time to go back over some old posts;-) Koray Atalag wrote: (in May...)
>Hi, > >Is there a specific way to represent genomic data of a patient (Either >Nucleic Acid sequences or protein sequences) in the Reference Models or is >the general purpose text data type is thought to be the solution? I think it >could be wise to create a new class with its own attributes, methods and >constraints right into the RM because with this speed of biologic evolution >I don't think the genetic code and concepts are going to change for a couple >million years! > this is true (assuming GM produce does not do it for us...), but the real issue is: what data structures are the users of this data using? THere will already be software, information models and so on of gene sequences, both in research and clinical medicine. With a structure like the DNA it is to think of many possible structures, depending on what the priorities of the users are, which might be - searching for particular sub-sequences, counting occurrences of some structure, determining over all statistics etc etc. THis is what we need to know. Also - what level of detail? It is easy to do ATCG sequences...but what if we need molecular level representation (e.g. if there are base pairs which are disrupted in some way)? And then we get onto proteins...I have no expertise in this area, but I guess that one way to diagnose certain genetic problems is to look for and characterise broken/bad proteins.... here we may have to represent the macro surface structure, the coiled structure, or even the amino acid structure. So.... I think this problem is a bit more complex than it looks. The answer for today is that openEHR would store this kind of data in a DV_ENCAPSULATED (either multimedia or parsable). - thomas - If you have any questions about using this list, please send a message to d.lloyd at openehr.org
