From 9d1fa4d6164cfe60ec17e206ac2798b589f4e9d7 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Mon, 5 Aug 2024 13:16:37 -0700 Subject: [PATCH] remove schemasheets yaml and combine with the main cmdr yaml --- src/cmdr/schema/cmdr.yaml | 253 ++++++++++++++++++++++++++++- src/cmdr/schema/from_sheets.yaml | 265 ------------------------------- 2 files changed, 252 insertions(+), 266 deletions(-) delete mode 100644 src/cmdr/schema/from_sheets.yaml diff --git a/src/cmdr/schema/cmdr.yaml b/src/cmdr/schema/cmdr.yaml index a5becb0..e3fb070 100644 --- a/src/cmdr/schema/cmdr.yaml +++ b/src/cmdr/schema/cmdr.yaml @@ -19,4 +19,255 @@ default_range: string imports: - linkml:types - - from_sheets + +classes: + Container: + from_schema: TEMP + slot_usage: + investigations: + inlined: true + inlined_as_list: true + multivalued: true + range: Investigation + material_processings: + inlined: true + inlined_as_list: true + multivalued: true + range: MaterialProcessing + materials: + inlined: true + inlined_as_list: true + multivalued: true + range: MaterialEntity + participations: + inlined: true + inlined_as_list: true + multivalued: true + range: Participation + specimen_collection_processes: + inlined: true + inlined_as_list: true + multivalued: true + range: SpecimenCollectionProcess + subjects: + inlined: true + inlined_as_list: true + multivalued: true + range: Subject + slots: + - materials + - participations + - material_processings + - specimen_collection_processes + - investigations + - subjects + tree_root: true + DataObject: + aliases: + - File + - Data + - DataFile + description: A DataFile Associated with a Subject or Investigation or MaterialEntity + from_schema: TEMP + see_also: + - include:DataFile + Investigation: + aliases: + - Study + - Proposal + description: General information about the Investigation + from_schema: TEMP + see_also: + - include:Study + slot_usage: + id: + identifier: true + range: uriorcurie + part_of: + range: Investigation + slots: + - id + - name + - part_of + MaterialEntity: + aliases: + - Substance + - Specimen + - Sample + - Biospecimen + - Biosample + description: Physical entity that is an input our output of a process from a Subject + from_schema: TEMP + see_also: + - include:Biospecimen + slot_usage: + concentration: + range: Quantity + id: + identifier: true + range: uriorcurie + source: + comments: + - this is a shortcut. to be expanded later. + range: Subject + used_in: + multivalued: true + range: Investigation + volume: + range: Quantity + slots: + - id + - name + - used_in + - source + - volume + - concentration + MaterialProcessing: + class_uri: OBI:0000094 + description: A planned process which results in physical changes in a specified + input material + from_schema: TEMP + is_a: Process + slot_usage: + has_input: + multivalued: true + range: MaterialEntity + has_output: + multivalued: true + range: MaterialEntity + slots: + - has_input + - has_output + Participation: + description: Subject/Study participation information + from_schema: TEMP + see_also: + - include:Participant + slot_usage: + id: + identifier: true + range: uriorcurie + includes: + range: Subject + involved_in: + multivalued: true + range: Investigation + slots: + - id + - name + - involved_in + - includes + Process: + abstract: true + description: A planned process resulting in a material or data + from_schema: TEMP + slot_usage: + has_input: + multivalued: true + has_output: + multivalued: true + id: + identifier: true + range: uriorcurie + slots: + - id + - name + - has_input + - has_output + Quantity: + from_schema: TEMP + slot_usage: + comparator: + range: string + has_numeric_value: + range: float + has_raw_value: + range: string + has_unit: + range: string + slots: + - has_raw_value + - has_numeric_value + - has_unit + - comparator + SpecimenCollectionProcess: + aliases: + - MaterialCollectionProcess + class_uri: OBI:0000659 + description: A planned process with the objective of collecting a specimen + from_schema: TEMP + is_a: Process + slot_usage: + has_input: + multivalued: true + range: Subject + has_output: + multivalued: true + range: MaterialEntity + slots: + - has_input + - has_output + Subject: + aliases: + - Site + - Participant + description: Demographic and clinical information about the subject + from_schema: TEMP + see_also: + - include:Participant + slot_usage: + id: + identifier: true + range: uriorcurie + slots: + - id + - name +slots: + comparator: + from_schema: TEMP + concentration: + from_schema: TEMP + has_input: + from_schema: TEMP + has_numeric_value: + from_schema: TEMP + has_output: + from_schema: TEMP + has_raw_value: + from_schema: TEMP + has_unit: + from_schema: TEMP + id: + from_schema: TEMP + includes: + from_schema: TEMP + investigations: + from_schema: TEMP + involved_in: + from_schema: TEMP + material_processings: + from_schema: TEMP + materials: + from_schema: TEMP + name: + from_schema: TEMP + part_of: + from_schema: TEMP + participations: + from_schema: TEMP + source: + from_schema: TEMP + specimen_collection_processes: + from_schema: TEMP + subjects: + from_schema: TEMP + used_in: + from_schema: TEMP + volume: + from_schema: TEMP +subsets: + potential_phi: + from_schema: TEMP + temporal_data: + from_schema: TEMP + diff --git a/src/cmdr/schema/from_sheets.yaml b/src/cmdr/schema/from_sheets.yaml deleted file mode 100644 index 47f75e2..0000000 --- a/src/cmdr/schema/from_sheets.yaml +++ /dev/null @@ -1,265 +0,0 @@ -classes: - Container: - from_schema: TEMP - slot_usage: - investigations: - inlined: true - inlined_as_list: true - multivalued: true - range: Investigation - material_processings: - inlined: true - inlined_as_list: true - multivalued: true - range: MaterialProcessing - materials: - inlined: true - inlined_as_list: true - multivalued: true - range: MaterialEntity - participations: - inlined: true - inlined_as_list: true - multivalued: true - range: Participation - specimen_collection_processes: - inlined: true - inlined_as_list: true - multivalued: true - range: SpecimenCollectionProcess - subjects: - inlined: true - inlined_as_list: true - multivalued: true - range: Subject - slots: - - materials - - participations - - material_processings - - specimen_collection_processes - - investigations - - subjects - tree_root: true - DataObject: - aliases: - - File - - Data - - DataFile - description: A DataFile Associated with a Subject or Investigation or MaterialEntity - from_schema: TEMP - see_also: - - include:DataFile - Investigation: - aliases: - - Study - - Proposal - description: General information about the Investigation - from_schema: TEMP - see_also: - - include:Study - slot_usage: - id: - identifier: true - range: uriorcurie - part_of: - range: Investigation - slots: - - id - - name - - part_of - MaterialEntity: - aliases: - - Substance - - Specimen - - Sample - - Biospecimen - - Biosample - description: Physical entity that is an input our output of a process from a Subject - from_schema: TEMP - see_also: - - include:Biospecimen - slot_usage: - concentration: - range: Quantity - id: - identifier: true - range: uriorcurie - source: - comments: - - this is a shortcut. to be expanded later. - range: Subject - used_in: - multivalued: true - range: Investigation - volume: - range: Quantity - slots: - - id - - name - - used_in - - source - - volume - - concentration - MaterialProcessing: - class_uri: OBI:0000094 - description: A planned process which results in physical changes in a specified - input material - from_schema: TEMP - is_a: Process - slot_usage: - has_input: - multivalued: true - range: MaterialEntity - has_output: - multivalued: true - range: MaterialEntity - slots: - - has_input - - has_output - Participation: - description: Subject/Study participation information - from_schema: TEMP - see_also: - - include:Participant - slot_usage: - id: - identifier: true - range: uriorcurie - includes: - range: Subject - involved_in: - multivalued: true - range: Investigation - slots: - - id - - name - - involved_in - - includes - Process: - abstract: true - description: A planned process resulting in a material or data - from_schema: TEMP - slot_usage: - has_input: - multivalued: true - has_output: - multivalued: true - id: - identifier: true - range: uriorcurie - slots: - - id - - name - - has_input - - has_output - Quantity: - from_schema: TEMP - slot_usage: - comparator: - range: string - has_numeric_value: - range: float - has_raw_value: - range: string - has_unit: - range: string - slots: - - has_raw_value - - has_numeric_value - - has_unit - - comparator - SpecimenCollectionProcess: - aliases: - - MaterialCollectionProcess - class_uri: OBI:0000659 - description: A planned process with the objective of collecting a specimen - from_schema: TEMP - is_a: Process - slot_usage: - has_input: - multivalued: true - range: Subject - has_output: - multivalued: true - range: MaterialEntity - slots: - - has_input - - has_output - Subject: - aliases: - - Site - - Participant - description: Demographic and clinical information about the subject - from_schema: TEMP - see_also: - - include:Participant - slot_usage: - id: - identifier: true - range: uriorcurie - slots: - - id - - name -default_prefix: TEMP -default_range: string -id: TEMP -imports: -- linkml:types -name: TEMP -prefixes: - OBI: http://purl.obolibrary.org/obo/OBI_ - RO: http://purl.obolibrary.org/obo/RO_ - TEMP: https://example.org/TEMP/ - cmdr: https://w3id.org/linkml/cmdr/ - linkml: https://w3id.org/linkml/ - omicsrus: https://example.org/omicsrus/ - sdo: http://schema.org/ - wikidata: http://www.wikidata.org/entity/ -slots: - comparator: - from_schema: TEMP - concentration: - from_schema: TEMP - has_input: - from_schema: TEMP - has_numeric_value: - from_schema: TEMP - has_output: - from_schema: TEMP - has_raw_value: - from_schema: TEMP - has_unit: - from_schema: TEMP - id: - from_schema: TEMP - includes: - from_schema: TEMP - investigations: - from_schema: TEMP - involved_in: - from_schema: TEMP - material_processings: - from_schema: TEMP - materials: - from_schema: TEMP - name: - from_schema: TEMP - part_of: - from_schema: TEMP - participations: - from_schema: TEMP - source: - from_schema: TEMP - specimen_collection_processes: - from_schema: TEMP - subjects: - from_schema: TEMP - used_in: - from_schema: TEMP - volume: - from_schema: TEMP -subsets: - potential_phi: - from_schema: TEMP - temporal_data: - from_schema: TEMP