Integrate a cell type ontology from NIF and OpenKnowledgeSpace/methodsOntology

[MFSY]

Cell type annotation is crucial to BBP data annotation. A lot of work already happened in collaboration with NIF and in the context of HBP :

• OpenKnowledgeSpace/methodsOntology which is imported in NIF

• hbp_cells.py from NIF

• cell type from the 2015 cell paper -neuron_ma2015.py

Now we need to consolidate all this work in one cell type ontology. A prerequisite would be to have competency questions ready (see #103).

[tgbugs]

The neuron_ma2015.py code needs to be adapted to export into the new format described below.

The full cell types ontology work is best documented here. There is also the phenotypes namespaces file, which has a namespace for bbp. The definitions in that file not correct because they currently use species general identifiers where they should be using species specific identifiers, but that is blocked by the need to finish the parcellation schemes work. If there are new definitions that you all need one easy place to start is by adding them to the bbp namespace and I can make sure that the required phenotypes are incorporated into the core of the neuron/phenotype ontology.

[MFSY]

Thank you for sharing this documentation. I'll quickly review the phenotypes namespaces and see if there are new needed definitions.
@srjimenez : it would be great if you can have a look too.