Adding new Namespace datasets

File format

A 'standard' format is available to use for adding new namespaces to the resource-generation pipeline. This format is a tab-delimited text file with the following columns:

1. ID - _a unique identifier for the namespace value required
2. ALTIDS - any alternative ids
3. LABEL - the preferred label for the namespace value required
4. SYNONYM - alternative labels, pipe-delimited
5. DESCRIPTION - documentation text
6. TYPE - the encoding for the namespace value (e.g., 'O' for pathology, 'C' for complex) required
7. SPECIES - the species associated with the namespace value, if any
8. XREF - equivalent values from other BEL namespaces, pipe-delimited. Must include a recognized prefix to be used for generating equivalences
9. OBSOLETE - flag obsolete values with '1'
10. PARENTS - any parent terms, valid for ID isA PARENT
11. CHILDREN - any child terms, valid for CHILD isA ID General information can be included at the top of the file, but must be preceded with a '#'.

Example data

Examples of namespace data in this format can be found for the following namespaces:

1. SFAM - Selventa protein families
2. SCHEM - Selventa legacy chemical names
3. SCOMP - Selventa named complexes
4. SDIS - Selventa legacy diseases

Integration into resource-generator pipeline

To add a namespace dataset in this format to your resource-generator pipeline, the following steps are required:

• In configuration.py:
• • initialize data object my_data = StandardCustomData(name='my-namespace-name', prefix='my-prefix')