| ... | ... | @@ -41,4 +41,26 @@ In practice: |
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|InChIKeys|`TSV`|A one-column file containing InChIKeys. This will fetch the corresponding molecular properties from the CC database.|
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|Key-feature pairs|`TSV`|A two-column file containing keys (first column) and features (second column). Features can be, for example, protein identifiers. Optionally, a third column can be included to specify the *weight* of the key-feature annotation.|
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|Key profiles|`TSV`|A multiple-column file containing keys (first column) and features (second column onwards). These can be, for example, NCI-60 profiles, or chemical-genetic interaction profiles. If a header is not included, the order of the columns should match the one used in the CC internally.|
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|Feature sets|`GMT`|A [GMT](http://software.broadinstitute.org/cancer/software/genepattern/file-formats-guide#GMT)-like file, typically used for gene sets. **First column:** Sample (signature) identifier. **Second column:** Agent (perturbagen, molecule, etc.) identifier. If empty, assume the same than first column. This is used in case it is necessary to aggregate downstream. **Third column:** Up features (genes). May be `NULL`. **Fourth column:** Down features (genes). If empty, assume that there is no direction in the gene set, and only take third column. May be `NULL`.| |
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|Feature sets|`GMT`|A [GMT](http://software.broadinstitute.org/cancer/software/genepattern/file-formats-guide#GMT)-like file, typically used for gene sets. **First column:** Sample (signature) identifier. **Second column:** Agent (perturbagen, molecule, etc.) identifier. If empty, assume the same than first column. This is used in case it is necessary to aggregate downstream. **Third column:** Up features (genes). Can be `NULL`. **Fourth column:** Down features (genes). If empty, assume that there is no direction in the gene set, and only take the third column. Can be `NULL`.|
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We highly recommend that, when designing the datasets, features are as explicit as possible. A good way to start would be the metanodes defined in the Bioteque:
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|Node|Abbreviation|
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|Assay|`ASY`|
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|Cell|`CLL`|
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|Chemical entity|`CHE`|
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|Compartment|`CMP`|
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|Domain|`DOM`|
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|Compound|`CPD`|
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|Gene/Protein|`GEN`|
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|Disease|`DIS`|
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|Molecular function|`MFN`|
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|Pathway/processes|`PWY`|
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|Protein class|`PCL`|
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|Perturbagen|`PGN`|
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|Symptom|`SYM`|
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|Tissue|`TIS`|
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|Pharmacologic class|`PHC`|
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Obviously, it is mandatory that the *vocabularies* used in the production phase and the mapping phase match. |
