They are both Same-AS I kept that in the comment to keep the separate from my side... -------------------- 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: Friday, May 11, 2012 5:41 AM >Subject: Re: [OPENMRS-DEV] Migrating concept mappings to 1.9 > > >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 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 >>> >>> >> >>________________________________ >> 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 lists...@listserv.iupui.edu with "SIGNOFF openmrs-devel-l" in the body (not the subject) of your e-mail. 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