Trying to wrap my mind about Gene Ontology. It is written here: http://geneontology.org/docs/ontology-documentation/
"The structure of GO can be described in terms of a graph, where each GO term is a node, and the relationships between the terms are edges between the nodes. GO is loosely hierarchical, with ‘child’ terms being more specialized than their ‘parent’ terms"
I wonder where can I look at this graph, or at least at most top level classes of it ? For each of three "molecular function", "bio process", "cellur component", sub-hierarchies at least how many classes on each top (I mean 1 level below root node) level ?
PS That thread is somewhat related: are there GO families?
PSPS Here is some nice collection of notebooks using python-GO-interface "ontobio" ( https://ontobio.readthedocs.io/en/latest/index.html ): https://nbviewer.jupyter.org/github/biolink/ontobio/tree/master/notebooks/
If you have programming experience you might parse the obo file and use a visualization package on the graph.
I am not sure if the sequence of the obo file would allow you to plot the first classes first (node with depth = 1 https://stackoverflow.com/questions/2603692/what-is-the-difference-between-tree-depth-and-height). But that is what I am assuming about the obo file sequence.
edit: looks like the connections to MF, BP and CC would be identified using links with "relations" (http://www.obofoundry.org/ontology/ro.html). This is what you could use to parse the OBO and create links. Nodes at depth =1 would be the first classes.
I understand that you're new to GO, so there may also be packages you can use for this (which also saves time). The GO graph is huge, so people may first filter their GO terms based on enrichment and then plot the graph.
Thank you very much for your answer ! What is the "obo file" ? Where is the link to download it ?
There are several, each with design for specific and general uses (http://geneontology.org/docs/download-ontology/).
People usually first conduct GO enrichment before visualization, as discussed in this thread: What'S The Best Way To View And Explore A Large Gene Ontology Dag?.
I am trying to solve your problem also, and I haven't been able to use the relations file yet. There must be a way to map relations to the OBO file (you may be able to use the "part_of" row in the OBO, I am unsure).
Here are all the unique labels in purl.obolibrary.org/obo/go.obo:
format-version, data-version, subsetdef, synonymtypedef, default-namespace, ontology, property_value, [Term], id, name, namespace, def, synonym, is_a, alt_id, subset, xref, disjoint_from, comment, is_obsolete, consider, relationship, intersection_of, created_by, creation_date, replaced_by, [Typedef], is_transitive, transitive_over, inverse_of, holds_over_chain, is_metadata_tag, is_class_level
The "relationship" row may be your best best for creating links in the graph.