idr0043-experimentA-bulkmap-config.yml

---
name: idr0043-uhlen-humanproteinatlas/experimentA
version: 1

defaults:
  # Should the column be processed when creating bulk-annotations (yes/no)
  include: no
  # Columns type of the bulk-annotations column
  type: string

  # If non-empty a string used to separate multiple fields in a column
  # White space will be stripped
  split: ;
  # Should this column be included in the clients (yes/no)
  includeclient: yes
  # Should this column be visible in the clients, if no the column should be
  # hidden in the client but will still be indexed by the searcher (yes/no)
  visible: yes
  # Should empty values be omitted from the client display
  omitempty: yes

columns:

  - name: Characteristics [Organism Part]
    clientname: Organism Part
    include: yes
  - name: Characteristics [Sex]
    clientname: Sex
    include: yes
  - name: Characteristics [Age]
    clientname: Age
    include: yes
  - name: Characteristics [Individual]
    clientname: Individual
    include: yes
  - name: Term Source 2 Accession
    clientname: SNOMED Identifier
    include: yes
  - name: Analysis Gene Annotation Build
    clientname: Ensembl version
    include: yes
  - name: Human Protein Atlas version
    clientname: Human Protein Atlas version
    include: yes

  ######################################################################
  # mapr groups
  ######################################################################

  - group:
      namespace: openmicroscopy.org/mapr/organism
      columns:
        - name: Characteristics [Organism]
          clientname: Organism
          include: yes

  - group:
      namespace: openmicroscopy.org/mapr/gene
      columns:
        - name: Comment [Gene Identifier] 1
          clientname: Gene Identifier
          include: yes
        - name: Comment [Gene Identifier] 1
          clientname: Gene Identifier URL
          clientvalue: http://www.ensembl.org/id/{{ value|urlencode }}
          include: yes
        - name: Comment [Gene Symbol] 1
          clientname: Gene Symbol
          include: yes
  - group:
      namespace: openmicroscopy.org/mapr/gene
      columns:
        - name: Comment [Gene Identifier] 2
          clientname: Gene Identifier
          include: yes
        - name: Comment [Gene Identifier] 2
          clientname: Gene Identifier URL
          clientvalue: http://www.ensembl.org/id/{{ value|urlencode }}
          include: yes
        - name: Comment [Gene Symbol] 2
          clientname: Gene Symbol
          include: yes

  - group:
      namespace: openmicroscopy.org/mapr/gene
      columns:
        - name: Comment [Gene Identifier] 3
          clientname: Gene Identifier
          include: yes
        - name: Comment [Gene Identifier] 3
          clientname: Gene Identifier URL
          clientvalue: http://www.ensembl.org/id/{{ value|urlencode }}
          include: yes
        - name: Comment [Gene Symbol] 3
          clientname: Gene Symbol
          include: yes

  - group:
      namespace: openmicroscopy.org/mapr/gene
      columns:
        - name: Comment [Gene Identifier] 4
          clientname: Gene Identifier
          include: yes
        - name: Comment [Gene Identifier] 4
          clientname: Gene Identifier URL
          clientvalue: http://www.ensembl.org/id/{{ value|urlencode }}
          include: yes
        - name: Comment [Gene Symbol] 4
          clientname: Gene Symbol
          include: yes

  - group:
      namespace: openmicroscopy.org/mapr/gene
      columns:
        - name: Comment [Gene Identifier] 5
          clientname: Gene Identifier
          include: yes
        - name: Comment [Gene Identifier] 5
          clientname: Gene Identifier URL
          clientvalue: http://www.ensembl.org/id/{{ value|urlencode }}
          include: yes
        - name: Comment [Gene Symbol] 5
          clientname: Gene Symbol
          include: yes

  - group:
      namespace: openmicroscopy.org/mapr/gene
      columns:
        - name: Comment [Gene Identifier] 6
          clientname: Gene Identifier
          include: yes
        - name: Comment [Gene Identifier] 6
          clientname: Gene Identifier URL
          clientvalue: http://www.ensembl.org/id/{{ value|urlencode }}
          include: yes
        - name: Comment [Gene Symbol] 6
          clientname: Gene Symbol
          include: yes

  - group:
      namespace: openmicroscopy.org/mapr/gene
      columns:
        - name: Comment [Gene Identifier] 7
          clientname: Gene Identifier
          include: yes
        - name: Comment [Gene Identifier] 7
          clientname: Gene Identifier URL
          clientvalue: http://www.ensembl.org/id/{{ value|urlencode }}
          include: yes
        - name: Comment [Gene Symbol] 7
          clientname: Gene Symbol
          include: yes

  - group:
      namespace: openmicroscopy.org/mapr/gene
      columns:
        - name: Comment [Gene Identifier] 8
          clientname: Gene Identifier
          include: yes
        - name: Comment [Gene Identifier] 8
          clientname: Gene Identifier URL
          clientvalue: http://www.ensembl.org/id/{{ value|urlencode }}
          include: yes
        - name: Comment [Gene Symbol] 8
          clientname: Gene Symbol
          include: yes

  - group:
      namespace: openmicroscopy.org/mapr/antibody
      columns:
        - name: Antibody identifier
          clientname: Antibody Identifier
          include: yes
          omitempty: no
        - name: Antibody identifier
          clientname: Antibody Identifier URL
          clientvalue: http://v18.proteinatlas.org/search/{{ value|urlencode }}
          include: yes

  - group:
      namespace: openmicroscopy.org/mapr/antibody/supplementary
      columns:
        - name: Antibody dilution
          clientname: Dilution Factor
          include: yes
        - name: Retrieval method
          clientname: Retrieval Method
          include: yes

advanced:
  ignore_missing_primary_key: yes
  primary_group_keys:
    - namespace: openmicroscopy.org/mapr/organism
      keys:
        - Organism
    - namespace: openmicroscopy.org/mapr/antibody
      keys:
        - Antibody Identifier
    - namespace: openmicroscopy.org/mapr/gene
      keys:
        - Gene Identifier
        - Gene Symbol