Rafal, I am confused... the mapping below is correct. For the plan, I would do 1, not 2 (just ignore the comment) I would make these probably SAME AS for "from excel and from UMLS". For 3, I presume we will keep one of the duplicate maps...and if I had to choose a map type (if there is no map id:) then I would pick NARROWER-THAN, but perhaps I should review the list of dupes first. -------------------- 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: 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 = 1 >| 2 | NARROWER-THAN = 2 >| 3 | BROADER-THAN = 3 >| 4 | Associated finding = 4 >| 5 | Associated morphology = 5 >| 6 | Associated procedure = 6 >| 7 | Associated with = 7 >| 8 | Causative agent >| 9 | Finding site >| 10 | Has specimen = 10 >| 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 | (Has specimen) >>>| Map Type: 17 | 5 | (Direct device) >>>| Map Type: 19 | 3 | (Direct substance) >>>| Map Type: 2 | 1880 | (NARROWER-THAN) >>>| Map Type: 24 | 18 | (Finding method) >>>| Map Type: 3 | 30841 | (BROADER-THAN) >>>| Map Type: 4 | 126 | (Associated finding) >>>| Map Type: 5 | 81 | (Associated morphology) >>>| Map Type: 6 | 19 | (Associated procedure) >>>| 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 > > _________________________________________ 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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