Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Refactor OWL restrictions #151

Open
wants to merge 1 commit into
base: main
Choose a base branch
from
Open

Refactor OWL restrictions #151

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
81 changes: 35 additions & 46 deletions omim2obo/main.py
View file
Open in desktop
Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Which data files and example identifiers are effected by this change?

None. It would indeed be a good idea to check builds or run tests after a change like this. We can't commit and examine the files in a diff, but I can do the same procedure we did recently, running it before and after and checking the .ofn diff. I believe it is deterministic, so I would expect to see no changes. So I think I'll do that. This is low prior, so I'm gonna push it farther down my stack.

  • @joeflack4 Low priority: Confirm no difference in outputs before/after this change.

Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

yes, i would test this to confirm everything is the same.

Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

without confirmation that the files are the same this should not be merged

Original file line number Diff line number Diff line change
Expand Up @@ -79,6 +79,33 @@ def get_curie_maps():
return maps


def add_subclassof_restriction(graph: Graph, predicate: URIRef, some_values_from: URIRef, on: URIRef) -> BNode:
"""Creates a subClassOf someValuesFrom restriction"""
b = BNode()
graph.add((b, RDF['type'], OWL['Restriction']))
graph.add((b, OWL['onProperty'], predicate))
graph.add((b, OWL['someValuesFrom'], some_values_from))
graph.add((on, RDFS['subClassOf'], b))
return b


def add_subclassof_restriction_with_evidence(
graph: Graph, predicate: URIRef, some_values_from: URIRef, on: URIRef, evidence: Union[str, Literal]
):
"""Creates a subClassOf someValuesFrom restriction, and adds an evidence axiom to it."""
evidence = Literal(evidence) if type(evidence) is str else evidence
# Add restriction on MIM class
b: BNode = add_subclassof_restriction(graph, predicate, some_values_from, on)
# Add axiom to restriction
b2 = BNode()
graph.add((b2, RDF['type'], OWL['Axiom']))
graph.add((b2, OWL['annotatedSource'], on))
graph.add((b2, OWL['annotatedProperty'], RDFS['subClassOf']))
graph.add((b2, OWL['annotatedTarget'], b))
graph.add((b2, BIOLINK['has_evidence'], evidence))
graph.add((b2, RDFS['comment'], evidence))


# Classes
class DeterministicBNode(BNode):
"""Overrides BNode to create a deterministic ID"""
Expand Down Expand Up @@ -238,11 +265,7 @@ def omim2obo(use_cache: bool = False):
graph.add((OMIM[mim_number], SKOS.exactMatch, NCBIGENE[entrez_id]))
for mim_number, entrez_id in pheno_map.items():
# RO['0002200'] = 'has phenotype'
b = BNode()
graph.add((b, RDF['type'], OWL['Restriction']))
graph.add((b, OWL['onProperty'], RO['0002200']))
graph.add((b, OWL['someValuesFrom'], OMIM[mim_number]))
graph.add((NCBIGENE[entrez_id], RDFS['subClassOf'], b))
add_subclassof_restriction(graph, RO['0002200'], OMIM[mim_number], NCBIGENE[entrez_id])
hgnc_symbol_id_map: Dict[str, str] = get_hgnc_symbol_id_map()
for mim_number, hgnc_symbol in hgnc_map.items():
graph.add((OMIM[mim_number], SKOS.exactMatch, HGNC_symbol[hgnc_symbol]))
Expand All @@ -265,18 +288,16 @@ def omim2obo(use_cache: bool = False):
# todo?: unused `mim_data` keys. Should they be used?
# - phenotype_label: Similar to p_lab in 'assocs', but has more info
# - gene_symbols
# - add cyto location
cyto_location: str = mim_data['cyto_location']
if cyto_location:
# What's 9606chr - joeflack4 2021/11/11
chr_id = '9606chr' + cyto_location
# RO:0002525 (is subsequence of)
# https://www.ebi.ac.uk/ols/ontologies/ro/properties?iri=http://purl.obolibrary.org/obo/RO_0002525
b = BNode()
graph.add((b, RDF['type'], OWL['Restriction']))
graph.add((b, OWL['onProperty'], RO['0002525']))
graph.add((b, OWL['someValuesFrom'], CHR[chr_id]))
graph.add((OMIM[mim_number], RDFS['subClassOf'], b))
add_subclassof_restriction(graph, RO['0002525'], CHR[chr_id], OMIM[mim_number])
assocs: List[Dict] = mim_data['phenotype_associations']
# - add associations
for assoc in assocs:
# p_lab currently not used
p_mim, p_lab, p_map_key, p_map_lab = \
Expand All @@ -289,54 +310,22 @@ def omim2obo(use_cache: bool = False):
if p_map_key == '1':
continue

# Precalc: determine mapping predicate
# RO:0003302 (causes or contributes to condition)
# https://www.ebi.ac.uk/ols/ontologies/ro/properties?iri=http://purl.obolibrary.org/obo/RO_0003302
# Provenance for this decision:
# - Multiple rows, same mapping key: https://github.com/monarch-initiative/omim/issues/75
# - Multiple rows, diff mapping keys: https://github.com/monarch-initiative/omim/issues/81
evidence = f'Evidence: ({p_map_key}) {p_map_lab}'
predicate = RO['0003302'] # default if `len(assocs) > 1`
if len(assocs) == 1:
predicate = MORBIDMAP_PHENOTYPE_MAPPING_KEY_PREDICATES[p_map_key]

evidence = Literal(f'Evidence: ({p_map_key}) {p_map_lab}')

# i. Add to MIM class
# noinspection DuplicatedCode b_and_b3_diff_results
b = BNode()
graph.add((b, RDF['type'], OWL['Restriction']))
graph.add((b, OWL['onProperty'], predicate))
graph.add((b, OWL['someValuesFrom'], OMIM[p_mim]))
graph.add((OMIM[mim_number], RDFS['subClassOf'], b))

# ii. add axiom
b2 = BNode()
graph.add((b2, RDF['type'], OWL['Axiom']))
graph.add((b2, OWL['annotatedSource'], OMIM[mim_number]))
graph.add((b2, OWL['annotatedProperty'], RDFS['subClassOf']))
graph.add((b2, OWL['annotatedTarget'], b))
graph.add((b2, BIOLINK['has_evidence'], evidence))
graph.add((b2, RDFS['comment'], evidence))

add_subclassof_restriction_with_evidence(graph, predicate, OMIM[p_mim], OMIM[mim_number], evidence)
if predicate in MORBIDMAP_PHENOTYPE_MAPPING_KEY_INVERSE_PREDICATES:
# The following code basically just adds the converse relation:
# If there is g2d in the previous code, we now, in addition, add d2g
inverse_predicate = MORBIDMAP_PHENOTYPE_MAPPING_KEY_INVERSE_PREDICATES[predicate]

# i. Add to MIM class
b = BNode()
graph.add((b, RDF['type'], OWL['Restriction']))
graph.add((b, OWL['onProperty'], inverse_predicate))
graph.add((b, OWL['someValuesFrom'], OMIM[mim_number]))
graph.add((OMIM[p_mim], RDFS['subClassOf'], b))

b2 = BNode()
graph.add((b2, RDF['type'], OWL['Axiom']))
graph.add((b2, OWL['annotatedSource'], OMIM[p_mim]))
graph.add((b2, OWL['annotatedProperty'], RDFS['subClassOf']))
graph.add((b2, OWL['annotatedTarget'], b))
graph.add((b2, BIOLINK['has_evidence'], evidence))
graph.add((b2, RDFS['comment'], evidence))
add_subclassof_restriction_with_evidence(
graph, inverse_predicate, OMIM[mim_number], OMIM[p_mim], evidence)

# PUBMED, UMLS
# How do we get these w/out relying on this ttl file? Possible? Where is it from? - joeflack4 2021/11/11
Expand Down