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 <andy_kan...@yahoo.com>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: andrew.kan...@dbmi.columbia.edu > Mobile: +1 (646) 469-2421 > Office: +1 (212) 305-4842 > Skype: akanter-ippnw > Yahoo: andy_kanter > > ------------------------------ > *From:* Rafal Korytkowski <ra...@openmrs.org> > *To:* openmrs-deve...@listserv.iupui.edu > *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 <andy_kan...@yahoo.com> 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: andrew.kan...@dbmi.columbia.edu > Mobile: +1 (646) 469-2421 > Office: +1 (212) 305-4842 > Skype: akanter-ippnw > Yahoo: andy_kanter > > ------------------------------ > *From:* Rafal Korytkowski <ra...@openmrs.org> > *To:* openmrs-deve...@listserv.iupui.edu > *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<lists...@listserv.iupui.edu?body=SIGNOFF%20openmrs-devel-l>from > OpenMRS Developers' mailing list > > > ------------------------------ > Click here to > unsubscribe<lists...@listserv.iupui.edu?body=SIGNOFF%20openmrs-devel-l>from > OpenMRS Developers' mailing list > > > ------------------------------ > Click here to > unsubscribe<lists...@listserv.iupui.edu?body=SIGNOFF%20openmrs-devel-l>from > OpenMRS Developers' mailing list > > > ------------------------------ > Click here to > unsubscribe<lists...@listserv.iupui.edu?body=SIGNOFF%20openmrs-devel-l>from > OpenMRS Developers' mailing list > _________________________________________ To unsubscribe from OpenMRS Developers' mailing list, send an e-mail to lists...@listserv.iupui.edu with "SIGNOFF openmrs-devel-l" in the body (not the subject) of your e-mail. 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