Use latest version of Orphanet

[cmungall]

Just noticed our pipeline was hardwired to download v1.2...

[cmungall]

Looking at diffs. Does not seem to be any major refactoring. Still these kinds of issues:

[cmungall]

2.0 distinguishes between exact an inexact mappings (axiom annotations on the xrefs)

[cmungall]

"Attributed"
"BTNT (broader term maps to a narrower term)"
"E (exact mapping (the terms and the concepts are equivalent))"
"Inclusion term (The term is included under a ICD10 category and has not its own code)"
"Index term"
"ND (not yet decided/unable to decide)"
"NTBT (narrower term maps to a broader term)"
"Specific code (The term has its own code in the ICD10)"
"W (incorrect mapping (two different concepts)"

[cmungall]

Not sure we can trust these. Took a random example:

[Term]
id: Orphanet:99931
name: Idiopathic pulmonary hemosiderosis
def: "Idiopathic pulmonary hemosiderosis is a respiratory disease due to repeated episodes of diffuse alveolar hemorrhage without any underlying apparent cause, most often in children. Anemia, cough, and pulmonary infiltrates on chest radiographs are found in majority of the patients." []
xref: ICD-10:E83.1+ {http://purl.obolibrary.org/obo/ECO_0000218="NTBT (narrower term maps to a broader term)"}
xref: ICD-10:J99.8* {http://purl.obolibrary.org/obo/ECO_0000218="Index term"}
xref: MeSH:C536281 {http://purl.obolibrary.org/obo/ECO_0000218="E (exact mapping (the terms and the concepts are equivalent))"}
**xref: OMIM:178550 {http://purl.obolibrary.org/obo/ECO_0000218="E (exact mapping (the terms and the concepts are equivalent))"}
**xref: OMIM:235500 {http://purl.obolibrary.org/obo/ECO_0000218="BTNT (broader term maps to a narrower term)"}
xref: UMLS:C0020807 {http://purl.obolibrary.org/obo/ECO_0000218="NTBT (narrower term maps to a broader term)"}
is_a: Orphanet:377788 ! disease
relationship: has_AgeOfOnset Orphanet:409946 ! Childhood
relationship: part_of Orphanet:264762 ! Primary interstitial lung disease in childhood and adulthood

ie.

• EXACT to OMIM:178550 ! Pulmonary Hemosiderosis
• BTNT to OMIM:235500 ! Hemosiderosis, Pulmonary, With Deficiency of Gamma-A Globulin

Except http://omim.org/entry/178550 seems to refer to something different from the Orphanet concept (which is idiopathic) "This rare disorder is characterized by the triad of hemoptysis, iron-deficiency anemia, and transient pulmonary infiltrates by roentgenography. The underlying pathogenetic mechanism is a propensity to recurrent intrapulmonary hemorrhage."

[nicolevasilevsky]

This issue was moved to monarch-initiative/monarch-disease-ontology-RETIRED#30