| rel(S,P,O) :~ cat relationships.tsv | |
| anc(S,O) :- rel(S,_,O). | |
| anc(S,O) :- anc(S,Z),anc(Z,O). | |
| main(X) :- anc(X, "GO:0005634"). |
| ## Original Ontology | |
| * IRI: http://purl.obolibrary.org/obo/ro.owl | |
| * VersionIRI: http://purl.obolibrary.org/obo/ro/releases/2018-05-11/ro.owl | |
| ## New Ontology | |
| * IRI: http://purl.obolibrary.org/obo/ro.owl |
| #!/usr/bin/env python3 | |
| """ | |
| Command line wrapper to mygene for bulk operations | |
| Type: | |
| bulkgene -h | |
| For instructions |
| Proposed schema for evolved processes. Evolved processes are either (1) the realization of a single function (2) a causally connected mereological sum of (1)s | |
| The schema could be generalized to other processes arise from non-evolved functions such as building a house. | |
| For simplicity this initial elucidation focuses on evolved processes (aka biological programs). | |
| Subsubmption hierarchy (`P` = process, `C` = independent continuant, `Q` = quality) | |
| * enabled by (aka has agent) `P->C` | |
| * has participant `P->C` | |
| * modifies or consumes (aka has initial participant) |
| fact(is_a(a,b)). | |
| fact(is_a(b,c)). | |
| rule((is_aT(A,B) :- is_a(A,B))). | |
| rule((is_aT(A,B) :- is_a(A,Z),is_aT(Z,B))). | |
| prove(Goal,[Goal]) :- | |
| fact(Goal). | |
| prove(Goal, [Rule|Steps]) :- | |
| Rule = rule( (Goal :- Body) ), |
| ## Type Definitions (contract) | |
| type Drug { | |
| id: ID! | |
| name: String! | |
| drugInteractions: [DrugInteraction] | |
| drugTargets: [DrugTarger] | |
| } | |
| type DrugTarget { |
https://docs.google.com/document/d/136NBEwqi0Jwon4h23m0BfDMMIn_TBx06o1pPXNz8HXk/edit
This API wraps a number of different more modular APIs and database engines or analysis services. The idea is that the API implementation will do the right thing - for example, using Solr for searches but injecting results with fast in-memory traversal of ontology graphs.
When starting up, configure with:
Bold Hypothesis: GO BPs can be cleanly separated into cellular processes and larger processes formed from assemblages of these. Any process should be diagrammable. If the diagram is expressed using cell parts and molecules, it is cellular. If the diagram is expressed using cells or tissues it is at a larger level of organization.
Additionally, we may have grouping classes which can abstract over both branches, in terms of some objective or phenotype. Examples are: growth (to increase the size of the organism or a part), immune system
README is empty
| # see thea/benchmarks directory | |
| TIME THEA CARO 0.0697942 | |
| MEM THEA CARO 1.885792 | |
| TIME THEA CL 1.38948 | |
| MEM THEA CL 8.553492 | |
| TIME THEA FBbt 19.0624 | |
| MEM THEA FBbt 38.238024 | |
| TIME THEA GO 411.418 | |
| MEM THEA GO 381.50792 | |
| TIME THEA SO 3.1424 |