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- ### Scinario 2: Map common annotations to networks
- =====================
- #### User Data
- * 2 human network files
- * Annnotation file for human genes
- Assume annotation table has the following columns:
- 1. NCBI Gene ID (Globally Unique)
- 2. Official Symbol (BRCA1, etc.)
- 3. Gene ontology terms (List of terms)
- 4. Aliases (IDs used in other databases)
- #### Steps
- 1. Load the annotation file as a global table. Use NCBI Gene ID as primary key
- 2. Load two human networks. It can be in same root or two different roots
- 3. At this point, we should assume networks have a column (usually NAME) with NCBI Gene ID.
- 4. Create links (i.e. create virtual columns) from global table to networks by using NCBI Gene ID and NAME column as join key.
- 5. The final network has only one "real" column, NAME. All others are virtual.
- __This is how Gene Ontology Import function is hadnling annotations (Gene Association files are loaded as global tables).__ Most of the annotation files for genes/proteins can be linked to the network in this way.
- ### Scinario 3: Import networks and annotations from web services
- =====================
- #### User Data
- * None. Just query to the services
- #### Steps
- 1. Send query to a web service.
- 2. Web service returns network(s) and annotations in their custom data structure. Usually, it contains at least one unique ID field for each node.
- 3. Convert returned data structure to CyNetwork. Use unique ID for NAME column of nodes.
- 4. Create global table for node annotations. Use uqinque ID as primary key for the global table.
- 5. Create links (i.e. create virtual columns) from global table to the new CyNetwork. Join key is the
- 6. Create edge columns in local table. In many cases, it does not make sense to create global table for edges since it usually contains network-specific values, such as edge score, publication links, etc.
- 7. Now, in the table browser, user can see node table with only one "real" column: NAME. All others are virtual. For edges, network has
- 8. Send another query.
- 9. Create a new network in existing network collection or create new root. It's user's choice.
- 10. Convert to CyNetwork. Again, use same unique ID as NAME.
- 11. For each annotation entry in the returned value, check the global table. If it exists, do not add. Otherwise, add a new row in the __global table__.
- 12. Link it to nodes.
- 13. Create local edge table values.
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