Andy, do we need to have two separate map types for "SAME-AS" and "SAME-AS from RxNORM" or the latter can be represented as "SAME-AS"?
-Rafał On 10 May 2012 19:21, Andrew Kanter <andy_kan...@yahoo.com> wrote: > 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: andrew.kan...@dbmi.columbia.edu > Mobile: +1 (646) 469-2421 > Office: +1 (212) 305-4842 > Skype: akanter-ippnw > Yahoo: andy_kanter > > ------------------------------ > *From:* Darius Jazayeri <djazayeri+...@gmail.com> > *To:* openmrs-deve...@listserv.iupui.edu > *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 <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 > > > ------------------------------ > 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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