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update bican biolink #206

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Merged
merged 19 commits into from
Oct 27, 2025
Merged

update bican biolink #206

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9b6ef74
updated biolink-model to current version in biolink repository
puja-trivedi Oct 24, 2025
626a139
reverting back to old biolink-model temporarily due to them added a n…
puja-trivedi Oct 24, 2025
7c12141
updated biolink-model to current version in biolink repository with a…
puja-trivedi Oct 24, 2025
ae5df9e
added 'relative frequency analysis result' class to bican_biolink
puja-trivedi Oct 24, 2025
585b22c
new bican_biolink with addional class: 'relative frequency analysis r…
puja-trivedi Oct 27, 2025
aa49431
removed attributes.yaml, pointing to the model directly using url
puja-trivedi Oct 27, 2025
23c0459
removed '.yaml' from import url
puja-trivedi Oct 27, 2025
7754971
added missing class: dataset and slot: version to bican_biolink
puja-trivedi Oct 27, 2025
0a99282
manually removed 'types' to resolve 'ValueError: Conflicting URIs (ht…
puja-trivedi Oct 27, 2025
b7b6e80
removing 'import: attributes' because slots in 'attributes.yaml' are …
puja-trivedi Oct 27, 2025
4263d6d
manually added 'type:unit' back to bican_biolink
puja-trivedi Oct 27, 2025
e041953
manually added 'type:iri type' back to bican_biolink
puja-trivedi Oct 27, 2025
568543e
manually added 'type:label type' back to bican_biolink
puja-trivedi Oct 27, 2025
3a008a1
manually added 'type:narrative text' back to bican_biolink
puja-trivedi Oct 27, 2025
715573f
manually added 'type:biological sequence' back to bican_biolink
puja-trivedi Oct 27, 2025
7918002
manually added 'type: symbol type' back to bican_biolink
puja-trivedi Oct 27, 2025
c1dae10
generate another formats for bke_taxonomy model(s)
Oct 27, 2025
e8e3ca0
generate another formats for genome_annotation model(s)
Oct 27, 2025
6d54e70
generate another formats for library_generation model(s)
Oct 27, 2025
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2,926 changes: 2,346 additions & 580 deletions biolink-model.yaml
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40 changes: 32 additions & 8 deletions erdiagram-autogen/anatomical_structure.md
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,6 @@ ParcellationAtlas {
string version
string id
iri_type iri
uriorcurieList category
stringList type
label_type name
narrative_text description
Expand All @@ -17,6 +16,10 @@ ParcellationAtlas {
uriorcurieList xref
label_type full_name
label_typeList synonym
float information_content
uriorcurieList equivalent_identifiers
uriorcurieList named_thing_category
uriorcurieList category
}
ParcellationAnnotationTermMap {
string subject_parcellation_term
Expand All @@ -32,7 +35,6 @@ AnatomicalAnnotationSet {
string version
string id
iri_type iri
uriorcurieList category
stringList type
label_type name
narrative_text description
Expand All @@ -41,6 +43,10 @@ AnatomicalAnnotationSet {
uriorcurieList xref
label_type full_name
label_typeList synonym
float information_content
uriorcurieList equivalent_identifiers
uriorcurieList named_thing_category
uriorcurieList category
}
ParcellationColorAssignment {
string subject_parcellation_term
Expand All @@ -52,7 +58,6 @@ ParcellationColorScheme {
string version
string id
iri_type iri
uriorcurieList category
stringList type
label_type name
narrative_text description
Expand All @@ -61,6 +66,10 @@ ParcellationColorScheme {
uriorcurieList xref
label_type full_name
label_typeList synonym
float information_content
uriorcurieList equivalent_identifiers
uriorcurieList named_thing_category
uriorcurieList category
}
ParcellationTerm {
integer ordinal
Expand All @@ -70,7 +79,6 @@ ParcellationTerm {
string version
string id
iri_type iri
uriorcurieList category
stringList type
label_type name
narrative_text description
Expand All @@ -79,6 +87,10 @@ ParcellationTerm {
uriorcurieList xref
label_type full_name
label_typeList synonym
float information_content
uriorcurieList equivalent_identifiers
uriorcurieList named_thing_category
uriorcurieList category
}
ParcellationTermSet {
integer ordinal
Expand All @@ -87,7 +99,6 @@ ParcellationTermSet {
string version
string id
iri_type iri
uriorcurieList category
stringList type
label_type name
narrative_text description
Expand All @@ -96,12 +107,15 @@ ParcellationTermSet {
uriorcurieList xref
label_type full_name
label_typeList synonym
float information_content
uriorcurieList equivalent_identifiers
uriorcurieList named_thing_category
uriorcurieList category
}
ParcellationTerminology {
string version
string id
iri_type iri
uriorcurieList category
stringList type
label_type name
narrative_text description
Expand All @@ -110,13 +124,16 @@ ParcellationTerminology {
uriorcurieList xref
label_type full_name
label_typeList synonym
float information_content
uriorcurieList equivalent_identifiers
uriorcurieList named_thing_category
uriorcurieList category
}
AnatomicalSpace {
string measures
string version
string id
iri_type iri
uriorcurieList category
stringList type
label_type name
narrative_text description
Expand All @@ -125,6 +142,10 @@ AnatomicalSpace {
uriorcurieList xref
label_type full_name
label_typeList synonym
float information_content
uriorcurieList equivalent_identifiers
uriorcurieList named_thing_category
uriorcurieList category
}
ImageDataset {
ANATOMICAL_DIRECTION x_direction
Expand All @@ -140,7 +161,6 @@ ImageDataset {
string version
string id
iri_type iri
uriorcurieList category
stringList type
label_type name
narrative_text description
Expand All @@ -149,6 +169,10 @@ ImageDataset {
uriorcurieList xref
label_type full_name
label_typeList synonym
float information_content
uriorcurieList equivalent_identifiers
uriorcurieList named_thing_category
uriorcurieList category
}

ParcellationAtlas ||--|o VersionedNamedThing : "revision_of"
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