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
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