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Add Udp case pages - ready to merge #1346
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kshefchek
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monarch-initiative:master
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kshefchek:udp-case-pages
Nov 28, 2016
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c12b096
first pass at case pages
kshefchek 2d60d82
add subject column to tables
kshefchek 236b559
fix UDP formatting
kshefchek ae35b72
remove case links
kshefchek 0ff51e9
replace person with case
kshefchek f37a3fc
manual copy of webapp.js
kshefchek 3580a3d
Merge remote-tracking branch 'origin/master' into udp-case-pages
kshefchek e7a3a58
break out phenogrid configuration into conf file
kshefchek 3779ff8
fixed analyze page bug introduced by last commit
kshefchek 75631f8
remove any hardcoding of configuration, raise error instead
kshefchek 1e04aa3
Merge remote-tracking branch 'upstream/master' into udp-case-pages
kshefchek d79ec0c
have table match filters on analyze page, fixes half of #1391
kshefchek 459fafc
fix broken id resolution test
kshefchek 7059fad
fix bugs in phenopackets, id resolution, phenogrid conf
kshefchek fa28273
Merge remote-tracking branch 'upstream/master' into udp-case-pages
kshefchek bf976b0
add support for patient phenopackets
kshefchek 8984b08
add disclaimer text, some clean up
kshefchek 1a77396
add download buttons
kshefchek 2b10378
add icons to download buttons
kshefchek f35546f
forgot to add phenopacket img and slash
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Original file line number | Diff line number | Diff line change |
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id: individual_gene | ||
schema_generating: true | ||
document_category: generic_association | ||
weight: 20 | ||
|
||
## Results table, horizontal | ||
result_weights: subject^6.0 object^5.0 | ||
|
||
## Ordering of facets, vertical | ||
filter_weights: subject_taxon_closure_label^3.5 object_taxon_closure_label^3.0 | ||
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## SOLR FIELD DEFINITIONS | ||
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fields: | ||
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## SUBJECT | ||
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- id: subject | ||
description: "The CURIE for oban:association_has_subject. May be disease, variant, gene, person, ...." | ||
display_name: Case | ||
type: string | ||
property: [] | ||
|
||
- id: subject_label | ||
description: "Label for association_subject. This will always be rdfs:label. Conventions may vary as to what goes in the label. For genes will be symbol, but we may choose to uniquify by prefixing with species" | ||
display_name: Case | ||
type: string | ||
property: [] | ||
searchable: true | ||
|
||
- id: subject_closure | ||
description: "Reflexive closure of association_has_subject. A list of CURIEs. If an individual, first traverse rdf:tpye. The default closure is subclass, but other may optionally be added depending on what type of association this is and what the class is. E.g. for expression associations, the object is an anatomy class, and the closure will include part_of" | ||
display_name: Case | ||
type: string | ||
cardinality: multi | ||
property: [] | ||
|
||
- id: subject_closure_label | ||
description: "Labels for subject_closure." | ||
display_name: Case | ||
type: string | ||
cardinality: multi | ||
property: [] | ||
searchable: true | ||
|
||
- id: subject_taxon | ||
description: "Taxonomic class of the subject. This is typically a CURIE of the form NCBITaxon:nnnn." | ||
display_name: Species | ||
type: string | ||
property: [] | ||
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||
- id: subject_taxon_label | ||
description: "Label of taxon." | ||
display_name: Species | ||
type: string | ||
property: [] | ||
searchable: true | ||
|
||
- id: subject_taxon_closure | ||
description: "Reflexive closure of taxon. ALWAYS up SubClassOf." | ||
display_name: Species | ||
type: string | ||
cardinality: multi | ||
property: [] | ||
|
||
- id: subject_taxon_closure_label | ||
description: "Labels for taxon_closure." | ||
display_name: Species | ||
type: string | ||
cardinality: multi | ||
property: [] | ||
searchable: true | ||
|
||
- id: object | ||
description: "The CURIE for oban:association_has_object. This is often, but not always an ontology class. E.g. for a gene-gene interaction it is an (arbitrary) member of the pair." | ||
display_name: Gene | ||
type: string | ||
property: [] | ||
|
||
- id: object_label | ||
description: "Label for association_object." | ||
display_name: Gene | ||
type: string | ||
property: [] | ||
searchable: true | ||
|
||
- id: object_closure | ||
description: "Reflexive closure of association_has_object. A list of CURIEs. If an individual, first traverse rdf:tpye. The default closure is subclass, but other may optionally be added depending on what type of association this is and what the class is. E.g. for expression associations, the object is an anatomy class, and the closure will include part_of" | ||
display_name: Gene | ||
type: string | ||
cardinality: multi | ||
property: [] | ||
|
||
- id: object_closure_label | ||
description: "Labels for object_class_closure." | ||
display_name: Gene | ||
type: string | ||
cardinality: multi | ||
property: [] | ||
searchable: true | ||
|
||
- id: object_taxon | ||
description: "Taxonomic class of the object. This is typically a CURIE of the form NCBITaxon:nnnn. This field may be unfilled when used with certain categories" | ||
display_name: Species | ||
type: string | ||
property: [] | ||
|
||
- id: object_taxon_label | ||
description: "Label of taxon." | ||
display_name: Species | ||
type: string | ||
property: [] | ||
searchable: true | ||
|
||
- id: object_taxon_closure | ||
description: "Reflexive closure of taxon. ALWAYS up SubClassOf." | ||
display_name: Species | ||
type: string | ||
cardinality: multi | ||
property: [] | ||
|
||
- id: object_taxon_closure_label | ||
description: "Labels for taxon_closure." | ||
display_name: Species | ||
type: string | ||
cardinality: multi | ||
property: [] | ||
searchable: true | ||
|
||
- id: evidence_object | ||
description: "List of CURIES of all entities that form part of the evidence graph." | ||
display_name: Evidence | ||
type: string | ||
cardinality: multi | ||
property: [] | ||
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||
- id: evidence_object_label | ||
description: "evidence object label" | ||
display_name: Evidence | ||
type: string | ||
cardinality: multi | ||
property: [] | ||
|
||
- id: evidence_object_closure | ||
description: "Closure for evidence object" | ||
display_name: Evidence | ||
type: string | ||
cardinality: multi | ||
property: [] | ||
|
||
- id: evidence_object_closure_label | ||
description: "List of CURIES of all entities that form part of the evidence closure." | ||
display_name: Evidence | ||
type: string | ||
cardinality: multi | ||
property: [] |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,156 @@ | ||
id: individual_phenotype | ||
schema_generating: true | ||
document_category: generic_association | ||
weight: 20 | ||
|
||
## Results table, horizontal | ||
result_weights: subject^6.0 object^5.0 | ||
|
||
## Ordering of facets, vertical | ||
filter_weights: subject_taxon_label^3.5 | ||
|
||
## SOLR FIELD DEFINITIONS | ||
|
||
fields: | ||
|
||
## SUBJECT | ||
|
||
- id: subject | ||
description: "The CURIE for oban:association_has_subject. May be disease, variant, gene, person, ...." | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. Here I would suggest "case" instead of "person" |
||
display_name: Case | ||
type: string | ||
property: [] | ||
|
||
- id: subject_label | ||
description: "Label for association_subject. This will always be rdfs:label. Conventions may vary as to what goes in the label. For genes will be symbol, but we may choose to uniquify by prefixing with species" | ||
display_name: Case | ||
type: string | ||
property: [] | ||
searchable: true | ||
|
||
- id: subject_closure | ||
description: "Reflexive closure of association_has_subject. A list of CURIEs. If an individual, first traverse rdf:tpye. The default closure is subclass, but other may optionally be added depending on what type of association this is and what the class is. E.g. for expression associations, the object is an anatomy class, and the closure will include part_of" | ||
display_name: Case | ||
type: string | ||
cardinality: multi | ||
property: [] | ||
|
||
- id: subject_closure_label | ||
description: "Labels for subject_closure." | ||
display_name: Case | ||
type: string | ||
cardinality: multi | ||
property: [] | ||
searchable: true | ||
|
||
- id: subject_taxon | ||
description: "Taxonomic class of the subject. This is typically a CURIE of the form NCBITaxon:nnnn." | ||
display_name: Species | ||
type: string | ||
property: [] | ||
|
||
- id: subject_taxon_label | ||
description: "Label of taxon." | ||
display_name: Species | ||
type: string | ||
property: [] | ||
searchable: true | ||
|
||
- id: subject_taxon_closure | ||
description: "Reflexive closure of taxon. ALWAYS up SubClassOf." | ||
display_name: Species | ||
type: string | ||
cardinality: multi | ||
property: [] | ||
|
||
- id: subject_taxon_closure_label | ||
description: "Labels for taxon_closure." | ||
display_name: Species | ||
type: string | ||
cardinality: multi | ||
property: [] | ||
searchable: true | ||
|
||
- id: object | ||
description: "The CURIE for oban:association_has_object. This is often, but not always an ontology class. E.g. for a gene-gene interaction it is an (arbitrary) member of the pair." | ||
display_name: Phenotype | ||
type: string | ||
property: [] | ||
|
||
- id: object_label | ||
description: "Label for association_object." | ||
display_name: Phenotype | ||
type: string | ||
property: [] | ||
searchable: true | ||
|
||
- id: object_closure | ||
description: "Reflexive closure of association_has_object. A list of CURIEs. If an individual, first traverse rdf:tpye. The default closure is subclass, but other may optionally be added depending on what type of association this is and what the class is. E.g. for expression associations, the object is an anatomy class, and the closure will include part_of" | ||
display_name: Phenotype | ||
type: string | ||
cardinality: multi | ||
property: [] | ||
|
||
- id: object_closure_label | ||
description: "Labels for object_class_closure." | ||
display_name: Phenotype | ||
type: string | ||
cardinality: multi | ||
property: [] | ||
searchable: true | ||
|
||
- id: object_taxon | ||
description: "Taxonomic class of the object. This is typically a CURIE of the form NCBITaxon:nnnn. This field may be unfilled when used with certain categories" | ||
display_name: Species | ||
type: string | ||
property: [] | ||
|
||
- id: object_taxon_label | ||
description: "Label of taxon." | ||
display_name: Species | ||
type: string | ||
property: [] | ||
searchable: true | ||
|
||
- id: object_taxon_closure | ||
description: "Reflexive closure of taxon. ALWAYS up SubClassOf." | ||
display_name: Species | ||
type: string | ||
cardinality: multi | ||
property: [] | ||
|
||
- id: object_taxon_closure_label | ||
description: "Labels for taxon_closure." | ||
display_name: Species | ||
type: string | ||
cardinality: multi | ||
property: [] | ||
searchable: true | ||
|
||
- id: evidence_object | ||
description: "List of CURIES of all entities that form part of the evidence graph." | ||
display_name: Evidence | ||
type: string | ||
cardinality: multi | ||
property: [] | ||
|
||
- id: evidence_object_label | ||
description: "evidence object label" | ||
display_name: Evidence | ||
type: string | ||
cardinality: multi | ||
property: [] | ||
|
||
- id: evidence_object_closure | ||
description: "Closure for evidence object" | ||
display_name: Evidence | ||
type: string | ||
cardinality: multi | ||
property: [] | ||
|
||
- id: evidence_object_closure_label | ||
description: "List of CURIES of all entities that form part of the evidence closure." | ||
display_name: Evidence | ||
type: string | ||
cardinality: multi | ||
property: [] |
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Here I would suggest "case" instead of person