Merge branch 'notebook_additions' of https://github.com/puja-trivedi/…

…models into notebook_additions

erdiagram-autogen/kbmodel.md

@@ -58,8 +58,9 @@ LibraryPool {
  integer avg_size_bp 
  float quantity_fmol 
  float quantity_pM 
- float concentration_nm 
+ float concentration_nM 
  integer volume_ul 
+ uriorcurieList xref 
  float tube_contents 
  string tube_barcode 
  integer read1_length 
@@ -113,7 +114,7 @@ Library {
  datetime creation_date 
  PassFailResult pass_fail_result 
  integer avg_size_bp 
- float concentration_nm 
+ float concentration_nM 
  float quantity_fmol 
  float quantity_ng 
  float input_quantity 
@@ -145,6 +146,7 @@ AmplifiedCdna {
  PassFailResult pass_fail_result 
  date creation_date 
  stringList cohort 
+ float quantity_ng 
  integer num_cycles 
  float percent_greater_than_400bp 
  string id 

json-schema-autogen/kbmodel.json

@@ -511,6 +511,10 @@
  "description": "QC metric to measure mRNA degradation of cDNA. Higher % is higher quality starting material. Over 400bp is used as a universal cutoff for intact (full length) vs degraded cDNA and is a common output from Bioanalyzer and Fragment Analyzer elecropheragrams.",
  "type": "number"
  },
+ "quantity_ng": {
+ "description": "Amount of cDNA produced after cDNA amplification measured in nanograms.",
+ "type": "number"
+ },
  "type": {
  "items": {
  "type": "string"
@@ -554,6 +558,7 @@
  "required": [
  "pass_fail_result",
  "cohort",
+ "quantity_ng",
  "num_cycles",
  "percent_greater_than_400bp",
  "id",
@@ -20912,7 +20917,7 @@
  },
  "type": "array"
  },
- "concentration_nm": {
+ "concentration_nM": {
  "description": "Concentration of library in terms of nM (nMol/L). Number of molecules is needed for accurate pooling of the libraries and for generating the number of target reads/cell in sequencing.",
  "type": "number"
  },
@@ -21358,7 +21363,7 @@
  },
  "type": "array"
  },
- "concentration_nm": {
+ "concentration_nM": {
  "description": "Library pool concentration as measured in nanomolarity (nMol/L)",
  "type": "number"
  },
@@ -21463,9 +21468,17 @@
  ]
  },
  "type": "array"
+ },
+ "xref": {
+ "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'.",
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
  }
  },
  "required": [
+ "xref",
  "tube_barcode",
  "read1_length",
  "read2_length",

jsonld-context-autogen/kbmodel.context.jsonld

@@ -858,7 +858,7 @@
  "@type": "@id",
  "@id": "biolink:composed_primarily_of"
  },
- "concentration_nm": {
+ "concentration_nM": {
  "@type": "xsd:float"
  },
  "concept_count_object": {

models_py-autogen/kbmodel.py

@@ -742,6 +742,7 @@ class AmplifiedCdna(Entity, ProvEntity):
  pass_fail_result: PassFailResult = Field(..., description="""Pass or Fail result based on qualitative assessment of cDNA yield and size.""")
  creation_date: Optional[date] = Field(None, description="""Date of cDNA amplification.""")
  cohort: List[str] = Field(default_factory=list, description="""cDNA amplification set, containing multiple amplified_cDNA_names that were processed at the same time.""")
+ quantity_ng: float = Field(..., description="""Amount of cDNA produced after cDNA amplification measured in nanograms.""")
  num_cycles: int = Field(..., description="""Number of PCR cycles used during cDNA amplification for this cDNA.""")
  percent_greater_than_400bp: float = Field(..., description="""QC metric to measure mRNA degradation of cDNA. Higher % is higher quality starting material. Over 400bp is used as a universal cutoff for intact (full length) vs degraded cDNA and is a common output from Bioanalyzer and Fragment Analyzer elecropheragrams.""")
  wasDerivedFrom: Optional[List[BarcodedCellSample]] = Field(default_factory=list)
@@ -766,7 +767,7 @@ class Library(Entity, ProvEntity):
  creation_date: Optional[datetime ] = Field(None, description="""Date of library construction.""")
  pass_fail_result: PassFailResult = Field(..., description="""Pass or Fail result based on qualitative assessment of library yield and size.""")
  avg_size_bp: int = Field(..., description="""Average size of the library in terms of base pairs. This is used to calculate the molarity before pooling and sequencing.""")
- concentration_nm: Optional[float] = Field(None, description="""Concentration of library in terms of nM (nMol/L). Number of molecules is needed for accurate pooling of the libraries and for generating the number of target reads/cell in sequencing.""")
+ concentration_nM: Optional[float] = Field(None, description="""Concentration of library in terms of nM (nMol/L). Number of molecules is needed for accurate pooling of the libraries and for generating the number of target reads/cell in sequencing.""")
  quantity_fmol: float = Field(..., description="""Amount of library generated in terms of femtomoles""")
  quantity_ng: Optional[float] = Field(None, description="""Amount of library generated in terms of nanograms""")
  input_quantity: float = Field(..., description="""Amount of cDNA going into library construction in nanograms.""")
@@ -815,8 +816,9 @@ class LibraryPool(Entity, ProvEntity):
  avg_size_bp: Optional[int] = Field(None, description="""Average insert size of library pool, measured in base pairs.""")
  quantity_fmol: Optional[float] = Field(None, description="""Amount of library pool in the tube as measured in femtamoles (fmol)""")
  quantity_pM: Optional[float] = Field(None, description="""Sequencer Loading Concentration as measured in pM (pmol/L). This is a value used by the SeqCore.""")
- concentration_nm: Optional[float] = Field(None, description="""Library pool concentration as measured in nanomolarity (nMol/L)""")
+ concentration_nM: Optional[float] = Field(None, description="""Library pool concentration as measured in nanomolarity (nMol/L)""")
  volume_ul: Optional[int] = Field(None, description="""Library pool volume as measured in ul""")
+ xref: List[str] = Field(default_factory=list, 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'.""")
  tube_contents: Optional[float] = Field(None, description="""The content concentration (nm).""")
  tube_barcode: str = Field(..., description="""Library Pool tube name as provided by the SeqCore (often a barcode). This tube is provided from the SeqCore and is part of the SeqCore tracking system.""")
  read1_length: int = Field(..., description="""Length of Read 1""")