diff --git a/data/exclusions-disease-gene.tsv b/data/exclusions-disease-gene.tsv index 070baf1..3d283a0 100644 --- a/data/exclusions-disease-gene.tsv +++ b/data/exclusions-disease-gene.tsv @@ -1,8 +1,8 @@ omim_id mondo_id mondo_label orcid exclusion_reason_comment -OMIM:603956 MONDO:0002974 cervical cancer' evidence of various genes involved -OMIM:619151 MONDO:0030894 AMED syndrome, digenic' digenic -OMIM:158901 MONDO:0008031 digenic -OMIM:108770 MONDO:0007171 atrial standstill 1' digenic -OMIM:620040 MONDO:0031057 dyskeratosis congenita, digenic' digenic -OMIM:619478 MONDO:0030355 facioscapulohumeral muscular dystrophy 4, digenic' digenic -OMIM:300818 MONDO:0010438 paroxysmal nocturnal hemoglobinuria 1 disease caused by a somatic mutation, therefore a gene association stating this is due to a germline mutation should not be added \ No newline at end of file +OMIM:603956 MONDO:0002974 cervical cancer' https://orcid.org/0000-0002-4142-7153 evidence of various genes involved +OMIM:619151 MONDO:0030894 "AMED syndrome, digenic'" https://orcid.org/0000-0002-4142-7153 digenic +OMIM:158901 MONDO:0008031 https://orcid.org/0000-0002-4142-7153 digenic +OMIM:108770 MONDO:0007171 atrial standstill 1' https://orcid.org/0000-0002-4142-7153 digenic +OMIM:620040 MONDO:0031057 "dyskeratosis congenita, digenic'" https://orcid.org/0000-0002-4142-7153 digenic +OMIM:619478 MONDO:0030355 "facioscapulohumeral muscular dystrophy 4, digenic'" https://orcid.org/0000-0002-4142-7153 digenic +OMIM:300818 MONDO:0010438 paroxysmal nocturnal hemoglobinuria 1 https://orcid.org/0000-0002-4142-7153 "disease caused by a somatic mutation, therefore a gene association stating this is due to a germline mutation should not be added" \ No newline at end of file diff --git a/omim2obo/main.py b/omim2obo/main.py index 152324f..42feba5 100644 --- a/omim2obo/main.py +++ b/omim2obo/main.py @@ -394,11 +394,13 @@ def omim2obo(use_cache: bool = False): if not p_mim or p_map_key == '1': continue - # Add restrictions: Gene->Disease non-causal (disease-defining) relationships + # Add restrictions: Gene->Disease non-causal / non-disease-defining relationships # - RO:0003302 docs: see MORBIDMAP_PHENOTYPE_MAPPING_KEY_PREDICATES # - Mapping key 3 = 'causal' (disease-defining). Handled separately below. if p_map_key != '3' or p_mim_excluded: - g2d_pred = MORBIDMAP_PHENOTYPE_MAPPING_KEY_PREDICATES[p_map_key] if len(assocs) == 1 else RO['0003302'] + g2d_pred = MORBIDMAP_PHENOTYPE_MAPPING_KEY_PREDICATES[p_map_key] \ + if len(assocs) == 1 and not p_mim_excluded \ + else RO['0003302'] orcid: Optional[URIRef] = exclusions_p_mim_orcid_map[p_mim] if p_mim_excluded else None add_subclassof_restriction_with_evidence_and_source( graph, g2d_pred, OMIM[p_mim], OMIM[gene_mim], evidence, orcid) diff --git a/sparql/disease-gene-relationships.sparql b/sparql/disease-gene-relationships.sparql index 8895cdb..d1359bb 100644 --- a/sparql/disease-gene-relationships.sparql +++ b/sparql/disease-gene-relationships.sparql @@ -24,6 +24,7 @@ WHERE { FILTER( ?PredUri IN ( + , , , ,