pnrobinson
commented
9 years ago Dear everybody, note that Orphanet terms such as Orphanet_98794 Angelman syndrome due to maternal 15q11q13 deletion are not really consistent with the remaining Orphanet "philosophy" of being a clinical disease ontology rather than a molecular one (the latter being much more OMIM's role). I do not think it makes much sense for us to include them because actually to be consistent you would need to have similar terms in a lot of other places. In fact, this is one of the exceptional places where Orphanet has more molecular detail than OMIM. The DO term and the OMIM term are exact synonyms, and the Orphanet term is a subclass thereof. -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: Melissa Haendel [notifications@github.com] Gesendet: Freitag, 13. März 2015 02:06 An: monarch-initiative/human-disease-ontology Betreff: [human-disease-ontology] OMIM labels (#9)
OMIM URIs are currently mostly leaf nodes (or merged as equiv classes if name is same as parent and there is only one child). However, there will occasionally be terms in DC or DO with the same label that don't meet requirements for the merge. Since we don't want to make equivalencies for these OMIM terms (or Decipher for that matter), these terms should be appended with (OMIM) in the label to distinguish them from their parents. For example, you could have:
DOID_1932 Angelman's syndrome --OMIM_105830 Angelman's syndrome --Orphanet_98794 Angelman syndrome due to maternal 15q11q13 deletion
Here for example, we might like to have OMIM appended like this: DOID_1932 Angelman's syndrome --OMIM_105830 Angelman's syndrome (OMIM) --Orphanet_98794 Angelman syndrome due to maternal 15q11q13 deletion
— Reply to this email directly or view it on GitHubhttps://github.com/monarch-initiative/human-disease-ontology/issues/9.
cmungall
mellybelly
OMIM URIs are currently mostly leaf nodes (or merged as equiv classes if name is same as parent and there is only one child). However, there will occasionally be terms in DC or DO with the same label that don't meet requirements for the merge. Since we don't want to make equivalencies for these OMIM terms (or Decipher for that matter), these terms should be appended with (OMIM) in the label to distinguish them from their parents. For example, you could have:
DOID_1932 Angelman's syndrome --OMIM_105830 Angelman's syndrome --Orphanet_98794 Angelman syndrome due to maternal 15q11q13 deletion
Here for example, we might like to have OMIM appended like this: DOID_1932 Angelman's syndrome --OMIM_105830 Angelman's syndrome (OMIM) --Orphanet_98794 Angelman syndrome due to maternal 15q11q13 deletion