diff --git a/cmat/clinvar_xml_io/clinvar_reference_record.py b/cmat/clinvar_xml_io/clinvar_reference_record.py index 90bd4f4e..a45c574f 100644 --- a/cmat/clinvar_xml_io/clinvar_reference_record.py +++ b/cmat/clinvar_xml_io/clinvar_reference_record.py @@ -2,7 +2,6 @@ from functools import cached_property from cmat.clinvar_xml_io.clinical_classification import ClinicalClassification - from cmat.clinvar_xml_io.clinvar_record import ClinVarRecord from cmat.clinvar_xml_io.xml_parsing import find_mandatory_unique_element, find_elements diff --git a/cmat/clinvar_xml_io/clinvar_set.py b/cmat/clinvar_xml_io/clinvar_set.py index 7f490b13..25b98267 100644 --- a/cmat/clinvar_xml_io/clinvar_set.py +++ b/cmat/clinvar_xml_io/clinvar_set.py @@ -1,4 +1,4 @@ -from cmat.clinvar_xml_io import ClinVarRecord +from cmat.clinvar_xml_io.clinvar_reference_record import ClinVarReferenceRecord from cmat.clinvar_xml_io.clinvar_submitted_record import ClinVarSubmittedRecord from cmat.clinvar_xml_io.xml_parsing import find_mandatory_unique_element, find_elements @@ -12,7 +12,7 @@ def __init__(self, cvs_xml, xsd_version): self.cvs_xml = cvs_xml rcv_elem = find_mandatory_unique_element(self.cvs_xml, 'ReferenceClinVarAssertion') - self.rcv = ClinVarRecord(rcv_elem, xsd_version) + self.rcv = ClinVarReferenceRecord(rcv_elem, xsd_version) scv_elems = find_elements(self.cvs_xml, 'ClinVarAssertion', allow_zero=False, allow_multiple=True) self.scvs = [ClinVarSubmittedRecord(elem, xsd_version, self.rcv) for elem in scv_elems] diff --git a/cmat/clinvar_xml_io/clinvar_submitted_record.py b/cmat/clinvar_xml_io/clinvar_submitted_record.py index 7934cea3..ed247e27 100644 --- a/cmat/clinvar_xml_io/clinvar_submitted_record.py +++ b/cmat/clinvar_xml_io/clinvar_submitted_record.py @@ -1,7 +1,7 @@ import logging from functools import cached_property -from cmat.clinvar_xml_io import ClinVarRecord +from cmat.clinvar_xml_io.clinvar_record import ClinVarRecord from cmat.clinvar_xml_io.xml_parsing import find_mandatory_unique_element logger = logging.getLogger(__name__) diff --git a/cmat/output_generation/clinvar_to_evidence_strings.py b/cmat/output_generation/clinvar_to_evidence_strings.py index 36d2c991..5c377d54 100644 --- a/cmat/output_generation/clinvar_to_evidence_strings.py +++ b/cmat/output_generation/clinvar_to_evidence_strings.py @@ -184,7 +184,7 @@ def clinvar_to_evidence_strings(string_to_efo_mappings, variant_to_gene_mappings # We catch exceptions but record when one is thrown, so that the pipeline will crash after processing all # records and printing the report. logger.error(f'Problem generating evidence for {clinvar_set.rcv.accession}') - logger.error(f'Error: {e}') + logger.error(f'Error: {repr(e)}') exception_raised = True continue diff --git a/tests/pipelines/resources/expected/automated_trait_mappings.tsv b/tests/pipelines/resources/expected/automated_trait_mappings.tsv index 4274e9a9..6950f88c 100644 --- a/tests/pipelines/resources/expected/automated_trait_mappings.tsv +++ b/tests/pipelines/resources/expected/automated_trait_mappings.tsv @@ -128,7 +128,7 @@ chédiak-higashi syndrome http://www.orpha.net/ORDO/Orphanet_167 chédiak-higash cobalamin c disease http://purl.obolibrary.org/obo/MONDO_0010184 methylmalonic aciduria and homocystinuria type cblC cobalamin c disease http://www.orpha.net/ORDO/Orphanet_26 Methylmalonic acidemia with homocystinuria cobalamin c disease http://www.orpha.net/ORDO/Orphanet_79282 Methylmalonic acidemia with homocystinuria, type cblC -coffin-siris syndrome 1 http://purl.obolibrary.org/obo/MONDO_0015452 Coffin-Siris syndrome +coffin-siris syndrome 1 http://purl.obolibrary.org/obo/MONDO_0007617 coffin-siris syndrome 1 cog1 congenital disorder of glycosylation http://purl.obolibrary.org/obo/MONDO_0012637 COG1-congenital disorder of glycosylation cog7 congenital disorder of glycosylation http://purl.obolibrary.org/obo/MONDO_0012118 COG7-congenital disorder of glycosylation cohen syndrome http://purl.obolibrary.org/obo/MONDO_0008999 cohen syndrome @@ -278,7 +278,7 @@ hepatoencephalopathy due to combined oxidative phosphorylation defect type 1 htt hereditary breast ovarian cancer syndrome http://purl.obolibrary.org/obo/MONDO_0003582 hereditary breast ovarian cancer syndrome hereditary cancer-predisposing syndrome http://purl.obolibrary.org/obo/MONDO_0015356 hereditary neoplastic syndrome hereditary diffuse gastric adenocarcinoma http://purl.obolibrary.org/obo/MONDO_0007648 hereditary diffuse gastric adenocarcinoma -hereditary diffuse leukoencephalopathy with spheroids http://www.orpha.net/ORDO/Orphanet_313808 Hereditary diffuse leukoencephalopathy with axonal spheroids and pigmented glia +hereditary diffuse leukoencephalopathy with spheroids http://www.orpha.net/ORDO/Orphanet_313808 Adult-onset leukoencephalopathy with axonal spheroids and pigmented glia hereditary hemorrhagic telangiectasia http://purl.obolibrary.org/obo/MONDO_0019180 hereditary hemorrhagic telangiectasia hereditary insensitivity to pain with anhidrosis http://purl.obolibrary.org/obo/MONDO_0009746 hereditary sensory and autonomic neuropathy type 4 hereditary nonpolyposis colorectal neoplasms http://www.ebi.ac.uk/efo/EFO_0009911 hereditary nonpolyposis colorectal carcinoma @@ -338,7 +338,7 @@ inflammatory skin and bowel disease, neonatal, 1 http://purl.obolibrary.org/obo/ intellectual developmental disorder, autosomal dominant 64 http://purl.obolibrary.org/obo/MONDO_0030934 intellectual developmental disorder, autosomal dominant 64 intellectual disability http://purl.obolibrary.org/obo/HP_0001249 intellectual disability intellectual disability, autosomal dominant 1 http://purl.obolibrary.org/obo/MONDO_0016459 2q23.1 microdeletion syndrome -intellectual disability, autosomal dominant 20 http://purl.obolibrary.org/obo/MONDO_0016456 5q14.3 microdeletion syndrome +intellectual disability, autosomal dominant 20 http://purl.obolibrary.org/obo/MONDO_0013266 intellectual disability, autosomal dominant 20 intellectual disability, autosomal dominant 5 http://purl.obolibrary.org/obo/MONDO_0012960 intellectual disability, autosomal dominant 5 intellectual disability, autosomal dominant 6 http://purl.obolibrary.org/obo/MONDO_0100172 intellectual disability, autosomal dominant intellectual disability, autosomal dominant 9 http://purl.obolibrary.org/obo/MONDO_0013656 intellectual disability, autosomal dominant 9 @@ -508,7 +508,7 @@ retinitis pigmentosa-deafness syndrome http://purl.obolibrary.org/obo/MONDO_0019 retinoblastoma http://purl.obolibrary.org/obo/MONDO_0008380 retinoblastoma rett syndrome http://purl.obolibrary.org/obo/MONDO_0010726 rett syndrome rett syndrome, congenital variant http://purl.obolibrary.org/obo/MONDO_0010726 Rett syndrome -rhabdoid tumor predisposition syndrome 2 http://purl.obolibrary.org/obo/MONDO_0016473 familial rhabdoid tumor +rhabdoid tumor predisposition syndrome 2 http://purl.obolibrary.org/obo/MONDO_0013224 rhabdoid tumor predisposition syndrome 2 rod-cone dystrophy http://www.orpha.net/ORDO/Orphanet_1872 Cone rod dystrophy rubinstein-taybi syndrome http://purl.obolibrary.org/obo/MONDO_0019188 rubinstein-taybi syndrome ryr1-related disorders http://www.ebi.ac.uk/efo/EFO_0009143 ryr1-related disorders diff --git a/tests/pipelines/resources/expected/google_sheets_table.tsv b/tests/pipelines/resources/expected/google_sheets_table.tsv index e2b46667..1b204d57 100644 --- a/tests/pipelines/resources/expected/google_sheets_table.tsv +++ b/tests/pipelines/resources/expected/google_sheets_table.tsv @@ -1,9 +1,9 @@ -gc1/gc2 polymorphism 1 NT expansion http://purl.obolibrary.org/obo/MONDO_0010739|Taqi polymorphism|MEDIUM|http://purl.obolibrary.org/obo/mondo.owl|NOT_CONTAINED http://www.orpha.net/ORDO/Orphanet_118803|solute carrier family 25 member 22|MEDIUM|https://www.orphadata.com/data/ontologies/ordo/last_version/ORDO_en_4.4.owl|NOT_CONTAINED http://purl.obolibrary.org/obo/MONDO_0009826|PA polymorphism of alpha-2-globulin|MEDIUM|http://purl.obolibrary.org/obo/mondo.owl|NOT_CONTAINED http://www.orpha.net/ORDO/Orphanet_122340|guanylate cyclase 2D, retinal|MEDIUM|https://www.orphadata.com/data/ontologies/ordo/last_version/ORDO_en_4.4.owl|NOT_CONTAINED +gc1/gc2 polymorphism 1 NT expansion http://purl.obolibrary.org/obo/MONDO_0010739|Taqi polymorphism|MEDIUM|http://purl.obolibrary.org/obo/mondo.owl|NOT_CONTAINED http://purl.obolibrary.org/obo/MONDO_0009826|PA polymorphism of alpha-2-globulin|MEDIUM|http://purl.obolibrary.org/obo/mondo.owl|NOT_CONTAINED http://www.orpha.net/ORDO/Orphanet_118803|solute carrier family 25 member 22|MEDIUM|https://www.orphadata.com/data/ontologies/ordo/last_version/ORDO_en_4.5.owl|NOT_CONTAINED http://www.orpha.net/ORDO/Orphanet_122340|guanylate cyclase 2D, retinal|MEDIUM|https://www.orphadata.com/data/ontologies/ordo/last_version/ORDO_en_4.5.owl|NOT_CONTAINED inherited immunodeficiency diseases 2 http://identifiers.org/medgen/C5197805|Inherited Immunodeficiency Diseases|HIGH|clinvar-xrefs|NOT_CONTAINED http://identifiers.org/medgen/C5197805|Inherited Immunodeficiency Diseases|HIGH|clinvar-xrefs|NOT_CONTAINED http://identifiers.org/mesh/D000081207|Inherited Immunodeficiency Diseases|HIGH|clinvar-xrefs|NOT_CONTAINED congenital muscular dystrophy, alpha-dystroglycan related 1 http://identifiers.org/medgen/CN239202|Congenital Muscular Dystrophy, alpha-dystroglycan related|HIGH|clinvar-xrefs|NOT_CONTAINED http://identifiers.org/medgen/CN239202|Congenital Muscular Dystrophy, alpha-dystroglycan related|HIGH|clinvar-xrefs|NOT_CONTAINED corneal dystrophy, recessive 1 http://identifiers.org/medgen/CN239343|Corneal Dystrophy, Recessive|HIGH|clinvar-xrefs|NOT_CONTAINED http://identifiers.org/medgen/CN239343|Corneal Dystrophy, Recessive|HIGH|clinvar-xrefs|NOT_CONTAINED -elfn1-related condition 1 http://purl.obolibrary.org/obo/MONDO_0045054|cancer-related condition|MEDIUM|http://purl.obolibrary.org/obo/mondo.owl|EFO_CURRENT http://purl.obolibrary.org/obo/MONDO_0021074|precancerous condition|MEDIUM|http://purl.obolibrary.org/obo/mondo.owl|EFO_CURRENT http://purl.obolibrary.org/obo/HP_0025256|Ameliorated by heat|MEDIUM|http://purl.obolibrary.org/obo/hp/hp-international.owl|NOT_CONTAINED http://purl.obolibrary.org/obo/HP_0032522|Ameliorated by immunosuppresion|MEDIUM|http://purl.obolibrary.org/obo/hp/hp-international.owl|NOT_CONTAINED http://www.orpha.net/ORDO/Orphanet_568065|EPHB4-related lymphatic-related hydrops fetalis|MEDIUM|https://www.orphadata.com/data/ontologies/ordo/last_version/ORDO_en_4.4.owl|NOT_CONTAINED http://www.orpha.net/ORDO/Orphanet_471012|RAS related|MEDIUM|https://www.orphadata.com/data/ontologies/ordo/last_version/ORDO_en_4.4.owl|NOT_CONTAINED +elfn1-related condition 1 http://purl.obolibrary.org/obo/MONDO_0045054|cancer-related condition|MEDIUM|http://purl.obolibrary.org/obo/mondo.owl|EFO_CURRENT http://purl.obolibrary.org/obo/MONDO_1040010|IRF6-related condition|MEDIUM|http://purl.obolibrary.org/obo/mondo.owl|NOT_CONTAINED http://purl.obolibrary.org/obo/HP_0025256|Ameliorated by heat|MEDIUM|http://purl.obolibrary.org/obo/hp/hp-international.owl|NOT_CONTAINED http://purl.obolibrary.org/obo/HP_0032522|Ameliorated by immunosuppresion|MEDIUM|http://purl.obolibrary.org/obo/hp/hp-international.owl|NOT_CONTAINED http://www.orpha.net/ORDO/Orphanet_568065|EPHB4-related lymphatic-related hydrops fetalis|MEDIUM|https://www.orphadata.com/data/ontologies/ordo/last_version/ORDO_en_4.5.owl|NOT_CONTAINED http://www.orpha.net/ORDO/Orphanet_471012|RAS related|MEDIUM|https://www.orphadata.com/data/ontologies/ordo/last_version/ORDO_en_4.5.owl|NOT_CONTAINED blepharophimosis, ptosis, and epicanthus inversus, type i 1 http://identifiers.org/medgen/C2931135|BLEPHAROPHIMOSIS, PTOSIS, AND EPICANTHUS INVERSUS, TYPE I|HIGH|clinvar-xrefs|NOT_CONTAINED http://identifiers.org/medgen/C2931135|BLEPHAROPHIMOSIS, PTOSIS, AND EPICANTHUS INVERSUS, TYPE I|HIGH|clinvar-xrefs|NOT_CONTAINED -autosomal dominant kcnq1-related disease 1 http://purl.obolibrary.org/obo/MONDO_0018832|HTRA1-related autosomal dominant cerebral small vessel disease|MEDIUM|http://purl.obolibrary.org/obo/mondo.owl|EFO_CURRENT http://purl.obolibrary.org/obo/MONDO_0000426|autosomal dominant disease|MEDIUM|http://purl.obolibrary.org/obo/mondo.owl|EFO_CURRENT http://purl.obolibrary.org/obo/HP_0000006|Autosomal dominant inheritance|MEDIUM|http://purl.obolibrary.org/obo/hp/hp-international.owl|EFO_CURRENT http://www.orpha.net/ORDO/Orphanet_482077|HTRA1-related autosomal dominant cerebral small vessel disease|MEDIUM|https://www.orphadata.com/data/ontologies/ordo/last_version/ORDO_en_4.4.owl|NOT_CONTAINED http://www.orpha.net/ORDO/Orphanet_497757|MME-related autosomal dominant Charcot Marie Tooth disease type 2|MEDIUM|https://www.orphadata.com/data/ontologies/ordo/last_version/ORDO_en_4.4.owl|NOT_CONTAINED http://purl.obolibrary.org/obo/HP_0003743|Genetic anticipation|MEDIUM|http://purl.obolibrary.org/obo/hp/hp-international.owl|NOT_CONTAINED +autosomal dominant kcnq1-related disease 1 http://purl.obolibrary.org/obo/MONDO_0018832|HTRA1-related autosomal dominant cerebral small vessel disease|MEDIUM|http://purl.obolibrary.org/obo/mondo.owl|EFO_CURRENT http://purl.obolibrary.org/obo/MONDO_0000426|autosomal dominant disease|MEDIUM|http://purl.obolibrary.org/obo/mondo.owl|EFO_CURRENT http://purl.obolibrary.org/obo/HP_0000006|Autosomal dominant inheritance|MEDIUM|http://purl.obolibrary.org/obo/hp/hp-international.owl|EFO_CURRENT http://www.orpha.net/ORDO/Orphanet_482077|HTRA1-related autosomal dominant cerebral small vessel disease|MEDIUM|https://www.orphadata.com/data/ontologies/ordo/last_version/ORDO_en_4.5.owl|NOT_CONTAINED http://www.orpha.net/ORDO/Orphanet_497757|MME-related autosomal dominant Charcot Marie Tooth disease type 2|MEDIUM|https://www.orphadata.com/data/ontologies/ordo/last_version/ORDO_en_4.5.owl|NOT_CONTAINED http://purl.obolibrary.org/obo/HP_0003743|Genetic anticipation|MEDIUM|http://purl.obolibrary.org/obo/hp/hp-international.owl|NOT_CONTAINED isolated nonsyndromic congenital heart disease 1 http://identifiers.org/medgen/CN239319|Isolated Nonsyndromic Congenital Heart Disease|HIGH|clinvar-xrefs|NOT_CONTAINED http://identifiers.org/medgen/CN239319|Isolated Nonsyndromic Congenital Heart Disease|HIGH|clinvar-xrefs|NOT_CONTAINED -simvastatin response - toxicity 1 http://www.ebi.ac.uk/efo/EFO_0011048|dermatological toxicity|MEDIUM|http://www.ebi.ac.uk/efo/efo.owl|EFO_CURRENT http://www.orpha.net/ORDO/Orphanet_529831|Letrozole toxicity|MEDIUM|https://www.orphadata.com/data/ontologies/ordo/last_version/ORDO_en_4.4.owl|NOT_CONTAINED http://purl.obolibrary.org/obo/MONDO_0010784|chloramphenicol toxicity|MEDIUM|http://purl.obolibrary.org/obo/mondo.owl|NOT_CONTAINED http://www.orpha.net/ORDO/Orphanet_565782|Methotrexate toxicity|MEDIUM|https://www.orphadata.com/data/ontologies/ordo/last_version/ORDO_en_4.4.owl|NOT_CONTAINED http://purl.obolibrary.org/obo/MONDO_0023176|formaldehyde poisoning|MEDIUM|http://purl.obolibrary.org/obo/mondo.owl|NOT_CONTAINED +simvastatin response - toxicity 1 http://www.ebi.ac.uk/efo/EFO_0011048|dermatological toxicity|MEDIUM|http://www.ebi.ac.uk/efo/efo.owl|EFO_CURRENT http://www.orpha.net/ORDO/Orphanet_529831|Letrozole toxicity|MEDIUM|https://www.orphadata.com/data/ontologies/ordo/last_version/ORDO_en_4.5.owl|NOT_CONTAINED http://www.orpha.net/ORDO/Orphanet_565782|Methotrexate toxicity|MEDIUM|https://www.orphadata.com/data/ontologies/ordo/last_version/ORDO_en_4.5.owl|NOT_CONTAINED http://purl.obolibrary.org/obo/MONDO_0027653|abacavir toxicity|MEDIUM|http://purl.obolibrary.org/obo/mondo.owl|NOT_CONTAINED http://purl.obolibrary.org/obo/MONDO_0023176|formaldehyde poisoning|MEDIUM|http://purl.obolibrary.org/obo/mondo.owl|NOT_CONTAINED diff --git a/tests/pipelines/resources/expected/trait_names_to_ontology_mappings.tsv b/tests/pipelines/resources/expected/trait_names_to_ontology_mappings.tsv index 7b7339dd..6bde0459 100644 --- a/tests/pipelines/resources/expected/trait_names_to_ontology_mappings.tsv +++ b/tests/pipelines/resources/expected/trait_names_to_ontology_mappings.tsv @@ -1,4 +1,4 @@ -#generated-date=2024-05-24 +#generated-date=2024-09-05 #ontology=EFO #clinvar_trait_name uri label 2-aminoadipic 2-oxoadipic aciduria http://purl.obolibrary.org/obo/MONDO_0008774 2-aminoadipic 2-oxoadipic aciduria @@ -132,7 +132,7 @@ chédiak-higashi syndrome http://www.orpha.net/ORDO/Orphanet_167 chédiak-higash cobalamin c disease http://purl.obolibrary.org/obo/MONDO_0010184 methylmalonic aciduria and homocystinuria type cblC cobalamin c disease http://www.orpha.net/ORDO/Orphanet_26 Methylmalonic acidemia with homocystinuria cobalamin c disease http://www.orpha.net/ORDO/Orphanet_79282 Methylmalonic acidemia with homocystinuria, type cblC -coffin-siris syndrome 1 http://purl.obolibrary.org/obo/MONDO_0015452 Coffin-Siris syndrome +coffin-siris syndrome 1 http://purl.obolibrary.org/obo/MONDO_0007617 coffin-siris syndrome 1 cog1 congenital disorder of glycosylation http://purl.obolibrary.org/obo/MONDO_0012637 COG1-congenital disorder of glycosylation cog7 congenital disorder of glycosylation http://purl.obolibrary.org/obo/MONDO_0012118 COG7-congenital disorder of glycosylation cohen syndrome http://purl.obolibrary.org/obo/MONDO_0008999 cohen syndrome @@ -283,7 +283,7 @@ hepatoencephalopathy due to combined oxidative phosphorylation defect type 1 htt hereditary breast ovarian cancer syndrome http://purl.obolibrary.org/obo/MONDO_0003582 hereditary breast ovarian cancer syndrome hereditary cancer-predisposing syndrome http://purl.obolibrary.org/obo/MONDO_0015356 hereditary neoplastic syndrome hereditary diffuse gastric adenocarcinoma http://purl.obolibrary.org/obo/MONDO_0007648 hereditary diffuse gastric adenocarcinoma -hereditary diffuse leukoencephalopathy with spheroids http://www.orpha.net/ORDO/Orphanet_313808 Hereditary diffuse leukoencephalopathy with axonal spheroids and pigmented glia +hereditary diffuse leukoencephalopathy with spheroids http://www.orpha.net/ORDO/Orphanet_313808 Adult-onset leukoencephalopathy with axonal spheroids and pigmented glia hereditary hemorrhagic telangiectasia http://purl.obolibrary.org/obo/MONDO_0019180 hereditary hemorrhagic telangiectasia hereditary insensitivity to pain with anhidrosis http://purl.obolibrary.org/obo/MONDO_0009746 hereditary sensory and autonomic neuropathy type 4 hereditary nonpolyposis colorectal neoplasms http://www.ebi.ac.uk/efo/EFO_0009911 hereditary nonpolyposis colorectal carcinoma @@ -344,7 +344,7 @@ inflammatory skin and bowel disease, neonatal, 1 http://purl.obolibrary.org/obo/ intellectual developmental disorder, autosomal dominant 64 http://purl.obolibrary.org/obo/MONDO_0030934 intellectual developmental disorder, autosomal dominant 64 intellectual disability http://purl.obolibrary.org/obo/HP_0001249 intellectual disability intellectual disability, autosomal dominant 1 http://purl.obolibrary.org/obo/MONDO_0016459 2q23.1 microdeletion syndrome -intellectual disability, autosomal dominant 20 http://purl.obolibrary.org/obo/MONDO_0016456 5q14.3 microdeletion syndrome +intellectual disability, autosomal dominant 20 http://purl.obolibrary.org/obo/MONDO_0013266 intellectual disability, autosomal dominant 20 intellectual disability, autosomal dominant 5 http://purl.obolibrary.org/obo/MONDO_0012960 intellectual disability, autosomal dominant 5 intellectual disability, autosomal dominant 6 http://purl.obolibrary.org/obo/MONDO_0100172 intellectual disability, autosomal dominant intellectual disability, autosomal dominant 9 http://purl.obolibrary.org/obo/MONDO_0013656 intellectual disability, autosomal dominant 9 @@ -517,7 +517,7 @@ retinitis pigmentosa-deafness syndrome http://purl.obolibrary.org/obo/MONDO_0019 retinoblastoma http://purl.obolibrary.org/obo/MONDO_0008380 retinoblastoma rett syndrome http://purl.obolibrary.org/obo/MONDO_0010726 rett syndrome rett syndrome, congenital variant http://purl.obolibrary.org/obo/MONDO_0010726 Rett syndrome -rhabdoid tumor predisposition syndrome 2 http://purl.obolibrary.org/obo/MONDO_0016473 familial rhabdoid tumor +rhabdoid tumor predisposition syndrome 2 http://purl.obolibrary.org/obo/MONDO_0013224 rhabdoid tumor predisposition syndrome 2 rod-cone dystrophy http://www.orpha.net/ORDO/Orphanet_1872 Cone rod dystrophy rubinstein-taybi syndrome http://purl.obolibrary.org/obo/MONDO_0019188 rubinstein-taybi syndrome ryr1-related disorders http://www.ebi.ac.uk/efo/EFO_0009143 ryr1-related disorders