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1 | github_issue | status | curation_notes | link | genetic basis | characterized by | iri | obo_id | parent_label | parent_curie | label | def | def_src | def_type | syn_exact | syn_broad | xrefs | skos_exact | skos_broad | Namespace | sc_axiom-INHERITANCE | sc_axiom-ANATOMY | sc_axiom-ONSET | sc_axiom-SYMP |
2 | ID | A oboInOwl:id | SC % | A rdfs:label | A obo:IAO_0000115 | >A oboInOwl:hasDbXref SPLIT=| | >AI dc11:type SPLIT=| | A oboInOwl:hasExactSynonym SPLIT=| | A oboInOwl:hasBroadSynonym SPLIT=| | A oboInOwl:hasDbXref SPLIT=| | A skos:exactMatch SPLIT=| | A skos:broadMatch SPLIT=| | A oboInOwl:hasOBONamespace | SC 'has material basis in' some % | SC 'disease has location' some % | SC 'has material basis in' some % | SC 'has symptom' some % | |||||||
3 | added | disease being converted to PS because it lists more than one gene (TGM5 = PSS2; CSTA = PSS4) which are now subtypes (they also cut across ORDO defined subgroupings, so it doesn't make sense to make it a subgroup) - not adding acral or generalized subgroups, or exfoliative ichthyosis (from ORDO) as there are discrepancies about which gene corresponds with each; most straightforward to follow OMIM and keep them as a single grouping xrefs: - remove existing ORDO, OMIM xrefs - leave existing MESH = correct - change ICD10CM xref to broadMatch synonyms: add synonyms from ORDO/GARD/MESH inheritance: all OMIM subtypes have autosomal recessive inheritance --> add here to grouping term definition: remove mention of genes & GARD source (references acral skin peeling only) - add NORD as source hierarchy: described in numerous publications as an ichthyosis; while dry skin is a consistent feature, scaling is not; the primary phenotype is peeling --> do NOT move as child of DOID:1697, keep as child of 'skin disease' | DOID:0060283 | peeling skin disease|deciduous skin|familial continuous skin peeling syndrome|keratosis exfoliativa congenita|PSS | OMIM:PS270300|ORDO:817|GARD:7347|UMLS_CUI:C1849193|SNOMEDCT_US_2023_03_01:724838009 | OMIM:PS270300|ORDO:817|GARD:7347|UMLS_CUI:C1849193|SNOMEDCT_US_2023_03_01:724838009 | autosomal recessive inheritance | skin peeling | ||||||||||||||||
4 | https://github.com/DiseaseOntology/HumanDiseaseOntology/issues/1276 | added | this is the only disease list as inflammatory or type B across all sources (add as exact synonyms) | OMIM:270300 | homozygous mutation in the CDSN gene on chromosome 6p21.33. | DOID:0070520 | DOID:0070520 | peeling skin syndrome | DOID:0060283 | peeling skin syndrome 1 | A peeling skin syndrome that has_material_basis_in homozygous mutation in the CDSN gene on chromosome 6p21.33. | url:https://pubmed.ncbi.nlm.nih.gov/20691404/|url:https://pubmed.ncbi.nlm.nih.gov/28584761 | curator inference from journal publication | PSS1|peeling skin syndrome type B|inflammatory peeling skin syndrome|generalized inflammatory peeling skin syndrome | OMIM:270300|UMLS_CUI:C5768235|UMLS_CUI:C5679693|ORDO:263553 | OMIM:270300|UMLS_CUI:C5768235|UMLS_CUI:C5679693|ORDO:263553 | disease_ontology | |||||||
5 | added | decided not to use characterized by statement for simplicity and because it could also apply to other PSS types (4/5?); acral PSS is probably historical OMIM name, which is why it's added here (and only here); the name has become more of a grouping = broadMatch (see NORD additional_notes, also evident in publications) | OMIM:609796 | homozygous or compound heterozygous mutation in the TGM5 gene on chromosome 15q15.2. | peeling most apparent on the hands and feet | DOID:0070521 | DOID:0070521 | peeling skin syndrome | DOID:0060283 | peeling skin syndrome 2 | A peeling skin syndrome that has_material_basis_in homozygous or compound heterozygous mutation in the TGM5 gene on chromosome 15q15.2. | url:https://pubmed.ncbi.nlm.nih.gov/16380904/|url:https://pubmed.ncbi.nlm.nih.gov/22036214/|url:https://medlineplus.gov/genetics/condition/peeling-skin-syndrome-2/ | curator inference from journal publication|curator inference from MedlinePlus encyclopedia | PSS2 | acral peeling skin syndrome|localized peeling skin syndrome|APSS | OMIM:609796|MESH:C536316|ORDO:263534|UMLS_CUI:C1853354|SNOMEDCT_US_2023_03_01:709416009|GARD:12863 | OMIM:609796|MESH:C536316|ORDO:263534|UMLS_CUI:C1853354|SNOMEDCT_US_2023_03_01:709416009|GARD:12863 | disease_ontology | ||||||
6 | added | going to create this disease with reservations - only 1 family reported - see OMIM_requests for publication suggesting the variant may not be pathogenic xrefs: not including UMLS_CUI because only has ORDO mapping and ORDO is a broadMatch | OMIM:616265 | homozygous mutation in the CHST8 gene on chromosome 19q13.11. | DOID:0070522 | DOID:0070522 | peeling skin syndrome | DOID:0060283 | peeling skin syndrome 3 | A peeling skin syndrome that has_material_basis_in homozygous mutation in the CHST8 gene on chromosome 19q13.11. | url:https://pubmed.ncbi.nlm.nih.gov/22289416/ | curator inference from journal publication | PSS3 | peeling skin syndrome type A | OMIM:616265 | OMIM:616265 | ORDO:263548 | disease_ontology | ||||||
7 | added | definition: leave out characterized by -> early papers describe basal/suprabasal issues but second source suggests higher level (though still lower than stratum corneum); all linked to CSTA - probable definition would include acral skin peeling (could be dorsal or palmar), leaving clearly denuded areas, aggravated by heat, moisture, and friction (last point may be true for most PSS) xrefs: - ORDO:289586 would be broad, links to UMLS_CUI:C1838440 for 'ICHTHYOSIS EXFOLIATIVA' which is linked to this OMIM and OMIM:146800 on DOID:0060877 (genetics suggest this is the same as IBS, see OMIM entry); ORDO/UMLS don't map to same OMIMs! SNOMED probably also broad --> since UMLS, ORDO, SNOMED multimap to DOIDs in inconsistent ways (likely exist due to phenotype/genotype or name confusion), I'm going to leave these off for now - MESH:C564309 lists CSTA gene = exact synonyms: - add broad synonyms, might be used in search - AREI is likely historical OMIM name (possibly prior to gene identifications) but has been used more broadly (at least including PSS5, full synonym anyway); acronym has only been used for this disease -> only include acronym here as broad, add full synoym here & PSS5 | OMIM:607936 | homozygous mutation in the CSTA gene on chromosome 3q21.1. | DOID:0070523 | DOID:0070523 | peeling skin syndrome | DOID:0060283 | peeling skin syndrome 4 | A peeling skin syndrome that has_material_basis_in homozygous mutation in the CSTA gene on chromosome 3q21.1. | url:https://pubmed.ncbi.nlm.nih.gov/21944047/|url:https://pubmed.ncbi.nlm.nih.gov/23534700/ | curator inference from journal publication | PSS4|ichthyosis bullosa of Siemens-like | autosomal recessive exfoliative ichthyosis|AREI|exfoliative ichthyosis|ichthyosis exfoliativa | OMIM:607936|MESH:C564309 | OMIM:607936|MESH:C564309 | disease_ontology | |||||||
8 | added | similar comments to PSS4 (only 1 paper) | OMIM:617115 | homozygous mutation in the SERPINB8 gene on chromosome 18q22.1. | DOID:0070524 | DOID:0070524 | peeling skin syndrome | DOID:0060283 | peeling skin syndrome 5 | A peeling skin syndrome that has_material_basis_in homozygous mutation in the SERPINB8 gene on chromosome 18q22.1. | url:https://pubmed.ncbi.nlm.nih.gov/27476651/ | curator inference from journal publication | PSS5 | exfoliative ichthyosis|ichthyosis exfoliativa|autosomal recessive exfoliative ichthyosis | OMIM:617115 | OMIM:617115 | disease_ontology | |||||||
9 | added | xref: UMLS not included for same reason as PSS3 | OMIM:618084 | homozygous mutation in the FLG2 gene on chromosome 1q21.3. | DOID:0070525 | DOID:0070525 | peeling skin syndrome | DOID:0060283 | peeling skin syndrome 6 | A peeling skin syndrome that has_material_basis_in homozygous mutation in the FLG2 gene on chromosome 1q21.3. | url:https://pubmed.ncbi.nlm.nih.gov/29505760/|url:https://pubmed.ncbi.nlm.nih.gov/29758285/ | curator inference from journal publication | PSS6 | peeling skin syndrome type A | OMIM:618084 | OMIM:618084 | ORDO:263548 | disease_ontology | ||||||
10 | added | PLACK syndrome, proposed by original authors, is used in every subsequent publication --> make name | OMIM:616295 | homozygous mutation in the CAST gene on chromosome 5q15. | peeling skin in association with leukonychia, acral punctate keratoses, cheilitis, and knuckle pads | DOID:0070526 | DOID:0070526 | skin disease | DOID:37 | PLACK syndrome | An skin disease characterized by peeling skin in association with leukonychia, acral punctate keratoses, cheilitis, and knuckle pads that has_material_basis_in homozygous mutation in the CAST gene on chromosome 5q15. | url:https://pubmed.ncbi.nlm.nih.gov/25683118/ | curator inference from journal publication | peeling skin with leukonychia, acral punctate keratoses, cheilitis, and knuckle pads | OMIM:616295|ORDO:444138|UMLS_CUI:C4225381|SNOMEDCT_US_2023_03_01:1237509001 | OMIM:616295|ORDO:444138|UMLS_CUI:C4225381|SNOMEDCT_US_2023_03_01:1237509001 | disease_ontology | autosomal recessive inheritance |