Command Line Interface

Pickling lots of BEL scripts

All of the BEL scripts in the current working directory (and sub-directories) can be pickled in-place with the following command (add -d to specify a different directory)

$ pybel-tools io convert -d ~/bms/aetionomy/

Getting Data in to the Cache

Before running the service, some data can be pre-loaded in your cache.

Loading Selventa Corpra

The Selventa Small Corpus and Large Corpus are two example BEL documents distributed by the OpenBEL framework. They are good examples of many types of BEL statements and can be used immediately to begin exploring. Add -v for more logging information during compilation. This is highly suggested for the first run, since it takes a while to cache all of the namespaces and annotations. This only has to be done once, and will be much faster the second time!

Small Corpus

$ pybel-tools ensure small_corpus -v

Large Corpus

$ pybel-tools ensure large_corpus -v

Loading Other Resources

Gene Families

$ pybel-tools ensure gene_families -v

Named Protein Complexes

$ pybel-tools ensure named_complexes -v

Uploading Precompiled BEL

A single network stored as a PyBEL gpickle can quickly be uploaded using the following code:

$ pybel-tools io upload -p /path/to/my_network.gpickle

Uploading Multiple Networks

Multiple networks in a given directory and sub-directories can be uploaded by adding the -r tag.

$ pybel-tools io upload -p ~/bms/aetionomy/ -r

Building Resources via OLS

Namespaces, annotations, and hierarchies can be created by querying the ontologies stored in the EBI Ontology Lookup Service.

Namespace

In order to convert UBERON to a namespace, the keyword inside the OLS, uberon is used as well as specifying the encoding type and the applicability domain. The -o option can be used to specify which file to write the output to.

$ pybel-tools namespace from_ols uberon --domain Other --encoding A

Alternatively, the ‘-b’ option can be used to specify an alternate OLS instance

$ pybel-tools namespace from_ols uberon --domain Other --encoding A -b https://localhost/ols