule pathways
* Key-metabolite pairs (exact nodes) (10-1; default = 5): `metabolites` [Default] / vocabulary: InChIKey
* Key-metabolite pairs (exact nodes): `metabolites` [Default] / vocabulary: InChIKey
* Key-metabolite pairs (neighbors) (10-1; default = 5): `metabolites_neighbors` / vocabulary: InChIKey
#### `C3.001` Signaling pathways
......