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BDSO - simplifying pipeline #168
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BDSO - simplifying pipeline
Aims:
A curation system that allows editor to link cell types and properties to taxonomy and non-taxonomy node IDs without being overwhelmed by columns
Auto-populated content input should be segregated from manually
curated content input.
Questions: General question - do we need all the comment/annotation
stuff? It doesn't get used much.
Current patterns - to merge down
brainCellRegionMinimalMarkers.yaml
Description: Drives annotation axioms and subClassOf axioms, excluding
markers
vars: gross_cell_type: "'cell'" # From YAML config for whole
taxonomy taxon: "'Vertebrata <vertebrates>'" # From YAML config
for whole taxonomy brain_region: "'regional part of brain'" #
From YAML config for whole taxonomy projection_type:
"'projection type'" # From curation to nodes
data_vars: cell_set_preferred_alias: "xsd:string" #
From Dendrogram/taxonomy brain_regionabbv: "xsd:string" #
Currently from Taxonomy config species_abbv: "xsd:string" #
Currently from Taxonomy config
list_vars: minimal_markers:
"'sequence_feature'" # From markers allen_markers:
"'sequence_feature'" # From curation to node IDs layers:
"'layer of neocortex'" # From curation to node IDs
data_listvars: alias_citations: "xsd:string" #
Curation to node IDs (based on hard to parse info in taxonomy?)
taxonomy_class.yaml
Example ROBOT template:
CCN202002013_class.tsv
Description: Linking to node IDs - some autogenerated. most curated.
logic:
annotation:
synonym axioms.
list_vars: Expresses: "'thing'" # Expression linked to leaf nodes.
vars: Classification: "'cell'" # Classifications linked to taxonomy nodes.
data_list_vars: Synonyms from taxonomy
Curated_synonyms: "xsd:string"
Classification_pub: "xsd:string"
Expresses_comment: "xsd:string"
Expresses_pub: "xsd:string"
data_vars: prefLabel: "xsd:string" Comment: "xsd:string"
Classification_comment: "xsd:string"
taxonomy_equivalent_class.yaml
DESCRIPTION: Rolls EC definitions - really only needs one var.
ROBOT_TEMPLATE_EXAMPLE
vars: Exemplar_SC: "'thing'" # contents same as exemplar
Exemplar: "'thing'"
taxonomy_minimal_markers.yaml
ROBOT TEMPALTE:
CCN202002013_minimalmarkers.tsv
Description: NS_Forerst minimal marker axioms. + part_of/has_soma_location depending on type
list_vars: Markers: "'thing'" # NS_Forest markers
vars:
taxonomy_non_taxonomy_classification.yaml
Description: Pulls in some additional/orthogonal classifications - CURATED
vars: Classification: "'cell'" # Driven from non-taxonomy nodes in YAML
Proposal
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