cmungall
commented
9 years ago From @pnrobinson on March 7, 2015 5:39
Hi everybody,
please note that OMIM's phenotype series while extremely useful do not attempt to be a full ontology. Orphanet's ORDO is an ontology of rare diseases that does cover this, and I would very much support us supporting and using ORDO, for the simple reason that we will be able to influence its development and because it is even now an extremely useful resource (it is of course still a WIP -- work in progress). I am a coauthor on a submitted manuscript on ORDO, and I am a coapplicant on an eRARE application with Ana Rath, who is leading ORDO development, and I have a very good feeling that ORDO will develop into something that will be really good for us. -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 Universit�t Berlin Institut f�r Medizinische Genetik und Humangenetik Charit� - Universit�tsmedizin 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: Nicole Washington [notifications@github.com] Gesendet: Freitag, 6. M�rz 2015 18:50 An: monarch-initiative/human-disease-ontology Betreff: [human-disease-ontology] fix grouping classes (#6)
i've been looking through our the ontology, i've found some issues.
many of the classes in the merged.obo are missing seemingly pedantic grouping classes.
for example,
id: OMIM:614480 name: Hypertriglyceridemia, Transient Infantile is_a: DOID:630 ! genetic disease
id: OMIM:145750 name: familial hypertriglyceridemia def: "A lipid metabolism disorder characterized by elevated triglyceride levels as a result of excess hepatic production of VLDL or heterozygous LPL deficiency." [url:http://en.wikipedia.org/wiki/Familial_hypertriglyceridemia] comment: OMIM mapping confirmed by DO. [SN]. synonym: "Pure hyperglyceridemia" EXACT [] xref: DOID:0050527 is_a: DOID:3146 ! lipid metabolism disorder is_a: DOID:630 ! genetic disease
are not related to one another except for both being genetic diseases. why isn't the former also a lipid metabolism disorder? or even better, why aren't they both classified as "hypertriglyceridemia"? that seems like a natural grouping class.
another
id: OMIM:606170 name: Genitopatellar Syndrome is_a: DOID:630 ! genetic disease
in the text there is the description, "The SBBYS variant of Ohdo syndrome (603736) is an allelic disorder with overlapping features."
but it is also not classified: [Term] id: OMIM:603736 name: Ohdo Syndrome, Sbbys Variant is_a: DOID:630 ! genetic disease
so i'd think they would be grouped together in some way.
when i just browse the ontology in protege, if you look under "genetic disease" there are many things that are siblings, but have nearly identical names, suggesting they should be subclasses of a more general disease, but are instead just a big fat flat list. some examples pulled only from A:
Acyl-coa Dehydrogenase * Deficiency Of Adams-oliver Syndrome Adrenal Hyperplasia, Congenital Arthrogryposis * (only 3 of the 6 are classified as subtypes) Atrial Fibrillation (only 4 of 8 are classified as subtypes) Atrial Septal Defect (only 4 of 8 are classified as subtypes) ... in fact, 2257 of the omim diseases in the merged file can't be classified into any upper-level grouping class at all except for a plain "genetic disease", which isn't too helpful.
migrated from monarch-initiative/disease-miner#8https://github.com/monarch-initiative/disease-miner/issues/8
� Reply to this email directly or view it on GitHubhttps://github.com/monarch-initiative/human-disease-ontology/issues/6.
nicolevasilevsky
From @nlwashington on March 6, 2015 17:50
i've been looking through our the ontology, i've found some issues.
many of the classes in the merged.obo are missing seemingly pedantic grouping classes.
for example,
id: OMIM:614480 name: Hypertriglyceridemia, Transient Infantile is_a: DOID:630 ! genetic disease
id: OMIM:145750 name: familial hypertriglyceridemia def: "A lipid metabolism disorder characterized by elevated triglyceride levels as a result of excess hepatic production of VLDL or heterozygous LPL deficiency." [url:http://en.wikipedia.org/wiki/Familial_hypertriglyceridemia] comment: OMIM mapping confirmed by DO. [SN]. synonym: "Pure hyperglyceridemia" EXACT [] xref: DOID:0050527 is_a: DOID:3146 ! lipid metabolism disorder is_a: DOID:630 ! genetic disease
are not related to one another except for both being genetic diseases. why isn't the former also a lipid metabolism disorder? or even better, why aren't they both classified as "hypertriglyceridemia"? that seems like a natural grouping class.
another
id: OMIM:606170 name: Genitopatellar Syndrome is_a: DOID:630 ! genetic disease
in the text there is the description, "The SBBYS variant of Ohdo syndrome (603736) is an allelic disorder with overlapping features."
but it is also not classified: [Term] id: OMIM:603736 name: Ohdo Syndrome, Sbbys Variant is_a: DOID:630 ! genetic disease
so i'd think they would be grouped together in some way.
when i just browse the ontology in protege, if you look under "genetic disease" there are many things that are siblings, but have nearly identical names, suggesting they should be subclasses of a more general disease, but are instead just a big fat flat list. some examples pulled only from A:
Acyl-coa Dehydrogenase * Deficiency Of Adams-oliver Syndrome Adrenal Hyperplasia, Congenital Arthrogryposis * (only 3 of the 6 are classified as subtypes) Atrial Fibrillation (only 4 of 8 are classified as subtypes) Atrial Septal Defect (only 4 of 8 are classified as subtypes) ... in fact, 2257 of the omim diseases in the merged file can't be classified into any upper-level grouping class at all except for a plain "genetic disease", which isn't too helpful.
migrated from https://github.com/monarch-initiative/disease-miner/issues/8
Copied from original issue: monarch-initiative/human-disease-ontology#6