new sample types

osc-em · Aug 5, 2024 · 8fdaa5b · 8fdaa5b
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diff --git a/examples/EMDataset-001.yaml b/examples/EMDataset-001.yaml
@@ -10,66 +10,74 @@ Instrument:
   CS: 2.7
 Acquisition:
   Holder: testitest
-OSCEMSample:
-  Grant:
-    - Grant_ID: SNF321
-      Funding_agency: SNF
-    - Grant_ID: Fundingofsomekind
-      Funding_agency: SNF
-  Author:
-    - Name:
-        FirstName: John
-        LastName: Doe
-      Email: [email protected]
-      Phone: "+4132112312"
-      ORCID: ORCID_123124151231
-      Organization:
-        Name_org: University of Blub
-        Type_org: Academic
-      Country: Switzerland
-    - Name:
-        FirstName: Jane
-        LastName: Doe
-      Email: [email protected]
-      Phone: "+4132112312"
-      ORCID: ORCID_123124151221
-      Organization:
-        Name_org: University of Blub
-        Type_org: Academic
-      Country: Switzerland
-  Sample:
-    Overall_Molecule:
-      Type: Complex
-      Name: Ribosome
-      Source: yeast
-      Molecular_weight: 3000000
-    Molecule:
-      - Name: Ribosome_
-        Type: polypeptide
-        Class: None of these
-        Sequence: MMKNMMKYMMMYSYKEKSEKRRWMMKREMMKYLELLNMRMNKWVKRMMMSRKRLLSRMNRLEKKNHMNDYKLMSYNFNKNSMMMKSMLSKLMMNLLENVMNGVDLKSGKSKMSGGNMMMSKPVMKENLNTVNMLFYYFLPNNKSYKYFNRMNMYLNKHMKNYKKLVKLNKNYSKSSYLLQDKLMMSNMFNNMMFNRNNMKYMNNNVNNLMSSLNMNSNNKSLYLSLLNKTLNNNLSNLYSNNNINKSIINNTLVNMSMLNNNYNNNNTTFNINNNLFNLLNLLNNNYNNNNNYNNMMSNTNMLLNNYNNNNNNNNNNKCNMHSKMKLERKNMMLNYLLKNEMMNKNQMWMSKMENNKMNNINNNNNMLKMNKENDKTNMFGYMMSYMDMLLGNMMNKSKKSNDMKMMMSKYFGLKEVNMTGMNLKYEFNNTEMLLKLMRKGMSKRKRTLSRMFRFRLKNRMPLLNDKGMLKNKMSNNLLKNLALNNNILNVEYNIKNVLFNSINNNNINNNNNNNMYNDMKDYYNNMSLENKKDLSLNNELLYKNMVGWSLLLKGKVGARKGKNRSNRMLMTKGSFKNNNLYIYNIFDDNSNNNGYTKDRLRLNYMKNSNFISYMDKSTNNGKLGMTLKVNIL
-        Natural_source: yeast
-        Taxonomy_ID_source: GCA_003054445.1
-        Expression_system: Pichia kudriavzevii
-        Taxonomy_ID_expression: GCA_003054445.1
-        Gene_name: Rib
-    Ligands:
-      - Present: false
-    Specimen:
-      Concentration: 0.3
-      pH: 7
-      Vitrification: false
-      Vitrification_cryogen: None
-      Humidity: 90
-      Temperature: 300
-      Staining: false
-      Embedding: false
-      Shadowing: false
-    Grid:
-      Manufacturer: Quantifoil
-      Material: Au
-      Mesh: 300
-      Film_support: false
-      Pretreatment_type: Glow discharge
-      Pretreatment_time: 30
-      Pretreatment_pressure: 0.000001
+  Detector: Falcon 4i
+  Detector_mode: counting
+  Dose_per_movie: 0.5
+  Datetime: "2024-01-01"
+  Binning_camera: 2
+  Pixel_size: 1.2
+oscemsample:
+  grant:
+    - grant_id: SNF321
+      funding_agency: SNF
+    - grant_id: Fundingofsomekind
+      funding_agency: SNF
+  # author:
+  #   - author_name:
+  #       first_name: John
+  #       last_name: Doe
+  #     email: [email protected]
+  #     phone: "+4132112312"
+  #     orcid: ORCID_123124151231
+  #     organization:
+  #       name_org: University of Blub
+  #       type_org: Academic
+  #     country: Switzerland
+  #   - author_name:
+  #       first_name: Jane
+  #       last_name: Doe
+  #     email: [email protected]
+  #     phone: "+4132112312"
+  #     orcid: ORCID_123124151221
+  #     organization:
+  #       name_org: University of Blub
+  #       type_org: Academic
+  #     country: Switzerland
+  sample:
+    overall_molecule:
+      type: Complex
+      name_sample: Ribosome
+      source: yeast
+      molecular_weight: 3000000
+    molecule:
+      - name_mol: Ribosome_
+        type: polypeptide
+        molecular_class: None of these
+        sequence: MMKNMMKYMMMYSYKEKSEKRRWMMKREMMKYLELLNMRMNKWVKRMMMSRKRLLSRMNRLEKKNHMNDYKLMSYNFNKNSMMMKSMLSKLMMNLLENVMNGVDLKSGKSKMSGGNMMMSKPVMKENLNTVNMLFYYFLPNNKSYKYFNRMNMYLNKHMKNYKKLVKLNKNYSKSSYLLQDKLMMSNMFNNMMFNRNNMKYMNNNVNNLMSSLNMNSNNKSLYLSLLNKTLNNNLSNLYSNNNINKSIINNTLVNMSMLNNNYNNNNTTFNINNNLFNLLNLLNNNYNNNNNYNNMMSNTNMLLNNYNNNNNNNNNNKCNMHSKMKLERKNMMLNYLLKNEMMNKNQMWMSKMENNKMNNINNNNNMLKMNKENDKTNMFGYMMSYMDMLLGNMMNKSKKSNDMKMMMSKYFGLKEVNMTGMNLKYEFNNTEMLLKLMRKGMSKRKRTLSRMFRFRLKNRMPLLNDKGMLKNKMSNNLLKNLALNNNILNVEYNIKNVLFNSINNNNINNNNNNNMYNDMKDYYNNMSLENKKDLSLNNELLYKNMVGWSLLLKGKVGARKGKNRSNRMLMTKGSFKNNNLYIYNIFDDNSNNNGYTKDRLRLNYMKNSNFISYMDKSTNNGKLGMTLKVNIL
+        natural_source: yeast
+        taxonomy_id_source: GCA_003054445.1
+        expression_system: Pichia kudriavzevii
+        taxonomy_id_expression: GCA_003054445.1
+        gene_name: Rib
+    ligands:
+      - present: false
+        smile: C1CCCCC1
+
+    specimen:
+      concentration: 0.3
+      ph: 7
+      vitrification: false
+      vitrification_cryogen: None
+      humidity: 90
+      temperature: 300
+      staining: false
+      embedding: false
+      shadowing: false
+    grid:
+      manufacturer: Quantifoil
+      material: Au
+      mesh: 300
+      film_support: false
+      pretreatment_type: Glow discharge
+      pretreatment_time: 30
+      pretreatment_pressure: 0.000001
diff --git a/project/excel/oscem_schemas.xlsx b/project/excel/oscem_schemas.xlsx
diff --git a/project/graphql/oscem_schemas.graphql b/project/graphql/oscem_schemas.graphql
@@ -32,19 +32,15 @@ type Acquisition
 
 type Author
   {
-    authorName: AuthorName!
-    email: String!
-    phone: String!
+    firstName: String
+    workStatus: Boolean
+    institution: [Institution]!
     orcid: String!
-    organization: Organization!
     country: String!
     role: String
-  }
-
-type AuthorName
-  {
-    firstName: String!
-    lastName: String!
+    name: String!
+    email: String!
+    workPhone: String!
   }
 
 type Base
@@ -84,7 +80,9 @@ type EMDataset
   {
     acquisition: Acquisition!
     instrument: Instrument!
-    oscemsample: OSCEMSample!
+    sample: Sample!
+    grants: [Grant]!
+    authors: [Author]!
   }
 
 type EnergyFilter
@@ -96,8 +94,12 @@ type EnergyFilter
 
 type Grant
   {
-    grantId: String!
-    fundingAgency: String!
+    name: String
+    funder: String
+    startDate: Date
+    endDate: Date
+    budget: QuantityValue
+    projectId: String
   }
 
 type Grid
@@ -129,6 +131,12 @@ type Imagehift
     yMax: Float
   }
 
+type Institution
+  {
+    nameOrg: String
+    typeOrg: OrganizationTypeEnum!
+  }
+
 type Instrument
   {
     microscope: String!
@@ -166,19 +174,6 @@ type NominalDefocus
     maximal: Float
   }
 
-type Organization
-  {
-    nameOrg: String
-    typeOrg: OrganizationTypeEnum!
-  }
-
-type OSCEMSample
-  {
-    grant: [Grant]!
-    author: [Author]
-    sample: Sample!
-  }
-
 type OverallMolecule
   {
     type: String!
@@ -187,12 +182,27 @@ type OverallMolecule
     molecularWeight: Float
   }
 
+type Person
+  {
+    name: String
+    firstName: String
+    workStatus: Boolean
+    email: String
+    workPhone: String
+  }
+
 type Phaseplate
   {
     used: Boolean!
     type: String!
   }
 
+type QuantityValue
+  {
+    hasValue: Double
+    hasUnit: String
+  }
+
 type Sample
   {
     overallMolecule: OverallMolecule!