New version openmrs_concepts_1.6.5_20120510.sql uploaded to CIEL dropbox. Rafal, please view this carefully as I generated things quickly... -------------------- Andrew S. Kanter, MD MPH
Asst. Prof. of Clinical Biomedical Informatics and Clinical Epidemiology Columbia University Email: [email protected] Mobile: +1 (646) 469-2421 Office: +1 (212) 305-4842 Skype: akanter-ippnw Yahoo: andy_kanter >________________________________ > From: Darius Jazayeri <[email protected]> >To: [email protected] >Sent: Thursday, May 10, 2012 11:47 AM >Subject: Re: [OPENMRS-DEV] Migrating concept mappings to 1.9 > > >Hi Rafal et al, > > >Andy and I just discussed this on the phone, and as he says below, the "Map >Type: #" comments in the MVP dictionary are totally unrelated to the actual >map type ids we introduce in 1.9. > > >Andy is going to (today if he has time) change those in his database so they >say something like "Map Type: SAME-AS" intstead, and re-export the dictionary >for us. > > >Is it straightforward to change the upgrade scripts so that they look for "Map >Type: NAME-OF-MAP-TYPE" instead? > > >-Darius > > >On Thu, May 10, 2012 at 7:30 AM, Andrew Kanter <[email protected]> wrote: > >Folks, >>I don't think the original comments had anything to do with the list which >>appears in OpenMRS now for mapping sources... so the original map presented >>was definitely wrong. Please see the bottom of this email for corrected maps >>from the existing comments to the new map types. >> >> >> >> >>Andy >> >>-------------------- >>Andrew S. Kanter, MD MPH >> >> >>Asst. Prof. of Clinical Biomedical Informatics and Clinical Epidemiology >> >>Columbia University >>Email: [email protected] >>Mobile: +1 (646) 469-2421 >>Office: +1 (212) 305-4842 >>Skype: akanter-ippnw >>Yahoo: andy_kanter >> >> >> >>>________________________________ >>> From: Rafal Korytkowski <[email protected]> >>>To: [email protected] >>> >>>Sent: Monday, May 7, 2012 11:04 AM >>>Subject: Re: [OPENMRS-DEV] Migrating concept mappings to 1.9 >>> >>> >>>Thanks Andy! When do you think you'll have time to look into that comments >>>and see if they can be matched with proper mapping types from 1.9? Below is >>>a full list of predefined mapping types in 1.9: >>> >>> >>>+---------------------+------------------------------- >>>| concept_map_type_id | name >>>+---------------------+------------------------------- >>>| 1 | SAME-AS = >>>| 2 | NARROWER-THAN >>>| 3 | BROADER-THAN >>>| 4 | Associated finding >>>| 5 | Associated morphology >>>| 6 | Associated procedure >>>| 7 | Associated with >>>| 8 | Causative agent >>>| 9 | Finding site >>>| 10 | Has specimen >>>| 11 | Laterality >>>| 12 | Severity >>>| 13 | Access >>>| 14 | After >>>| 15 | Clinical course >>>| 16 | Component >>>| 17 | Direct device >>>| 18 | Direct morphology >>>| 19 | Direct substance >>>| 20 | Due to >>>| 21 | Episodicity >>>| 22 | Finding context >>>| 23 | Finding informer >>>| 24 | Finding method >>>| 25 | Has active ingredient >>>| 26 | Has definitional manifestation >>>| 27 | Has dose form >>>| 28 | Has focus >>>| 29 | Has intent >>>| 30 | Has interpretation >>>| 31 | Indirect device >>>| 32 | Indirect morphology >>>| 33 | Interprets >>>| 34 | Measurement method >>>| 35 | Method >>>| 36 | Occurrence >>>| 37 | Part of >>>| 38 | Pathological process >>>| 39 | Priority >>>| 40 | Procedure context >>>| 41 | Procedure device >>>| 42 | Procedure morphology >>>| 43 | Procedure site >>>| 44 | Procedure site - Direct >>>| 45 | Procedure site - Indirect >>>| 46 | Property >>>| 47 | Recipient category >>>| 48 | Revision status >>>| 49 | Route of administration >>>| 50 | Scale type >>>| 51 | Specimen procedure >>>| 52 | Specimen source identity >>>| 53 | Specimen source morphology >>>| 54 | Specimen source topography >>>| 55 | Specimen substance >>>| 56 | Subject of information >>>| 57 | Subject relationship context >>>| 58 | Surgical approach >>>| 59 | Temporal context >>>| 60 | Time aspect >>>| 61 | Using access device >>>| 62 | Using device >>>| 63 | Using energy >>>| 64 | Using substance >>>| 65 | IS A >>>| 66 | MAY BE A >>>| 67 | MOVED FROM >>>| 68 | MOVED TO >>>| 69 | REPLACED BY >>>| 70 | WAS A >>>+---------------------+------------------------------- >>> >>>-Rafał >>> >>> >>> >>>On 4 May 2012 23:35, Andrew Kanter <[email protected]> wrote: >>> >>>Yes, we did that from IMO and I included in that in some... however, it is >>>not at all consistent. Where we have it, we should use it. There shouldn't >>>be dupes with the same map type. I will look through this... >>>> >>>> >>>>Thanks! >>>>Andy >>>> >>>> >>>>P.S. Great news about MDS... now just need to fix the concepts :) >>>> >>>>-------------------- >>>>Andrew S. Kanter, MD MPH >>>> >>>>- Director of Health Information Systems/Medical Informatics >>>>Millennium Villages Project, Earth Institute, Columbia University >>>>- Asst. Prof. of Clinical Biomedical Informatics and Clinical Epidemiology >>>>Columbia University >>>> >>>>Email: [email protected] >>>>Mobile: +1 (646) 469-2421 >>>>Office: +1 (212) 305-4842 >>>>Skype: akanter-ippnw >>>>Yahoo: andy_kanter >>>> >>>> >>>> >>>>>________________________________ >>>>> From: Rafal Korytkowski <[email protected]> >>>>>To: [email protected] >>>>>Sent: Friday, May 4, 2012 11:08 AM >>>>>Subject: [OPENMRS-DEV] Migrating concept mappings to 1.9 >>>>> >>>>> >>>>>Hi Andy, >>>>> >>>>>We have noticed that MVP uses the comment field in the concept_map table. >>>>>We are considering using that to determine the right map type in 1.9. >>>>> >>>>>I ran the following query select comment, count(*) from concept_map group >>>>>by comment; The results are below. I have also added corresponding map >>>>>types from 1.9, but I am not sure if they match right now. We could >>>>>correct them if needed. >>>>> >>>>>+----------------------+----------+ >>>>>| comment | count(*) | >>>>>+----------------------+----------+ >>>>>| NULL | 15516 | >>>>>| From Excel | 2381 | >>>>>| From UMLS RxNORM Map | 3010 | >>>>> | Map Type: 1 | 46897 | => SAME AS >>>>>| Map Type: 10 | 1 | Mistake... should be Map Type: 3 >>>>>| Map Type: 17 | 5 | => Associated with >>>>>| Map Type: 19 | 3 | => Associated with >>>>>| Map Type: 2 | 1880 |=> BROADER-THAN >>>>>| Map Type: 24 | 18 | => Associated procedure >>>>>| Map Type: 3 | 30841 | => NARROWER-THAN >>>>>| Map Type: 4 | 126 | => Associated finding >>>>>| Map Type: 5 | 81 | => Associated Morphology >>>>>| Map Type: 6 | 19 | => Finding Site >>>>>| Map Type: 7 | 2 | => Associated with >>>>> >>>>>+----------------------+----------+ >>>>>14 rows in set (2.12 sec) >>>>> >>>>>Here's the proposed migration algorithm: >>>>> >>>>>(1) if the comment matches "Map Type: (\d+)" then use that to determine >>>>>the map type, and drop it >>>>> >>>>>(2) otherwise move the comment to concept_reference_term.description (even >>>>>though it doesn't really belong there) >>>>> >>>>>(3) delete duplicate concept_reference_terms (having same source and >>>>>source_code), though this means we may lose some concept_map.comment data >>>>> >>>>> >>>>>The reason for these changes is: TRUNK-3296: Found multiple reference terms >>>>>https://tickets.openmrs.org/browse/TRUNK-3296 >>>>>-Rafał >>>>> >>>>>________________________________ >>>>> Click here to unsubscribe from OpenMRS Developers' mailing list >>>>> >>>>> >>>> >>>>________________________________ >>>> Click here to unsubscribe from OpenMRS Developers' mailing list >>> >>> >>>________________________________ >>> Click here to unsubscribe from OpenMRS Developers' mailing list >>> >>> >> >>________________________________ >> Click here to unsubscribe from OpenMRS Developers' mailing list > >________________________________ > Click here to unsubscribe from OpenMRS Developers' mailing list > > _________________________________________ To unsubscribe from OpenMRS Developers' mailing list, send an e-mail to [email protected] with "SIGNOFF openmrs-devel-l" in the body (not the subject) of your e-mail. 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