process documentation added

docs/main-flow.md

@@ -0,0 +1,9 @@
+# Build Process Flow
+
+Project build process works as follows:
+
+1. Related structure graph is downloaded from Allen, eg. http://api.brain-map.org/api/v2/structure_graph_download/8.json
+2. Using the [LinkML-OWL](https://github.com/linkml/linkml-owl) structure graph is converted to the owl. This template (https://github.com/hkir-dev/primate_brain_atlas_ontology/blob/main/src/linkml/structure_graph_schema.yaml) is utilized for the conversion.
+3. Related bridge files are downloaded from the [UBERON](https://github.com/obophenotype/uberon/tree/master/src/ontology/bridge) repo. In this case uberon-bridge-to-pba.obo and uberon-bridge-to-aba.obo
+4. Using the [ROBOT](http://robot.obolibrary.org/) ontology templating tool, external links to the related atlas pages are generated (linkouts.owl). Eg. https://github.com/hkir-dev/human_brain_atlas_ontology/blob/main/src/templates/linkouts.tsv. This template generates external links to the related atlas web pages http://atlas.brain-map.org/atlas?atlas=138322605#structure=10499
+5. Finally all ontologies (linkouts.owl, structure graph ontology and bridges) are merged and the uberon import module added to the output ontology.

mkdocs.yaml

@@ -24,6 +24,7 @@ nav:
   - Getting started: index.md
   - Cite: cite.md
   - How-to guides:
+      - PBAO workflow: main-flow.md
       - Standard ODK workflows:
           - Overview: odk-workflows/index.md
           - Editors Workflow: odk-workflows/EditorsWorkflow.md