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MESH:C538119 Hirschsprung disease ganglioneuroblastoma #16

Closed cmungall closed 6 years ago

cmungall commented 9 years ago

hir

cmungall commented 9 years ago

underlying cause

[Term]
id: Orphanet:2151
name: Hirschsprung disease - ganglioneuroblastoma
xref: ICD-10:Q43.1 {http://purl.obolibrary.org/obo/ECO_0000218="NTBT (narrower term maps to a broader term)"}
xref: MeSH:C538119 {http://purl.obolibrary.org/obo/ECO_0000218="E (exact mapping (the terms and the concepts are equivalent))"}
xref: UMLS:C2751683 {http://purl.obolibrary.org/obo/ECO_0000218="Attributed"}
is_a: Orphanet:377789 ! malformation syndrome
relationship: part_of Orphanet:108969 ! Syndromic intestinal malformation
relationship: part_of Orphanet:117573 ! Syndromic anorectal malformation

Should probably be merged with

[Term]
id: OMIM:613013
name: Neuroblastoma, Susceptibility To, 2
synonym: "NBLST2" EXACT []
synonym: "NEUROBLASTOMA, SUSCEPTIBILITY TO, 2; NBLST2" EXACT []
synonym: "Neuroblastoma With Hirschsprung Disease" EXACT []
xref: Orphanet:635 !  Neuroblastoma
xref: UMLS:C2751682
xref: UMLS:C2751683

however, the xref in OMIM is to a more general class, and the Ordo has no xref.

text mining may fail here due to the qualifier "ganglio" in ORDO

pnrobinson commented 9 years ago

Hm, I do not think that Hirschsprung disease ganglioneuroblastoma is a valid disease...

Dr. med. Peter N. Robinson, MSc. Professor of Medical Genomics Professor in the Bioinformatics Division of the Department of Mathematics and Computer Science of the Freie Universität Berlin Institut für Medizinische Genetik und Humangenetik Charité - Universitätsmedizin Berlin Augustenburger Platz 1 13353 Berlin Germany +4930 450566006 Mobile: 0160 93769872 peter.robinson@charite.de http://compbio.charite.de http://www.human-phenotype-ontology.org Introduction to Bio-Ontologies: http://www.crcpress.com/product/isbn/9781439836651 I have learned from my mistakes, and I am sure I can repeat them exactly ORCID ID:http://orcid.org/0000-0002-0736-9199 Scopus Author ID 7403719646 Appointment request: http://doodle.com/pnrobinson

Von: Chris Mungall [notifications@github.com] Gesendet: Dienstag, 28. Juli 2015 16:45 An: monarch-initiative/monarch-disease-ontology Betreff: Re: [monarch-disease-ontology] MESH:C538119 Hirschsprung disease ganglioneuroblastoma (#16)

underlying cause

[Term] id: Orphanet:2151 name: Hirschsprung disease - ganglioneuroblastoma xref: ICD-10:Q43.1 {http://purl.obolibrary.org/obo/ECO_0000218="NTBT (narrower term maps to a broader term)"} xref: MeSH:C538119 {http://purl.obolibrary.org/obo/ECO_0000218="E (exact mapping (the terms and the concepts are equivalent))"} xref: UMLS:C2751683 {http://purl.obolibrary.org/obo/ECO_0000218="Attributed"} is_a: Orphanet:377789 ! malformation syndrome relationship: part_of Orphanet:108969 ! Syndromic intestinal malformation relationship: part_of Orphanet:117573 ! Syndromic anorectal malformation

Should probably be merged with

[Term] id: OMIM:613013 name: Neuroblastoma, Susceptibility To, 2 synonym: "NBLST2" EXACT [] synonym: "NEUROBLASTOMA, SUSCEPTIBILITY TO, 2; NBLST2" EXACT [] synonym: "Neuroblastoma With Hirschsprung Disease" EXACT [] xref: Orphanet:635 ! Neuroblastoma xref: UMLS:C2751682 xref: UMLS:C2751683

however, the xref in OMIM is to a more general class, and the Ordo has no xref.

text mining may fail here due to the qualifier "ganglio" in ORDO

— Reply to this email directly or view it on GitHubhttps://github.com/monarch-initiative/monarch-disease-ontology/issues/16#issuecomment-125634333.

cmungall commented 9 years ago

Can you elaborate?

would you agree this is a disease http://www.omim.org/entry/613013

but the synonyms with neuroblastoma are invalid?

pnrobinson commented 9 years ago

The neuroblastoma is a complication of the Hirschsprung, but I do not think it should be listed as a separate disease. If we did that, then we would need to split all known diseases into 100 subtypes each! -Peter

Dr. med. Peter N. Robinson, MSc. Professor of Medical Genomics Professor in the Bioinformatics Division of the Department of Mathematics and Computer Science of the Freie Universität Berlin Institut für Medizinische Genetik und Humangenetik Charité - Universitätsmedizin Berlin Augustenburger Platz 1 13353 Berlin Germany +4930 450566006 Mobile: 0160 93769872 peter.robinson@charite.de http://compbio.charite.de http://www.human-phenotype-ontology.org Introduction to Bio-Ontologies: http://www.crcpress.com/product/isbn/9781439836651 I have learned from my mistakes, and I am sure I can repeat them exactly ORCID ID:http://orcid.org/0000-0002-0736-9199 Scopus Author ID 7403719646 Appointment request: http://doodle.com/pnrobinson

Von: Chris Mungall [notifications@github.com] Gesendet: Dienstag, 28. Juli 2015 17:12 An: monarch-initiative/monarch-disease-ontology Cc: Robinson, Peter Betreff: Re: [monarch-disease-ontology] MESH:C538119 Hirschsprung disease ganglioneuroblastoma (#16)

Can you elaborate?

would you agree this is a disease http://www.omim.org/entry/613013

but the synonyms with neuroblastoma are invalid?

— Reply to this email directly or view it on GitHubhttps://github.com/monarch-initiative/monarch-disease-ontology/issues/16#issuecomment-125644367.

pnrobinson commented 9 years ago

btw note that OMIM is implying they are the same disease while Orphanet is splitting them.

Dr. med. Peter N. Robinson, MSc. Professor of Medical Genomics Professor in the Bioinformatics Division of the Department of Mathematics and Computer Science of the Freie Universität Berlin Institut für Medizinische Genetik und Humangenetik Charité - Universitätsmedizin Berlin Augustenburger Platz 1 13353 Berlin Germany +4930 450566006 Mobile: 0160 93769872 peter.robinson@charite.de http://compbio.charite.de http://www.human-phenotype-ontology.org Introduction to Bio-Ontologies: http://www.crcpress.com/product/isbn/9781439836651 I have learned from my mistakes, and I am sure I can repeat them exactly ORCID ID:http://orcid.org/0000-0002-0736-9199 Scopus Author ID 7403719646 Appointment request: http://doodle.com/pnrobinson

Von: Chris Mungall [notifications@github.com] Gesendet: Dienstag, 28. Juli 2015 17:12 An: monarch-initiative/monarch-disease-ontology Cc: Robinson, Peter Betreff: Re: [monarch-disease-ontology] MESH:C538119 Hirschsprung disease ganglioneuroblastoma (#16)

Can you elaborate?

would you agree this is a disease http://www.omim.org/entry/613013

but the synonyms with neuroblastoma are invalid?

— Reply to this email directly or view it on GitHubhttps://github.com/monarch-initiative/monarch-disease-ontology/issues/16#issuecomment-125644367.