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updates to library_gen #210

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Merged
merged 8 commits into from
Nov 16, 2025
Merged

updates to library_gen #210

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4458489
added local_name to xref. xref will now store NIMP id
puja-trivedi Nov 15, 2025
fc65605
generate another formats for library_generation model(s)
Nov 15, 2025
9fd3157
changed library_pool attribute from local_tube_id to tube_interal_lab…
puja-trivedi Nov 15, 2025
26d27b9
Merge branch 'lib_gen_20251115' of https://github.com/puja-trivedi/mo…
puja-trivedi Nov 15, 2025
1024540
generate another formats for library_generation model(s)
Nov 15, 2025
6934189
temporarily 'ignored' BICAN UUID column because in the jsonld-context…
puja-trivedi Nov 16, 2025
73e001b
Merge branch 'lib_gen_20251115' of https://github.com/puja-trivedi/mo…
puja-trivedi Nov 16, 2025
a36a61e
generate another formats for library_generation model(s)
Nov 16, 2025
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23 changes: 12 additions & 11 deletions erdiagram-autogen/library_generation.md
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Original file line number Diff line number Diff line change
Expand Up @@ -31,6 +31,7 @@ ProvEntity {
}
DissectionRoiPolygon {
label_type name
uriorcurieList xref
string id
iri_type iri
uriorcurieList category
Expand Down Expand Up @@ -198,14 +199,14 @@ DissectionRoiDelineation {
}
LibraryPool {
label_type name
string local_tube_id
uriorcurieList xref
string tube_internal_label
string id
iri_type iri
stringList type
narrative_text description
boolean deprecated
stringList provided_by
uriorcurieList xref
label_type full_name
label_typeList synonym
float information_content
Expand All @@ -215,13 +216,13 @@ LibraryPool {
}
LibraryAliquot {
label_type name
uriorcurieList xref
string id
iri_type iri
stringList type
narrative_text description
boolean deprecated
stringList provided_by
uriorcurieList xref
label_type full_name
label_typeList synonym
float information_content
Expand All @@ -231,6 +232,7 @@ LibraryAliquot {
}
Library {
label_type name
uriorcurieList xref
integer average_size_bp
float concentration_nm
library_prep_pass_fail library_result
Expand All @@ -243,7 +245,6 @@ Library {
narrative_text description
boolean deprecated
stringList provided_by
uriorcurieList xref
label_type full_name
label_typeList synonym
float information_content
Expand All @@ -253,6 +254,7 @@ Library {
}
AmplifiedCdna {
label_type name
uriorcurieList xref
float amplified_cDNA_quantity_ng
amplified_cdna_rna_amplification_pass_fail amplified_cDNA_result
float percent_cdna_longer_than_400bp
Expand All @@ -262,7 +264,6 @@ AmplifiedCdna {
narrative_text description
boolean deprecated
stringList provided_by
uriorcurieList xref
label_type full_name
label_typeList synonym
float information_content
Expand All @@ -272,14 +273,14 @@ AmplifiedCdna {
}
BarcodedCellSample {
label_type name
uriorcurieList xref
integer number_of_expected_cells
string id
iri_type iri
stringList type
narrative_text description
boolean deprecated
stringList provided_by
uriorcurieList xref
label_type full_name
label_typeList synonym
float information_content
Expand All @@ -289,6 +290,7 @@ BarcodedCellSample {
}
EnrichedCellSample {
label_type name
uriorcurieList xref
string enrichment_population
string enriched_cell_oligo_name
string histone_modification_marker
Expand All @@ -298,7 +300,6 @@ EnrichedCellSample {
narrative_text description
boolean deprecated
stringList provided_by
uriorcurieList xref
label_type full_name
label_typeList synonym
float information_content
Expand All @@ -308,6 +309,7 @@ EnrichedCellSample {
}
DissociatedCellSample {
label_type name
uriorcurieList xref
dissociated_cell_sample_cell_prep_type cell_prep_type
dissociated_cell_sample_cell_label_barcode dissociated_cell_oligo_name
string id
Expand All @@ -316,7 +318,6 @@ DissociatedCellSample {
narrative_text description
boolean deprecated
stringList provided_by
uriorcurieList xref
label_type full_name
label_typeList synonym
float information_content
Expand All @@ -326,14 +327,14 @@ DissociatedCellSample {
}
TissueSample {
label_type name
uriorcurieList xref
stringList structure
string id
iri_type iri
stringList type
narrative_text description
boolean deprecated
stringList provided_by
uriorcurieList xref
label_type full_name
label_typeList synonym
float information_content
Expand All @@ -343,13 +344,13 @@ TissueSample {
}
BrainSlab {
label_type name
uriorcurieList xref
string id
iri_type iri
stringList type
narrative_text description
boolean deprecated
stringList provided_by
uriorcurieList xref
label_type full_name
label_typeList synonym
float information_content
Expand All @@ -359,6 +360,7 @@ BrainSlab {
}
Donor {
label_type name
uriorcurieList xref
sex biological_sex
string age_at_death_description
age_at_death_reference_point age_at_death_reference_point
Expand All @@ -372,7 +374,6 @@ Donor {
narrative_text description
boolean deprecated
stringList provided_by
uriorcurieList xref
label_type full_name
label_typeList synonym
float information_content
Expand Down
24 changes: 17 additions & 7 deletions json-schema-autogen/library_generation.json
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Original file line number Diff line number Diff line change
Expand Up @@ -2093,6 +2093,16 @@
"string",
"null"
]
},
"xref": {
"description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.",
"items": {
"type": "string"
},
"type": [
"array",
"null"
]
}
},
"required": [
Expand Down Expand Up @@ -3691,13 +3701,6 @@
"null"
]
},
"local_tube_id": {
"description": "Library Pool Tube local name. Label of the tube containing the library pool, which is made up of multiple library_aliquots. This is a Library Lab local tube name, before the pool is aliquoted to the Seq Core provided tube 'Library Pool Tube Name'.",
"type": [
"string",
"null"
]
},
"name": {
"description": "Library lab's library pool name. For some labs this may be the same as \"Libray pool tube local name\". Other labs distinguish between the local tube label of the library pool and the library pool name provided to SeqCore for tracking. Local Pool Name is used to communicate sequencing status between SeqCore and Library Labs.",
"type": [
Expand Down Expand Up @@ -3725,6 +3728,13 @@
"null"
]
},
"tube_internal_label": {
"description": "Library Pool Tube local name. Label of the tube containing the library pool, which is made up of multiple library_aliquots. This is a Library Lab local tube name, before the pool is aliquoted to the Seq Core provided tube 'Library Pool Tube Name'.",
"type": [
"string",
"null"
]
},
"type": {
"items": {
"type": "string"
Expand Down
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