FHIR Chat · R4 MolecularSequence composite search params

Stream: genomics

Topic: R4 MolecularSequence composite search params

Michael Calderero (Nov 15 2018 at 08:31):

Hi,

I'm looking at MolecularSequence composite search parameters i.e. referenceseqid-coordinate and chromosome-coordinate. Taking an example for chromosome-coordinate (excerpt only):

        <code value="chromosome-coordinate"/>
        <base value="MolecularSequence"/>
        <type value="composite"/>
        <expression value="MolecularSequence"/>
        <component>
          <definition value="http://hl7.org/fhir/SearchParameter/MolecularSequence-chromosome"/>
          <expression value="referenceSeq.chromosome"/>
        </component>
        <component>
          <definition value="http://hl7.org/fhir/SearchParameter/MolecularSequence-start"/>
          <expression value="variant.start"/>
        </component>
        <component>
          <definition value="http://hl7.org/fhir/SearchParameter/MolecularSequence-end"/>
          <expression value="variant.end"/>
        </component>

Since MolecularSequence.variant's cardinality allows it to appear more than once in the resource, I would think the aforementioned search parameter will allow the following search [baseurl]/MolecularSequence?chromosome-coordinate=X$0$3 to match the resource below:

MolecularSequence:
  referenceSeq:
    chromosome:
      system: whatever-system
      code: X
  variant:
    start: 0
    end: 1
  variant:
    start: 2
    end: 3

i.e. start:0 is in the first variant property while end:3 is in the second variant property.

Is that the expected behavior or is my understanding of composite search parameters incorrect?

Michael Calderero (Nov 15 2018 at 08:40):

My assumption for this search parameter is that it would not match the resource above but would match this one instead (i.e. start:0 and end:3 are within the same variant property):

MolecularSequence:
  referenceSeq:
    chromosome:
      system: whatever-system
      code: X
  variant:
    start: 0
    end: 3
  variant:
    start: 5
    end: 6

Kevin Power (Nov 15 2018 at 15:15):

I agree with your assessment. You can do range searches on start/end if needed.

Michael Calderero (Nov 16 2018 at 02:37):

Sorry I'm still confused. What's the expected behavior of this search parameter? Is it expected to match the first example or the second one?

If the second example, then I would think the search parameter definition needs to be changed to:

        <code value="chromosome-coordinate"/>
        <base value="MolecularSequence"/>
        <type value="composite"/>
        <expression value="MolecularSequence.variant"/>
        <component>
          <definition value="http://hl7.org/fhir/SearchParameter/MolecularSequence-chromosome"/>
          <expression value="%resource.referenceSeq.chromosome"/>
        </component>
        <component>
          <definition value="http://hl7.org/fhir/SearchParameter/MolecularSequence-start"/>
          <expression value="start"/>
        </component>
        <component>
          <definition value="http://hl7.org/fhir/SearchParameter/MolecularSequence-end"/>
          <expression value="end"/>
        </component>

i.e. which is what this definition was in STU3.

Kevin Power (Nov 16 2018 at 03:05):

When I said I agree with your assessment, the intention is to match when a variant instance matches both the start and end criteria. I do remember that when I was adding the second composite search param, I was getting some build issues. I need to do some research into how to structure this search param.

Kevin Power (Nov 16 2018 at 22:34):

I have created a pull request with a fix, and have asked if it is possible to get the fix merged in. While looking at the fix, I have made some additional changes as well.
See the pull request 286
I created some new search params, and tried to make it clear how to search for sequences for given "windows", and also for sequences with variants at given locations. I welcome comments/questions/concerns.
@Patrick Werner @James Jones @ Bob Milius @Gil Alterovitz @Michael Calderero

Jamie Jones (Nov 20 2018 at 14:57):

@Kevin Power The changes look right and good to me from how I understand the composite searches :thumbs_up:

Kevin Power (Nov 20 2018 at 14:58):

Many thanks @James Jones

Patrick Werner (Nov 20 2018 at 15:01):

looks good to me as well. I'm currently trying to get the Resources into hapi to be able to test it

Kevin Power (Nov 20 2018 at 15:18):

Thanks @Patrick Werner - Keep us updated on your progress with HAPI.

Kevin Power (Nov 26 2018 at 12:38):

FYI - Grahame merged the MolecularSequence search param changes. If anyone reviews the changes and has questions please respond here. @Michael Calderero

Michael Calderero (Nov 27 2018 at 06:42):

I checked the updated definitions from build.fhir.org and I see the following:

1. http://hl7.org/fhir/SearchParameter/MolecularSequence-chromosome-window-coordinate composite

        <expression value="MolecularSequence.referenceSeq"/>
        <xpathUsage value="normal"/>
        <multipleOr value="false"/>
        <multipleAnd value="true"/>
        <modifier value="missing"/>
        <component>
          <definition value="http://hl7.org/fhir/SearchParameter/MolecularSequence-chromosome"/>
          <expression value="chromosome"/>
        </component>
        <component>
          <definition value="http://hl7.org/fhir/SearchParameter/MolecularSequence-window-start"/>
          <expression value="start"/>
        </component>
        <component>
          <definition value="http://hl7.org/fhir/SearchParameter/MolecularSequence-window-end"/>
          <expression value="end"/>
        </component>

but MolecularSequence.referenceSeq doesn't have start and end properties. Perhaps the windowStart and windowEnd should have been used instead?

2. http://hl7.org/fhir/SearchParameter/MolecularSequence-referenceseqid-window-coordinate

        <expression value="MolecularSequence.referenceSeq"/>
        <xpathUsage value="normal"/>
        <multipleOr value="false"/>
        <multipleAnd value="true"/>
        <modifier value="missing"/>
        <component>
          <definition value="http://hl7.org/fhir/SearchParameter/MolecularSequence-referenceseqid"/>
          <expression value="referenceSeqId"/>
        </component>
        <component>
          <definition value="http://hl7.org/fhir/SearchParameter/MolecularSequence-window-start"/>
          <expression value="start"/>
        </component>
        <component>
          <definition value="http://hl7.org/fhir/SearchParameter/MolecularSequence-window-end"/>
          <expression value="end"/>
        </component>

Same as number 1 (i.e. I think windowStart and windowEnd should have been used instead).

@Kevin Power