From fad7b1ba62d15af9b295840d58c10c2d406b7caf Mon Sep 17 00:00:00 2001 From: juwitte Date: Wed, 20 Aug 2025 12:22:08 +0000 Subject: [PATCH 01/10] fix: changed enzyme url to identifier list --- .../classes/enzyme.py | 9 ++-- tests/example_data/bacteria.json | 54 ++++++++++++++----- 2 files changed, 45 insertions(+), 18 deletions(-) diff --git a/src/microbial_strain_data_model/classes/enzyme.py b/src/microbial_strain_data_model/classes/enzyme.py index 01e964b..61a6ec5 100644 --- a/src/microbial_strain_data_model/classes/enzyme.py +++ b/src/microbial_strain_data_model/classes/enzyme.py @@ -1,6 +1,7 @@ from typing_extensions import Annotated -from pydantic import BaseModel, ConfigDict, StringConstraints, Field, HttpUrl +from pydantic import BaseModel, ConfigDict, StringConstraints, Field +from microbial_strain_data_model.classes.identifier import Identifier from microbial_strain_data_model.classes.links import RelationLink, SourceLink @@ -24,11 +25,7 @@ class Enzyme(BaseModel): title="EC Number", description="An EC number defined by the Enzyme Commission", ) - url: HttpUrl | None = Field( - default=None, - title="URL", - description="Uniform Resource Locator of a resource on the Internet", - ) + identifier: list[Identifier] = Field(default_factory=list, title="Identifier") alternateName: list[str] = Field(default_factory=list, title="Alternate Name") active: bool | None = Field( default=None, title="Active", description="Is this enzyme active" diff --git a/tests/example_data/bacteria.json b/tests/example_data/bacteria.json index deeb417..01787fa 100644 --- a/tests/example_data/bacteria.json +++ b/tests/example_data/bacteria.json @@ -329,14 +329,19 @@ "tracp5b" ], "hasECNumber": "3.1.3.2", + "identifier": [ + { + "name": "Brenda", + "value": "https://www.brenda-enzymes.org/enzyme.php?ecno=3.1.3.2" + } + ], "name": "acid phosphatase", "relatedData": [ "/relatedData/0" ], "source": [ "/sources/0" - ], - "url": "https://www.brenda-enzymes.org/enzyme.php?ecno=3.1.3.2" + ] }, { "active": true, @@ -353,11 +358,16 @@ "secreted alkaline phosphatase" ], "hasECNumber": "3.1.3.1", + "identifier": [ + { + "name": "Brenda", + "value": "https://www.brenda-enzymes.org/enzyme.php?ecno=3.1.3.1" + } + ], "name": "alkaline phosphatase", "source": [ "/sources/0" - ], - "url": "https://www.brenda-enzymes.org/enzyme.php?ecno=3.1.3.1" + ] }, { "active": false, @@ -374,11 +384,16 @@ "chymotrypsin ii" ], "hasECNumber": "3.4.21.1", + "identifier": [ + { + "name": "Brenda", + "value": "https://www.brenda-enzymes.org/enzyme.php?ecno=3.4.21.1" + } + ], "name": "alpha-chymotrypsin", "source": [ "/sources/0" - ], - "url": "https://www.brenda-enzymes.org/enzyme.php?ecno=3.4.21.1" + ] }, { "active": false, @@ -395,11 +410,16 @@ "alphafuc" ], "hasECNumber": "3.2.1.51", + "identifier": [ + { + "name": "Brenda", + "value": "https://www.brenda-enzymes.org/enzyme.php?ecno=3.2.1.51" + } + ], "name": "alpha-fucosidase", "source": [ "/sources/0" - ], - "url": "https://www.brenda-enzymes.org/enzyme.php?ecno=3.2.1.51" + ] }, { "active": false, @@ -415,11 +435,16 @@ "streptococcal acid glycoprotein" ], "hasECNumber": "3.5.3.6", + "identifier": [ + { + "name": "Brenda", + "value": "https://www.brenda-enzymes.org/enzyme.php?ecno=3.5.3.6" + } + ], "name": "arginine dihydrolase", "source": [ "/sources/0" - ], - "url": "https://www.brenda-enzymes.org/enzyme.php?ecno=3.5.3.6" + ] }, { "active": true, @@ -436,11 +461,16 @@ "betagal" ], "hasECNumber": "3.2.1.23", + "identifier": [ + { + "name": "Brenda", + "value": "https://www.brenda-enzymes.org/enzyme.php?ecno=3.2.1.23" + } + ], "name": "beta-galactosidase", "source": [ "/sources/0" - ], - "url": "https://www.brenda-enzymes.org/enzyme.php?ecno=3.2.1.23" + ] } ], "fattyAcidProfiles": [ From 0750861a452582031d4c8afe9a952e99ce40290b Mon Sep 17 00:00:00 2001 From: juwitte Date: Wed, 20 Aug 2025 12:33:01 +0000 Subject: [PATCH 02/10] feat: add KindOfUtilization enum BREAKING CHANGE: --- .../classes/enums.py | 23 +++++++++++++++++++ .../classes/metabolitetest.py | 7 ++++-- 2 files changed, 28 insertions(+), 2 deletions(-) diff --git a/src/microbial_strain_data_model/classes/enums.py b/src/microbial_strain_data_model/classes/enums.py index 0d4eec7..02201e3 100644 --- a/src/microbial_strain_data_model/classes/enums.py +++ b/src/microbial_strain_data_model/classes/enums.py @@ -480,3 +480,26 @@ class CurationMode(str, Enum): manual = "manual" automated = "automated" unknown = "unknown" + + +class KindOfUtilization(str, Enum): + """ + Types of utilization + + Args: + assimilation: assimilation + buildsAcidFrom: builds acid from + degradation: degradation + energySource: energy source + fermentation: fermentation + hydrolysis: hydrolysis + reduction: reduction + """ + + assimilation = "assimilation" + buildsAcidFrom = "builds acid from" + degradation = "degradation" + energySource = "energy source" + fermentation = "fermentation" + hydrolysis = "hydrolysis" + reduction = "reduction" diff --git a/src/microbial_strain_data_model/classes/metabolitetest.py b/src/microbial_strain_data_model/classes/metabolitetest.py index 610f91f..3fba6a8 100644 --- a/src/microbial_strain_data_model/classes/metabolitetest.py +++ b/src/microbial_strain_data_model/classes/metabolitetest.py @@ -1,6 +1,9 @@ from pydantic import BaseModel, ConfigDict, Field -from microbial_strain_data_model.classes.enums import MetaboliteTestType +from microbial_strain_data_model.classes.enums import ( + MetaboliteTestType, + KindOfUtilization, +) from microbial_strain_data_model.classes.links import RelationLink @@ -25,7 +28,7 @@ class MetaboliteTest(BaseModel): protocol: str | None = Field( default=None, title="Protocol", description="What test was used" ) - kindOfUtilization: str | None = Field( + kindOfUtilization: KindOfUtilization | None = Field( default=None, title="Kind Of Utilization", description="Only relevant if the type is utilization, " From 9a115e9250e99d5c5697e244161a0237e6723331 Mon Sep 17 00:00:00 2001 From: juwitte Date: Wed, 20 Aug 2025 12:41:50 +0000 Subject: [PATCH 03/10] feat: add lastUpdate to source and logo to identifier --- src/microbial_strain_data_model/classes/identifier.py | 5 +++++ src/microbial_strain_data_model/classes/source.py | 3 +++ 2 files changed, 8 insertions(+) diff --git a/src/microbial_strain_data_model/classes/identifier.py b/src/microbial_strain_data_model/classes/identifier.py index cf0d236..72f447e 100644 --- a/src/microbial_strain_data_model/classes/identifier.py +++ b/src/microbial_strain_data_model/classes/identifier.py @@ -25,6 +25,11 @@ class Identifier(BaseModel): title="URL", description="Uniform Resource Locator of a resource on the Internet", ) + logo: HttpUrl | None = Field( + default=None, + title="Logo", + description="Logo of the Identifier Organization (e.g. DOI, ORCID, ROR, ...)", + ) class IdentifierStrain(Identifier): diff --git a/src/microbial_strain_data_model/classes/source.py b/src/microbial_strain_data_model/classes/source.py index 05ce6f5..cbe3446 100644 --- a/src/microbial_strain_data_model/classes/source.py +++ b/src/microbial_strain_data_model/classes/source.py @@ -27,6 +27,9 @@ class Source(BaseModel): dateRecorded: Date = Field( default_factory=Date.today, title="Date Recorded", strict=False ) + lastUpdate: Date | None = Field( + default=None, title="Date of last update", strict=False + ) author: list[Person] = Field(default_factory=list, title="Author") publisher: list[Organization] = Field(default_factory=list, title="Publisher") From 2e487dc77b970e4fe0df666f6d58736ccfec46bb Mon Sep 17 00:00:00 2001 From: juwitte Date: Wed, 20 Aug 2025 12:46:19 +0000 Subject: [PATCH 04/10] feat: add GCMethod enum BREAKING CHANGE: --- src/microbial_strain_data_model/classes/enums.py | 13 +++++++++++++ .../classes/gccontent.py | 6 +++++- tests/example_data/bacteria.json | 3 ++- 3 files changed, 20 insertions(+), 2 deletions(-) diff --git a/src/microbial_strain_data_model/classes/enums.py b/src/microbial_strain_data_model/classes/enums.py index 02201e3..572f4dc 100644 --- a/src/microbial_strain_data_model/classes/enums.py +++ b/src/microbial_strain_data_model/classes/enums.py @@ -503,3 +503,16 @@ class KindOfUtilization(str, Enum): fermentation = "fermentation" hydrolysis = "hydrolysis" reduction = "reduction" + + +class GCMethod(str, Enum): + """ + Methods for GC measurement + + Args: + experimental: experimental + genomeSequence: genome sequence + """ + + experimental = "experimental" + genomeSequence = "genome sequence" diff --git a/src/microbial_strain_data_model/classes/gccontent.py b/src/microbial_strain_data_model/classes/gccontent.py index 2d62681..1dff4d5 100644 --- a/src/microbial_strain_data_model/classes/gccontent.py +++ b/src/microbial_strain_data_model/classes/gccontent.py @@ -1,6 +1,7 @@ from typing_extensions import Annotated from pydantic import BaseModel, ConfigDict, Field +from microbial_strain_data_model.classes.enums import GCMethod from microbial_strain_data_model.classes.links import SourceLink @@ -14,11 +15,14 @@ class GCContent(BaseModel): str_strip_whitespace=True, ) - method: str | None = Field( + method: GCMethod | None = Field( default=None, title="Method", description="Name of the method used to measure the GC content", ) + noteMethod: str | None = Field( + default=None, title="Note Method", description="Note about the used method" + ) value: Annotated[float, Field(ge=0, le=100)] = Field( title="Percent Value", description="Percent value of how much percent of the DNA is GC pairs", diff --git a/tests/example_data/bacteria.json b/tests/example_data/bacteria.json index 01787fa..6b64a8e 100644 --- a/tests/example_data/bacteria.json +++ b/tests/example_data/bacteria.json @@ -549,7 +549,8 @@ ], "gcContent": [ { - "method": "thermal denaturion, midpoint method (Tm)", + "method": "experimental", + "noteMethod": "thermal denaturion, midpoint method (Tm)", "source": [ "/sources/0" ], From 261a78dc1da2b286fcd968f4efe8dd90779855fd Mon Sep 17 00:00:00 2001 From: juwitte Date: Thu, 21 Aug 2025 10:26:42 +0000 Subject: [PATCH 05/10] feat: add OxygenRelation Enum --- .../classes/enums.py | 27 +++++++++++++++++++ .../classes/oxygenrelation.py | 3 ++- 2 files changed, 29 insertions(+), 1 deletion(-) diff --git a/src/microbial_strain_data_model/classes/enums.py b/src/microbial_strain_data_model/classes/enums.py index 572f4dc..4051e04 100644 --- a/src/microbial_strain_data_model/classes/enums.py +++ b/src/microbial_strain_data_model/classes/enums.py @@ -516,3 +516,30 @@ class GCMethod(str, Enum): experimental = "experimental" genomeSequence = "genome sequence" + + +class OxygenTolerance(str, Enum): + """ + How does the strain tolerate Oxygen + + Args: + aerobe: aerobe + aerotolerant: aerotolerant + anaerobe: anaerobe + facultativeAerobe: facultative aerobe + facultativeAnaerobe: facultative anaerobe + microaerophile: microaerophile + microaerotolerant: microaerotolerant + obligateAerobe: obligate aerobe + obligateAnaerobe: obligate anaerobe + """ + + aerobe = "aerobe" + aerotolerant = "aerotolerant" + anaerobe = "anaerobe" + facultativeAerobe = "facultative aerobe" + facultativeAnaerobe = "facultative anaerobe" + microaerophile = "microaerophile" + microaerotolerant = "microaerotolerant" + obligateAerobe = "obligate aerobe" + obligateAnaerobe = "obligate anaerobe" diff --git a/src/microbial_strain_data_model/classes/oxygenrelation.py b/src/microbial_strain_data_model/classes/oxygenrelation.py index 57526a5..554cdba 100644 --- a/src/microbial_strain_data_model/classes/oxygenrelation.py +++ b/src/microbial_strain_data_model/classes/oxygenrelation.py @@ -1,5 +1,6 @@ from pydantic import BaseModel, ConfigDict, Field +from microbial_strain_data_model.classes.enums import OxygenTolerance from microbial_strain_data_model.classes.links import RelationLink, SourceLink @@ -13,7 +14,7 @@ class OxygenRelation(BaseModel): str_strip_whitespace=True, ) - oxygenRelation: str = Field( + oxygenRelation: OxygenTolerance = Field( title="Oxygen Relation", description="Aerobic, anaerobic etc." ) relatedData: list[RelationLink] = Field( From 3e2370e8f4544bf0ba6bf8daf716ee28f0d3d664 Mon Sep 17 00:00:00 2001 From: juwitte Date: Thu, 21 Aug 2025 10:31:37 +0000 Subject: [PATCH 06/10] fix: change concentration of tolerance test to float value, was string --- src/microbial_strain_data_model/classes/tolerance.py | 2 +- tests/example_data/bacteria.json | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/src/microbial_strain_data_model/classes/tolerance.py b/src/microbial_strain_data_model/classes/tolerance.py index db87f4c..596018f 100644 --- a/src/microbial_strain_data_model/classes/tolerance.py +++ b/src/microbial_strain_data_model/classes/tolerance.py @@ -17,7 +17,7 @@ class ToleranceTest(BaseModel): ) reaction: ToleranceReaction = Field(title="Reaction") - concentration: str | None = Field( + concentration: float | None = Field( default=None, title="Concentration", description="Concentration value" ) unit: ConcentrationUnit = Field( diff --git a/tests/example_data/bacteria.json b/tests/example_data/bacteria.json index 6b64a8e..cc69405 100644 --- a/tests/example_data/bacteria.json +++ b/tests/example_data/bacteria.json @@ -1518,7 +1518,7 @@ ], "tests": [ { - "concentration": "30", + "concentration": 30, "reaction": "sensitive", "unit": "g/L" } @@ -1550,7 +1550,7 @@ ], "tests": [ { - "concentration": "10", + "concentration": 10, "reaction": "resistant", "unit": "g/L" } @@ -1581,7 +1581,7 @@ ], "tests": [ { - "concentration": "30", + "concentration": 30, "reaction": "intermediate", "unit": "g/L" } From 0f7f34aa288bd6cb64da45fcb7614adadccb53ff Mon Sep 17 00:00:00 2001 From: juwitte Date: Fri, 29 Aug 2025 08:48:53 +0000 Subject: [PATCH 07/10] refactor(restructure): restructure information of origin, morphology and growthcondtion into new classes the goal is to reduce top level elements and make the standard easier to understand BREAKING CHANGE: --- bin/python/build_docs_schema_excel.py | 4 +- docs/graph.md | 238 +++--- docs/python/microbe.md | 2 +- ... creation_date.md => 01. creation_date.md} | 2 +- docs/schema/01. version.md | 5 - ...3. organismType.md => 02. organismType.md} | 2 +- .../{04. morphType.md => 03. morphType.md} | 2 +- .../{07. typeStrain.md => 04. typeStrain.md} | 6 +- docs/schema/{08. taxon.md => 05. taxon.md} | 71 +- docs/schema/05. unifiedTypeStrain.md | 8 - docs/schema/06. origin.md | 542 ++++++++++++++ docs/schema/06. unifiedTaxon.md | 147 ---- docs/schema/{11. legal.md => 07. legal.md} | 59 +- docs/schema/08. oxygenRelation.md | 55 ++ ...ming.md => 09. multiCellComplexForming.md} | 8 +- docs/schema/09. sample.md | 203 ----- docs/schema/10. isolation.md | 179 ----- docs/schema/10. morphology.md | 206 ++++++ ...poreFormation.md => 11. sporeFormation.md} | 12 +- docs/schema/12. cellShape.md | 23 - ...{19. temperature.md => 12. temperature.md} | 24 +- docs/schema/13. oxygenRelation.md | 32 - docs/schema/{20. ph.md => 13. ph.md} | 24 +- .../{21. identifier.md => 14. identifier.md} | 21 +- docs/schema/15. cellSize.md | 92 --- ...ctedPersons.md => 15. connectedPersons.md} | 27 +- docs/schema/16. motility.md | 56 -- ... pathogenicity.md => 16. pathogenicity.md} | 12 +- .../{24. bioSafety.md => 17. bioSafety.md} | 10 +- docs/schema/17. colony.md | 74 -- .../{25. sequences.md => 18. sequences.md} | 33 +- .../{26. gcContent.md => 19. gcContent.md} | 22 +- .../{27. literature.md => 20. literature.md} | 78 +- ...onstituents.md => 21. wallConstituents.md} | 29 +- ...idProfiles.md => 22. fattyAcidProfiles.md} | 39 +- .../{30. staining.md => 23. staining.md} | 8 +- .../{31. hemolysis.md => 24. hemolysis.md} | 8 +- ...vationMedia.md => 25. cultivationMedia.md} | 12 +- .../{33. halophily.md => 26. halophily.md} | 47 +- .../{34. tolerances.md => 27. tolerances.md} | 45 +- docs/schema/28. enzymes.md | 107 +++ ...{36. metabolites.md => 29. metabolites.md} | 49 +- ...plications.md => 30. knownApplications.md} | 6 +- ...{38. collections.md => 31. collections.md} | 96 ++- .../{39. otherMedia.md => 32. otherMedia.md} | 14 +- ...{40. relatedData.md => 33. relatedData.md} | 6 +- .../schema/{41. sources.md => 34. sources.md} | 107 ++- docs/schema/35. enzymes.md | 62 -- schema/microbe_schema.json | 697 +++++++++--------- .../classes/cellshape.py | 19 - .../classes/chemicalsubstance.py | 28 +- .../classes/colony.py | 28 - .../classes/enums.py | 20 - .../{growthrange.py => growthcondition.py} | 45 +- .../classes/isolation.py | 42 -- .../classes/isolationtag.py | 36 + .../classes/{motility.py => morphology.py} | 14 +- .../classes/origin.py | 89 +++ .../classes/person.py | 19 - .../classes/sample.py | 76 -- .../classes/size.py | 19 - .../{microbe.py => strain.py} | 69 +- tests/example_data/bacteria.json | 314 +++----- tests/test_check_example_data.py | 4 +- tests/test_isolation_source.py | 18 +- tests/test_microbe.py | 14 +- 66 files changed, 2232 insertions(+), 2233 deletions(-) rename docs/schema/{02. creation_date.md => 01. creation_date.md} (69%) delete mode 100644 docs/schema/01. version.md rename docs/schema/{03. organismType.md => 02. organismType.md} (93%) rename docs/schema/{04. morphType.md => 03. morphType.md} (87%) rename docs/schema/{07. typeStrain.md => 04. typeStrain.md} (70%) rename docs/schema/{08. taxon.md => 05. taxon.md} (52%) delete mode 100644 docs/schema/05. unifiedTypeStrain.md create mode 100644 docs/schema/06. origin.md delete mode 100644 docs/schema/06. unifiedTaxon.md rename docs/schema/{11. legal.md => 07. legal.md} (67%) create mode 100644 docs/schema/08. oxygenRelation.md rename docs/schema/{14. multiCellComplexForming.md => 09. multiCellComplexForming.md} (66%) delete mode 100644 docs/schema/09. sample.md delete mode 100644 docs/schema/10. isolation.md create mode 100644 docs/schema/10. morphology.md rename docs/schema/{18. sporeFormation.md => 11. sporeFormation.md} (70%) delete mode 100644 docs/schema/12. cellShape.md rename docs/schema/{19. temperature.md => 12. temperature.md} (70%) delete mode 100644 docs/schema/13. oxygenRelation.md rename docs/schema/{20. ph.md => 13. ph.md} (76%) rename docs/schema/{21. identifier.md => 14. identifier.md} (62%) delete mode 100644 docs/schema/15. cellSize.md rename docs/schema/{22. connectedPersons.md => 15. connectedPersons.md} (60%) delete mode 100644 docs/schema/16. motility.md rename docs/schema/{23. pathogenicity.md => 16. pathogenicity.md} (84%) rename docs/schema/{24. bioSafety.md => 17. bioSafety.md} (77%) delete mode 100644 docs/schema/17. colony.md rename docs/schema/{25. sequences.md => 18. sequences.md} (70%) rename docs/schema/{26. gcContent.md => 19. gcContent.md} (58%) rename docs/schema/{27. literature.md => 20. literature.md} (58%) rename docs/schema/{28. wallConstituents.md => 21. wallConstituents.md} (61%) rename docs/schema/{29. fattyAcidProfiles.md => 22. fattyAcidProfiles.md} (59%) rename docs/schema/{30. staining.md => 23. staining.md} (81%) rename docs/schema/{31. hemolysis.md => 24. hemolysis.md} (83%) rename docs/schema/{32. cultivationMedia.md => 25. cultivationMedia.md} (62%) rename docs/schema/{33. halophily.md => 26. halophily.md} (73%) rename docs/schema/{34. tolerances.md => 27. tolerances.md} (72%) create mode 100644 docs/schema/28. enzymes.md rename docs/schema/{36. metabolites.md => 29. metabolites.md} (66%) rename docs/schema/{37. knownApplications.md => 30. knownApplications.md} (70%) rename docs/schema/{38. collections.md => 31. collections.md} (66%) rename docs/schema/{39. otherMedia.md => 32. otherMedia.md} (71%) rename docs/schema/{40. relatedData.md => 33. relatedData.md} (78%) rename docs/schema/{41. sources.md => 34. sources.md} (61%) delete mode 100644 docs/schema/35. enzymes.md delete mode 100644 src/microbial_strain_data_model/classes/cellshape.py delete mode 100644 src/microbial_strain_data_model/classes/colony.py rename src/microbial_strain_data_model/classes/{growthrange.py => growthcondition.py} (61%) delete mode 100644 src/microbial_strain_data_model/classes/isolation.py create mode 100644 src/microbial_strain_data_model/classes/isolationtag.py rename src/microbial_strain_data_model/classes/{motility.py => morphology.py} (60%) create mode 100644 src/microbial_strain_data_model/classes/origin.py delete mode 100644 src/microbial_strain_data_model/classes/sample.py rename src/microbial_strain_data_model/{microbe.py => strain.py} (72%) diff --git a/bin/python/build_docs_schema_excel.py b/bin/python/build_docs_schema_excel.py index 8d64cd8..d1e1c66 100644 --- a/bin/python/build_docs_schema_excel.py +++ b/bin/python/build_docs_schema_excel.py @@ -4,7 +4,7 @@ import json import pandas as pd -from microbial_strain_data_model.microbe import Microbe +from microbial_strain_data_model.strain import Strain # ruff: noqa: C901 @@ -39,7 +39,7 @@ def write_documentation(name, title, type, format, description, id, is_req): def parse_schema() -> None: - mi = Microbe.model_json_schema() + mi = Strain.model_json_schema() main_schema_path = Path("schema/microbe_schema.json") with main_schema_path.open("w") as f_out: f_out.write(json.dumps(mi, indent=2)) diff --git a/docs/graph.md b/docs/graph.md index ca32f14..5e4330d 100644 --- a/docs/graph.md +++ b/docs/graph.md @@ -22,15 +22,21 @@ yeast filamentous } -class `Taxon`{ +class `TypeStrain`{ +typeStrain: boolean +source: string +} + +class `TaxonWithSource`{ name: string -taxonRank: TaxonRank -taxonStatus: TaxonStatus +taxonRank: TaxonRank | null +taxonStatus: TaxonStatus | null identifier: array[Identifier] scientificName: ScientificName | null alternateName: string parentTaxon: Taxon | null sameAs: string +source: string } class `TaxonRank`{ @@ -58,6 +64,7 @@ name: string value: string propertyID: string | null url: string | null +logo: string | null } class `ScientificName`{ @@ -65,29 +72,27 @@ name: string author: string } -class `TypeStrain`{ -typeStrain: boolean -source: string -} - -class `TaxonWithSource`{ +class `Taxon`{ name: string -taxonRank: TaxonRank -taxonStatus: TaxonStatus +taxonRank: TaxonRank | null +taxonStatus: TaxonStatus | null identifier: array[Identifier] scientificName: ScientificName | null alternateName: string parentTaxon: Taxon | null sameAs: string -source: string } -class `Sample`{ -date: string | null +class `Origin`{ +sampleDate: string | null country: Country | null description: string | null locationCreated: Location | null tags: array[IsolationTag] +sampler: Person | null +isolationDate: string | null +isolatedAt: Organization | null +isolator: Person | null source: string } @@ -147,10 +152,9 @@ level2: string | null level3: string | null } -class `Isolation`{ -date: string | null -isolatedAt: Organization | null -source: string +class `Person`{ +name: string +identifier: array[Identifier] } class `Organization`{ @@ -199,26 +203,41 @@ value: string url: string | null } -class `CellShape`{ -cellShape: string -source: string -} - class `OxygenRelation`{ -oxygenRelation: string +oxygenRelation: OxygenTolerance relatedData: string source: string } +class `OxygenTolerance`{ +<> +aerobe +aerotolerant +anaerobe +facultative aerobe +facultative anaerobe +microaerophile +microaerotolerant +obligate aerobe +obligate anaerobe +} + class `MultiCell`{ multiCellComplexForming: boolean relatedData: string source: string } -class `CellSize`{ +class `Morphology`{ +cellShape: string cellLength: Size cellWidth: Size +motile: boolean | null +flagellum: boolean | null +flagellumArrangement: FlagellumArrangement | null +gliding: boolean | null +colonySize: Size | null +colonyColor: ColonyColor | null source: string } @@ -234,14 +253,6 @@ class `SizeUnit`{ mm } -class `Motility`{ -motile: boolean | null -flagellum: boolean | null -flagellumArrangement: FlagellumArrangement | null -gliding: boolean | null -source: string -} - class `FlagellumArrangement`{ <> Polar @@ -249,12 +260,6 @@ Peritrichous Monotrichous polar } -class `Colony`{ -size: Size | null -color: ColonyColor | null -source: string -} - class `ColonyColor`{ <> white @@ -324,6 +329,7 @@ name: string value: string propertyID: string | null url: string | null +logo: string | null source: string } @@ -401,11 +407,18 @@ other } class `GCContent`{ -method: string | null +method: GCMethod | null +noteMethod: string | null value: number source: string } +class `GCMethod`{ +<> +experimental +genome sequence +} + class `Literature`{ name: string | null url: string | null @@ -415,11 +428,6 @@ publisher: array[Organization] source: string } -class `Person`{ -name: string -identifier: array[Identifier] -} - class `CellWall`{ name: string | null identifier: array[Identifier] @@ -534,7 +542,7 @@ intermediate class `ToleranceTest`{ reaction: ToleranceReaction -concentration: string | null +concentration: number | null unit: ConcentrationUnit relatedData: string } @@ -542,7 +550,7 @@ relatedData: string class `Enzyme`{ name: string | null hasECNumber: string -url: string | null +identifier: array[Identifier] alternateName: string active: boolean | null relatedData: string @@ -561,7 +569,7 @@ class `MetaboliteTest`{ type: MetaboliteTestType active: boolean | null protocol: string | null -kindOfUtilization: string | null +kindOfUtilization: KindOfUtilization | null relatedData: string } @@ -571,6 +579,17 @@ utilization production } +class `KindOfUtilization`{ +<> +assimilation +builds acid from +degradation +energy source +fermentation +hydrolysis +reduction +} + class `Application`{ application: string source: string @@ -639,9 +658,10 @@ sourceType: SourceType mode: CurationMode name: string | null url: string | null -identifiers: array[Identifier] +identifier: array[Identifier] datePublished: string | null dateRecorded: string +lastUpdate: string | null author: array[Person] publisher: array[Organization] } @@ -660,24 +680,17 @@ automated unknown } -class `Microbe`{ -version: string +class `Strain`{ creation_date: string organismType: OrganismType morphType: Morph | null -unifiedTypeStrain: boolean | null -unifiedTaxon: Taxon | null typeStrain: array[TypeStrain] taxon: array[TaxonWithSource] -sample: array[Sample] -isolation: array[Isolation] +origin: array[Origin] legal: array[Legal] -cellShape: array[CellShape] oxygenRelation: array[OxygenRelation] multiCellComplexForming: array[MultiCell] -cellSize: array[CellSize] -motility: array[Motility] -colony: array[Colony] +morphology: array[Morphology] sporeFormation: array[Spore] temperature: array[Growth[C]] ph: array[Growth[pH]] @@ -704,110 +717,111 @@ relatedData: array[RelatedData] sources: array[Source] } -`Microbe` ..> `OrganismType` -`Microbe` ..> `Morph` -`Microbe` ..> `Taxon` -`Taxon` ..> `TaxonRank` -`Taxon` ..> `TaxonStatus` -`Taxon` ..> `Identifier` -`Taxon` ..> `ScientificName` -`Taxon` ..> `Taxon` -`Microbe` ..> `TypeStrain` -`Microbe` ..> `TaxonWithSource` +`Strain` ..> `OrganismType` +`Strain` ..> `Morph` +`Strain` ..> `TypeStrain` +`Strain` ..> `TaxonWithSource` `TaxonWithSource` ..> `TaxonRank` `TaxonWithSource` ..> `TaxonStatus` `TaxonWithSource` ..> `Identifier` `TaxonWithSource` ..> `ScientificName` `TaxonWithSource` ..> `Taxon` -`Microbe` ..> `Sample` -`Sample` ..> `Country` +`Taxon` ..> `TaxonRank` +`Taxon` ..> `TaxonStatus` +`Taxon` ..> `Identifier` +`Taxon` ..> `ScientificName` +`Taxon` ..> `Taxon` +`Strain` ..> `Origin` +`Origin` ..> `Country` `Country` ..> `CountryHistoricalAlpha2` `Country` ..> `CountryOtherCodes` `Country` ..> `Identifier` -`Sample` ..> `Location` +`Origin` ..> `Location` `Location` ..> `GeoPoint` -`Sample` ..> `IsolationTag` -`Microbe` ..> `Isolation` -`Isolation` ..> `Organization` +`Origin` ..> `IsolationTag` +`Origin` ..> `Person` +`Person` ..> `Identifier` +`Origin` ..> `Organization` `Organization` ..> `Identifier` `Organization` ..> `Address` -`Microbe` ..> `Legal` +`Origin` ..> `Person` +`Strain` ..> `Legal` `Legal` ..> `NagoyaRestrictions` `Legal` ..> `microbial_strain_data_model__classes__legal__Restriction` `microbial_strain_data_model__classes__legal__Restriction` ..> `Country` -`Microbe` ..> `CellShape` -`Microbe` ..> `OxygenRelation` -`Microbe` ..> `MultiCell` -`Microbe` ..> `CellSize` -`CellSize` ..> `Size` +`Strain` ..> `OxygenRelation` +`OxygenRelation` ..> `OxygenTolerance` +`Strain` ..> `MultiCell` +`Strain` ..> `Morphology` +`Morphology` ..> `Size` `Size` ..> `SizeUnit` -`CellSize` ..> `Size` -`Microbe` ..> `Motility` -`Motility` ..> `FlagellumArrangement` -`Microbe` ..> `Colony` -`Colony` ..> `Size` -`Colony` ..> `ColonyColor` -`Microbe` ..> `Spore` +`Morphology` ..> `Size` +`Morphology` ..> `FlagellumArrangement` +`Morphology` ..> `Size` +`Morphology` ..> `ColonyColor` +`Strain` ..> `Spore` `Spore` ..> `SporeType` -`Microbe` ..> `Growth[C]` +`Strain` ..> `Growth[C]` `Growth[C]` ..> `GrowthRange[C]` -`Microbe` ..> `Growth[pH]` +`Strain` ..> `Growth[pH]` `Growth[pH]` ..> `GrowthRange[pH]` -`Microbe` ..> `IdentifierStrain` -`Microbe` ..> `ConnectedPerson` +`Strain` ..> `IdentifierStrain` +`Strain` ..> `ConnectedPerson` `ConnectedPerson` ..> `Identifier` `ConnectedPerson` ..> `PersonRole` -`Microbe` ..> `Pathogen` +`Strain` ..> `Pathogen` `Pathogen` ..> `Host` `Pathogen` ..> `PathogenLevel` -`Microbe` ..> `BioSafety` -`Microbe` ..> `Sequence` +`Strain` ..> `BioSafety` +`Strain` ..> `Sequence` `Sequence` ..> `SequenceType` `Sequence` ..> `SequenceLevel` `Sequence` ..> `Identifier` -`Microbe` ..> `GCContent` -`Microbe` ..> `Literature` +`Strain` ..> `GCContent` +`GCContent` ..> `GCMethod` +`Strain` ..> `Literature` `Literature` ..> `Person` -`Person` ..> `Identifier` `Literature` ..> `Organization` -`Microbe` ..> `CellWall` +`Strain` ..> `CellWall` `CellWall` ..> `Identifier` -`Microbe` ..> `FattyAcidProfile` +`Strain` ..> `FattyAcidProfile` `FattyAcidProfile` ..> `FattyAcid` `FattyAcid` ..> `Identifier` -`Microbe` ..> `Staining` +`Strain` ..> `Staining` `Staining` ..> `StainingValue` -`Microbe` ..> `Hemolysis` +`Strain` ..> `Hemolysis` `Hemolysis` ..> `HemolysisBlood` `Hemolysis` ..> `HemolysisType` -`Microbe` ..> `CultivationMedia` -`Microbe` ..> `Halophil` +`Strain` ..> `CultivationMedia` +`Strain` ..> `Halophil` `Halophil` ..> `Identifier` `Halophil` ..> `ConcentrationUnit` `Halophil` ..> `GrowthRange_ConcentrationUnit_` `GrowthRange_ConcentrationUnit_` ..> `ConcentrationUnit` -`Microbe` ..> `Tolerance` +`Strain` ..> `Tolerance` `Tolerance` ..> `Identifier` `Tolerance` ..> `ToleranceReaction` `Tolerance` ..> `ConcentrationUnit` `Tolerance` ..> `ToleranceTest` `ToleranceTest` ..> `ToleranceReaction` `ToleranceTest` ..> `ConcentrationUnit` -`Microbe` ..> `Enzyme` -`Microbe` ..> `Metabolite` +`Strain` ..> `Enzyme` +`Enzyme` ..> `Identifier` +`Strain` ..> `Metabolite` `Metabolite` ..> `Identifier` `Metabolite` ..> `MetaboliteTest` `MetaboliteTest` ..> `MetaboliteTestType` -`Microbe` ..> `Application` -`Microbe` ..> `Collection` +`MetaboliteTest` ..> `KindOfUtilization` +`Strain` ..> `Application` +`Strain` ..> `Collection` `Collection` ..> `Identifier` `Collection` ..> `Address` `Collection` ..> `microbial_strain_data_model__classes__enums__Restriction` `Collection` ..> `SupplyForm` `Collection` ..> `Person` -`Microbe` ..> `OtherMedia` -`Microbe` ..> `RelatedData` -`Microbe` ..> `Source` +`Strain` ..> `OtherMedia` +`Strain` ..> `RelatedData` +`Strain` ..> `Source` `Source` ..> `SourceType` `Source` ..> `CurationMode` `Source` ..> `Identifier` diff --git a/docs/python/microbe.md b/docs/python/microbe.md index 800c5d6..63509ee 100644 --- a/docs/python/microbe.md +++ b/docs/python/microbe.md @@ -1,3 +1,3 @@ # Main Class -::: microbial_strain_data_model.microbe.Microbe +::: microbial_strain_data_model.strain.Strain diff --git a/docs/schema/02. creation_date.md b/docs/schema/01. creation_date.md similarity index 69% rename from docs/schema/02. creation_date.md rename to docs/schema/01. creation_date.md index 901b9d4..cef948b 100644 --- a/docs/schema/02. creation_date.md +++ b/docs/schema/01. creation_date.md @@ -1,5 +1,5 @@ --- -## 02. creation_date +## 01. creation_date Creation Date **string** diff --git a/docs/schema/01. version.md b/docs/schema/01. version.md deleted file mode 100644 index 4cb5c08..0000000 --- a/docs/schema/01. version.md +++ /dev/null @@ -1,5 +0,0 @@ ---- -## 01. version -Version `Required` - -**string** diff --git a/docs/schema/03. organismType.md b/docs/schema/02. organismType.md similarity index 93% rename from docs/schema/03. organismType.md rename to docs/schema/02. organismType.md index 5d42e86..41e7c5c 100644 --- a/docs/schema/03. organismType.md +++ b/docs/schema/02. organismType.md @@ -1,5 +1,5 @@ --- -## 03. organismType +## 02. organismType OrganismType `Required` Description: diff --git a/docs/schema/04. morphType.md b/docs/schema/03. morphType.md similarity index 87% rename from docs/schema/04. morphType.md rename to docs/schema/03. morphType.md index 002852d..8ff4b96 100644 --- a/docs/schema/04. morphType.md +++ b/docs/schema/03. morphType.md @@ -1,5 +1,5 @@ --- -## 04. morphType +## 03. morphType Morph Type Description: diff --git a/docs/schema/07. typeStrain.md b/docs/schema/04. typeStrain.md similarity index 70% rename from docs/schema/07. typeStrain.md rename to docs/schema/04. typeStrain.md index 91908c3..1fc08c8 100644 --- a/docs/schema/07. typeStrain.md +++ b/docs/schema/04. typeStrain.md @@ -1,17 +1,17 @@ --- -## 07. typeStrain +## 04. typeStrain Type Strain `Required` **array[object]** --- -## 07.1. typeStrain.typeStrain +## 04.1. typeStrain.typeStrain Type Strain `Required` **boolean** --- -## 07.2. typeStrain.source +## 04.2. typeStrain.source Source `Required` Description: diff --git a/docs/schema/08. taxon.md b/docs/schema/05. taxon.md similarity index 52% rename from docs/schema/08. taxon.md rename to docs/schema/05. taxon.md index d19648b..03bb198 100644 --- a/docs/schema/08. taxon.md +++ b/docs/schema/05. taxon.md @@ -1,34 +1,20 @@ --- -## 08. taxon +## 05. taxon Taxon `Required` **array[object]** --- -## 08.1. taxon.name +## 05.1. taxon.name Name `Required` **string** --- -## 08.2. taxon.taxonRank -TaxonRank `Required` +## 05.2. taxon.taxonRank +Taxon Rank -Description: -> Valid ranks of taxonomy -> -> Attributes: -> subspecies: subspecies -> species: species -> section: section -> genus: genus -> family: family -> order: order -> tax_class: class -> phylum: phylum -> domain: domain - -**string** +**string, null** Enum: @@ -43,18 +29,10 @@ Enum: domain --- -## 08.3. taxon.taxonStatus -TaxonStatus `Required` +## 05.3. taxon.taxonStatus +Taxon Status -Description: -> Valid taxon status -> -> Attributes: -> proposed: Proposed -> valid: Validly published -> valid_synonym: Validly published synonym - -**string** +**string, null** Enum: @@ -63,7 +41,7 @@ Enum: validly published synonym --- -## 08.4. taxon.identifier +## 05.4. taxon.identifier Identifier Description: @@ -72,7 +50,7 @@ Description: **array[object]** --- -## 08.4.1. taxon.identifier.name +## 05.4.1. taxon.identifier.name Name `Required` Description: @@ -81,7 +59,7 @@ Description: **string** --- -## 08.4.2. taxon.identifier.value +## 05.4.2. taxon.identifier.value Value `Required` Description: @@ -90,7 +68,7 @@ Description: **string** --- -## 08.4.3. taxon.identifier.propertyID +## 05.4.3. taxon.identifier.propertyID Property ID Description: @@ -99,7 +77,7 @@ Description: **string, null** --- -## 08.4.4. taxon.identifier.url +## 05.4.4. taxon.identifier.url URL Description: @@ -108,43 +86,52 @@ Description: **string, null** --- -## 08.5. taxon.scientificName +## 05.4.5. taxon.identifier.logo +Logo + +Description: +> Logo of the Identifier Organization (e.g. DOI, ORCID, ROR, ...) + +**string, null** + +--- +## 05.5. taxon.scientificName Scientific Name **object, null** --- -## 08.5.1. taxon.scientificName.name +## 05.5.1. taxon.scientificName.name Name `Required` **string** --- -## 08.5.2. taxon.scientificName.author +## 05.5.2. taxon.scientificName.author Author `Required` **string** --- -## 08.6. taxon.alternateName +## 05.6. taxon.alternateName Alternate Name **array[string]** --- -## 08.7. taxon.parentTaxon +## 05.7. taxon.parentTaxon Parent Taxon **object, null** --- -## 08.8. taxon.sameAs +## 05.8. taxon.sameAs Same As **array[string]** --- -## 08.9. taxon.source +## 05.9. taxon.source Source `Required` Description: diff --git a/docs/schema/05. unifiedTypeStrain.md b/docs/schema/05. unifiedTypeStrain.md deleted file mode 100644 index 69d5241..0000000 --- a/docs/schema/05. unifiedTypeStrain.md +++ /dev/null @@ -1,8 +0,0 @@ ---- -## 05. unifiedTypeStrain -Unified Type Strain - -Description: -> Is this strain type for unified species - -**boolean, null** diff --git a/docs/schema/06. origin.md b/docs/schema/06. origin.md new file mode 100644 index 0000000..539e8a4 --- /dev/null +++ b/docs/schema/06. origin.md @@ -0,0 +1,542 @@ +--- +## 06. origin +Origin + +Description: +> Sample and isolation data + +**array[object]** + +--- +## 06.1. origin.sampleDate +Date + +Description: +> Date of sampling, using date range format of dublin core: 'YYYY-MM-DD/YYYY-MM-DD' ether side can be empty defining an open ended range, only the year is mandatory, e.g. '/1978' means before 1978 + +**string, null** + +--- +## 06.2. origin.country +Country + +Description: +> Country where the sample material originated from + +**object, null** + +--- +## 06.2.1. origin.country.name +Country name `Required` + +Description: +> Country code, see ISO 3166-1 alpha-2 + +**string, string, string** + +--- +## 06.2.2. origin.country.identifier +Identifier + +Description: +> Identifier of every Kind, compare to schema.org PropertyValue class + +**array[object]** + +--- +## 06.2.2.1. origin.country.identifier.name +Name `Required` + +Description: +> Name of the identifier + +**string** + +--- +## 06.2.2.2. origin.country.identifier.value +Value `Required` + +Description: +> Value of the identifier (can also be a URL) + +**string** + +--- +## 06.2.2.3. origin.country.identifier.propertyID +Property ID + +Description: +> See schema.org/propertyID + +**string, null** + +--- +## 06.2.2.4. origin.country.identifier.url +URL + +Description: +> Uniform Resource Locator of a resource on the Internet + +**string, null** + +--- +## 06.2.2.5. origin.country.identifier.logo +Logo + +Description: +> Logo of the Identifier Organization (e.g. DOI, ORCID, ROR, ...) + +**string, null** + +--- +## 06.2.3. origin.country.conventionOfBiologicalDiversityParty +Is Convention Of Biological Diversity Party + +**boolean, null** + +--- +## 06.2.4. origin.country.cartagenaProtocolParty +Is Cartagena Protocol Party + +**boolean, null** + +--- +## 06.2.5. origin.country.nagoyaProtocolParty +Is Nagoya Protocol Party + +**boolean, null** + +--- +## 06.2.6. origin.country.nagoyaKualaLumpurParty +Is Nagoya Kuala Lumpur Party + +**boolean, null** + +--- +## 06.3. origin.description +Description + +Description: +> Description of the sample + +**string, null** + +--- +## 06.4. origin.locationCreated +Location Created + +Description: +> Location where the sample was taken + +**object, null** + +--- +## 06.4.1. origin.locationCreated.name +Name + +Description: +> Name of the location, e.g. 'Lake Como' + +**string, null** + +--- +## 06.4.2. origin.locationCreated.description +Description + +Description: +> Description of the location + +**string, null** + +--- +## 06.4.3. origin.locationCreated.geo +Geo + +Description: +> Precise location coordinates + +**object, null** + +--- +## 06.4.3.1. origin.locationCreated.geo.latitude +Latitude `Required` + +Description: +> Should be a float value between -90 and 90 + +**number, string** + +--- +## 06.4.3.2. origin.locationCreated.geo.longitude +Longitude `Required` + +Description: +> Should be a float value between -180 and 180 + +**number, string** + +--- +## 06.4.3.3. origin.locationCreated.geo.elevation +Elevation + +**number, null** + +--- +## 06.4.3.4. origin.locationCreated.geo.precision +Precision + +**number, null** + +--- +## 06.5. origin.tags +Isolation Source Tags + +Description: +> Isolation tag system, original used by BacDive + +**array[object]** + +--- +## 06.5.1. origin.tags.level1 +Level 1 `Required` + +**string** + +--- +## 06.5.2. origin.tags.level2 +Level 2 + +**string, null** + +--- +## 06.5.3. origin.tags.level3 +Level 3 + +**string, null** + +--- +## 06.6. origin.sampler +Sampler + +Description: +> Person that sampled the material + +**object, null** + +--- +## 06.6.1. origin.sampler.name +Name `Required` + +Description: +> Name of the person, preferable: [Last], [First] + +**string** + +--- +## 06.6.2. origin.sampler.identifier +Identifier + +Description: +> Person identifiers like ORCID + +**array[object]** + +--- +## 06.6.2.1. origin.sampler.identifier.name +Name `Required` + +Description: +> Name of the identifier + +**string** + +--- +## 06.6.2.2. origin.sampler.identifier.value +Value `Required` + +Description: +> Value of the identifier (can also be a URL) + +**string** + +--- +## 06.6.2.3. origin.sampler.identifier.propertyID +Property ID + +Description: +> See schema.org/propertyID + +**string, null** + +--- +## 06.6.2.4. origin.sampler.identifier.url +URL + +Description: +> Uniform Resource Locator of a resource on the Internet + +**string, null** + +--- +## 06.6.2.5. origin.sampler.identifier.logo +Logo + +Description: +> Logo of the Identifier Organization (e.g. DOI, ORCID, ROR, ...) + +**string, null** + +--- +## 06.7. origin.isolationDate +Date + +Description: +> Date of isolation from the sample material, using date range format of dublin core:'YYYY-MM-DD/YYYY-MM-DD' ether side can be empty defining an open ended range, only the year is mandatory, e.g. '/1978' means before 1978 + +**string, null** + +--- +## 06.8. origin.isolatedAt +Isolated At + +Description: +> Institute where the strain was isolated from the sample + +**object, null** + +--- +## 06.8.1. origin.isolatedAt.name +Name `Required` + +Description: +> Short name of the organization + +**string** + +--- +## 06.8.2. origin.isolatedAt.identifier +Identifier + +Description: +> Identifiers of the organization, e.g. ROR + +**array[object]** + +--- +## 06.8.2.1. origin.isolatedAt.identifier.name +Name `Required` + +Description: +> Name of the identifier + +**string** + +--- +## 06.8.2.2. origin.isolatedAt.identifier.value +Value `Required` + +Description: +> Value of the identifier (can also be a URL) + +**string** + +--- +## 06.8.2.3. origin.isolatedAt.identifier.propertyID +Property ID + +Description: +> See schema.org/propertyID + +**string, null** + +--- +## 06.8.2.4. origin.isolatedAt.identifier.url +URL + +Description: +> Uniform Resource Locator of a resource on the Internet + +**string, null** + +--- +## 06.8.2.5. origin.isolatedAt.identifier.logo +Logo + +Description: +> Logo of the Identifier Organization (e.g. DOI, ORCID, ROR, ...) + +**string, null** + +--- +## 06.8.3. origin.isolatedAt.legalName +Legal Name + +Description: +> Full legal name of the organization + +**string, null** + +--- +## 06.8.4. origin.isolatedAt.address +Address + +Description: +> Address of the organization + +**object, null** + +--- +## 06.8.4.1. origin.isolatedAt.address.addressCountry +Country + +Description: +> Country code, see ISO 3166-1 alpha-2 + +**string, null** + +--- +## 06.8.4.2. origin.isolatedAt.address.addressRegion +Region + +Description: +> Region within the country + +**string, null** + +--- +## 06.8.4.3. origin.isolatedAt.address.addressLocality +Locality + +Description: +> Locality within the region + +**string, null** + +--- +## 06.8.4.4. origin.isolatedAt.address.postOfficeBoxNumber +Post Office Box Number + +**string, null** + +--- +## 06.8.4.5. origin.isolatedAt.address.postalCode +Postal Code + +**string, null** + +--- +## 06.8.4.6. origin.isolatedAt.address.streetAddress +Street Address + +Description: +> Name of the street and number within street + +**string, null** + +--- +## 06.8.5. origin.isolatedAt.url +URL + +Description: +> Link to homepage + +**string, null** + +--- +## 06.8.6. origin.isolatedAt.email +Email + +Description: +> Contact email + +**string, null** + +--- +## 06.8.7. origin.isolatedAt.logo +Logo + +Description: +> Link to logo + +**string, null** + +--- +## 06.9. origin.isolator +Isolator + +Description: +> Person that isolated the strain from the sample + +**object, null** + +--- +## 06.9.1. origin.isolator.name +Name `Required` + +Description: +> Name of the person, preferable: [Last], [First] + +**string** + +--- +## 06.9.2. origin.isolator.identifier +Identifier + +Description: +> Person identifiers like ORCID + +**array[object]** + +--- +## 06.9.2.1. origin.isolator.identifier.name +Name `Required` + +Description: +> Name of the identifier + +**string** + +--- +## 06.9.2.2. origin.isolator.identifier.value +Value `Required` + +Description: +> Value of the identifier (can also be a URL) + +**string** + +--- +## 06.9.2.3. origin.isolator.identifier.propertyID +Property ID + +Description: +> See schema.org/propertyID + +**string, null** + +--- +## 06.9.2.4. origin.isolator.identifier.url +URL + +Description: +> Uniform Resource Locator of a resource on the Internet + +**string, null** + +--- +## 06.9.2.5. origin.isolator.identifier.logo +Logo + +Description: +> Logo of the Identifier Organization (e.g. DOI, ORCID, ROR, ...) + +**string, null** + +--- +## 06.10. origin.source +Source `Required` + +Description: +> List of JSON paths to source object + +**array[string]** diff --git a/docs/schema/06. unifiedTaxon.md b/docs/schema/06. unifiedTaxon.md deleted file mode 100644 index 6a3650d..0000000 --- a/docs/schema/06. unifiedTaxon.md +++ /dev/null @@ -1,147 +0,0 @@ ---- -## 06. unifiedTaxon -Unified Taxon - -Description: -> Evaluated and updated taxonomy - -**object, null** - ---- -## 06.1. unifiedTaxon.name -Name `Required` - -**string** - ---- -## 06.2. unifiedTaxon.taxonRank -TaxonRank `Required` - -Description: -> Valid ranks of taxonomy -> -> Attributes: -> subspecies: subspecies -> species: species -> section: section -> genus: genus -> family: family -> order: order -> tax_class: class -> phylum: phylum -> domain: domain - -**string** - -Enum: - - subspecies - species - section - genus - family - order - class - phylum - domain - ---- -## 06.3. unifiedTaxon.taxonStatus -TaxonStatus `Required` - -Description: -> Valid taxon status -> -> Attributes: -> proposed: Proposed -> valid: Validly published -> valid_synonym: Validly published synonym - -**string** - -Enum: - - proposed - validly published - validly published synonym - ---- -## 06.4. unifiedTaxon.identifier -Identifier - -Description: -> Identifier of every Kind, compare to schema.org PropertyValue class - -**array[object]** - ---- -## 06.4.1. unifiedTaxon.identifier.name -Name `Required` - -Description: -> Name of the identifier - -**string** - ---- -## 06.4.2. unifiedTaxon.identifier.value -Value `Required` - -Description: -> Value of the identifier (can also be a URL) - -**string** - ---- -## 06.4.3. unifiedTaxon.identifier.propertyID -Property ID - -Description: -> See schema.org/propertyID - -**string, null** - ---- -## 06.4.4. unifiedTaxon.identifier.url -URL - -Description: -> Uniform Resource Locator of a resource on the Internet - -**string, null** - ---- -## 06.5. unifiedTaxon.scientificName -Scientific Name - -**object, null** - ---- -## 06.5.1. unifiedTaxon.scientificName.name -Name `Required` - -**string** - ---- -## 06.5.2. unifiedTaxon.scientificName.author -Author `Required` - -**string** - ---- -## 06.6. unifiedTaxon.alternateName -Alternate Name - -**array[string]** - ---- -## 06.7. unifiedTaxon.parentTaxon -Parent Taxon - -**object, null** - ---- -## 06.8. unifiedTaxon.sameAs -Same As - -**array[string]** diff --git a/docs/schema/11. legal.md b/docs/schema/07. legal.md similarity index 67% rename from docs/schema/11. legal.md rename to docs/schema/07. legal.md index d62d2a9..7b8cddd 100644 --- a/docs/schema/11. legal.md +++ b/docs/schema/07. legal.md @@ -1,23 +1,23 @@ --- -## 11. legal +## 07. legal Legal **array[object]** --- -## 11.1. legal.dualUse +## 07.1. legal.dualUse Dual Use **boolean, null** --- -## 11.2. legal.quarantineEU +## 07.2. legal.quarantineEU Quarantine EU **boolean, null** --- -## 11.3. legal.nagoyaRestrictions +## 07.3. legal.nagoyaRestrictions NagoyaRestrictions `Required` Description: @@ -37,7 +37,7 @@ Enum: Strain probably in scope, please contact the culture collection --- -## 11.4. legal.qps +## 07.4. legal.qps QPS Description: @@ -46,7 +46,7 @@ Description: **boolean, null** --- -## 11.5. legal.gras +## 07.5. legal.gras GRAS Description: @@ -55,7 +55,7 @@ Description: **boolean, null** --- -## 11.6. legal.gmo +## 07.6. legal.gmo GMO Description: @@ -64,7 +64,7 @@ Description: **boolean, null** --- -## 11.7. legal.gmoInformation +## 07.7. legal.gmoInformation GMO Information Description: @@ -73,7 +73,7 @@ Description: **string, null** --- -## 11.8. legal.otherRestrictions +## 07.8. legal.otherRestrictions Other Restrictions Description: @@ -82,7 +82,7 @@ Description: **array[object]** --- -## 11.8.1. legal.otherRestrictions.name +## 07.8.1. legal.otherRestrictions.name Name `Required` Description: @@ -91,7 +91,7 @@ Description: **string** --- -## 11.8.2. legal.otherRestrictions.country +## 07.8.2. legal.otherRestrictions.country Country Description: @@ -100,7 +100,7 @@ Description: **object, null** --- -## 11.8.2.1. legal.otherRestrictions.country.name +## 07.8.2.1. legal.otherRestrictions.country.name Country name `Required` Description: @@ -109,7 +109,7 @@ Description: **string, string, string** --- -## 11.8.2.2. legal.otherRestrictions.country.identifier +## 07.8.2.2. legal.otherRestrictions.country.identifier Identifier Description: @@ -118,7 +118,7 @@ Description: **array[object]** --- -## 11.8.2.2.1. legal.otherRestrictions.country.identifier.name +## 07.8.2.2.1. legal.otherRestrictions.country.identifier.name Name `Required` Description: @@ -127,7 +127,7 @@ Description: **string** --- -## 11.8.2.2.2. legal.otherRestrictions.country.identifier.value +## 07.8.2.2.2. legal.otherRestrictions.country.identifier.value Value `Required` Description: @@ -136,7 +136,7 @@ Description: **string** --- -## 11.8.2.2.3. legal.otherRestrictions.country.identifier.propertyID +## 07.8.2.2.3. legal.otherRestrictions.country.identifier.propertyID Property ID Description: @@ -145,7 +145,7 @@ Description: **string, null** --- -## 11.8.2.2.4. legal.otherRestrictions.country.identifier.url +## 07.8.2.2.4. legal.otherRestrictions.country.identifier.url URL Description: @@ -154,31 +154,40 @@ Description: **string, null** --- -## 11.8.2.3. legal.otherRestrictions.country.conventionOfBiologicalDiversityParty +## 07.8.2.2.5. legal.otherRestrictions.country.identifier.logo +Logo + +Description: +> Logo of the Identifier Organization (e.g. DOI, ORCID, ROR, ...) + +**string, null** + +--- +## 07.8.2.3. legal.otherRestrictions.country.conventionOfBiologicalDiversityParty Is Convention Of Biological Diversity Party **boolean, null** --- -## 11.8.2.4. legal.otherRestrictions.country.cartagenaProtocolParty +## 07.8.2.4. legal.otherRestrictions.country.cartagenaProtocolParty Is Cartagena Protocol Party **boolean, null** --- -## 11.8.2.5. legal.otherRestrictions.country.nagoyaProtocolParty +## 07.8.2.5. legal.otherRestrictions.country.nagoyaProtocolParty Is Nagoya Protocol Party **boolean, null** --- -## 11.8.2.6. legal.otherRestrictions.country.nagoyaKualaLumpurParty +## 07.8.2.6. legal.otherRestrictions.country.nagoyaKualaLumpurParty Is Nagoya Kuala Lumpur Party **boolean, null** --- -## 11.8.3. legal.otherRestrictions.authority +## 07.8.3. legal.otherRestrictions.authority Authority Description: @@ -187,7 +196,7 @@ Description: **string, null** --- -## 11.8.4. legal.otherRestrictions.value +## 07.8.4. legal.otherRestrictions.value Value `Required` Description: @@ -196,7 +205,7 @@ Description: **string** --- -## 11.8.5. legal.otherRestrictions.url +## 07.8.5. legal.otherRestrictions.url URL Description: @@ -205,7 +214,7 @@ Description: **string, null** --- -## 11.9. legal.source +## 07.9. legal.source Source `Required` Description: diff --git a/docs/schema/08. oxygenRelation.md b/docs/schema/08. oxygenRelation.md new file mode 100644 index 0000000..9f41a38 --- /dev/null +++ b/docs/schema/08. oxygenRelation.md @@ -0,0 +1,55 @@ +--- +## 08. oxygenRelation +Oxygen Relation + +**array[object]** + +--- +## 08.1. oxygenRelation.oxygenRelation +OxygenTolerance `Required` + +Description: +> How does the strain tolerate Oxygen +> +> Args: +> aerobe: aerobe +> aerotolerant: aerotolerant +> anaerobe: anaerobe +> facultativeAerobe: facultative aerobe +> facultativeAnaerobe: facultative anaerobe +> microaerophile: microaerophile +> microaerotolerant: microaerotolerant +> obligateAerobe: obligate aerobe +> obligateAnaerobe: obligate anaerobe + +**string** + +Enum: + + aerobe + aerotolerant + anaerobe + facultative aerobe + facultative anaerobe + microaerophile + microaerotolerant + obligate aerobe + obligate anaerobe + +--- +## 08.2. oxygenRelation.relatedData +Related Data + +Description: +> JSON paths to relation object + +**array[string]** + +--- +## 08.3. oxygenRelation.source +Source `Required` + +Description: +> List of JSON paths to source object + +**array[string]** diff --git a/docs/schema/14. multiCellComplexForming.md b/docs/schema/09. multiCellComplexForming.md similarity index 66% rename from docs/schema/14. multiCellComplexForming.md rename to docs/schema/09. multiCellComplexForming.md index 37ec4e2..f063614 100644 --- a/docs/schema/14. multiCellComplexForming.md +++ b/docs/schema/09. multiCellComplexForming.md @@ -1,11 +1,11 @@ --- -## 14. multiCellComplexForming +## 09. multiCellComplexForming Multi Cell Complex Forming **array[object]** --- -## 14.1. multiCellComplexForming.multiCellComplexForming +## 09.1. multiCellComplexForming.multiCellComplexForming Multi Cell Complex Forming `Required` Description: @@ -14,7 +14,7 @@ Description: **boolean** --- -## 14.2. multiCellComplexForming.relatedData +## 09.2. multiCellComplexForming.relatedData Related Data Description: @@ -23,7 +23,7 @@ Description: **array[string]** --- -## 14.3. multiCellComplexForming.source +## 09.3. multiCellComplexForming.source Source `Required` Description: diff --git a/docs/schema/09. sample.md b/docs/schema/09. sample.md deleted file mode 100644 index 9848b6d..0000000 --- a/docs/schema/09. sample.md +++ /dev/null @@ -1,203 +0,0 @@ ---- -## 09. sample -Sample - -**array[object]** - ---- -## 09.1. sample.date -Date - -Description: -> Date of Sampling, using date range format of dublin core: 'YYYY-MM-DD/YYYY-MM-DD' ether side can be empty defining an open ended range, only the year is mandatory, e.g. '/1978' means before 1978 - -**string, null** - ---- -## 09.2. sample.country -Country - -**object, null** - ---- -## 09.2.1. sample.country.name -Country name `Required` - -Description: -> Country code, see ISO 3166-1 alpha-2 - -**string, string, string** - ---- -## 09.2.2. sample.country.identifier -Identifier - -Description: -> Identifier of every Kind, compare to schema.org PropertyValue class - -**array[object]** - ---- -## 09.2.2.1. sample.country.identifier.name -Name `Required` - -Description: -> Name of the identifier - -**string** - ---- -## 09.2.2.2. sample.country.identifier.value -Value `Required` - -Description: -> Value of the identifier (can also be a URL) - -**string** - ---- -## 09.2.2.3. sample.country.identifier.propertyID -Property ID - -Description: -> See schema.org/propertyID - -**string, null** - ---- -## 09.2.2.4. sample.country.identifier.url -URL - -Description: -> Uniform Resource Locator of a resource on the Internet - -**string, null** - ---- -## 09.2.3. sample.country.conventionOfBiologicalDiversityParty -Is Convention Of Biological Diversity Party - -**boolean, null** - ---- -## 09.2.4. sample.country.cartagenaProtocolParty -Is Cartagena Protocol Party - -**boolean, null** - ---- -## 09.2.5. sample.country.nagoyaProtocolParty -Is Nagoya Protocol Party - -**boolean, null** - ---- -## 09.2.6. sample.country.nagoyaKualaLumpurParty -Is Nagoya Kuala Lumpur Party - -**boolean, null** - ---- -## 09.3. sample.description -Description - -**string, null** - ---- -## 09.4. sample.locationCreated -Location Created - -**object, null** - ---- -## 09.4.1. sample.locationCreated.name -Name - -Description: -> Name of the location, e.g. 'Lake Como' - -**string, null** - ---- -## 09.4.2. sample.locationCreated.description -Description - -Description: -> Description of the location - -**string, null** - ---- -## 09.4.3. sample.locationCreated.geo -Geo - -Description: -> Precise location coordinates - -**object, null** - ---- -## 09.4.3.1. sample.locationCreated.geo.latitude -Latitude `Required` - -Description: -> Should be a float value between -90 and 90 - -**number, string** - ---- -## 09.4.3.2. sample.locationCreated.geo.longitude -Longitude `Required` - -Description: -> Should be a float value between -180 and 180 - -**number, string** - ---- -## 09.4.3.3. sample.locationCreated.geo.elevation -Elevation - -**number, null** - ---- -## 09.4.3.4. sample.locationCreated.geo.precision -Precision - -**number, null** - ---- -## 09.5. sample.tags -Isolation Source Tags - -Description: -> Isolation tag system, original used by BacDive - -**array[object]** - ---- -## 09.5.1. sample.tags.level1 -Level 1 `Required` - -**string** - ---- -## 09.5.2. sample.tags.level2 -Level 2 - -**string, null** - ---- -## 09.5.3. sample.tags.level3 -Level 3 - -**string, null** - ---- -## 09.6. sample.source -Source `Required` - -Description: -> List of JSON paths to source object - -**array[string]** diff --git a/docs/schema/10. isolation.md b/docs/schema/10. isolation.md deleted file mode 100644 index b37a2e1..0000000 --- a/docs/schema/10. isolation.md +++ /dev/null @@ -1,179 +0,0 @@ ---- -## 10. isolation -Isolation - -**array[object]** - ---- -## 10.1. isolation.date -Date - -Description: -> Date of Isolation, using date range format of dublin core: 'YYYY-MM-DD/YYYY-MM-DD' ether side can be empty defining an open ended range, only the year is mandatory, e.g. '/1978' means before 1978 - -**string, null** - ---- -## 10.2. isolation.isolatedAt -Isolated At - -Description: -> Institute where the isolation happened - -**object, null** - ---- -## 10.2.1. isolation.isolatedAt.name -Name `Required` - -Description: -> Short name of the organization - -**string** - ---- -## 10.2.2. isolation.isolatedAt.identifier -Identifier - -Description: -> Identifiers of the organization, e.g. ROR - -**array[object]** - ---- -## 10.2.2.1. isolation.isolatedAt.identifier.name -Name `Required` - -Description: -> Name of the identifier - -**string** - ---- -## 10.2.2.2. isolation.isolatedAt.identifier.value -Value `Required` - -Description: -> Value of the identifier (can also be a URL) - -**string** - ---- -## 10.2.2.3. isolation.isolatedAt.identifier.propertyID -Property ID - -Description: -> See schema.org/propertyID - -**string, null** - ---- -## 10.2.2.4. isolation.isolatedAt.identifier.url -URL - -Description: -> Uniform Resource Locator of a resource on the Internet - -**string, null** - ---- -## 10.2.3. isolation.isolatedAt.legalName -Legal Name - -Description: -> Full legal name of the organization - -**string, null** - ---- -## 10.2.4. isolation.isolatedAt.address -Address - -Description: -> Address of the organization - -**object, null** - ---- -## 10.2.4.1. isolation.isolatedAt.address.addressCountry -Country - -Description: -> Country code, see ISO 3166-1 alpha-2 - -**string, null** - ---- -## 10.2.4.2. isolation.isolatedAt.address.addressRegion -Region - -Description: -> Region within the country - -**string, null** - ---- -## 10.2.4.3. isolation.isolatedAt.address.addressLocality -Locality - -Description: -> Locality within the region - -**string, null** - ---- -## 10.2.4.4. isolation.isolatedAt.address.postOfficeBoxNumber -Post Office Box Number - -**string, null** - ---- -## 10.2.4.5. isolation.isolatedAt.address.postalCode -Postal Code - -**string, null** - ---- -## 10.2.4.6. isolation.isolatedAt.address.streetAddress -Street Address - -Description: -> Name of the street and number within street - -**string, null** - ---- -## 10.2.5. isolation.isolatedAt.url -URL - -Description: -> Link to homepage - -**string, null** - ---- -## 10.2.6. isolation.isolatedAt.email -Email - -Description: -> Contact email - -**string, null** - ---- -## 10.2.7. isolation.isolatedAt.logo -Logo - -Description: -> Link to logo - -**string, null** - ---- -## 10.3. isolation.source -Source `Required` - -Description: -> List of JSON paths to source object - -**array[string]** diff --git a/docs/schema/10. morphology.md b/docs/schema/10. morphology.md new file mode 100644 index 0000000..78567a5 --- /dev/null +++ b/docs/schema/10. morphology.md @@ -0,0 +1,206 @@ +--- +## 10. morphology +Morphology + +Description: +> Morphology information + +**array[object]** + +--- +## 10.1. morphology.cellShape +Cell Shape `Required` + +Description: +> The shape type the cells + +**string** + +--- +## 10.2. morphology.cellLength +Size `Required` + +Description: +> size object, use only for micro and millimeter + +**object** + +--- +## 10.2.1. morphology.cellLength.minimal +Minimal `Required` + +**number** + +--- +## 10.2.2. morphology.cellLength.maximal +Maximal `Required` + +**number** + +--- +## 10.2.3. morphology.cellLength.unit +SizeUnit `Required` + +Description: +> Valid size options for microbes +> +> Attributes: +> µm: µm +> mm: mm + +**string** + +Enum: + + µm + mm + +--- +## 10.3. morphology.cellWidth +Size `Required` + +Description: +> size object, use only for micro and millimeter + +**object** + +--- +## 10.3.1. morphology.cellWidth.minimal +Minimal `Required` + +**number** + +--- +## 10.3.2. morphology.cellWidth.maximal +Maximal `Required` + +**number** + +--- +## 10.3.3. morphology.cellWidth.unit +SizeUnit `Required` + +Description: +> Valid size options for microbes +> +> Attributes: +> µm: µm +> mm: mm + +**string** + +Enum: + + µm + mm + +--- +## 10.4. morphology.motile +Motile + +Description: +> Are the cells of this strain are motile + +**boolean, null** + +--- +## 10.5. morphology.flagellum +Flagellum + +Description: +> Do the cells have flagella + +**boolean, null** + +--- +## 10.6. morphology.flagellumArrangement +Flagellum Arrangement + +Description: +> How are the flagella arranged + +**string, null** + +Enum: + + Polar + Peritrichous + Monotrichous polar + +--- +## 10.7. morphology.gliding +Gliding + +Description: +> Cells can be motile by gliding instead of having flagella + +**boolean, null** + +--- +## 10.8. morphology.colonySize +Size of Colony + +**object, null** + +--- +## 10.8.1. morphology.colonySize.minimal +Minimal `Required` + +**number** + +--- +## 10.8.2. morphology.colonySize.maximal +Maximal `Required` + +**number** + +--- +## 10.8.3. morphology.colonySize.unit +SizeUnit `Required` + +Description: +> Valid size options for microbes +> +> Attributes: +> µm: µm +> mm: mm + +**string** + +Enum: + + µm + mm + +--- +## 10.9. morphology.colonyColor +Color of Colony + +Description: +> Color of the colony on the + +**string, null** + +Enum: + + white + cream + yellowish + orange + pink + red + buff + darkbrown + reyish + tannish + beige + brownish + +--- +## 10.10. morphology.source +Source `Required` + +Description: +> List of JSON paths to source object + +**array[string]** diff --git a/docs/schema/18. sporeFormation.md b/docs/schema/11. sporeFormation.md similarity index 70% rename from docs/schema/18. sporeFormation.md rename to docs/schema/11. sporeFormation.md index 94eea58..ea75ba6 100644 --- a/docs/schema/18. sporeFormation.md +++ b/docs/schema/11. sporeFormation.md @@ -1,17 +1,17 @@ --- -## 18. sporeFormation +## 11. sporeFormation Spore Formation **array[object]** --- -## 18.1. sporeFormation.sporeBuilding +## 11.1. sporeFormation.sporeBuilding sporeBuilding **boolean, null** --- -## 18.2. sporeFormation.typeOfSpore +## 11.2. sporeFormation.typeOfSpore SporeType `Required` Description: @@ -29,13 +29,13 @@ Enum: endospore --- -## 18.3. sporeFormation.sporeEjection +## 11.3. sporeFormation.sporeEjection Spore Ejection **string, null** --- -## 18.4. sporeFormation.relatedData +## 11.4. sporeFormation.relatedData Related Data Description: @@ -44,7 +44,7 @@ Description: **array[string]** --- -## 18.5. sporeFormation.source +## 11.5. sporeFormation.source Source `Required` Description: diff --git a/docs/schema/12. cellShape.md b/docs/schema/12. cellShape.md deleted file mode 100644 index 07e3f9c..0000000 --- a/docs/schema/12. cellShape.md +++ /dev/null @@ -1,23 +0,0 @@ ---- -## 12. cellShape -Cell Shape - -**array[object]** - ---- -## 12.1. cellShape.cellShape -Cell Shape `Required` - -Description: -> The shape type the cells - -**string** - ---- -## 12.2. cellShape.source -Source `Required` - -Description: -> List of JSON paths to source object - -**array[string]** diff --git a/docs/schema/19. temperature.md b/docs/schema/12. temperature.md similarity index 70% rename from docs/schema/19. temperature.md rename to docs/schema/12. temperature.md index 83ee463..9f778a2 100644 --- a/docs/schema/19. temperature.md +++ b/docs/schema/12. temperature.md @@ -1,11 +1,11 @@ --- -## 19. temperature +## 12. temperature Temperature **array[object]** --- -## 19.1. temperature.optimal +## 12.1. temperature.optimal Optimal Description: @@ -14,7 +14,7 @@ Description: **number, null** --- -## 19.2. temperature.minimal +## 12.2. temperature.minimal Minimal Description: @@ -23,7 +23,7 @@ Description: **number, null** --- -## 19.3. temperature.maximal +## 12.3. temperature.maximal Maximal Description: @@ -32,13 +32,13 @@ Description: **number, null** --- -## 19.4. temperature.unit +## 12.4. temperature.unit Unit `Required` **string** --- -## 19.5. temperature.tests +## 12.5. temperature.tests Tests Description: @@ -47,7 +47,7 @@ Description: **array[object]** --- -## 19.5.1. temperature.tests.minimal +## 12.5.1. temperature.tests.minimal Minimal Description: @@ -56,7 +56,7 @@ Description: **number, null** --- -## 19.5.2. temperature.tests.maximal +## 12.5.2. temperature.tests.maximal Maximal Description: @@ -65,13 +65,13 @@ Description: **number, null** --- -## 19.5.3. temperature.tests.unit +## 12.5.3. temperature.tests.unit Unit `Required` **string** --- -## 19.5.4. temperature.tests.growth +## 12.5.4. temperature.tests.growth Growth `Required` Description: @@ -80,7 +80,7 @@ Description: **boolean** --- -## 19.5.5. temperature.tests.relatedData +## 12.5.5. temperature.tests.relatedData Related Data Description: @@ -89,7 +89,7 @@ Description: **array[string]** --- -## 19.6. temperature.source +## 12.6. temperature.source Source `Required` Description: diff --git a/docs/schema/13. oxygenRelation.md b/docs/schema/13. oxygenRelation.md deleted file mode 100644 index 7ae931a..0000000 --- a/docs/schema/13. oxygenRelation.md +++ /dev/null @@ -1,32 +0,0 @@ ---- -## 13. oxygenRelation -Oxygen Relation - -**array[object]** - ---- -## 13.1. oxygenRelation.oxygenRelation -Oxygen Relation `Required` - -Description: -> Aerobic, anaerobic etc. - -**string** - ---- -## 13.2. oxygenRelation.relatedData -Related Data - -Description: -> JSON paths to relation object - -**array[string]** - ---- -## 13.3. oxygenRelation.source -Source `Required` - -Description: -> List of JSON paths to source object - -**array[string]** diff --git a/docs/schema/20. ph.md b/docs/schema/13. ph.md similarity index 76% rename from docs/schema/20. ph.md rename to docs/schema/13. ph.md index d99622f..8245300 100644 --- a/docs/schema/20. ph.md +++ b/docs/schema/13. ph.md @@ -1,11 +1,11 @@ --- -## 20. ph +## 13. ph pH **array[object]** --- -## 20.1. ph.optimal +## 13.1. ph.optimal Optimal Description: @@ -14,7 +14,7 @@ Description: **number, null** --- -## 20.2. ph.minimal +## 13.2. ph.minimal Minimal Description: @@ -23,7 +23,7 @@ Description: **number, null** --- -## 20.3. ph.maximal +## 13.3. ph.maximal Maximal Description: @@ -32,13 +32,13 @@ Description: **number, null** --- -## 20.4. ph.unit +## 13.4. ph.unit Unit `Required` **string** --- -## 20.5. ph.tests +## 13.5. ph.tests Tests Description: @@ -47,7 +47,7 @@ Description: **array[object]** --- -## 20.5.1. ph.tests.minimal +## 13.5.1. ph.tests.minimal Minimal Description: @@ -56,7 +56,7 @@ Description: **number, null** --- -## 20.5.2. ph.tests.maximal +## 13.5.2. ph.tests.maximal Maximal Description: @@ -65,13 +65,13 @@ Description: **number, null** --- -## 20.5.3. ph.tests.unit +## 13.5.3. ph.tests.unit Unit `Required` **string** --- -## 20.5.4. ph.tests.growth +## 13.5.4. ph.tests.growth Growth `Required` Description: @@ -80,7 +80,7 @@ Description: **boolean** --- -## 20.5.5. ph.tests.relatedData +## 13.5.5. ph.tests.relatedData Related Data Description: @@ -89,7 +89,7 @@ Description: **array[string]** --- -## 20.6. ph.source +## 13.6. ph.source Source `Required` Description: diff --git a/docs/schema/21. identifier.md b/docs/schema/14. identifier.md similarity index 62% rename from docs/schema/21. identifier.md rename to docs/schema/14. identifier.md index 36fb17a..35f5a0a 100644 --- a/docs/schema/21. identifier.md +++ b/docs/schema/14. identifier.md @@ -1,11 +1,11 @@ --- -## 21. identifier +## 14. identifier Identifier **array[object]** --- -## 21.1. identifier.name +## 14.1. identifier.name Name `Required` Description: @@ -14,7 +14,7 @@ Description: **string** --- -## 21.2. identifier.value +## 14.2. identifier.value Value `Required` Description: @@ -23,7 +23,7 @@ Description: **string** --- -## 21.3. identifier.propertyID +## 14.3. identifier.propertyID Property ID Description: @@ -32,7 +32,7 @@ Description: **string, null** --- -## 21.4. identifier.url +## 14.4. identifier.url URL Description: @@ -41,7 +41,16 @@ Description: **string, null** --- -## 21.5. identifier.source +## 14.5. identifier.logo +Logo + +Description: +> Logo of the Identifier Organization (e.g. DOI, ORCID, ROR, ...) + +**string, null** + +--- +## 14.6. identifier.source Source `Required` Description: diff --git a/docs/schema/15. cellSize.md b/docs/schema/15. cellSize.md deleted file mode 100644 index 1e906fe..0000000 --- a/docs/schema/15. cellSize.md +++ /dev/null @@ -1,92 +0,0 @@ ---- -## 15. cellSize -Cell Size - -**array[object]** - ---- -## 15.1. cellSize.cellLength -Size `Required` - -Description: -> size object, use only for micro and millimeter - -**object** - ---- -## 15.1.1. cellSize.cellLength.minimal -Minimal `Required` - -**number** - ---- -## 15.1.2. cellSize.cellLength.maximal -Maximal `Required` - -**number** - ---- -## 15.1.3. cellSize.cellLength.unit -SizeUnit `Required` - -Description: -> Valid size options for microbes -> -> Attributes: -> µm: µm -> mm: mm - -**string** - -Enum: - - µm - mm - ---- -## 15.2. cellSize.cellWidth -Size `Required` - -Description: -> size object, use only for micro and millimeter - -**object** - ---- -## 15.2.1. cellSize.cellWidth.minimal -Minimal `Required` - -**number** - ---- -## 15.2.2. cellSize.cellWidth.maximal -Maximal `Required` - -**number** - ---- -## 15.2.3. cellSize.cellWidth.unit -SizeUnit `Required` - -Description: -> Valid size options for microbes -> -> Attributes: -> µm: µm -> mm: mm - -**string** - -Enum: - - µm - mm - ---- -## 15.3. cellSize.source -Source `Required` - -Description: -> List of JSON paths to source object - -**array[string]** diff --git a/docs/schema/22. connectedPersons.md b/docs/schema/15. connectedPersons.md similarity index 60% rename from docs/schema/22. connectedPersons.md rename to docs/schema/15. connectedPersons.md index 1290b19..5d28b99 100644 --- a/docs/schema/22. connectedPersons.md +++ b/docs/schema/15. connectedPersons.md @@ -1,11 +1,11 @@ --- -## 22. connectedPersons +## 15. connectedPersons Connected Persons **array[object]** --- -## 22.1. connectedPersons.name +## 15.1. connectedPersons.name Name `Required` Description: @@ -14,7 +14,7 @@ Description: **string** --- -## 22.2. connectedPersons.identifier +## 15.2. connectedPersons.identifier Identifier Description: @@ -23,7 +23,7 @@ Description: **array[object]** --- -## 22.2.1. connectedPersons.identifier.name +## 15.2.1. connectedPersons.identifier.name Name `Required` Description: @@ -32,7 +32,7 @@ Description: **string** --- -## 22.2.2. connectedPersons.identifier.value +## 15.2.2. connectedPersons.identifier.value Value `Required` Description: @@ -41,7 +41,7 @@ Description: **string** --- -## 22.2.3. connectedPersons.identifier.propertyID +## 15.2.3. connectedPersons.identifier.propertyID Property ID Description: @@ -50,7 +50,7 @@ Description: **string, null** --- -## 22.2.4. connectedPersons.identifier.url +## 15.2.4. connectedPersons.identifier.url URL Description: @@ -59,7 +59,16 @@ Description: **string, null** --- -## 22.3. connectedPersons.role +## 15.2.5. connectedPersons.identifier.logo +Logo + +Description: +> Logo of the Identifier Organization (e.g. DOI, ORCID, ROR, ...) + +**string, null** + +--- +## 15.3. connectedPersons.role Role **string, null** @@ -71,7 +80,7 @@ Enum: other --- -## 22.4. connectedPersons.source +## 15.4. connectedPersons.source Source `Required` Description: diff --git a/docs/schema/16. motility.md b/docs/schema/16. motility.md deleted file mode 100644 index 3b03b73..0000000 --- a/docs/schema/16. motility.md +++ /dev/null @@ -1,56 +0,0 @@ ---- -## 16. motility -Motility - -**array[object]** - ---- -## 16.1. motility.motile -Motile - -Description: -> Are the cells of this strain are motile - -**boolean, null** - ---- -## 16.2. motility.flagellum -Flagellum - -Description: -> Do the cells have flagella - -**boolean, null** - ---- -## 16.3. motility.flagellumArrangement -Flagellum Arrangement - -Description: -> How are the flagella arranged - -**string, null** - -Enum: - - Polar - Peritrichous - Monotrichous polar - ---- -## 16.4. motility.gliding -Gliding - -Description: -> Cells can be motile by gliding instead of having flagella - -**boolean, null** - ---- -## 16.5. motility.source -Source `Required` - -Description: -> List of JSON paths to source object - -**array[string]** diff --git a/docs/schema/23. pathogenicity.md b/docs/schema/16. pathogenicity.md similarity index 84% rename from docs/schema/23. pathogenicity.md rename to docs/schema/16. pathogenicity.md index 0e0a57e..44856c0 100644 --- a/docs/schema/23. pathogenicity.md +++ b/docs/schema/16. pathogenicity.md @@ -1,11 +1,11 @@ --- -## 23. pathogenicity +## 16. pathogenicity pathogenicity **array[object]** --- -## 23.1. pathogenicity.host +## 16.1. pathogenicity.host Host `Required` Description: @@ -35,7 +35,7 @@ Enum: fungi --- -## 23.2. pathogenicity.pathogen +## 16.2. pathogenicity.pathogen PathogenLevel `Required` Description: @@ -55,7 +55,7 @@ Enum: obligate --- -## 23.3. pathogenicity.classification +## 16.3. pathogenicity.classification Classification Description: @@ -64,7 +64,7 @@ Description: **string, null** --- -## 23.4. pathogenicity.url +## 16.4. pathogenicity.url URL Description: @@ -73,7 +73,7 @@ Description: **string, null** --- -## 23.5. pathogenicity.source +## 16.5. pathogenicity.source Source `Required` Description: diff --git a/docs/schema/24. bioSafety.md b/docs/schema/17. bioSafety.md similarity index 77% rename from docs/schema/24. bioSafety.md rename to docs/schema/17. bioSafety.md index 9f5ed0b..a53ddba 100644 --- a/docs/schema/24. bioSafety.md +++ b/docs/schema/17. bioSafety.md @@ -1,11 +1,11 @@ --- -## 24. bioSafety +## 17. bioSafety Bio Safety **array[object]** --- -## 24.1. bioSafety.riskgroup +## 17.1. bioSafety.riskgroup Riskgroup `Required` Description: @@ -14,7 +14,7 @@ Description: **string** --- -## 24.2. bioSafety.classification +## 17.2. bioSafety.classification Classification Description: @@ -23,7 +23,7 @@ Description: **string, null** --- -## 24.3. bioSafety.url +## 17.3. bioSafety.url URL Description: @@ -32,7 +32,7 @@ Description: **string, null** --- -## 24.4. bioSafety.source +## 17.4. bioSafety.source Source `Required` Description: diff --git a/docs/schema/17. colony.md b/docs/schema/17. colony.md deleted file mode 100644 index c66aa7e..0000000 --- a/docs/schema/17. colony.md +++ /dev/null @@ -1,74 +0,0 @@ ---- -## 17. colony -Colony - -**array[object]** - ---- -## 17.1. colony.size -Size of Colony - -**object, null** - ---- -## 17.1.1. colony.size.minimal -Minimal `Required` - -**number** - ---- -## 17.1.2. colony.size.maximal -Maximal `Required` - -**number** - ---- -## 17.1.3. colony.size.unit -SizeUnit `Required` - -Description: -> Valid size options for microbes -> -> Attributes: -> µm: µm -> mm: mm - -**string** - -Enum: - - µm - mm - ---- -## 17.2. colony.color -Color of Colony - -Description: -> Color of the colony on the - -**string, null** - -Enum: - - white - cream - yellowish - orange - pink - red - buff - darkbrown - reyish - tannish - beige - brownish - ---- -## 17.3. colony.source -Source `Required` - -Description: -> List of JSON paths to source object - -**array[string]** diff --git a/docs/schema/25. sequences.md b/docs/schema/18. sequences.md similarity index 70% rename from docs/schema/25. sequences.md rename to docs/schema/18. sequences.md index 3c3b1b0..be90152 100644 --- a/docs/schema/25. sequences.md +++ b/docs/schema/18. sequences.md @@ -1,11 +1,11 @@ --- -## 25. sequences +## 18. sequences Sequences **array[object]** --- -## 25.1. sequences.type +## 18.1. sequences.type SequenceType `Required` Description: @@ -23,7 +23,7 @@ Enum: protein --- -## 25.2. sequences.level +## 18.2. sequences.level SequenceLevel `Required` Description: @@ -47,25 +47,25 @@ Enum: other --- -## 25.3. sequences.accessionNumber +## 18.3. sequences.accessionNumber Accession Number `Required` **string** --- -## 25.4. sequences.description +## 18.4. sequences.description Description **string, null** --- -## 25.5. sequences.length +## 18.5. sequences.length Length **string, null** --- -## 25.6. sequences.identifier +## 18.6. sequences.identifier Identifier Description: @@ -74,7 +74,7 @@ Description: **array[object]** --- -## 25.6.1. sequences.identifier.name +## 18.6.1. sequences.identifier.name Name `Required` Description: @@ -83,7 +83,7 @@ Description: **string** --- -## 25.6.2. sequences.identifier.value +## 18.6.2. sequences.identifier.value Value `Required` Description: @@ -92,7 +92,7 @@ Description: **string** --- -## 25.6.3. sequences.identifier.propertyID +## 18.6.3. sequences.identifier.propertyID Property ID Description: @@ -101,7 +101,7 @@ Description: **string, null** --- -## 25.6.4. sequences.identifier.url +## 18.6.4. sequences.identifier.url URL Description: @@ -110,7 +110,16 @@ Description: **string, null** --- -## 25.7. sequences.source +## 18.6.5. sequences.identifier.logo +Logo + +Description: +> Logo of the Identifier Organization (e.g. DOI, ORCID, ROR, ...) + +**string, null** + +--- +## 18.7. sequences.source Source `Required` Description: diff --git a/docs/schema/26. gcContent.md b/docs/schema/19. gcContent.md similarity index 58% rename from docs/schema/26. gcContent.md rename to docs/schema/19. gcContent.md index 4c92554..d78d1fc 100644 --- a/docs/schema/26. gcContent.md +++ b/docs/schema/19. gcContent.md @@ -1,11 +1,11 @@ --- -## 26. gcContent +## 19. gcContent GC Content **array[object]** --- -## 26.1. gcContent.method +## 19.1. gcContent.method Method Description: @@ -13,8 +13,22 @@ Description: **string, null** +Enum: + + experimental + genome sequence + +--- +## 19.2. gcContent.noteMethod +Note Method + +Description: +> Note about the used method + +**string, null** + --- -## 26.2. gcContent.value +## 19.3. gcContent.value Percent Value `Required` Description: @@ -23,7 +37,7 @@ Description: **number** --- -## 26.3. gcContent.source +## 19.4. gcContent.source Source `Required` Description: diff --git a/docs/schema/27. literature.md b/docs/schema/20. literature.md similarity index 58% rename from docs/schema/27. literature.md rename to docs/schema/20. literature.md index f34074b..d87942e 100644 --- a/docs/schema/27. literature.md +++ b/docs/schema/20. literature.md @@ -1,29 +1,29 @@ --- -## 27. literature +## 20. literature Literature **array[object]** --- -## 27.1. literature.name +## 20.1. literature.name Name **string, null** --- -## 27.2. literature.url +## 20.2. literature.url URL **string, null** --- -## 27.3. literature.datePublished +## 20.3. literature.datePublished Date Published **string, null** --- -## 27.4. literature.author +## 20.4. literature.author Author Description: @@ -32,7 +32,7 @@ Description: **array[object]** --- -## 27.4.1. literature.author.name +## 20.4.1. literature.author.name Name `Required` Description: @@ -41,7 +41,7 @@ Description: **string** --- -## 27.4.2. literature.author.identifier +## 20.4.2. literature.author.identifier Identifier Description: @@ -50,7 +50,7 @@ Description: **array[object]** --- -## 27.4.2.1. literature.author.identifier.name +## 20.4.2.1. literature.author.identifier.name Name `Required` Description: @@ -59,7 +59,7 @@ Description: **string** --- -## 27.4.2.2. literature.author.identifier.value +## 20.4.2.2. literature.author.identifier.value Value `Required` Description: @@ -68,7 +68,7 @@ Description: **string** --- -## 27.4.2.3. literature.author.identifier.propertyID +## 20.4.2.3. literature.author.identifier.propertyID Property ID Description: @@ -77,7 +77,7 @@ Description: **string, null** --- -## 27.4.2.4. literature.author.identifier.url +## 20.4.2.4. literature.author.identifier.url URL Description: @@ -86,7 +86,16 @@ Description: **string, null** --- -## 27.5. literature.publisher +## 20.4.2.5. literature.author.identifier.logo +Logo + +Description: +> Logo of the Identifier Organization (e.g. DOI, ORCID, ROR, ...) + +**string, null** + +--- +## 20.5. literature.publisher Publisher Description: @@ -95,7 +104,7 @@ Description: **array[object]** --- -## 27.5.1. literature.publisher.name +## 20.5.1. literature.publisher.name Name `Required` Description: @@ -104,7 +113,7 @@ Description: **string** --- -## 27.5.2. literature.publisher.identifier +## 20.5.2. literature.publisher.identifier Identifier Description: @@ -113,7 +122,7 @@ Description: **array[object]** --- -## 27.5.2.1. literature.publisher.identifier.name +## 20.5.2.1. literature.publisher.identifier.name Name `Required` Description: @@ -122,7 +131,7 @@ Description: **string** --- -## 27.5.2.2. literature.publisher.identifier.value +## 20.5.2.2. literature.publisher.identifier.value Value `Required` Description: @@ -131,7 +140,7 @@ Description: **string** --- -## 27.5.2.3. literature.publisher.identifier.propertyID +## 20.5.2.3. literature.publisher.identifier.propertyID Property ID Description: @@ -140,7 +149,7 @@ Description: **string, null** --- -## 27.5.2.4. literature.publisher.identifier.url +## 20.5.2.4. literature.publisher.identifier.url URL Description: @@ -149,7 +158,16 @@ Description: **string, null** --- -## 27.5.3. literature.publisher.legalName +## 20.5.2.5. literature.publisher.identifier.logo +Logo + +Description: +> Logo of the Identifier Organization (e.g. DOI, ORCID, ROR, ...) + +**string, null** + +--- +## 20.5.3. literature.publisher.legalName Legal Name Description: @@ -158,7 +176,7 @@ Description: **string, null** --- -## 27.5.4. literature.publisher.address +## 20.5.4. literature.publisher.address Address Description: @@ -167,7 +185,7 @@ Description: **object, null** --- -## 27.5.4.1. literature.publisher.address.addressCountry +## 20.5.4.1. literature.publisher.address.addressCountry Country Description: @@ -176,7 +194,7 @@ Description: **string, null** --- -## 27.5.4.2. literature.publisher.address.addressRegion +## 20.5.4.2. literature.publisher.address.addressRegion Region Description: @@ -185,7 +203,7 @@ Description: **string, null** --- -## 27.5.4.3. literature.publisher.address.addressLocality +## 20.5.4.3. literature.publisher.address.addressLocality Locality Description: @@ -194,19 +212,19 @@ Description: **string, null** --- -## 27.5.4.4. literature.publisher.address.postOfficeBoxNumber +## 20.5.4.4. literature.publisher.address.postOfficeBoxNumber Post Office Box Number **string, null** --- -## 27.5.4.5. literature.publisher.address.postalCode +## 20.5.4.5. literature.publisher.address.postalCode Postal Code **string, null** --- -## 27.5.4.6. literature.publisher.address.streetAddress +## 20.5.4.6. literature.publisher.address.streetAddress Street Address Description: @@ -215,7 +233,7 @@ Description: **string, null** --- -## 27.5.5. literature.publisher.url +## 20.5.5. literature.publisher.url URL Description: @@ -224,7 +242,7 @@ Description: **string, null** --- -## 27.5.6. literature.publisher.email +## 20.5.6. literature.publisher.email Email Description: @@ -233,7 +251,7 @@ Description: **string, null** --- -## 27.5.7. literature.publisher.logo +## 20.5.7. literature.publisher.logo Logo Description: @@ -242,7 +260,7 @@ Description: **string, null** --- -## 27.6. literature.source +## 20.6. literature.source Source `Required` Description: diff --git a/docs/schema/28. wallConstituents.md b/docs/schema/21. wallConstituents.md similarity index 61% rename from docs/schema/28. wallConstituents.md rename to docs/schema/21. wallConstituents.md index 5746f59..0a3617f 100644 --- a/docs/schema/28. wallConstituents.md +++ b/docs/schema/21. wallConstituents.md @@ -1,11 +1,11 @@ --- -## 28. wallConstituents +## 21. wallConstituents Wall Constituents **array[object]** --- -## 28.1. wallConstituents.name +## 21.1. wallConstituents.name Name of Chemical Substance Description: @@ -14,7 +14,7 @@ Description: **string, null** --- -## 28.2. wallConstituents.identifier +## 21.2. wallConstituents.identifier Identifier Description: @@ -23,7 +23,7 @@ Description: **array[object]** --- -## 28.2.1. wallConstituents.identifier.name +## 21.2.1. wallConstituents.identifier.name Name `Required` Description: @@ -32,7 +32,7 @@ Description: **string** --- -## 28.2.2. wallConstituents.identifier.value +## 21.2.2. wallConstituents.identifier.value Value `Required` Description: @@ -41,7 +41,7 @@ Description: **string** --- -## 28.2.3. wallConstituents.identifier.propertyID +## 21.2.3. wallConstituents.identifier.propertyID Property ID Description: @@ -50,7 +50,7 @@ Description: **string, null** --- -## 28.2.4. wallConstituents.identifier.url +## 21.2.4. wallConstituents.identifier.url URL Description: @@ -59,7 +59,16 @@ Description: **string, null** --- -## 28.3. wallConstituents.alternateName +## 21.2.5. wallConstituents.identifier.logo +Logo + +Description: +> Logo of the Identifier Organization (e.g. DOI, ORCID, ROR, ...) + +**string, null** + +--- +## 21.3. wallConstituents.alternateName Alternate Name Description: @@ -68,13 +77,13 @@ Description: **array[string]** --- -## 28.4. wallConstituents.percent +## 21.4. wallConstituents.percent Percent **number, null** --- -## 28.5. wallConstituents.source +## 21.5. wallConstituents.source Source `Required` Description: diff --git a/docs/schema/29. fattyAcidProfiles.md b/docs/schema/22. fattyAcidProfiles.md similarity index 59% rename from docs/schema/29. fattyAcidProfiles.md rename to docs/schema/22. fattyAcidProfiles.md index b704f3e..8e5606a 100644 --- a/docs/schema/29. fattyAcidProfiles.md +++ b/docs/schema/22. fattyAcidProfiles.md @@ -1,11 +1,11 @@ --- -## 29. fattyAcidProfiles +## 22. fattyAcidProfiles Fatty Acid Profile **array[object]** --- -## 29.1. fattyAcidProfiles.profile +## 22.1. fattyAcidProfiles.profile Profile Description: @@ -14,7 +14,7 @@ Description: **array[object]** --- -## 29.1.1. fattyAcidProfiles.profile.name +## 22.1.1. fattyAcidProfiles.profile.name Name of Chemical Substance Description: @@ -23,7 +23,7 @@ Description: **string, null** --- -## 29.1.2. fattyAcidProfiles.profile.identifier +## 22.1.2. fattyAcidProfiles.profile.identifier Identifier Description: @@ -32,7 +32,7 @@ Description: **array[object]** --- -## 29.1.2.1. fattyAcidProfiles.profile.identifier.name +## 22.1.2.1. fattyAcidProfiles.profile.identifier.name Name `Required` Description: @@ -41,7 +41,7 @@ Description: **string** --- -## 29.1.2.2. fattyAcidProfiles.profile.identifier.value +## 22.1.2.2. fattyAcidProfiles.profile.identifier.value Value `Required` Description: @@ -50,7 +50,7 @@ Description: **string** --- -## 29.1.2.3. fattyAcidProfiles.profile.identifier.propertyID +## 22.1.2.3. fattyAcidProfiles.profile.identifier.propertyID Property ID Description: @@ -59,7 +59,7 @@ Description: **string, null** --- -## 29.1.2.4. fattyAcidProfiles.profile.identifier.url +## 22.1.2.4. fattyAcidProfiles.profile.identifier.url URL Description: @@ -68,7 +68,16 @@ Description: **string, null** --- -## 29.1.3. fattyAcidProfiles.profile.alternateName +## 22.1.2.5. fattyAcidProfiles.profile.identifier.logo +Logo + +Description: +> Logo of the Identifier Organization (e.g. DOI, ORCID, ROR, ...) + +**string, null** + +--- +## 22.1.3. fattyAcidProfiles.profile.alternateName Alternate Name Description: @@ -77,19 +86,19 @@ Description: **array[string]** --- -## 29.1.4. fattyAcidProfiles.profile.percent +## 22.1.4. fattyAcidProfiles.profile.percent Percent **number, null** --- -## 29.1.5. fattyAcidProfiles.profile.ecl +## 22.1.5. fattyAcidProfiles.profile.ecl ECL **string, null** --- -## 29.2. fattyAcidProfiles.library +## 22.2. fattyAcidProfiles.library Library Description: @@ -98,7 +107,7 @@ Description: **string, null** --- -## 29.3. fattyAcidProfiles.software +## 22.3. fattyAcidProfiles.software Software Description: @@ -107,7 +116,7 @@ Description: **string, null** --- -## 29.4. fattyAcidProfiles.relatedData +## 22.4. fattyAcidProfiles.relatedData Related Data Description: @@ -116,7 +125,7 @@ Description: **array[string]** --- -## 29.5. fattyAcidProfiles.source +## 22.5. fattyAcidProfiles.source Source `Required` Description: diff --git a/docs/schema/30. staining.md b/docs/schema/23. staining.md similarity index 81% rename from docs/schema/30. staining.md rename to docs/schema/23. staining.md index 7494b95..275a6ff 100644 --- a/docs/schema/30. staining.md +++ b/docs/schema/23. staining.md @@ -1,17 +1,17 @@ --- -## 30. staining +## 23. staining Stainings **array[object]** --- -## 30.1. staining.name +## 23.1. staining.name Name `Required` **string** --- -## 30.2. staining.value +## 23.2. staining.value StainingValue `Required` Description: @@ -31,7 +31,7 @@ Enum: variable --- -## 30.3. staining.source +## 23.3. staining.source Source `Required` Description: diff --git a/docs/schema/31. hemolysis.md b/docs/schema/24. hemolysis.md similarity index 83% rename from docs/schema/31. hemolysis.md rename to docs/schema/24. hemolysis.md index eaeb3a9..e0199d8 100644 --- a/docs/schema/31. hemolysis.md +++ b/docs/schema/24. hemolysis.md @@ -1,11 +1,11 @@ --- -## 31. hemolysis +## 24. hemolysis Hemolysis **array[object]** --- -## 31.1. hemolysis.blood +## 24.1. hemolysis.blood HemolysisBlood `Required` Description: @@ -25,7 +25,7 @@ Enum: unknown --- -## 31.2. hemolysis.hemolysisType +## 24.2. hemolysis.hemolysisType HemolysisType `Required` Description: @@ -45,7 +45,7 @@ Enum: gamma --- -## 31.3. hemolysis.source +## 24.3. hemolysis.source Source `Required` Description: diff --git a/docs/schema/32. cultivationMedia.md b/docs/schema/25. cultivationMedia.md similarity index 62% rename from docs/schema/32. cultivationMedia.md rename to docs/schema/25. cultivationMedia.md index e2a6fb1..6bfe743 100644 --- a/docs/schema/32. cultivationMedia.md +++ b/docs/schema/25. cultivationMedia.md @@ -1,29 +1,29 @@ --- -## 32. cultivationMedia +## 25. cultivationMedia Cultivation Media **array[object]** --- -## 32.1. cultivationMedia.name +## 25.1. cultivationMedia.name Name `Required` **string** --- -## 32.2. cultivationMedia.url +## 25.2. cultivationMedia.url URL **string, null** --- -## 32.3. cultivationMedia.reagentUsed +## 25.3. cultivationMedia.reagentUsed Reagent Used **array[string]** --- -## 32.4. cultivationMedia.source +## 25.4. cultivationMedia.source Source `Required` Description: @@ -32,7 +32,7 @@ Description: **array[string]** --- -## 32.5. cultivationMedia.relatedData +## 25.5. cultivationMedia.relatedData Related Data Description: diff --git a/docs/schema/33. halophily.md b/docs/schema/26. halophily.md similarity index 73% rename from docs/schema/33. halophily.md rename to docs/schema/26. halophily.md index 13da59e..634130f 100644 --- a/docs/schema/33. halophily.md +++ b/docs/schema/26. halophily.md @@ -1,11 +1,11 @@ --- -## 33. halophily +## 26. halophily Halophily **array[object]** --- -## 33.1. halophily.name +## 26.1. halophily.name Name of Chemical Substance Description: @@ -14,7 +14,7 @@ Description: **string, null** --- -## 33.2. halophily.identifier +## 26.2. halophily.identifier Identifier Description: @@ -23,7 +23,7 @@ Description: **array[object]** --- -## 33.2.1. halophily.identifier.name +## 26.2.1. halophily.identifier.name Name `Required` Description: @@ -32,7 +32,7 @@ Description: **string** --- -## 33.2.2. halophily.identifier.value +## 26.2.2. halophily.identifier.value Value `Required` Description: @@ -41,7 +41,7 @@ Description: **string** --- -## 33.2.3. halophily.identifier.propertyID +## 26.2.3. halophily.identifier.propertyID Property ID Description: @@ -50,7 +50,7 @@ Description: **string, null** --- -## 33.2.4. halophily.identifier.url +## 26.2.4. halophily.identifier.url URL Description: @@ -59,7 +59,16 @@ Description: **string, null** --- -## 33.3. halophily.alternateName +## 26.2.5. halophily.identifier.logo +Logo + +Description: +> Logo of the Identifier Organization (e.g. DOI, ORCID, ROR, ...) + +**string, null** + +--- +## 26.3. halophily.alternateName Alternate Name Description: @@ -68,7 +77,7 @@ Description: **array[string]** --- -## 33.4. halophily.optimal +## 26.4. halophily.optimal Optimal Description: @@ -77,7 +86,7 @@ Description: **number, null** --- -## 33.5. halophily.minimal +## 26.5. halophily.minimal Minimal Description: @@ -86,7 +95,7 @@ Description: **number, null** --- -## 33.6. halophily.maximal +## 26.6. halophily.maximal Maximal Description: @@ -95,7 +104,7 @@ Description: **number, null** --- -## 33.7. halophily.unit +## 26.7. halophily.unit ConcentrationUnit `Required` Description: @@ -118,7 +127,7 @@ Enum: unknown --- -## 33.8. halophily.tests +## 26.8. halophily.tests Tests Description: @@ -127,7 +136,7 @@ Description: **array[object]** --- -## 33.8.1. halophily.tests.minimal +## 26.8.1. halophily.tests.minimal Minimal Description: @@ -136,7 +145,7 @@ Description: **number, null** --- -## 33.8.2. halophily.tests.maximal +## 26.8.2. halophily.tests.maximal Maximal Description: @@ -145,7 +154,7 @@ Description: **number, null** --- -## 33.8.3. halophily.tests.unit +## 26.8.3. halophily.tests.unit ConcentrationUnit `Required` Description: @@ -168,7 +177,7 @@ Enum: unknown --- -## 33.8.4. halophily.tests.growth +## 26.8.4. halophily.tests.growth Growth `Required` Description: @@ -177,7 +186,7 @@ Description: **boolean** --- -## 33.8.5. halophily.tests.relatedData +## 26.8.5. halophily.tests.relatedData Related Data Description: @@ -186,7 +195,7 @@ Description: **array[string]** --- -## 33.9. halophily.source +## 26.9. halophily.source Source `Required` Description: diff --git a/docs/schema/34. tolerances.md b/docs/schema/27. tolerances.md similarity index 72% rename from docs/schema/34. tolerances.md rename to docs/schema/27. tolerances.md index 3d7450f..373b561 100644 --- a/docs/schema/34. tolerances.md +++ b/docs/schema/27. tolerances.md @@ -1,11 +1,11 @@ --- -## 34. tolerances +## 27. tolerances Tolerances **array[object]** --- -## 34.1. tolerances.name +## 27.1. tolerances.name Name of Chemical Substance Description: @@ -14,7 +14,7 @@ Description: **string, null** --- -## 34.2. tolerances.identifier +## 27.2. tolerances.identifier Identifier Description: @@ -23,7 +23,7 @@ Description: **array[object]** --- -## 34.2.1. tolerances.identifier.name +## 27.2.1. tolerances.identifier.name Name `Required` Description: @@ -32,7 +32,7 @@ Description: **string** --- -## 34.2.2. tolerances.identifier.value +## 27.2.2. tolerances.identifier.value Value `Required` Description: @@ -41,7 +41,7 @@ Description: **string** --- -## 34.2.3. tolerances.identifier.propertyID +## 27.2.3. tolerances.identifier.propertyID Property ID Description: @@ -50,7 +50,7 @@ Description: **string, null** --- -## 34.2.4. tolerances.identifier.url +## 27.2.4. tolerances.identifier.url URL Description: @@ -59,7 +59,16 @@ Description: **string, null** --- -## 34.3. tolerances.alternateName +## 27.2.5. tolerances.identifier.logo +Logo + +Description: +> Logo of the Identifier Organization (e.g. DOI, ORCID, ROR, ...) + +**string, null** + +--- +## 27.3. tolerances.alternateName Alternate Name Description: @@ -68,7 +77,7 @@ Description: **array[string]** --- -## 34.4. tolerances.reaction +## 27.4. tolerances.reaction Reaction **string, null** @@ -80,7 +89,7 @@ Enum: intermediate --- -## 34.5. tolerances.mic +## 27.5. tolerances.mic MIC Description: @@ -89,7 +98,7 @@ Description: **string, null** --- -## 34.6. tolerances.unit +## 27.6. tolerances.unit Unit **string, null** @@ -103,7 +112,7 @@ Enum: unknown --- -## 34.7. tolerances.tests +## 27.7. tolerances.tests Tests Description: @@ -112,7 +121,7 @@ Description: **array[object]** --- -## 34.7.1. tolerances.tests.reaction +## 27.7.1. tolerances.tests.reaction ToleranceReaction `Required` Description: @@ -132,16 +141,16 @@ Enum: intermediate --- -## 34.7.2. tolerances.tests.concentration +## 27.7.2. tolerances.tests.concentration Concentration Description: > Concentration value -**string, null** +**number, null** --- -## 34.7.3. tolerances.tests.unit +## 27.7.3. tolerances.tests.unit ConcentrationUnit `Required` Description: @@ -164,7 +173,7 @@ Enum: unknown --- -## 34.7.4. tolerances.tests.relatedData +## 27.7.4. tolerances.tests.relatedData Related Data Description: @@ -173,7 +182,7 @@ Description: **array[string]** --- -## 34.8. tolerances.source +## 27.8. tolerances.source Source `Required` Description: diff --git a/docs/schema/28. enzymes.md b/docs/schema/28. enzymes.md new file mode 100644 index 0000000..a206f76 --- /dev/null +++ b/docs/schema/28. enzymes.md @@ -0,0 +1,107 @@ +--- +## 28. enzymes +Enzymes + +**array[object]** + +--- +## 28.1. enzymes.name +Name + +**string, null** + +--- +## 28.2. enzymes.hasECNumber +EC Number `Required` + +Description: +> An EC number defined by the Enzyme Commission + +**string** + +--- +## 28.3. enzymes.identifier +Identifier + +Description: +> Identifier of every Kind, compare to schema.org PropertyValue class + +**array[object]** + +--- +## 28.3.1. enzymes.identifier.name +Name `Required` + +Description: +> Name of the identifier + +**string** + +--- +## 28.3.2. enzymes.identifier.value +Value `Required` + +Description: +> Value of the identifier (can also be a URL) + +**string** + +--- +## 28.3.3. enzymes.identifier.propertyID +Property ID + +Description: +> See schema.org/propertyID + +**string, null** + +--- +## 28.3.4. enzymes.identifier.url +URL + +Description: +> Uniform Resource Locator of a resource on the Internet + +**string, null** + +--- +## 28.3.5. enzymes.identifier.logo +Logo + +Description: +> Logo of the Identifier Organization (e.g. DOI, ORCID, ROR, ...) + +**string, null** + +--- +## 28.4. enzymes.alternateName +Alternate Name + +**array[string]** + +--- +## 28.5. enzymes.active +Active + +Description: +> Is this enzyme active + +**boolean, null** + +--- +## 28.6. enzymes.relatedData +Related Data + +Description: +> JSON paths to relation object + +**array[string]** + +--- +## 28.7. enzymes.source +Source `Required` + +Description: +> List of JSON paths to source object + +**array[string]** diff --git a/docs/schema/36. metabolites.md b/docs/schema/29. metabolites.md similarity index 66% rename from docs/schema/36. metabolites.md rename to docs/schema/29. metabolites.md index a84094c..27d6c91 100644 --- a/docs/schema/36. metabolites.md +++ b/docs/schema/29. metabolites.md @@ -1,11 +1,11 @@ --- -## 36. metabolites +## 29. metabolites Metabolites **array[object]** --- -## 36.1. metabolites.name +## 29.1. metabolites.name Name of Chemical Substance Description: @@ -14,7 +14,7 @@ Description: **string, null** --- -## 36.2. metabolites.identifier +## 29.2. metabolites.identifier Identifier Description: @@ -23,7 +23,7 @@ Description: **array[object]** --- -## 36.2.1. metabolites.identifier.name +## 29.2.1. metabolites.identifier.name Name `Required` Description: @@ -32,7 +32,7 @@ Description: **string** --- -## 36.2.2. metabolites.identifier.value +## 29.2.2. metabolites.identifier.value Value `Required` Description: @@ -41,7 +41,7 @@ Description: **string** --- -## 36.2.3. metabolites.identifier.propertyID +## 29.2.3. metabolites.identifier.propertyID Property ID Description: @@ -50,7 +50,7 @@ Description: **string, null** --- -## 36.2.4. metabolites.identifier.url +## 29.2.4. metabolites.identifier.url URL Description: @@ -59,7 +59,16 @@ Description: **string, null** --- -## 36.3. metabolites.alternateName +## 29.2.5. metabolites.identifier.logo +Logo + +Description: +> Logo of the Identifier Organization (e.g. DOI, ORCID, ROR, ...) + +**string, null** + +--- +## 29.3. metabolites.alternateName Alternate Name Description: @@ -68,7 +77,7 @@ Description: **array[string]** --- -## 36.4. metabolites.tests +## 29.4. metabolites.tests Tests Description: @@ -77,7 +86,7 @@ Description: **array[object]** --- -## 36.4.1. metabolites.tests.type +## 29.4.1. metabolites.tests.type MetaboliteTestType `Required` Description: @@ -95,7 +104,7 @@ Enum: production --- -## 36.4.2. metabolites.tests.active +## 29.4.2. metabolites.tests.active Active Description: @@ -104,7 +113,7 @@ Description: **boolean, null** --- -## 36.4.3. metabolites.tests.protocol +## 29.4.3. metabolites.tests.protocol Protocol Description: @@ -113,7 +122,7 @@ Description: **string, null** --- -## 36.4.4. metabolites.tests.kindOfUtilization +## 29.4.4. metabolites.tests.kindOfUtilization Kind Of Utilization Description: @@ -121,8 +130,18 @@ Description: **string, null** +Enum: + + assimilation + builds acid from + degradation + energy source + fermentation + hydrolysis + reduction + --- -## 36.4.5. metabolites.tests.relatedData +## 29.4.5. metabolites.tests.relatedData Related Data Description: @@ -131,7 +150,7 @@ Description: **array[string]** --- -## 36.5. metabolites.source +## 29.5. metabolites.source Source `Required` Description: diff --git a/docs/schema/37. knownApplications.md b/docs/schema/30. knownApplications.md similarity index 70% rename from docs/schema/37. knownApplications.md rename to docs/schema/30. knownApplications.md index 36ba7ab..ffa56c1 100644 --- a/docs/schema/37. knownApplications.md +++ b/docs/schema/30. knownApplications.md @@ -1,11 +1,11 @@ --- -## 37. knownApplications +## 30. knownApplications Known Applications **array[object]** --- -## 37.1. knownApplications.application +## 30.1. knownApplications.application Application `Required` Description: @@ -14,7 +14,7 @@ Description: **string** --- -## 37.2. knownApplications.source +## 30.2. knownApplications.source Source `Required` Description: diff --git a/docs/schema/38. collections.md b/docs/schema/31. collections.md similarity index 66% rename from docs/schema/38. collections.md rename to docs/schema/31. collections.md index 7c05ae5..8d19188 100644 --- a/docs/schema/38. collections.md +++ b/docs/schema/31. collections.md @@ -1,11 +1,11 @@ --- -## 38. collections +## 31. collections Collections **array[object]** --- -## 38.1. collections.name +## 31.1. collections.name Name `Required` Description: @@ -14,7 +14,7 @@ Description: **string** --- -## 38.2. collections.identifier +## 31.2. collections.identifier Identifier Description: @@ -23,7 +23,7 @@ Description: **array[object]** --- -## 38.2.1. collections.identifier.name +## 31.2.1. collections.identifier.name Name `Required` Description: @@ -32,7 +32,7 @@ Description: **string** --- -## 38.2.2. collections.identifier.value +## 31.2.2. collections.identifier.value Value `Required` Description: @@ -41,7 +41,7 @@ Description: **string** --- -## 38.2.3. collections.identifier.propertyID +## 31.2.3. collections.identifier.propertyID Property ID Description: @@ -50,7 +50,7 @@ Description: **string, null** --- -## 38.2.4. collections.identifier.url +## 31.2.4. collections.identifier.url URL Description: @@ -59,7 +59,16 @@ Description: **string, null** --- -## 38.3. collections.legalName +## 31.2.5. collections.identifier.logo +Logo + +Description: +> Logo of the Identifier Organization (e.g. DOI, ORCID, ROR, ...) + +**string, null** + +--- +## 31.3. collections.legalName Legal Name Description: @@ -68,7 +77,7 @@ Description: **string, null** --- -## 38.4. collections.address +## 31.4. collections.address Address Description: @@ -77,7 +86,7 @@ Description: **object, null** --- -## 38.4.1. collections.address.addressCountry +## 31.4.1. collections.address.addressCountry Country Description: @@ -86,7 +95,7 @@ Description: **string, null** --- -## 38.4.2. collections.address.addressRegion +## 31.4.2. collections.address.addressRegion Region Description: @@ -95,7 +104,7 @@ Description: **string, null** --- -## 38.4.3. collections.address.addressLocality +## 31.4.3. collections.address.addressLocality Locality Description: @@ -104,19 +113,19 @@ Description: **string, null** --- -## 38.4.4. collections.address.postOfficeBoxNumber +## 31.4.4. collections.address.postOfficeBoxNumber Post Office Box Number **string, null** --- -## 38.4.5. collections.address.postalCode +## 31.4.5. collections.address.postalCode Postal Code **string, null** --- -## 38.4.6. collections.address.streetAddress +## 31.4.6. collections.address.streetAddress Street Address Description: @@ -125,7 +134,7 @@ Description: **string, null** --- -## 38.5. collections.url +## 31.5. collections.url URL Description: @@ -134,7 +143,7 @@ Description: **string, null** --- -## 38.6. collections.email +## 31.6. collections.email Email Description: @@ -143,7 +152,7 @@ Description: **string, null** --- -## 38.7. collections.logo +## 31.7. collections.logo Logo Description: @@ -152,7 +161,7 @@ Description: **string, null** --- -## 38.8. collections.resourceNumber +## 31.8. collections.resourceNumber Resource Number `Required` Description: @@ -161,7 +170,7 @@ Description: **string** --- -## 38.9. collections.available +## 31.9. collections.available Availability Description: @@ -170,7 +179,7 @@ Description: **boolean, null** --- -## 38.10. collections.catalogUrl +## 31.10. collections.catalogUrl Catalog URL Description: @@ -179,7 +188,7 @@ Description: **string, null** --- -## 38.11. collections.restrictionsOnUse +## 31.11. collections.restrictionsOnUse Restrictions On Use Description: @@ -194,7 +203,7 @@ Enum: For commercial development a special agreement is requested --- -## 38.12. collections.policyUrl +## 31.12. collections.policyUrl Policy URL Description: @@ -203,7 +212,7 @@ Description: **string, null** --- -## 38.13. collections.axenicCulture +## 31.13. collections.axenicCulture Axenic Culture Description: @@ -212,7 +221,7 @@ Description: **boolean, null** --- -## 38.14. collections.supplyForms +## 31.14. collections.supplyForms Supply Forms Description: @@ -221,7 +230,7 @@ Description: **array[string]** --- -## 38.15. collections.history +## 31.15. collections.history History Description: @@ -230,7 +239,7 @@ Description: **string, null** --- -## 38.16. collections.depositionDate +## 31.16. collections.depositionDate Deposition Date Description: @@ -239,7 +248,7 @@ Description: **string, null** --- -## 38.17. collections.depositor +## 31.17. collections.depositor Depositor Description: @@ -248,7 +257,7 @@ Description: **object, null** --- -## 38.17.1. collections.depositor.name +## 31.17.1. collections.depositor.name Name `Required` Description: @@ -257,7 +266,7 @@ Description: **string** --- -## 38.17.2. collections.depositor.identifier +## 31.17.2. collections.depositor.identifier Identifier Description: @@ -266,7 +275,7 @@ Description: **array[object]** --- -## 38.17.2.1. collections.depositor.identifier.name +## 31.17.2.1. collections.depositor.identifier.name Name `Required` Description: @@ -275,7 +284,7 @@ Description: **string** --- -## 38.17.2.2. collections.depositor.identifier.value +## 31.17.2.2. collections.depositor.identifier.value Value `Required` Description: @@ -284,7 +293,7 @@ Description: **string** --- -## 38.17.2.3. collections.depositor.identifier.propertyID +## 31.17.2.3. collections.depositor.identifier.propertyID Property ID Description: @@ -293,7 +302,7 @@ Description: **string, null** --- -## 38.17.2.4. collections.depositor.identifier.url +## 31.17.2.4. collections.depositor.identifier.url URL Description: @@ -302,7 +311,16 @@ Description: **string, null** --- -## 38.18. collections.depositedAs +## 31.17.2.5. collections.depositor.identifier.logo +Logo + +Description: +> Logo of the Identifier Organization (e.g. DOI, ORCID, ROR, ...) + +**string, null** + +--- +## 31.18. collections.depositedAs Deposited as Description: @@ -311,7 +329,7 @@ Description: **string, null** --- -## 38.19. collections.registeredCollection +## 31.19. collections.registeredCollection Registered Collection Description: @@ -320,7 +338,7 @@ Description: **boolean, null** --- -## 38.20. collections.mtaFile +## 31.20. collections.mtaFile MTA file Description: @@ -329,7 +347,7 @@ Description: **string, null** --- -## 38.21. collections.absFile +## 31.21. collections.absFile ABS related file Description: @@ -338,7 +356,7 @@ Description: **string, null** --- -## 38.22. collections.source +## 31.22. collections.source Source `Required` Description: diff --git a/docs/schema/39. otherMedia.md b/docs/schema/32. otherMedia.md similarity index 71% rename from docs/schema/39. otherMedia.md rename to docs/schema/32. otherMedia.md index b366aea..c902ab3 100644 --- a/docs/schema/39. otherMedia.md +++ b/docs/schema/32. otherMedia.md @@ -1,11 +1,11 @@ --- -## 39. otherMedia +## 32. otherMedia Other Media **array[object]** --- -## 39.1. otherMedia.url +## 32.1. otherMedia.url URL Description: @@ -14,13 +14,13 @@ Description: **string, null** --- -## 39.2. otherMedia.name +## 32.2. otherMedia.name Name **string, null** --- -## 39.3. otherMedia.description +## 32.3. otherMedia.description Description Description: @@ -29,7 +29,7 @@ Description: **string, null** --- -## 39.4. otherMedia.usageInfo +## 32.4. otherMedia.usageInfo Usage Information Description: @@ -38,13 +38,13 @@ Description: **string, null** --- -## 39.5. otherMedia.additionalType +## 32.5. otherMedia.additionalType Additional Type **string, null** --- -## 39.6. otherMedia.source +## 32.6. otherMedia.source Source `Required` Description: diff --git a/docs/schema/40. relatedData.md b/docs/schema/33. relatedData.md similarity index 78% rename from docs/schema/40. relatedData.md rename to docs/schema/33. relatedData.md index e1b89c8..038345c 100644 --- a/docs/schema/40. relatedData.md +++ b/docs/schema/33. relatedData.md @@ -1,11 +1,11 @@ --- -## 40. relatedData +## 33. relatedData Related Data **array[object]** --- -## 40.1. relatedData.relation +## 33.1. relatedData.relation Relation `Required` Description: @@ -14,7 +14,7 @@ Description: **string** --- -## 40.2. relatedData.source +## 33.2. relatedData.source Source `Required` Description: diff --git a/docs/schema/41. sources.md b/docs/schema/34. sources.md similarity index 61% rename from docs/schema/41. sources.md rename to docs/schema/34. sources.md index a00653f..8cf3191 100644 --- a/docs/schema/41. sources.md +++ b/docs/schema/34. sources.md @@ -1,11 +1,11 @@ --- -## 41. sources +## 34. sources Sources `Required` **array[object]** --- -## 41.1. sources.sourceType +## 34.1. sources.sourceType SourceType `Required` Description: @@ -25,7 +25,7 @@ Enum: dataset --- -## 41.2. sources.mode +## 34.2. sources.mode CurationMode `Required` Description: @@ -45,19 +45,19 @@ Enum: unknown --- -## 41.3. sources.name +## 34.3. sources.name Name **string, null** --- -## 41.4. sources.url +## 34.4. sources.url URL **string, null** --- -## 41.5. sources.identifiers +## 34.5. sources.identifier Identifier Description: @@ -66,7 +66,7 @@ Description: **array[object]** --- -## 41.5.1. sources.identifiers.name +## 34.5.1. sources.identifier.name Name `Required` Description: @@ -75,7 +75,7 @@ Description: **string** --- -## 41.5.2. sources.identifiers.value +## 34.5.2. sources.identifier.value Value `Required` Description: @@ -84,7 +84,7 @@ Description: **string** --- -## 41.5.3. sources.identifiers.propertyID +## 34.5.3. sources.identifier.propertyID Property ID Description: @@ -93,7 +93,7 @@ Description: **string, null** --- -## 41.5.4. sources.identifiers.url +## 34.5.4. sources.identifier.url URL Description: @@ -102,13 +102,22 @@ Description: **string, null** --- -## 41.6. sources.datePublished +## 34.5.5. sources.identifier.logo +Logo + +Description: +> Logo of the Identifier Organization (e.g. DOI, ORCID, ROR, ...) + +**string, null** + +--- +## 34.6. sources.datePublished Date Published **string, null** --- -## 41.7. sources.dateRecorded +## 34.7. sources.dateRecorded Date Recorded **string** @@ -118,7 +127,13 @@ Format: date --- -## 41.8. sources.author +## 34.8. sources.lastUpdate +Date of last update + +**string, null** + +--- +## 34.9. sources.author Author Description: @@ -127,7 +142,7 @@ Description: **array[object]** --- -## 41.8.1. sources.author.name +## 34.9.1. sources.author.name Name `Required` Description: @@ -136,7 +151,7 @@ Description: **string** --- -## 41.8.2. sources.author.identifier +## 34.9.2. sources.author.identifier Identifier Description: @@ -145,7 +160,7 @@ Description: **array[object]** --- -## 41.8.2.1. sources.author.identifier.name +## 34.9.2.1. sources.author.identifier.name Name `Required` Description: @@ -154,7 +169,7 @@ Description: **string** --- -## 41.8.2.2. sources.author.identifier.value +## 34.9.2.2. sources.author.identifier.value Value `Required` Description: @@ -163,7 +178,7 @@ Description: **string** --- -## 41.8.2.3. sources.author.identifier.propertyID +## 34.9.2.3. sources.author.identifier.propertyID Property ID Description: @@ -172,7 +187,7 @@ Description: **string, null** --- -## 41.8.2.4. sources.author.identifier.url +## 34.9.2.4. sources.author.identifier.url URL Description: @@ -181,7 +196,16 @@ Description: **string, null** --- -## 41.9. sources.publisher +## 34.9.2.5. sources.author.identifier.logo +Logo + +Description: +> Logo of the Identifier Organization (e.g. DOI, ORCID, ROR, ...) + +**string, null** + +--- +## 34.10. sources.publisher Publisher Description: @@ -190,7 +214,7 @@ Description: **array[object]** --- -## 41.9.1. sources.publisher.name +## 34.10.1. sources.publisher.name Name `Required` Description: @@ -199,7 +223,7 @@ Description: **string** --- -## 41.9.2. sources.publisher.identifier +## 34.10.2. sources.publisher.identifier Identifier Description: @@ -208,7 +232,7 @@ Description: **array[object]** --- -## 41.9.2.1. sources.publisher.identifier.name +## 34.10.2.1. sources.publisher.identifier.name Name `Required` Description: @@ -217,7 +241,7 @@ Description: **string** --- -## 41.9.2.2. sources.publisher.identifier.value +## 34.10.2.2. sources.publisher.identifier.value Value `Required` Description: @@ -226,7 +250,7 @@ Description: **string** --- -## 41.9.2.3. sources.publisher.identifier.propertyID +## 34.10.2.3. sources.publisher.identifier.propertyID Property ID Description: @@ -235,7 +259,7 @@ Description: **string, null** --- -## 41.9.2.4. sources.publisher.identifier.url +## 34.10.2.4. sources.publisher.identifier.url URL Description: @@ -244,7 +268,16 @@ Description: **string, null** --- -## 41.9.3. sources.publisher.legalName +## 34.10.2.5. sources.publisher.identifier.logo +Logo + +Description: +> Logo of the Identifier Organization (e.g. DOI, ORCID, ROR, ...) + +**string, null** + +--- +## 34.10.3. sources.publisher.legalName Legal Name Description: @@ -253,7 +286,7 @@ Description: **string, null** --- -## 41.9.4. sources.publisher.address +## 34.10.4. sources.publisher.address Address Description: @@ -262,7 +295,7 @@ Description: **object, null** --- -## 41.9.4.1. sources.publisher.address.addressCountry +## 34.10.4.1. sources.publisher.address.addressCountry Country Description: @@ -271,7 +304,7 @@ Description: **string, null** --- -## 41.9.4.2. sources.publisher.address.addressRegion +## 34.10.4.2. sources.publisher.address.addressRegion Region Description: @@ -280,7 +313,7 @@ Description: **string, null** --- -## 41.9.4.3. sources.publisher.address.addressLocality +## 34.10.4.3. sources.publisher.address.addressLocality Locality Description: @@ -289,19 +322,19 @@ Description: **string, null** --- -## 41.9.4.4. sources.publisher.address.postOfficeBoxNumber +## 34.10.4.4. sources.publisher.address.postOfficeBoxNumber Post Office Box Number **string, null** --- -## 41.9.4.5. sources.publisher.address.postalCode +## 34.10.4.5. sources.publisher.address.postalCode Postal Code **string, null** --- -## 41.9.4.6. sources.publisher.address.streetAddress +## 34.10.4.6. sources.publisher.address.streetAddress Street Address Description: @@ -310,7 +343,7 @@ Description: **string, null** --- -## 41.9.5. sources.publisher.url +## 34.10.5. sources.publisher.url URL Description: @@ -319,7 +352,7 @@ Description: **string, null** --- -## 41.9.6. sources.publisher.email +## 34.10.6. sources.publisher.email Email Description: @@ -328,7 +361,7 @@ Description: **string, null** --- -## 41.9.7. sources.publisher.logo +## 34.10.7. sources.publisher.logo Logo Description: diff --git a/docs/schema/35. enzymes.md b/docs/schema/35. enzymes.md deleted file mode 100644 index 3c20cbd..0000000 --- a/docs/schema/35. enzymes.md +++ /dev/null @@ -1,62 +0,0 @@ ---- -## 35. enzymes -Enzymes - -**array[object]** - ---- -## 35.1. enzymes.name -Name - -**string, null** - ---- -## 35.2. enzymes.hasECNumber -EC Number `Required` - -Description: -> An EC number defined by the Enzyme Commission - -**string** - ---- -## 35.3. enzymes.url -URL - -Description: -> Uniform Resource Locator of a resource on the Internet - -**string, null** - ---- -## 35.4. enzymes.alternateName -Alternate Name - -**array[string]** - ---- -## 35.5. enzymes.active -Active - -Description: -> Is this enzyme active - -**boolean, null** - ---- -## 35.6. enzymes.relatedData -Related Data - -Description: -> JSON paths to relation object - -**array[string]** - ---- -## 35.7. enzymes.source -Source `Required` - -Description: -> List of JSON paths to source object - -**array[string]** diff --git a/schema/microbe_schema.json b/schema/microbe_schema.json index beb56e9..3025c1a 100644 --- a/schema/microbe_schema.json +++ b/schema/microbe_schema.json @@ -166,64 +166,6 @@ "title": "BioSafety", "type": "object" }, - "CellShape": { - "additionalProperties": false, - "description": "Cell shape of the strain", - "properties": { - "cellShape": { - "description": "The shape type the cells", - "title": "Cell Shape", - "type": "string" - }, - "source": { - "description": "List of JSON paths to source object", - "items": { - "pattern": "^\\/sources\\/\\d+$", - "type": "string" - }, - "title": "Source", - "type": "array" - } - }, - "required": [ - "cellShape", - "source" - ], - "title": "CellShape", - "type": "object" - }, - "CellSize": { - "additionalProperties": false, - "description": "object to hold cell size information", - "properties": { - "cellLength": { - "$ref": "#/$defs/Size", - "description": "", - "title": "Cell Length" - }, - "cellWidth": { - "$ref": "#/$defs/Size", - "description": "", - "title": "Cell Width" - }, - "source": { - "description": "List of JSON paths to source object", - "items": { - "pattern": "^\\/sources\\/\\d+$", - "type": "string" - }, - "title": "Source", - "type": "array" - } - }, - "required": [ - "cellLength", - "cellWidth", - "source" - ], - "title": "CellSize", - "type": "object" - }, "CellWall": { "additionalProperties": false, "description": "Cell Wall constituent - ChemSubstance + percent of CellWall", @@ -575,51 +517,6 @@ "title": "Collection", "type": "object" }, - "Colony": { - "additionalProperties": false, - "description": "Colony information of a microorganism/strain", - "properties": { - "color": { - "anyOf": [ - { - "$ref": "#/$defs/ColonyColor" - }, - { - "type": "null" - } - ], - "default": null, - "description": "Color of the colony on the", - "title": "Color of Colony" - }, - "size": { - "anyOf": [ - { - "$ref": "#/$defs/Size" - }, - { - "type": "null" - } - ], - "default": null, - "title": "Size of Colony" - }, - "source": { - "description": "List of JSON paths to source object", - "items": { - "pattern": "^\\/sources\\/\\d+$", - "type": "string" - }, - "title": "Source", - "type": "array" - } - }, - "required": [ - "source" - ], - "title": "Colony", - "type": "object" - }, "ColonyColor": { "description": "Valid colors for colonies\n\nAttributes:\n white: white\n cream: cream\n yellowish: yellowish\n orange: orange\n pink: pink\n red: red\n buff: buff\n darkbrown: darkbrown\n reyish: reyish\n tannish: tannish\n beige: beige\n brownish: brownish", "enum": [ @@ -909,6 +806,13 @@ "title": "EC Number", "type": "string" }, + "identifier": { + "items": { + "$ref": "#/$defs/Identifier" + }, + "title": "Identifier", + "type": "array" + }, "name": { "anyOf": [ { @@ -938,22 +842,6 @@ }, "title": "Source", "type": "array" - }, - "url": { - "anyOf": [ - { - "format": "uri", - "maxLength": 2083, - "minLength": 1, - "type": "string" - }, - { - "type": "null" - } - ], - "default": null, - "description": "Uniform Resource Locator of a resource on the Internet", - "title": "URL" } }, "required": [ @@ -1105,7 +993,7 @@ "method": { "anyOf": [ { - "type": "string" + "$ref": "#/$defs/GCMethod" }, { "type": "null" @@ -1115,6 +1003,19 @@ "description": "Name of the method used to measure the GC content", "title": "Method" }, + "noteMethod": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "default": null, + "description": "Note about the used method", + "title": "Note Method" + }, "source": { "description": "List of JSON paths to source object", "items": { @@ -1139,6 +1040,15 @@ "title": "GCContent", "type": "object" }, + "GCMethod": { + "description": "Methods for GC measurement\n\nArgs:\n experimental: experimental\n genomeSequence: genome sequence", + "enum": [ + "experimental", + "genome sequence" + ], + "title": "GCMethod", + "type": "string" + }, "GeoPoint": { "additionalProperties": false, "description": "Geopoint / Coordinate object", @@ -1683,6 +1593,22 @@ "additionalProperties": false, "description": "Identifier of every Kind, compare to schema.org PropertyValue class", "properties": { + "logo": { + "anyOf": [ + { + "format": "uri", + "maxLength": 2083, + "minLength": 1, + "type": "string" + }, + { + "type": "null" + } + ], + "default": null, + "description": "Logo of the Identifier Organization (e.g. DOI, ORCID, ROR, ...)", + "title": "Logo" + }, "name": { "description": "Name of the identifier", "title": "Name", @@ -1733,6 +1659,22 @@ "IdentifierStrain": { "additionalProperties": false, "properties": { + "logo": { + "anyOf": [ + { + "format": "uri", + "maxLength": 2083, + "minLength": 1, + "type": "string" + }, + { + "type": "null" + } + ], + "default": null, + "description": "Logo of the Identifier Organization (e.g. DOI, ORCID, ROR, ...)", + "title": "Logo" + }, "name": { "description": "Name of the identifier", "title": "Name", @@ -1790,53 +1732,6 @@ "title": "IdentifierStrain", "type": "object" }, - "Isolation": { - "additionalProperties": false, - "description": "Isolation event information", - "properties": { - "date": { - "anyOf": [ - { - "pattern": "^(?:\\d{4}[-\\._]?\\d{0,2}[-\\._]?\\d{0,2})?/?(?:\\d{4}[-\\._]?\\d{0,2}[-\\._]?\\d{0,2})?$", - "type": "string" - }, - { - "type": "null" - } - ], - "default": null, - "description": "Date of Isolation, using date range format of dublin core: 'YYYY-MM-DD/YYYY-MM-DD' ether side can be empty defining an open ended range, only the year is mandatory, e.g. '/1978' means before 1978", - "title": "Date" - }, - "isolatedAt": { - "anyOf": [ - { - "$ref": "#/$defs/Organization" - }, - { - "type": "null" - } - ], - "default": null, - "description": "Institute where the isolation happened", - "title": "Isolated At" - }, - "source": { - "description": "List of JSON paths to source object", - "items": { - "pattern": "^\\/sources\\/\\d+$", - "type": "string" - }, - "title": "Source", - "type": "array" - } - }, - "required": [ - "source" - ], - "title": "Isolation", - "type": "object" - }, "IsolationTag": { "additionalProperties": false, "description": "Isolation tag system, original used by BacDive", @@ -1876,6 +1771,20 @@ "title": "IsolationTag", "type": "object" }, + "KindOfUtilization": { + "description": "Types of utilization\n\nArgs:\n assimilation: assimilation\n buildsAcidFrom: builds acid from\n degradation: degradation\n energySource: energy source\n fermentation: fermentation\n hydrolysis: hydrolysis\n reduction: reduction", + "enum": [ + "assimilation", + "builds acid from", + "degradation", + "energy source", + "fermentation", + "hydrolysis", + "reduction" + ], + "title": "KindOfUtilization", + "type": "string" + }, "Legal": { "additionalProperties": false, "description": "Legal information of the strain", @@ -2182,7 +2091,7 @@ "kindOfUtilization": { "anyOf": [ { - "type": "string" + "$ref": "#/$defs/KindOfUtilization" }, { "type": "null" @@ -2244,10 +2153,50 @@ "title": "Morph", "type": "string" }, - "Motility": { + "Morphology": { "additionalProperties": false, - "description": "Information on motility of a Strain", + "description": "Morphology of a cell", "properties": { + "cellLength": { + "$ref": "#/$defs/Size", + "description": "Length of a cell", + "title": "Cell Length" + }, + "cellShape": { + "description": "The shape type the cells", + "title": "Cell Shape", + "type": "string" + }, + "cellWidth": { + "$ref": "#/$defs/Size", + "description": "Width of a cell", + "title": "Cell Width" + }, + "colonyColor": { + "anyOf": [ + { + "$ref": "#/$defs/ColonyColor" + }, + { + "type": "null" + } + ], + "default": null, + "description": "Color of the colony on the", + "title": "Color of Colony" + }, + "colonySize": { + "anyOf": [ + { + "$ref": "#/$defs/Size" + }, + { + "type": "null" + } + ], + "default": null, + "title": "Size of Colony" + }, "flagellum": { "anyOf": [ { @@ -2311,9 +2260,12 @@ } }, "required": [ + "cellShape", + "cellLength", + "cellWidth", "source" ], - "title": "Motility", + "title": "Morphology", "type": "object" }, "MultiCell": { @@ -2469,21 +2421,22 @@ "title": "Organization", "type": "object" }, - "OtherMedia": { + "Origin": { "additionalProperties": false, - "description": "A Media object e.g. Photo, Video, Document, etc", + "description": "Isolation event information\n Sample = The material probe in which the strain was found\n Isolation = Isolation of the strain from the sample", "properties": { - "additionalType": { + "country": { "anyOf": [ { - "type": "string" + "$ref": "#/$defs/Country" }, { "type": "null" } ], "default": null, - "title": "Additional Type" + "description": "Country where the sample material originated from", + "title": "Country" }, "description": { "anyOf": [ @@ -2495,20 +2448,152 @@ } ], "default": null, - "description": "Description of the medium and the content in the medium", + "description": "Description of the sample", "title": "Description" }, - "name": { + "isolatedAt": { "anyOf": [ { - "type": "string" + "$ref": "#/$defs/Organization" }, { "type": "null" } ], "default": null, - "title": "Name" + "description": "Institute where the strain was isolated from the sample", + "title": "Isolated At" + }, + "isolationDate": { + "anyOf": [ + { + "pattern": "^(?:\\d{4}[-\\._]?\\d{0,2}[-\\._]?\\d{0,2})?/?(?:\\d{4}[-\\._]?\\d{0,2}[-\\._]?\\d{0,2})?$", + "type": "string" + }, + { + "type": "null" + } + ], + "default": null, + "description": "Date of isolation from the sample material, using date range format of dublin core:'YYYY-MM-DD/YYYY-MM-DD' ether side can be empty defining an open ended range, only the year is mandatory, e.g. '/1978' means before 1978", + "title": "Date" + }, + "isolator": { + "anyOf": [ + { + "$ref": "#/$defs/Person" + }, + { + "type": "null" + } + ], + "default": null, + "description": "Person that isolated the strain from the sample", + "title": "Isolator" + }, + "locationCreated": { + "anyOf": [ + { + "$ref": "#/$defs/Location" + }, + { + "type": "null" + } + ], + "default": null, + "description": "Location where the sample was taken", + "title": "Location Created" + }, + "sampleDate": { + "anyOf": [ + { + "pattern": "^(?:\\d{4}[-\\._]?\\d{0,2}[-\\._]?\\d{0,2})?/?(?:\\d{4}[-\\._]?\\d{0,2}[-\\._]?\\d{0,2})?$", + "type": "string" + }, + { + "type": "null" + } + ], + "default": null, + "description": "Date of sampling, using date range format of dublin core: 'YYYY-MM-DD/YYYY-MM-DD' ether side can be empty defining an open ended range, only the year is mandatory, e.g. '/1978' means before 1978", + "title": "Date" + }, + "sampler": { + "anyOf": [ + { + "$ref": "#/$defs/Person" + }, + { + "type": "null" + } + ], + "default": null, + "description": "Person that sampled the material", + "title": "Sampler" + }, + "source": { + "description": "List of JSON paths to source object", + "items": { + "pattern": "^\\/sources\\/\\d+$", + "type": "string" + }, + "title": "Source", + "type": "array" + }, + "tags": { + "items": { + "$ref": "#/$defs/IsolationTag" + }, + "title": "Isolation Source Tags", + "type": "array" + } + }, + "required": [ + "source" + ], + "title": "Origin", + "type": "object" + }, + "OtherMedia": { + "additionalProperties": false, + "description": "A Media object e.g. Photo, Video, Document, etc", + "properties": { + "additionalType": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "default": null, + "title": "Additional Type" + }, + "description": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "default": null, + "description": "Description of the medium and the content in the medium", + "title": "Description" + }, + "name": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "default": null, + "title": "Name" }, "source": { "description": "List of JSON paths to source object", @@ -2560,9 +2645,9 @@ "description": "OxygenRelation of the strain", "properties": { "oxygenRelation": { + "$ref": "#/$defs/OxygenTolerance", "description": "Aerobic, anaerobic etc.", - "title": "Oxygen Relation", - "type": "string" + "title": "Oxygen Relation" }, "relatedData": { "description": "JSON paths to relation object", @@ -2590,6 +2675,22 @@ "title": "OxygenRelation", "type": "object" }, + "OxygenTolerance": { + "description": "How does the strain tolerate Oxygen\n\nArgs:\n aerobe: aerobe\n aerotolerant: aerotolerant\n anaerobe: anaerobe\n facultativeAerobe: facultative aerobe\n facultativeAnaerobe: facultative anaerobe\n microaerophile: microaerophile\n microaerotolerant: microaerotolerant\n obligateAerobe: obligate aerobe\n obligateAnaerobe: obligate anaerobe", + "enum": [ + "aerobe", + "aerotolerant", + "anaerobe", + "facultative aerobe", + "facultative anaerobe", + "microaerophile", + "microaerotolerant", + "obligate aerobe", + "obligate anaerobe" + ], + "title": "OxygenTolerance", + "type": "string" + }, "Pathogen": { "additionalProperties": false, "description": "Pathogen, defining Host, pathogenicity and under what classification", @@ -2720,83 +2821,6 @@ "title": "RelatedData", "type": "object" }, - "Sample": { - "additionalProperties": false, - "description": "Information on the Sampling event of that Strain", - "properties": { - "country": { - "anyOf": [ - { - "$ref": "#/$defs/Country" - }, - { - "type": "null" - } - ], - "default": null, - "title": "Country" - }, - "date": { - "anyOf": [ - { - "pattern": "^(?:\\d{4}[-\\._]?\\d{0,2}[-\\._]?\\d{0,2})?/?(?:\\d{4}[-\\._]?\\d{0,2}[-\\._]?\\d{0,2})?$", - "type": "string" - }, - { - "type": "null" - } - ], - "default": null, - "description": "Date of Sampling, using date range format of dublin core: 'YYYY-MM-DD/YYYY-MM-DD' ether side can be empty defining an open ended range, only the year is mandatory, e.g. '/1978' means before 1978", - "title": "Date" - }, - "description": { - "anyOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "default": null, - "title": "Description" - }, - "locationCreated": { - "anyOf": [ - { - "$ref": "#/$defs/Location" - }, - { - "type": "null" - } - ], - "default": null, - "title": "Location Created" - }, - "source": { - "description": "List of JSON paths to source object", - "items": { - "pattern": "^\\/sources\\/\\d+$", - "type": "string" - }, - "title": "Source", - "type": "array" - }, - "tags": { - "items": { - "$ref": "#/$defs/IsolationTag" - }, - "title": "Isolation Source Tags", - "type": "array" - } - }, - "required": [ - "source" - ], - "title": "Sample", - "type": "object" - }, "ScientificName": { "additionalProperties": false, "description": "Scientific name", @@ -2968,13 +2992,26 @@ "title": "Date Recorded", "type": "string" }, - "identifiers": { + "identifier": { "items": { "$ref": "#/$defs/Identifier" }, "title": "Identifier", "type": "array" }, + "lastUpdate": { + "anyOf": [ + { + "format": "date", + "type": "string" + }, + { + "type": "null" + } + ], + "default": null, + "title": "Date of last update" + }, "mode": { "$ref": "#/$defs/CurationMode", "description": "Mode of curation", @@ -3212,18 +3249,32 @@ "title": "Scientific Name" }, "taxonRank": { - "$ref": "#/$defs/TaxonRank", + "anyOf": [ + { + "$ref": "#/$defs/TaxonRank" + }, + { + "type": "null" + } + ], + "default": null, "title": "Taxon Rank" }, "taxonStatus": { - "$ref": "#/$defs/TaxonStatus", + "anyOf": [ + { + "$ref": "#/$defs/TaxonStatus" + }, + { + "type": "null" + } + ], + "default": null, "title": "Taxon Status" } }, "required": [ - "name", - "taxonRank", - "taxonStatus" + "name" ], "title": "Taxon", "type": "object" @@ -3317,18 +3368,32 @@ "type": "array" }, "taxonRank": { - "$ref": "#/$defs/TaxonRank", + "anyOf": [ + { + "$ref": "#/$defs/TaxonRank" + }, + { + "type": "null" + } + ], + "default": null, "title": "Taxon Rank" }, "taxonStatus": { - "$ref": "#/$defs/TaxonStatus", + "anyOf": [ + { + "$ref": "#/$defs/TaxonStatus" + }, + { + "type": "null" + } + ], + "default": null, "title": "Taxon Status" } }, "required": [ "name", - "taxonRank", - "taxonStatus", "source" ], "title": "TaxonWithSource", @@ -3443,7 +3508,7 @@ "concentration": { "anyOf": [ { - "type": "string" + "type": "number" }, { "type": "null" @@ -3580,7 +3645,7 @@ } }, "additionalProperties": false, - "description": "Microbe - main class of the new microbial data standard", + "description": "Microbial Strain - main class of the new microbial strain data standard", "properties": { "bioSafety": { "description": "", @@ -3590,22 +3655,6 @@ "title": "Bio Safety", "type": "array" }, - "cellShape": { - "description": "", - "items": { - "$ref": "#/$defs/CellShape" - }, - "title": "Cell Shape", - "type": "array" - }, - "cellSize": { - "description": "", - "items": { - "$ref": "#/$defs/CellSize" - }, - "title": "Cell Size", - "type": "array" - }, "collections": { "description": "", "items": { @@ -3614,14 +3663,6 @@ "title": "Collections", "type": "array" }, - "colony": { - "description": "", - "items": { - "$ref": "#/$defs/Colony" - }, - "title": "Colony", - "type": "array" - }, "connectedPersons": { "description": "", "items": { @@ -3691,14 +3732,6 @@ "title": "Identifier", "type": "array" }, - "isolation": { - "description": "", - "items": { - "$ref": "#/$defs/Isolation" - }, - "title": "Isolation", - "type": "array" - }, "knownApplications": { "description": "", "items": { @@ -3744,12 +3777,12 @@ "description": "Applicable and required for fungi only", "title": "Morph Type" }, - "motility": { - "description": "", + "morphology": { + "description": "Morphology information", "items": { - "$ref": "#/$defs/Motility" + "$ref": "#/$defs/Morphology" }, - "title": "Motility", + "title": "Morphology", "type": "array" }, "multiCellComplexForming": { @@ -3765,6 +3798,14 @@ "description": "", "title": "Organism Type" }, + "origin": { + "description": "Sample and isolation data", + "items": { + "$ref": "#/$defs/Origin" + }, + "title": "Origin", + "type": "array" + }, "otherMedia": { "description": "", "items": { @@ -3805,14 +3846,6 @@ "title": "Related Data", "type": "array" }, - "sample": { - "description": "", - "items": { - "$ref": "#/$defs/Sample" - }, - "title": "Sample", - "type": "array" - }, "sequences": { "description": "", "items": { @@ -3877,37 +3910,6 @@ "title": "Type Strain", "type": "array" }, - "unifiedTaxon": { - "anyOf": [ - { - "$ref": "#/$defs/Taxon" - }, - { - "type": "null" - } - ], - "default": null, - "description": "Evaluated and updated taxonomy", - "title": "Unified Taxon" - }, - "unifiedTypeStrain": { - "anyOf": [ - { - "type": "boolean" - }, - { - "type": "null" - } - ], - "default": null, - "description": "Is this strain type for unified species", - "title": "Unified Type Strain" - }, - "version": { - "const": "0.6", - "title": "Version", - "type": "string" - }, "wallConstituents": { "description": "", "items": { @@ -3918,12 +3920,11 @@ } }, "required": [ - "version", "organismType", "typeStrain", "taxon", "sources" ], - "title": "Microbe", + "title": "Strain", "type": "object" } diff --git a/src/microbial_strain_data_model/classes/cellshape.py b/src/microbial_strain_data_model/classes/cellshape.py deleted file mode 100644 index 70d7c9d..0000000 --- a/src/microbial_strain_data_model/classes/cellshape.py +++ /dev/null @@ -1,19 +0,0 @@ -from pydantic import BaseModel, ConfigDict, Field - -from microbial_strain_data_model.classes.links import SourceLink - - -class CellShape(BaseModel): - """Cell shape of the strain""" - - model_config = ConfigDict( - strict=True, - extra="forbid", - revalidate_instances="always", - str_strip_whitespace=True, - ) - - cellShape: str = Field(title="Cell Shape", description="The shape type the cells") - source: list[SourceLink] = Field( - title="Source", description="List of JSON paths to source object" - ) diff --git a/src/microbial_strain_data_model/classes/chemicalsubstance.py b/src/microbial_strain_data_model/classes/chemicalsubstance.py index 7bf54e6..f9cca95 100644 --- a/src/microbial_strain_data_model/classes/chemicalsubstance.py +++ b/src/microbial_strain_data_model/classes/chemicalsubstance.py @@ -1,14 +1,12 @@ from typing_extensions import Annotated -from microbial_strain_data_model.classes.enums import ConcentrationUnit -from microbial_strain_data_model.classes.metabolitetest import MetaboliteTest -from microbial_strain_data_model.utils.functions import check_not_completely_empty - from pydantic import BaseModel, ConfigDict, Field, model_validator -from microbial_strain_data_model.classes.growthrange import Growth +from microbial_strain_data_model.classes.enums import ConcentrationUnit +from microbial_strain_data_model.classes.growthcondition import GrowthRange +from microbial_strain_data_model.classes.metabolitetest import MetaboliteTest from microbial_strain_data_model.classes.identifier import Identifier - from microbial_strain_data_model.classes.links import SourceLink +from microbial_strain_data_model.utils.functions import check_not_completely_empty class ChemicalSubstance(BaseModel): @@ -70,7 +68,7 @@ class FattyAcid(ChemicalSubstance): ecl: str | None = Field(default=None, title="ECL") -class Halophil(Growth[ConcentrationUnit], ChemicalSubstance): +class Halophil(ChemicalSubstance): """Halophily abilities of a Strain""" model_config = ConfigDict( @@ -79,6 +77,22 @@ class Halophil(Growth[ConcentrationUnit], ChemicalSubstance): revalidate_instances="always", str_strip_whitespace=True, ) + minimal: float | None = Field( + default=None, title="Optimal", description="Single optimal growth value" + ) + maximal: float | None = Field( + default=None, title="Optimal", description="Single optimal growth value" + ) + optimal: float | None = Field( + default=None, title="Optimal", description="Single optimal growth value" + ) + unit: ConcentrationUnit = Field(title="Unit", description="") + + tests: list[GrowthRange] = Field( + default_factory=list, + title="Tests", + description="List of tests and if the strain grows in tested ranges", + ) source: list[SourceLink] = Field( title="Source", description="List of JSON paths to source object" diff --git a/src/microbial_strain_data_model/classes/colony.py b/src/microbial_strain_data_model/classes/colony.py deleted file mode 100644 index 7a15cb4..0000000 --- a/src/microbial_strain_data_model/classes/colony.py +++ /dev/null @@ -1,28 +0,0 @@ -from pydantic import BaseModel, ConfigDict, Field, model_validator - -from microbial_strain_data_model.classes.enums import ColonyColor -from microbial_strain_data_model.classes.size import Size -from microbial_strain_data_model.utils.functions import check_not_completely_empty - -from microbial_strain_data_model.classes.links import SourceLink - - -class Colony(BaseModel): - """Colony information of a microorganism/strain""" - - model_config = ConfigDict( - strict=True, - extra="forbid", - revalidate_instances="always", - str_strip_whitespace=True, - ) - - size: Size | None = Field(default=None, title="Size of Colony") - color: ColonyColor | None = Field( - default=None, title="Color of Colony", description="Color of the colony on the" - ) - source: list[SourceLink] = Field( - title="Source", description="List of JSON paths to source object" - ) - - _check_values = model_validator(mode="after")(check_not_completely_empty) diff --git a/src/microbial_strain_data_model/classes/enums.py b/src/microbial_strain_data_model/classes/enums.py index 4051e04..c1f3aa0 100644 --- a/src/microbial_strain_data_model/classes/enums.py +++ b/src/microbial_strain_data_model/classes/enums.py @@ -1,9 +1,4 @@ from enum import Enum -from typing import Literal, TypeAlias - - -CelsiusUnit: TypeAlias = Literal["C"] -PHUnit: TypeAlias = Literal["pH"] # ruff: noqa: E501 @@ -282,21 +277,6 @@ class PathogenLevel(str, Enum): obligate = "obligate" -class PersonRole(str, Enum): - """ - Valid roles for persons related to strain - - Attributes: - sampler: sampler - isolator: isolator - other: other - """ - - sampler = "sampler" - isolator = "isolator" - other = "other" - - class SequenceType(str, Enum): """ Valid sequence types diff --git a/src/microbial_strain_data_model/classes/growthrange.py b/src/microbial_strain_data_model/classes/growthcondition.py similarity index 61% rename from src/microbial_strain_data_model/classes/growthrange.py rename to src/microbial_strain_data_model/classes/growthcondition.py index b8617f0..83825ce 100644 --- a/src/microbial_strain_data_model/classes/growthrange.py +++ b/src/microbial_strain_data_model/classes/growthcondition.py @@ -1,12 +1,9 @@ -from typing import Generic, TypeVar from pydantic import BaseModel, ConfigDict, Field from microbial_strain_data_model.classes.links import SourceLink, RelationLink -T = TypeVar("T") - -class GrowthRange(BaseModel, Generic[T]): +class GrowthRange(BaseModel): """Single grow condition test""" model_config = ConfigDict( @@ -22,7 +19,6 @@ class GrowthRange(BaseModel, Generic[T]): maximal: float | None = Field( default=None, title="Maximal", description="Maximal value of tested range" ) - unit: T growth: bool = Field( title="Growth", description="Does the strain grow within this range?" ) @@ -33,7 +29,7 @@ class GrowthRange(BaseModel, Generic[T]): ) -class Growth(BaseModel, Generic[T]): +class GrowthCondition(BaseModel): """Optimal and tested information about growing a Strain""" model_config = ConfigDict( @@ -43,21 +39,42 @@ class Growth(BaseModel, Generic[T]): str_strip_whitespace=True, ) - optimal: float | None = Field( - default=None, title="Optimal", description="Single optimal growth value" + optimalTemperature: float | None = Field( + default=None, + title="Optimal", + description="Single optimal growth temperature value in celsius", ) - minimal: float | None = Field( - default=None, title="Minimal", description="Known minimal growth value" + minimalTemperature: float | None = Field( + default=None, + title="Minimal", + description="Known minimal growth temperature value in celsius", ) - maximal: float | None = Field( - default=None, title="Maximal", description="Known maximal growth value" + maximalTemperature: float | None = Field( + default=None, + title="Maximal", + description="Known maximal growth temperature value in celsius", + ) + testsTemperature: list[GrowthRange] = Field( + default_factory=list, + title="Tests", + description="List of tests and if the strain grows in tested ranges", + ) + + optimalPh: float | None = Field( + default=None, title="Optimal", description="Single optimal growth pH value" ) - unit: T - tests: list[GrowthRange[T]] = Field( + minimalPh: float | None = Field( + default=None, title="Minimal", description="Known minimal growth pH value" + ) + maximalPh: float | None = Field( + default=None, title="Maximal", description="Known maximal growth pH value" + ) + testsPh: list[GrowthRange] = Field( default_factory=list, title="Tests", description="List of tests and if the strain grows in tested ranges", ) + source: list[SourceLink] = Field( title="Source", description="List of JSON paths to source object" ) diff --git a/src/microbial_strain_data_model/classes/isolation.py b/src/microbial_strain_data_model/classes/isolation.py deleted file mode 100644 index 50a89c6..0000000 --- a/src/microbial_strain_data_model/classes/isolation.py +++ /dev/null @@ -1,42 +0,0 @@ -from typing_extensions import Annotated -from pydantic import BaseModel, ConfigDict, Field, StringConstraints - -from microbial_strain_data_model.classes.organization import Organization -from microbial_strain_data_model.classes.links import SourceLink - - -class Isolation(BaseModel): - """Isolation event information""" - - model_config = ConfigDict( - strict=True, - extra="forbid", - revalidate_instances="always", - str_strip_whitespace=True, - ) - - date: ( - Annotated[ - str, - StringConstraints( - strip_whitespace=True, - to_upper=True, - pattern=r"^(?:\d{4}[-\._]?\d{0,2}[-\._]?\d{0,2})?/?(?:\d{4}[-\._]?\d{0,2}[-\._]?\d{0,2})?$", - ), - ] - | None - ) = Field( - default=None, - title="Date", - description="Date of Isolation, using date range format of dublin core: " - "'YYYY-MM-DD/YYYY-MM-DD' ether side can be empty defining an open ended " - "range, only the year is mandatory, e.g. '/1978' means before 1978", - ) - isolatedAt: Organization | None = Field( - default=None, - title="Isolated At", - description="Institute where the isolation happened", - ) - source: list[SourceLink] = Field( - title="Source", description="List of JSON paths to source object" - ) diff --git a/src/microbial_strain_data_model/classes/isolationtag.py b/src/microbial_strain_data_model/classes/isolationtag.py new file mode 100644 index 0000000..704ae87 --- /dev/null +++ b/src/microbial_strain_data_model/classes/isolationtag.py @@ -0,0 +1,36 @@ +from typing_extensions import Self +from pydantic import BaseModel, ConfigDict, Field, model_validator +from anytree.resolver import Resolver, ChildResolverError + +from microbial_strain_data_model.data.isolation_sources_tree import root + + +class IsolationTag(BaseModel): + """Isolation tag system, original used by BacDive""" + + model_config = ConfigDict( + strict=True, + extra="forbid", + revalidate_instances="always", + str_strip_whitespace=True, + ) + + level1: str = Field(title="Level 1") + level2: str | None = Field(default=None, title="Level 2") + level3: str | None = Field(default=None, title="Level 3") + + @model_validator(mode="after") + def check_isolation_tag(self) -> Self: + resolver = Resolver("name") + path = "" + self.level1 + for x in [self.level2, self.level3]: + if isinstance(x, str): + path += "/" + path += x + try: + resolver.get(root, path) + except ChildResolverError as e: + raise ValueError from ValueError( + f"Isolation Source Tags are not valid isolation tag path: {e}" + ) + return self diff --git a/src/microbial_strain_data_model/classes/motility.py b/src/microbial_strain_data_model/classes/morphology.py similarity index 60% rename from src/microbial_strain_data_model/classes/motility.py rename to src/microbial_strain_data_model/classes/morphology.py index 494d9d8..14f9f89 100644 --- a/src/microbial_strain_data_model/classes/motility.py +++ b/src/microbial_strain_data_model/classes/morphology.py @@ -1,11 +1,12 @@ from pydantic import BaseModel, ConfigDict, Field -from microbial_strain_data_model.classes.enums import FlagellumArrangement +from microbial_strain_data_model.classes.enums import ColonyColor, FlagellumArrangement from microbial_strain_data_model.classes.links import SourceLink +from microbial_strain_data_model.classes.size import Size -class Motility(BaseModel): - """Information on motility of a Strain""" +class Morphology(BaseModel): + """Morphology of a cell""" model_config = ConfigDict( strict=True, @@ -14,6 +15,9 @@ class Motility(BaseModel): str_strip_whitespace=True, ) + cellShape: str = Field(title="Cell Shape", description="The shape type the cells") + cellLength: Size = Field(title="Cell Length", description="Length of a cell") + cellWidth: Size = Field(title="Cell Width", description="Width of a cell") motile: bool | None = Field( default=None, title="Motile", @@ -32,6 +36,10 @@ class Motility(BaseModel): title="Gliding", description="Cells can be motile by gliding instead of having flagella", ) + colonySize: Size | None = Field(default=None, title="Size of Colony") + colonyColor: ColonyColor | None = Field( + default=None, title="Color of Colony", description="Color of the colony on the" + ) source: list[SourceLink] = Field( title="Source", description="List of JSON paths to source object" ) diff --git a/src/microbial_strain_data_model/classes/origin.py b/src/microbial_strain_data_model/classes/origin.py new file mode 100644 index 0000000..9516ef9 --- /dev/null +++ b/src/microbial_strain_data_model/classes/origin.py @@ -0,0 +1,89 @@ +from typing_extensions import Annotated +from pydantic import BaseModel, ConfigDict, Field, StringConstraints + +from microbial_strain_data_model.classes.country import Country +from microbial_strain_data_model.classes.isolationtag import IsolationTag +from microbial_strain_data_model.classes.location import Location +from microbial_strain_data_model.classes.organization import Organization +from microbial_strain_data_model.classes.links import SourceLink +from microbial_strain_data_model.classes.person import Person + + +class Origin(BaseModel): + """ + Isolation event information + Sample = The material probe in which the strain was found + Isolation = Isolation of the strain from the sample + """ + + model_config = ConfigDict( + strict=True, + extra="forbid", + revalidate_instances="always", + str_strip_whitespace=True, + ) + + sampleDate: ( + Annotated[ + str, + StringConstraints( + strip_whitespace=True, + to_upper=True, + pattern=r"^(?:\d{4}[-\._]?\d{0,2}[-\._]?\d{0,2})?/?(?:\d{4}[-\._]?\d{0,2}[-\._]?\d{0,2})?$", + ), + ] + | None + ) = Field( + default=None, + title="Date", + description="Date of sampling, using date range format of dublin core: " + "'YYYY-MM-DD/YYYY-MM-DD' ether side can be empty defining an open ended " + "range, only the year is mandatory, e.g. '/1978' means before 1978", + ) + country: Country | None = Field( + default=None, + title="Country", + description="Country where the sample material originated from", + ) + description: str | None = Field( + default=None, title="Description", description="Description of the sample" + ) + locationCreated: Location | None = Field( + default=None, + title="Location Created", + description="Location where the sample was taken", + ) + tags: list[IsolationTag] = Field(default_factory=list, title="Isolation Source Tags") + sampler: Person | None = Field( + default=None, title="Sampler", description="Person that sampled the material" + ) + isolationDate: ( + Annotated[ + str, + StringConstraints( + strip_whitespace=True, + to_upper=True, + pattern=r"^(?:\d{4}[-\._]?\d{0,2}[-\._]?\d{0,2})?/?(?:\d{4}[-\._]?\d{0,2}[-\._]?\d{0,2})?$", + ), + ] + | None + ) = Field( + default=None, + title="Date", + description="Date of isolation from the sample material, using date range format" + " of dublin core:'YYYY-MM-DD/YYYY-MM-DD' ether side can be empty defining an open" + " ended range, only the year is mandatory, e.g. '/1978' means before 1978", + ) + isolatedAt: Organization | None = Field( + default=None, + title="Isolated At", + description="Institute where the strain was isolated from the sample", + ) + isolator: Person | None = Field( + default=None, + title="Isolator", + description="Person that isolated the strain from the sample", + ) + source: list[SourceLink] = Field( + title="Source", description="List of JSON paths to source object" + ) diff --git a/src/microbial_strain_data_model/classes/person.py b/src/microbial_strain_data_model/classes/person.py index 459d18a..1b799fe 100644 --- a/src/microbial_strain_data_model/classes/person.py +++ b/src/microbial_strain_data_model/classes/person.py @@ -1,9 +1,6 @@ from pydantic import BaseModel, ConfigDict, Field -from microbial_strain_data_model.classes.enums import PersonRole from microbial_strain_data_model.classes.identifier import Identifier -from microbial_strain_data_model.classes.links import SourceLink - class Person(BaseModel): """Person""" @@ -23,19 +20,3 @@ class Person(BaseModel): title="Identifier", description="Person identifiers like ORCID", ) - - -class ConnectedPerson(Person): - """Connected Person = Person + Role""" - - model_config = ConfigDict( - strict=True, - extra="forbid", - revalidate_instances="always", - str_strip_whitespace=True, - ) - - role: PersonRole | None = Field(default=None, title="Role") - source: list[SourceLink] = Field( - title="Source", description="List of JSON paths to source object" - ) diff --git a/src/microbial_strain_data_model/classes/sample.py b/src/microbial_strain_data_model/classes/sample.py deleted file mode 100644 index 261faae..0000000 --- a/src/microbial_strain_data_model/classes/sample.py +++ /dev/null @@ -1,76 +0,0 @@ -from typing_extensions import Annotated, Self -from pydantic import BaseModel, ConfigDict, Field, StringConstraints, model_validator -from anytree.resolver import Resolver, ChildResolverError - -from microbial_strain_data_model.data.isolation_sources_tree import root -from microbial_strain_data_model.classes.country import Country -from microbial_strain_data_model.classes.location import Location - -from microbial_strain_data_model.classes.links import SourceLink - - -class IsolationTag(BaseModel): - """Isolation tag system, original used by BacDive""" - - model_config = ConfigDict( - strict=True, - extra="forbid", - revalidate_instances="always", - str_strip_whitespace=True, - ) - - level1: str = Field(title="Level 1") - level2: str | None = Field(default=None, title="Level 2") - level3: str | None = Field(default=None, title="Level 3") - - @model_validator(mode="after") - def check_isolation_tag(self) -> Self: - resolver = Resolver("name") - path = "" + self.level1 - for x in [self.level2, self.level3]: - if isinstance(x, str): - path += "/" - path += x - try: - resolver.get(root, path) - except ChildResolverError as e: - raise ValueError from ValueError( - f"Isolation Source Tags are not valid isolation tag path: {e}" - ) - return self - - -class Sample(BaseModel): - """Information on the Sampling event of that Strain""" - - model_config = ConfigDict( - strict=True, - extra="forbid", - revalidate_instances="always", - str_strip_whitespace=True, - ) - - date: ( - Annotated[ - str, - StringConstraints( - strip_whitespace=True, - to_upper=True, - pattern=r"^(?:\d{4}[-\._]?\d{0,2}[-\._]?\d{0,2})?/?(?:\d{4}[-\._]?\d{0,2}[-\._]?\d{0,2})?$", - ), - ] - | None - ) = Field( - default=None, - title="Date", - description="Date of Sampling, using date range format of dublin core: " - "'YYYY-MM-DD/YYYY-MM-DD' ether side can be empty defining an open ended " - "range, only the year is mandatory, e.g. '/1978' means before 1978", - ) - country: Country | None = Field(default=None, title="Country") - description: str | None = Field(default=None, title="Description") - locationCreated: Location | None = Field(default=None, title="Location Created") - tags: list[IsolationTag] = Field(default_factory=list, title="Isolation Source Tags") - source: list[SourceLink] = Field( - title="Source", description="List of JSON paths to source object" - ) diff --git a/src/microbial_strain_data_model/classes/size.py b/src/microbial_strain_data_model/classes/size.py index 894aee7..0830b78 100644 --- a/src/microbial_strain_data_model/classes/size.py +++ b/src/microbial_strain_data_model/classes/size.py @@ -2,8 +2,6 @@ from microbial_strain_data_model.classes.enums import SizeUnit -from microbial_strain_data_model.classes.links import SourceLink - class Size(BaseModel): """size object, use only for micro and millimeter""" @@ -18,20 +16,3 @@ class Size(BaseModel): minimal: PositiveFloat = Field(title="Minimal") maximal: PositiveFloat = Field(title="Maximal") unit: SizeUnit = Field(title="Unit") - - -class CellSize(BaseModel): - """object to hold cell size information""" - - model_config = ConfigDict( - strict=True, - extra="forbid", - revalidate_instances="always", - str_strip_whitespace=True, - ) - - cellLength: Size = Field(title="Cell Length", description="") - cellWidth: Size = Field(title="Cell Width", description="") - source: list[SourceLink] = Field( - title="Source", description="List of JSON paths to source object" - ) diff --git a/src/microbial_strain_data_model/microbe.py b/src/microbial_strain_data_model/strain.py similarity index 72% rename from src/microbial_strain_data_model/microbe.py rename to src/microbial_strain_data_model/strain.py index be83392..d18c031 100644 --- a/src/microbial_strain_data_model/microbe.py +++ b/src/microbial_strain_data_model/strain.py @@ -1,55 +1,45 @@ from pydantic_extra_types.pendulum_dt import Date -from typing import Literal from pydantic import BaseModel, ConfigDict, Field from microbial_strain_data_model.classes.application import Application from microbial_strain_data_model.classes.biosafety import BioSafety -from microbial_strain_data_model.classes.cellshape import CellShape from microbial_strain_data_model.classes.chemicalsubstance import ( CellWall, Halophil, Metabolite, ) -from microbial_strain_data_model.classes.colony import Colony from microbial_strain_data_model.classes.cultivationmedia import CultivationMedia from microbial_strain_data_model.classes.enzyme import Enzyme from microbial_strain_data_model.classes.fattyacidprofile import FattyAcidProfile from microbial_strain_data_model.classes.gccontent import GCContent -from microbial_strain_data_model.classes.growthrange import Growth +from microbial_strain_data_model.classes.growthcondition import GrowthCondition from microbial_strain_data_model.classes.hemolysis import Hemolysis from microbial_strain_data_model.classes.legal import Legal from microbial_strain_data_model.classes.literature import Literature +from microbial_strain_data_model.classes.morphology import Morphology from microbial_strain_data_model.classes.multicell import MultiCell from microbial_strain_data_model.classes.organization import Collection from microbial_strain_data_model.classes.othermedia import OtherMedia from microbial_strain_data_model.classes.oxygenrelation import OxygenRelation from microbial_strain_data_model.classes.pathogen import Pathogen -from microbial_strain_data_model.classes.person import ConnectedPerson from microbial_strain_data_model.classes.identifier import IdentifierStrain -from microbial_strain_data_model.classes.isolation import Isolation -from microbial_strain_data_model.classes.motility import Motility +from microbial_strain_data_model.classes.origin import Origin from microbial_strain_data_model.classes.relateddata import RelatedData -from microbial_strain_data_model.classes.sample import Sample from microbial_strain_data_model.classes.sequence import Sequence -from microbial_strain_data_model.classes.size import CellSize from microbial_strain_data_model.classes.source import Source from microbial_strain_data_model.classes.spore import Spore from microbial_strain_data_model.classes.staining import Staining -from microbial_strain_data_model.classes.taxon import Taxon, TaxonWithSource, TypeStrain +from microbial_strain_data_model.classes.taxon import TaxonWithSource, TypeStrain from microbial_strain_data_model.classes.tolerance import Tolerance from microbial_strain_data_model.classes.enums import ( - CelsiusUnit, Morph, OrganismType, - PHUnit, ) -class Microbe(BaseModel): - """Microbe - main class of the new microbial data standard""" - - version: Literal["0.6"] +class Strain(BaseModel): + """Microbial Strain - main class of the new microbial strain data standard""" creation_date: Date = Field(default_factory=Date.today) @@ -64,37 +54,18 @@ class Microbe(BaseModel): frozen=True, ) - unifiedTypeStrain: bool | None = Field( - default=None, - title="Unified Type Strain", - description="Is this strain type for unified species", - frozen=True, - ) - - unifiedTaxon: Taxon | None = Field( - default=None, - title="Unified Taxon", - description="Evaluated and updated taxonomy", - ) - # lists of data objects typeStrain: list[TypeStrain] = Field(title="Type Strain", description="") taxon: list[TaxonWithSource] = Field(title="Taxon", description="") - sample: list[Sample] = Field(default_factory=list, title="Sample", description="") - - isolation: list[Isolation] = Field( - default_factory=list, title="Isolation", description="" + origin: list[Origin] = Field( + default_factory=list, title="Origin", description="Sample and isolation data" ) legal: list[Legal] = Field(default_factory=list, title="Legal", description="") - cellShape: list[CellShape] = Field( - default_factory=list, title="Cell Shape", description="" - ) - oxygenRelation: list[OxygenRelation] = Field( default_factory=list, title="Oxygen Relation", @@ -107,38 +78,26 @@ class Microbe(BaseModel): description="", ) - cellSize: list[CellSize] = Field( - default_factory=list, title="Cell Size", description="" - ) - - motility: list[Motility] = Field( - default_factory=list, title="Motility", description="" + morphology: list[Morphology] = Field( + default_factory=list, title="Morphology", description="Morphology information" ) - colony: list[Colony] = Field(default_factory=list, title="Colony", description="") - sporeFormation: list[Spore] = Field( default_factory=list, title="Spore Formation", description="", ) - temperature: list[Growth[CelsiusUnit]] = Field( - default_factory=list, title="Temperature", description="" + growthConditions: list[GrowthCondition] = Field( + default_factory=list, + title="Growth conditions", + description="Temperature and pH values", ) - ph: list[Growth[PHUnit]] = Field(default_factory=list, title="pH", description="") - identifier: list[IdentifierStrain] = Field( default_factory=list, title="Identifier", description="" ) - connectedPersons: list[ConnectedPerson] = Field( - default_factory=list, - title="Connected Persons", - description="", - ) - pathogenicity: list[Pathogen] = Field( default_factory=list, title="pathogenicity", description="" ) diff --git a/tests/example_data/bacteria.json b/tests/example_data/bacteria.json index cc69405..18da9d3 100644 --- a/tests/example_data/bacteria.json +++ b/tests/example_data/bacteria.json @@ -17,31 +17,6 @@ "url": null } ], - "cellShape": [ - { - "cellShape": "coccus", - "source": [ - "/sources/0" - ] - } - ], - "cellSize": [ - { - "cellLength": { - "maximal": 2.2, - "minimal": 1.3, - "unit": "\u00b5m" - }, - "cellWidth": { - "maximal": 0.8, - "minimal": 0.5, - "unit": "\u00b5m" - }, - "source": [ - "/sources/0" - ] - } - ], "collections": [ { "address": null, @@ -255,24 +230,6 @@ "url": "https://catalogue-crbip.pasteur.fr/" } ], - "colony": [], - "connectedPersons": [ - { - "identifier": [ - { - "name": "ORCiD", - "propertyID": "https://www.wikidata.org/wiki/Property:P496", - "url": null, - "value": "https://orcid.org/0000-0001-6433-5270" - } - ], - "name": "J.-W. Bae", - "role": "isolator", - "source": [ - "/sources/0" - ] - } - ], "cultivationMedia": [ { "name": "PYG MEDIUM (MODIFIED) (DSMZ Medium 104)", @@ -557,6 +514,54 @@ "value": 47.8 } ], + "growthConditions": [ + { + "maximalPh": null, + "maximalTemperature": null, + "minimalPh": null, + "minimalTemperature": null, + "optimalPh": 7.0, + "optimalTemperature": 37.0, + "source": [ + "/sources/0" + ], + "testsPh": [ + { + "growth": true, + "maximal": 9.0, + "minimal": 6.0 + }, + { + "growth": true, + "maximal": 7.0, + "minimal": 7.0, + "relatedData": [ + "/relatedData/0" + ] + } + ], + "testsTemperature": [ + { + "growth": true, + "maximal": 39.0, + "minimal": 30.0 + }, + { + "growth": false, + "maximal": 43.0, + "minimal": 45.0 + }, + { + "growth": true, + "maximal": 36, + "minimal": 36, + "relatedData": [ + "/relatedData/0" + ] + } + ] + } + ], "halophily": [ { "alternateName": [ @@ -592,8 +597,7 @@ "minimal": 0.0, "relatedData": [ "/relatedData/0" - ], - "unit": "g/g%" + ] } ], "unit": "g/g%" @@ -734,29 +738,6 @@ "value": "34969" } ], - "isolation": [ - { - "date": null, - "isolatedAt": { - "address": null, - "email": null, - "identifier": [ - { - "name": "ROR", - "propertyID": "https://www.wikidata.org/wiki/Property:P6782", - "url": null, - "value": "https://ror.org/03ep23f07" - } - ], - "legalName": null, - "name": "Korea Research Institute of Bioscience and Biotechnology", - "url": null - }, - "source": [ - "/sources/0" - ] - } - ], "knownApplications": [ { "application": "Production of substance x", @@ -1098,8 +1079,19 @@ } ], "morphType": null, - "motility": [ + "morphology": [ { + "cellLength": { + "maximal": 2.2, + "minimal": 1.3, + "unit": "\u00b5m" + }, + "cellShape": "coccus", + "cellWidth": { + "maximal": 0.8, + "minimal": 0.5, + "unit": "\u00b5m" + }, "flagellum": true, "flagellumArrangement": null, "gliding": false, @@ -1118,6 +1110,49 @@ } ], "organismType": "Bacteria", + "origin": [ + { + "country": null, + "description": "soil of landfill site", + "isolatedAt": { + "address": null, + "email": null, + "identifier": [ + { + "name": "ROR", + "propertyID": "https://www.wikidata.org/wiki/Property:P6782", + "url": null, + "value": "https://ror.org/03ep23f07" + } + ], + "legalName": null, + "name": "Korea Research Institute of Bioscience and Biotechnology", + "url": null + }, + "isolationDate": null, + "locationCreated": { + "description": null, + "geo": { + "elevation": null, + "latitude": 36.03901723905223, + "longitude": 129.365704500591, + "precision": null + }, + "name": "Pohang" + }, + "sampleDate": "/2011-09-12", + "source": [ + "/sources/0" + ], + "tags": [ + { + "level1": "#Environmental", + "level2": "#Terrestrial", + "level3": "#Soil" + } + ] + } + ], "otherMedia": [ { "additionalType": "image", @@ -1167,34 +1202,6 @@ ] } ], - "ph": [ - { - "maximal": null, - "minimal": null, - "optimal": 7.0, - "source": [ - "/sources/0" - ], - "tests": [ - { - "growth": true, - "maximal": 9.0, - "minimal": 6.0, - "unit": "pH" - }, - { - "growth": true, - "maximal": 7.0, - "minimal": 7.0, - "relatedData": [ - "/relatedData/0" - ], - "unit": "pH" - } - ], - "unit": "pH" - } - ], "relatedData": [ { "relation": "growthCondition", @@ -1203,33 +1210,6 @@ ] } ], - "sample": [ - { - "country": null, - "date": "/2011-09-12", - "description": "soil of landfill site", - "locationCreated": { - "description": null, - "geo": { - "elevation": null, - "latitude": 36.03901723905223, - "longitude": 129.365704500591, - "precision": null - }, - "name": "Pohang" - }, - "source": [ - "/sources/0" - ], - "tags": [ - { - "level1": "#Environmental", - "level2": "#Terrestrial", - "level3": "#Soil" - } - ] - } - ], "sequences": [ { "accessionNumber": "LC019782", @@ -1461,40 +1441,6 @@ "taxonStatus": "validly published" } ], - "temperature": [ - { - "maximal": null, - "minimal": null, - "optimal": 37.0, - "source": [ - "/sources/0" - ], - "tests": [ - { - "growth": true, - "maximal": 39.0, - "minimal": 30.0, - "unit": "C" - }, - { - "growth": false, - "maximal": 43.0, - "minimal": 45.0, - "unit": "C" - }, - { - "growth": true, - "maximal": 36, - "minimal": 36, - "relatedData": [ - "/relatedData/0" - ], - "unit": "C" - } - ], - "unit": "C" - } - ], "tolerances": [ { "alternateName": [ @@ -1597,58 +1543,6 @@ "typeStrain": true } ], - "unifiedTaxon": { - "alternateName": [ - "Butyribacterium limosum", - "Bacteroides limosus" - ], - "identifier": [ - { - "name": "LPSN", - "propertyID": "https://www.wikidata.org/wiki/Property:P1991", - "url": "https://lpsn.dsmz.de/species/eubacterium-limosum", - "value": "https://lpsn.dsmz.de/species/eubacterium-limosum" - }, - { - "name": "NCBI:txid", - "propertyID": "https://www.wikidata.org/wiki/Property:P685", - "url": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1736", - "value": "1736" - } - ], - "name": "Eubacterium limosum", - "parentTaxon": { - "alternateName": [], - "identifier": [ - { - "name": "LPSN", - "propertyID": "https://www.wikidata.org/wiki/Property:P1991", - "url": "https://lpsn.dsmz.de/genus/eubacterium", - "value": "https://lpsn.dsmz.de/genus/eubacterium" - } - ], - "name": "Eubacterium", - "parentTaxon": null, - "sameAs": [], - "scientificName": { - "author": "Pr\u00e9vot 1938 (Approved Lists 1980)", - "name": "Eubacterium" - }, - "taxonRank": "genus", - "taxonStatus": "validly published" - }, - "sameAs": [ - "https://www.gbif.org/species/3226415/metrics" - ], - "scientificName": { - "author": "(Eggerth 1935) Pr\u00e9vot 1938 (Approved Lists 1980)", - "name": "Eubacterium limosum" - }, - "taxonRank": "species", - "taxonStatus": "validly published" - }, - "unifiedTypeStrain": true, - "version": "0.6", "wallConstituents": [ { "alternateName": [ diff --git a/tests/test_check_example_data.py b/tests/test_check_example_data.py index b4b926e..a1d613f 100644 --- a/tests/test_check_example_data.py +++ b/tests/test_check_example_data.py @@ -1,7 +1,7 @@ from pathlib import Path -from microbial_strain_data_model.microbe import Microbe +from microbial_strain_data_model.strain import Strain def test_validate_bacteria_example() -> None: with Path("./tests/example_data/bacteria.json").open("r") as f_in: - Microbe.model_validate_json(f_in.read()) + Strain.model_validate_json(f_in.read()) diff --git a/tests/test_isolation_source.py b/tests/test_isolation_source.py index e893e3c..cecea14 100644 --- a/tests/test_isolation_source.py +++ b/tests/test_isolation_source.py @@ -1,40 +1,42 @@ import pytest -from microbial_strain_data_model.classes import sample +from microbial_strain_data_model.classes import isolationtag def test_isolation_tag_system_1(): - assert sample.IsolationTag(level1="#Environmental") + assert isolationtag.IsolationTag(level1="#Environmental") def test_isolation_tag_system_2(): - assert sample.IsolationTag(level1="#Environmental", level2="#Terrestrial") + assert isolationtag.IsolationTag(level1="#Environmental", level2="#Terrestrial") def test_isolation_tag_system_3(): - assert sample.IsolationTag( + assert isolationtag.IsolationTag( level1="#Environmental", level2="#Terrestrial", level3="#Geologic" ) def test_no_data(): with pytest.raises(ValueError, match=r".*"): - sample.IsolationTag() + isolationtag.IsolationTag() def test_wrong_category_1(): with pytest.raises(ValueError, match=r".*"): - sample.IsolationTag(level1="#StarWars", level2="#Terrestrial", level3="#Geologic") + isolationtag.IsolationTag( + level1="#StarWars", level2="#Terrestrial", level3="#Geologic" + ) def test_wrong_category_2(): with pytest.raises(ValueError, match=r".*"): - sample.IsolationTag( + isolationtag.IsolationTag( level1="#Environmental", level2="#StarWars", level3="#Geologic" ) def test_wrong_category_3(): with pytest.raises(ValueError, match=r".*"): - sample.IsolationTag( + isolationtag.IsolationTag( level1="#Environmental", level2="#Terrestrial", level3="#StarWars" ) diff --git a/tests/test_microbe.py b/tests/test_microbe.py index 78864ee..59d609d 100644 --- a/tests/test_microbe.py +++ b/tests/test_microbe.py @@ -1,18 +1,17 @@ from microbial_strain_data_model.classes.enums import OrganismType from microbial_strain_data_model.classes.taxon import TaxonRank, TaxonStatus import pytest -from microbial_strain_data_model.microbe import Microbe +from microbial_strain_data_model.strain import Strain # ruff: noqa: E501 @pytest.fixture def micro(): - return Microbe( - version="0.6", + return Strain( organismType=OrganismType.bacteria, typeStrain=[{"typeStrain": False, "source": ["/sources/0"]}], - sample=[ + origin=[ { "tags": [ {"level1": "#Host", "level2": "#Fishes", "level3": "#Zebrafish"} @@ -68,13 +67,12 @@ def micro(): ) -def test_microbe(micro: Microbe) -> None: +def test_microbe(micro: Strain) -> None: assert micro.organismType == "Bacteria" -def test_populate_new_class(micro: Microbe) -> None: - new_micro = Microbe( - version=micro.version, +def test_populate_new_class(micro: Strain) -> None: + new_micro = Strain( organismType=micro.organismType, typeStrain=micro.typeStrain, taxon=micro.taxon, From 0c6e9bf7533729290d5d26c399871e132a2f4d9b Mon Sep 17 00:00:00 2001 From: juwitte Date: Fri, 29 Aug 2025 09:11:06 +0000 Subject: [PATCH 08/10] refactor(restructure): restructure data multicallcomplex and oxygenrelation into other classes BREAKING CHANGE: --- docs/graph.md | 120 ++--- docs/schema/08. oxygenRelation.md | 2 +- docs/schema/12. growthConditions.md | 161 +++++++ docs/schema/12. temperature.md | 98 ---- .../{14. identifier.md => 13. identifier.md} | 14 +- docs/schema/13. ph.md | 98 ---- ... pathogenicity.md => 14. pathogenicity.md} | 12 +- .../{17. bioSafety.md => 15. bioSafety.md} | 10 +- docs/schema/15. connectedPersons.md | 89 ---- .../{18. sequences.md => 16. sequences.md} | 26 +- .../{19. gcContent.md => 17. gcContent.md} | 10 +- .../{20. literature.md => 18. literature.md} | 64 +-- ...onstituents.md => 19. wallConstituents.md} | 22 +- ...idProfiles.md => 20. fattyAcidProfiles.md} | 32 +- .../{23. staining.md => 21. staining.md} | 8 +- .../{24. hemolysis.md => 22. hemolysis.md} | 8 +- ...vationMedia.md => 23. cultivationMedia.md} | 12 +- .../{26. halophily.md => 24. halophily.md} | 69 +-- .../{27. tolerances.md => 25. tolerances.md} | 36 +- .../schema/{28. enzymes.md => 26. enzymes.md} | 26 +- ...{29. metabolites.md => 27. metabolites.md} | 32 +- ...plications.md => 28. knownApplications.md} | 6 +- ...{31. collections.md => 29. collections.md} | 82 ++-- .../{32. otherMedia.md => 30. otherMedia.md} | 14 +- ...{33. relatedData.md => 31. relatedData.md} | 6 +- .../schema/{34. sources.md => 32. sources.md} | 82 ++-- schema/microbe_schema.json | 429 ++++-------------- .../classes/enums.py | 6 +- .../classes/growthcondition.py | 5 + .../classes/morphology.py | 5 + .../classes/multicell.py | 26 -- .../classes/oxygenrelation.py | 27 -- src/microbial_strain_data_model/strain.py | 14 - tests/example_data/bacteria.json | 19 +- 34 files changed, 558 insertions(+), 1112 deletions(-) create mode 100644 docs/schema/12. growthConditions.md delete mode 100644 docs/schema/12. temperature.md rename docs/schema/{14. identifier.md => 13. identifier.md} (77%) delete mode 100644 docs/schema/13. ph.md rename docs/schema/{16. pathogenicity.md => 14. pathogenicity.md} (84%) rename docs/schema/{17. bioSafety.md => 15. bioSafety.md} (77%) delete mode 100644 docs/schema/15. connectedPersons.md rename docs/schema/{18. sequences.md => 16. sequences.md} (76%) rename docs/schema/{19. gcContent.md => 17. gcContent.md} (79%) rename docs/schema/{20. literature.md => 18. literature.md} (64%) rename docs/schema/{21. wallConstituents.md => 19. wallConstituents.md} (69%) rename docs/schema/{22. fattyAcidProfiles.md => 20. fattyAcidProfiles.md} (64%) rename docs/schema/{23. staining.md => 21. staining.md} (81%) rename docs/schema/{24. hemolysis.md => 22. hemolysis.md} (83%) rename docs/schema/{25. cultivationMedia.md => 23. cultivationMedia.md} (62%) rename docs/schema/{26. halophily.md => 24. halophily.md} (64%) rename docs/schema/{27. tolerances.md => 25. tolerances.md} (76%) rename docs/schema/{28. enzymes.md => 26. enzymes.md} (73%) rename docs/schema/{29. metabolites.md => 27. metabolites.md} (75%) rename docs/schema/{30. knownApplications.md => 28. knownApplications.md} (70%) rename docs/schema/{31. collections.md => 29. collections.md} (71%) rename docs/schema/{32. otherMedia.md => 30. otherMedia.md} (71%) rename docs/schema/{33. relatedData.md => 31. relatedData.md} (78%) rename docs/schema/{34. sources.md => 32. sources.md} (68%) delete mode 100644 src/microbial_strain_data_model/classes/multicell.py delete mode 100644 src/microbial_strain_data_model/classes/oxygenrelation.py diff --git a/docs/graph.md b/docs/graph.md index 5e4330d..778413f 100644 --- a/docs/graph.md +++ b/docs/graph.md @@ -203,31 +203,6 @@ value: string url: string | null } -class `OxygenRelation`{ -oxygenRelation: OxygenTolerance -relatedData: string -source: string -} - -class `OxygenTolerance`{ -<> -aerobe -aerotolerant -anaerobe -facultative aerobe -facultative anaerobe -microaerophile -microaerotolerant -obligate aerobe -obligate anaerobe -} - -class `MultiCell`{ -multiCellComplexForming: boolean -relatedData: string -source: string -} - class `Morphology`{ cellShape: string cellLength: Size @@ -238,6 +213,7 @@ flagellumArrangement: FlagellumArrangement | null gliding: boolean | null colonySize: Size | null colonyColor: ColonyColor | null +multiCellComplexForming: boolean | null source: string } @@ -290,38 +266,37 @@ spore endospore } -class `Growth[C]`{ -optimal: number | null -minimal: number | null -maximal: number | null -unit: string -tests: array[GrowthRange[C]] +class `GrowthCondition`{ +optimalTemperature: number | null +minimalTemperature: number | null +maximalTemperature: number | null +testsTemperature: array[GrowthRange] +optimalPh: number | null +minimalPh: number | null +maximalPh: number | null +testsPh: array[GrowthRange] +oxygenRelation: OxygenTolerance | null source: string } -class `GrowthRange[C]`{ +class `GrowthRange`{ minimal: number | null maximal: number | null -unit: string growth: boolean relatedData: string } -class `Growth[pH]`{ -optimal: number | null -minimal: number | null -maximal: number | null -unit: string -tests: array[GrowthRange[pH]] -source: string -} - -class `GrowthRange[pH]`{ -minimal: number | null -maximal: number | null -unit: string -growth: boolean -relatedData: string +class `OxygenTolerance`{ +<> +aerobe +aerotolerant +anaerobe +facultative aerobe +facultative anaerobe +microaerophile +microaerotolerant +obligate aerobe +obligate anaerobe } class `IdentifierStrain`{ @@ -333,20 +308,6 @@ logo: string | null source: string } -class `ConnectedPerson`{ -name: string -identifier: array[Identifier] -role: PersonRole | null -source: string -} - -class `PersonRole`{ -<> -sampler -isolator -other -} - class `Pathogen`{ host: Host pathogen: PathogenLevel @@ -497,11 +458,11 @@ class `Halophil`{ name: string | null identifier: array[Identifier] alternateName: string -optimal: number | null minimal: number | null maximal: number | null +optimal: number | null unit: ConcentrationUnit -tests: array[GrowthRange_ConcentrationUnit_] +tests: array[GrowthRange] source: string } @@ -514,14 +475,6 @@ v/v% unknown } -class `GrowthRange_ConcentrationUnit_`{ -minimal: number | null -maximal: number | null -unit: ConcentrationUnit -growth: boolean -relatedData: string -} - class `Tolerance`{ name: string | null identifier: array[Identifier] @@ -688,14 +641,10 @@ typeStrain: array[TypeStrain] taxon: array[TaxonWithSource] origin: array[Origin] legal: array[Legal] -oxygenRelation: array[OxygenRelation] -multiCellComplexForming: array[MultiCell] morphology: array[Morphology] sporeFormation: array[Spore] -temperature: array[Growth[C]] -ph: array[Growth[pH]] +growthConditions: array[GrowthCondition] identifier: array[IdentifierStrain] -connectedPersons: array[ConnectedPerson] pathogenicity: array[Pathogen] bioSafety: array[BioSafety] sequences: array[Sequence] @@ -749,9 +698,6 @@ sources: array[Source] `Legal` ..> `NagoyaRestrictions` `Legal` ..> `microbial_strain_data_model__classes__legal__Restriction` `microbial_strain_data_model__classes__legal__Restriction` ..> `Country` -`Strain` ..> `OxygenRelation` -`OxygenRelation` ..> `OxygenTolerance` -`Strain` ..> `MultiCell` `Strain` ..> `Morphology` `Morphology` ..> `Size` `Size` ..> `SizeUnit` @@ -761,14 +707,11 @@ sources: array[Source] `Morphology` ..> `ColonyColor` `Strain` ..> `Spore` `Spore` ..> `SporeType` -`Strain` ..> `Growth[C]` -`Growth[C]` ..> `GrowthRange[C]` -`Strain` ..> `Growth[pH]` -`Growth[pH]` ..> `GrowthRange[pH]` +`Strain` ..> `GrowthCondition` +`GrowthCondition` ..> `GrowthRange` +`GrowthCondition` ..> `GrowthRange` +`GrowthCondition` ..> `OxygenTolerance` `Strain` ..> `IdentifierStrain` -`Strain` ..> `ConnectedPerson` -`ConnectedPerson` ..> `Identifier` -`ConnectedPerson` ..> `PersonRole` `Strain` ..> `Pathogen` `Pathogen` ..> `Host` `Pathogen` ..> `PathogenLevel` @@ -796,8 +739,7 @@ sources: array[Source] `Strain` ..> `Halophil` `Halophil` ..> `Identifier` `Halophil` ..> `ConcentrationUnit` -`Halophil` ..> `GrowthRange_ConcentrationUnit_` -`GrowthRange_ConcentrationUnit_` ..> `ConcentrationUnit` +`Halophil` ..> `GrowthRange` `Strain` ..> `Tolerance` `Tolerance` ..> `Identifier` `Tolerance` ..> `ToleranceReaction` diff --git a/docs/schema/08. oxygenRelation.md b/docs/schema/08. oxygenRelation.md index 9f41a38..a58a13d 100644 --- a/docs/schema/08. oxygenRelation.md +++ b/docs/schema/08. oxygenRelation.md @@ -11,7 +11,7 @@ OxygenTolerance `Required` Description: > How does the strain tolerate Oxygen > -> Args: +> Attributes: > aerobe: aerobe > aerotolerant: aerotolerant > anaerobe: anaerobe diff --git a/docs/schema/12. growthConditions.md b/docs/schema/12. growthConditions.md new file mode 100644 index 0000000..9b2705b --- /dev/null +++ b/docs/schema/12. growthConditions.md @@ -0,0 +1,161 @@ +--- +## 12. growthConditions +Growth conditions + +Description: +> Temperature and pH values + +**array[object]** + +--- +## 12.1. growthConditions.optimalTemperature +Optimal + +Description: +> Single optimal growth temperature value in celsius + +**number, null** + +--- +## 12.2. growthConditions.minimalTemperature +Minimal + +Description: +> Known minimal growth temperature value in celsius + +**number, null** + +--- +## 12.3. growthConditions.maximalTemperature +Maximal + +Description: +> Known maximal growth temperature value in celsius + +**number, null** + +--- +## 12.4. growthConditions.testsTemperature +Tests + +Description: +> List of tests and if the strain grows in tested ranges + +**array[object]** + +--- +## 12.4.1. growthConditions.testsTemperature.minimal +Minimal + +Description: +> Minimal value of tested range + +**number, null** + +--- +## 12.4.2. growthConditions.testsTemperature.maximal +Maximal + +Description: +> Maximal value of tested range + +**number, null** + +--- +## 12.4.3. growthConditions.testsTemperature.growth +Growth `Required` + +Description: +> Does the strain grow within this range? + +**boolean** + +--- +## 12.4.4. growthConditions.testsTemperature.relatedData +Related Data + +Description: +> JSON paths to relation object + +**array[string]** + +--- +## 12.5. growthConditions.optimalPh +Optimal + +Description: +> Single optimal growth pH value + +**number, null** + +--- +## 12.6. growthConditions.minimalPh +Minimal + +Description: +> Known minimal growth pH value + +**number, null** + +--- +## 12.7. growthConditions.maximalPh +Maximal + +Description: +> Known maximal growth pH value + +**number, null** + +--- +## 12.8. growthConditions.testsPh +Tests + +Description: +> List of tests and if the strain grows in tested ranges + +**array[object]** + +--- +## 12.8.1. growthConditions.testsPh.minimal +Minimal + +Description: +> Minimal value of tested range + +**number, null** + +--- +## 12.8.2. growthConditions.testsPh.maximal +Maximal + +Description: +> Maximal value of tested range + +**number, null** + +--- +## 12.8.3. growthConditions.testsPh.growth +Growth `Required` + +Description: +> Does the strain grow within this range? + +**boolean** + +--- +## 12.8.4. growthConditions.testsPh.relatedData +Related Data + +Description: +> JSON paths to relation object + +**array[string]** + +--- +## 12.9. growthConditions.source +Source `Required` + +Description: +> List of JSON paths to source object + +**array[string]** diff --git a/docs/schema/12. temperature.md b/docs/schema/12. temperature.md deleted file mode 100644 index 9f778a2..0000000 --- a/docs/schema/12. temperature.md +++ /dev/null @@ -1,98 +0,0 @@ ---- -## 12. temperature -Temperature - -**array[object]** - ---- -## 12.1. temperature.optimal -Optimal - -Description: -> Single optimal growth value - -**number, null** - ---- -## 12.2. temperature.minimal -Minimal - -Description: -> Known minimal growth value - -**number, null** - ---- -## 12.3. temperature.maximal -Maximal - -Description: -> Known maximal growth value - -**number, null** - ---- -## 12.4. temperature.unit -Unit `Required` - -**string** - ---- -## 12.5. temperature.tests -Tests - -Description: -> List of tests and if the strain grows in tested ranges - -**array[object]** - ---- -## 12.5.1. temperature.tests.minimal -Minimal - -Description: -> Minimal value of tested range - -**number, null** - ---- -## 12.5.2. temperature.tests.maximal -Maximal - -Description: -> Maximal value of tested range - -**number, null** - ---- -## 12.5.3. temperature.tests.unit -Unit `Required` - -**string** - ---- -## 12.5.4. temperature.tests.growth -Growth `Required` - -Description: -> Does the strain grow within this range? - -**boolean** - ---- -## 12.5.5. temperature.tests.relatedData -Related Data - -Description: -> JSON paths to relation object - -**array[string]** - ---- -## 12.6. temperature.source -Source `Required` - -Description: -> List of JSON paths to source object - -**array[string]** diff --git a/docs/schema/14. identifier.md b/docs/schema/13. identifier.md similarity index 77% rename from docs/schema/14. identifier.md rename to docs/schema/13. identifier.md index 35f5a0a..66f6cac 100644 --- a/docs/schema/14. identifier.md +++ b/docs/schema/13. identifier.md @@ -1,11 +1,11 @@ --- -## 14. identifier +## 13. identifier Identifier **array[object]** --- -## 14.1. identifier.name +## 13.1. identifier.name Name `Required` Description: @@ -14,7 +14,7 @@ Description: **string** --- -## 14.2. identifier.value +## 13.2. identifier.value Value `Required` Description: @@ -23,7 +23,7 @@ Description: **string** --- -## 14.3. identifier.propertyID +## 13.3. identifier.propertyID Property ID Description: @@ -32,7 +32,7 @@ Description: **string, null** --- -## 14.4. identifier.url +## 13.4. identifier.url URL Description: @@ -41,7 +41,7 @@ Description: **string, null** --- -## 14.5. identifier.logo +## 13.5. identifier.logo Logo Description: @@ -50,7 +50,7 @@ Description: **string, null** --- -## 14.6. identifier.source +## 13.6. identifier.source Source `Required` Description: diff --git a/docs/schema/13. ph.md b/docs/schema/13. ph.md deleted file mode 100644 index 8245300..0000000 --- a/docs/schema/13. ph.md +++ /dev/null @@ -1,98 +0,0 @@ ---- -## 13. ph -pH - -**array[object]** - ---- -## 13.1. ph.optimal -Optimal - -Description: -> Single optimal growth value - -**number, null** - ---- -## 13.2. ph.minimal -Minimal - -Description: -> Known minimal growth value - -**number, null** - ---- -## 13.3. ph.maximal -Maximal - -Description: -> Known maximal growth value - -**number, null** - ---- -## 13.4. ph.unit -Unit `Required` - -**string** - ---- -## 13.5. ph.tests -Tests - -Description: -> List of tests and if the strain grows in tested ranges - -**array[object]** - ---- -## 13.5.1. ph.tests.minimal -Minimal - -Description: -> Minimal value of tested range - -**number, null** - ---- -## 13.5.2. ph.tests.maximal -Maximal - -Description: -> Maximal value of tested range - -**number, null** - ---- -## 13.5.3. ph.tests.unit -Unit `Required` - -**string** - ---- -## 13.5.4. ph.tests.growth -Growth `Required` - -Description: -> Does the strain grow within this range? - -**boolean** - ---- -## 13.5.5. ph.tests.relatedData -Related Data - -Description: -> JSON paths to relation object - -**array[string]** - ---- -## 13.6. ph.source -Source `Required` - -Description: -> List of JSON paths to source object - -**array[string]** diff --git a/docs/schema/16. pathogenicity.md b/docs/schema/14. pathogenicity.md similarity index 84% rename from docs/schema/16. pathogenicity.md rename to docs/schema/14. pathogenicity.md index 44856c0..4b6c172 100644 --- a/docs/schema/16. pathogenicity.md +++ b/docs/schema/14. pathogenicity.md @@ -1,11 +1,11 @@ --- -## 16. pathogenicity +## 14. pathogenicity pathogenicity **array[object]** --- -## 16.1. pathogenicity.host +## 14.1. pathogenicity.host Host `Required` Description: @@ -35,7 +35,7 @@ Enum: fungi --- -## 16.2. pathogenicity.pathogen +## 14.2. pathogenicity.pathogen PathogenLevel `Required` Description: @@ -55,7 +55,7 @@ Enum: obligate --- -## 16.3. pathogenicity.classification +## 14.3. pathogenicity.classification Classification Description: @@ -64,7 +64,7 @@ Description: **string, null** --- -## 16.4. pathogenicity.url +## 14.4. pathogenicity.url URL Description: @@ -73,7 +73,7 @@ Description: **string, null** --- -## 16.5. pathogenicity.source +## 14.5. pathogenicity.source Source `Required` Description: diff --git a/docs/schema/17. bioSafety.md b/docs/schema/15. bioSafety.md similarity index 77% rename from docs/schema/17. bioSafety.md rename to docs/schema/15. bioSafety.md index a53ddba..2dc801c 100644 --- a/docs/schema/17. bioSafety.md +++ b/docs/schema/15. bioSafety.md @@ -1,11 +1,11 @@ --- -## 17. bioSafety +## 15. bioSafety Bio Safety **array[object]** --- -## 17.1. bioSafety.riskgroup +## 15.1. bioSafety.riskgroup Riskgroup `Required` Description: @@ -14,7 +14,7 @@ Description: **string** --- -## 17.2. bioSafety.classification +## 15.2. bioSafety.classification Classification Description: @@ -23,7 +23,7 @@ Description: **string, null** --- -## 17.3. bioSafety.url +## 15.3. bioSafety.url URL Description: @@ -32,7 +32,7 @@ Description: **string, null** --- -## 17.4. bioSafety.source +## 15.4. bioSafety.source Source `Required` Description: diff --git a/docs/schema/15. connectedPersons.md b/docs/schema/15. connectedPersons.md deleted file mode 100644 index 5d28b99..0000000 --- a/docs/schema/15. connectedPersons.md +++ /dev/null @@ -1,89 +0,0 @@ ---- -## 15. connectedPersons -Connected Persons - -**array[object]** - ---- -## 15.1. connectedPersons.name -Name `Required` - -Description: -> Name of the person, preferable: [Last], [First] - -**string** - ---- -## 15.2. connectedPersons.identifier -Identifier - -Description: -> Person identifiers like ORCID - -**array[object]** - ---- -## 15.2.1. connectedPersons.identifier.name -Name `Required` - -Description: -> Name of the identifier - -**string** - ---- -## 15.2.2. connectedPersons.identifier.value -Value `Required` - -Description: -> Value of the identifier (can also be a URL) - -**string** - ---- -## 15.2.3. connectedPersons.identifier.propertyID -Property ID - -Description: -> See schema.org/propertyID - -**string, null** - ---- -## 15.2.4. connectedPersons.identifier.url -URL - -Description: -> Uniform Resource Locator of a resource on the Internet - -**string, null** - ---- -## 15.2.5. connectedPersons.identifier.logo -Logo - -Description: -> Logo of the Identifier Organization (e.g. DOI, ORCID, ROR, ...) - -**string, null** - ---- -## 15.3. connectedPersons.role -Role - -**string, null** - -Enum: - - sampler - isolator - other - ---- -## 15.4. connectedPersons.source -Source `Required` - -Description: -> List of JSON paths to source object - -**array[string]** diff --git a/docs/schema/18. sequences.md b/docs/schema/16. sequences.md similarity index 76% rename from docs/schema/18. sequences.md rename to docs/schema/16. sequences.md index be90152..8c35321 100644 --- a/docs/schema/18. sequences.md +++ b/docs/schema/16. sequences.md @@ -1,11 +1,11 @@ --- -## 18. sequences +## 16. sequences Sequences **array[object]** --- -## 18.1. sequences.type +## 16.1. sequences.type SequenceType `Required` Description: @@ -23,7 +23,7 @@ Enum: protein --- -## 18.2. sequences.level +## 16.2. sequences.level SequenceLevel `Required` Description: @@ -47,25 +47,25 @@ Enum: other --- -## 18.3. sequences.accessionNumber +## 16.3. sequences.accessionNumber Accession Number `Required` **string** --- -## 18.4. sequences.description +## 16.4. sequences.description Description **string, null** --- -## 18.5. sequences.length +## 16.5. sequences.length Length **string, null** --- -## 18.6. sequences.identifier +## 16.6. sequences.identifier Identifier Description: @@ -74,7 +74,7 @@ Description: **array[object]** --- -## 18.6.1. sequences.identifier.name +## 16.6.1. sequences.identifier.name Name `Required` Description: @@ -83,7 +83,7 @@ Description: **string** --- -## 18.6.2. sequences.identifier.value +## 16.6.2. sequences.identifier.value Value `Required` Description: @@ -92,7 +92,7 @@ Description: **string** --- -## 18.6.3. sequences.identifier.propertyID +## 16.6.3. sequences.identifier.propertyID Property ID Description: @@ -101,7 +101,7 @@ Description: **string, null** --- -## 18.6.4. sequences.identifier.url +## 16.6.4. sequences.identifier.url URL Description: @@ -110,7 +110,7 @@ Description: **string, null** --- -## 18.6.5. sequences.identifier.logo +## 16.6.5. sequences.identifier.logo Logo Description: @@ -119,7 +119,7 @@ Description: **string, null** --- -## 18.7. sequences.source +## 16.7. sequences.source Source `Required` Description: diff --git a/docs/schema/19. gcContent.md b/docs/schema/17. gcContent.md similarity index 79% rename from docs/schema/19. gcContent.md rename to docs/schema/17. gcContent.md index d78d1fc..14c0e98 100644 --- a/docs/schema/19. gcContent.md +++ b/docs/schema/17. gcContent.md @@ -1,11 +1,11 @@ --- -## 19. gcContent +## 17. gcContent GC Content **array[object]** --- -## 19.1. gcContent.method +## 17.1. gcContent.method Method Description: @@ -19,7 +19,7 @@ Enum: genome sequence --- -## 19.2. gcContent.noteMethod +## 17.2. gcContent.noteMethod Note Method Description: @@ -28,7 +28,7 @@ Description: **string, null** --- -## 19.3. gcContent.value +## 17.3. gcContent.value Percent Value `Required` Description: @@ -37,7 +37,7 @@ Description: **number** --- -## 19.4. gcContent.source +## 17.4. gcContent.source Source `Required` Description: diff --git a/docs/schema/20. literature.md b/docs/schema/18. literature.md similarity index 64% rename from docs/schema/20. literature.md rename to docs/schema/18. literature.md index d87942e..7d481ae 100644 --- a/docs/schema/20. literature.md +++ b/docs/schema/18. literature.md @@ -1,29 +1,29 @@ --- -## 20. literature +## 18. literature Literature **array[object]** --- -## 20.1. literature.name +## 18.1. literature.name Name **string, null** --- -## 20.2. literature.url +## 18.2. literature.url URL **string, null** --- -## 20.3. literature.datePublished +## 18.3. literature.datePublished Date Published **string, null** --- -## 20.4. literature.author +## 18.4. literature.author Author Description: @@ -32,7 +32,7 @@ Description: **array[object]** --- -## 20.4.1. literature.author.name +## 18.4.1. literature.author.name Name `Required` Description: @@ -41,7 +41,7 @@ Description: **string** --- -## 20.4.2. literature.author.identifier +## 18.4.2. literature.author.identifier Identifier Description: @@ -50,7 +50,7 @@ Description: **array[object]** --- -## 20.4.2.1. literature.author.identifier.name +## 18.4.2.1. literature.author.identifier.name Name `Required` Description: @@ -59,7 +59,7 @@ Description: **string** --- -## 20.4.2.2. literature.author.identifier.value +## 18.4.2.2. literature.author.identifier.value Value `Required` Description: @@ -68,7 +68,7 @@ Description: **string** --- -## 20.4.2.3. literature.author.identifier.propertyID +## 18.4.2.3. literature.author.identifier.propertyID Property ID Description: @@ -77,7 +77,7 @@ Description: **string, null** --- -## 20.4.2.4. literature.author.identifier.url +## 18.4.2.4. literature.author.identifier.url URL Description: @@ -86,7 +86,7 @@ Description: **string, null** --- -## 20.4.2.5. literature.author.identifier.logo +## 18.4.2.5. literature.author.identifier.logo Logo Description: @@ -95,7 +95,7 @@ Description: **string, null** --- -## 20.5. literature.publisher +## 18.5. literature.publisher Publisher Description: @@ -104,7 +104,7 @@ Description: **array[object]** --- -## 20.5.1. literature.publisher.name +## 18.5.1. literature.publisher.name Name `Required` Description: @@ -113,7 +113,7 @@ Description: **string** --- -## 20.5.2. literature.publisher.identifier +## 18.5.2. literature.publisher.identifier Identifier Description: @@ -122,7 +122,7 @@ Description: **array[object]** --- -## 20.5.2.1. literature.publisher.identifier.name +## 18.5.2.1. literature.publisher.identifier.name Name `Required` Description: @@ -131,7 +131,7 @@ Description: **string** --- -## 20.5.2.2. literature.publisher.identifier.value +## 18.5.2.2. literature.publisher.identifier.value Value `Required` Description: @@ -140,7 +140,7 @@ Description: **string** --- -## 20.5.2.3. literature.publisher.identifier.propertyID +## 18.5.2.3. literature.publisher.identifier.propertyID Property ID Description: @@ -149,7 +149,7 @@ Description: **string, null** --- -## 20.5.2.4. literature.publisher.identifier.url +## 18.5.2.4. literature.publisher.identifier.url URL Description: @@ -158,7 +158,7 @@ Description: **string, null** --- -## 20.5.2.5. literature.publisher.identifier.logo +## 18.5.2.5. literature.publisher.identifier.logo Logo Description: @@ -167,7 +167,7 @@ Description: **string, null** --- -## 20.5.3. literature.publisher.legalName +## 18.5.3. literature.publisher.legalName Legal Name Description: @@ -176,7 +176,7 @@ Description: **string, null** --- -## 20.5.4. literature.publisher.address +## 18.5.4. literature.publisher.address Address Description: @@ -185,7 +185,7 @@ Description: **object, null** --- -## 20.5.4.1. literature.publisher.address.addressCountry +## 18.5.4.1. literature.publisher.address.addressCountry Country Description: @@ -194,7 +194,7 @@ Description: **string, null** --- -## 20.5.4.2. literature.publisher.address.addressRegion +## 18.5.4.2. literature.publisher.address.addressRegion Region Description: @@ -203,7 +203,7 @@ Description: **string, null** --- -## 20.5.4.3. literature.publisher.address.addressLocality +## 18.5.4.3. literature.publisher.address.addressLocality Locality Description: @@ -212,19 +212,19 @@ Description: **string, null** --- -## 20.5.4.4. literature.publisher.address.postOfficeBoxNumber +## 18.5.4.4. literature.publisher.address.postOfficeBoxNumber Post Office Box Number **string, null** --- -## 20.5.4.5. literature.publisher.address.postalCode +## 18.5.4.5. literature.publisher.address.postalCode Postal Code **string, null** --- -## 20.5.4.6. literature.publisher.address.streetAddress +## 18.5.4.6. literature.publisher.address.streetAddress Street Address Description: @@ -233,7 +233,7 @@ Description: **string, null** --- -## 20.5.5. literature.publisher.url +## 18.5.5. literature.publisher.url URL Description: @@ -242,7 +242,7 @@ Description: **string, null** --- -## 20.5.6. literature.publisher.email +## 18.5.6. literature.publisher.email Email Description: @@ -251,7 +251,7 @@ Description: **string, null** --- -## 20.5.7. literature.publisher.logo +## 18.5.7. literature.publisher.logo Logo Description: @@ -260,7 +260,7 @@ Description: **string, null** --- -## 20.6. literature.source +## 18.6. literature.source Source `Required` Description: diff --git a/docs/schema/21. wallConstituents.md b/docs/schema/19. wallConstituents.md similarity index 69% rename from docs/schema/21. wallConstituents.md rename to docs/schema/19. wallConstituents.md index 0a3617f..56a7d2c 100644 --- a/docs/schema/21. wallConstituents.md +++ b/docs/schema/19. wallConstituents.md @@ -1,11 +1,11 @@ --- -## 21. wallConstituents +## 19. wallConstituents Wall Constituents **array[object]** --- -## 21.1. wallConstituents.name +## 19.1. wallConstituents.name Name of Chemical Substance Description: @@ -14,7 +14,7 @@ Description: **string, null** --- -## 21.2. wallConstituents.identifier +## 19.2. wallConstituents.identifier Identifier Description: @@ -23,7 +23,7 @@ Description: **array[object]** --- -## 21.2.1. wallConstituents.identifier.name +## 19.2.1. wallConstituents.identifier.name Name `Required` Description: @@ -32,7 +32,7 @@ Description: **string** --- -## 21.2.2. wallConstituents.identifier.value +## 19.2.2. wallConstituents.identifier.value Value `Required` Description: @@ -41,7 +41,7 @@ Description: **string** --- -## 21.2.3. wallConstituents.identifier.propertyID +## 19.2.3. wallConstituents.identifier.propertyID Property ID Description: @@ -50,7 +50,7 @@ Description: **string, null** --- -## 21.2.4. wallConstituents.identifier.url +## 19.2.4. wallConstituents.identifier.url URL Description: @@ -59,7 +59,7 @@ Description: **string, null** --- -## 21.2.5. wallConstituents.identifier.logo +## 19.2.5. wallConstituents.identifier.logo Logo Description: @@ -68,7 +68,7 @@ Description: **string, null** --- -## 21.3. wallConstituents.alternateName +## 19.3. wallConstituents.alternateName Alternate Name Description: @@ -77,13 +77,13 @@ Description: **array[string]** --- -## 21.4. wallConstituents.percent +## 19.4. wallConstituents.percent Percent **number, null** --- -## 21.5. wallConstituents.source +## 19.5. wallConstituents.source Source `Required` Description: diff --git a/docs/schema/22. fattyAcidProfiles.md b/docs/schema/20. fattyAcidProfiles.md similarity index 64% rename from docs/schema/22. fattyAcidProfiles.md rename to docs/schema/20. fattyAcidProfiles.md index 8e5606a..057d527 100644 --- a/docs/schema/22. fattyAcidProfiles.md +++ b/docs/schema/20. fattyAcidProfiles.md @@ -1,11 +1,11 @@ --- -## 22. fattyAcidProfiles +## 20. fattyAcidProfiles Fatty Acid Profile **array[object]** --- -## 22.1. fattyAcidProfiles.profile +## 20.1. fattyAcidProfiles.profile Profile Description: @@ -14,7 +14,7 @@ Description: **array[object]** --- -## 22.1.1. fattyAcidProfiles.profile.name +## 20.1.1. fattyAcidProfiles.profile.name Name of Chemical Substance Description: @@ -23,7 +23,7 @@ Description: **string, null** --- -## 22.1.2. fattyAcidProfiles.profile.identifier +## 20.1.2. fattyAcidProfiles.profile.identifier Identifier Description: @@ -32,7 +32,7 @@ Description: **array[object]** --- -## 22.1.2.1. fattyAcidProfiles.profile.identifier.name +## 20.1.2.1. fattyAcidProfiles.profile.identifier.name Name `Required` Description: @@ -41,7 +41,7 @@ Description: **string** --- -## 22.1.2.2. fattyAcidProfiles.profile.identifier.value +## 20.1.2.2. fattyAcidProfiles.profile.identifier.value Value `Required` Description: @@ -50,7 +50,7 @@ Description: **string** --- -## 22.1.2.3. fattyAcidProfiles.profile.identifier.propertyID +## 20.1.2.3. fattyAcidProfiles.profile.identifier.propertyID Property ID Description: @@ -59,7 +59,7 @@ Description: **string, null** --- -## 22.1.2.4. fattyAcidProfiles.profile.identifier.url +## 20.1.2.4. fattyAcidProfiles.profile.identifier.url URL Description: @@ -68,7 +68,7 @@ Description: **string, null** --- -## 22.1.2.5. fattyAcidProfiles.profile.identifier.logo +## 20.1.2.5. fattyAcidProfiles.profile.identifier.logo Logo Description: @@ -77,7 +77,7 @@ Description: **string, null** --- -## 22.1.3. fattyAcidProfiles.profile.alternateName +## 20.1.3. fattyAcidProfiles.profile.alternateName Alternate Name Description: @@ -86,19 +86,19 @@ Description: **array[string]** --- -## 22.1.4. fattyAcidProfiles.profile.percent +## 20.1.4. fattyAcidProfiles.profile.percent Percent **number, null** --- -## 22.1.5. fattyAcidProfiles.profile.ecl +## 20.1.5. fattyAcidProfiles.profile.ecl ECL **string, null** --- -## 22.2. fattyAcidProfiles.library +## 20.2. fattyAcidProfiles.library Library Description: @@ -107,7 +107,7 @@ Description: **string, null** --- -## 22.3. fattyAcidProfiles.software +## 20.3. fattyAcidProfiles.software Software Description: @@ -116,7 +116,7 @@ Description: **string, null** --- -## 22.4. fattyAcidProfiles.relatedData +## 20.4. fattyAcidProfiles.relatedData Related Data Description: @@ -125,7 +125,7 @@ Description: **array[string]** --- -## 22.5. fattyAcidProfiles.source +## 20.5. fattyAcidProfiles.source Source `Required` Description: diff --git a/docs/schema/23. staining.md b/docs/schema/21. staining.md similarity index 81% rename from docs/schema/23. staining.md rename to docs/schema/21. staining.md index 275a6ff..98e82e2 100644 --- a/docs/schema/23. staining.md +++ b/docs/schema/21. staining.md @@ -1,17 +1,17 @@ --- -## 23. staining +## 21. staining Stainings **array[object]** --- -## 23.1. staining.name +## 21.1. staining.name Name `Required` **string** --- -## 23.2. staining.value +## 21.2. staining.value StainingValue `Required` Description: @@ -31,7 +31,7 @@ Enum: variable --- -## 23.3. staining.source +## 21.3. staining.source Source `Required` Description: diff --git a/docs/schema/24. hemolysis.md b/docs/schema/22. hemolysis.md similarity index 83% rename from docs/schema/24. hemolysis.md rename to docs/schema/22. hemolysis.md index e0199d8..1da4ae3 100644 --- a/docs/schema/24. hemolysis.md +++ b/docs/schema/22. hemolysis.md @@ -1,11 +1,11 @@ --- -## 24. hemolysis +## 22. hemolysis Hemolysis **array[object]** --- -## 24.1. hemolysis.blood +## 22.1. hemolysis.blood HemolysisBlood `Required` Description: @@ -25,7 +25,7 @@ Enum: unknown --- -## 24.2. hemolysis.hemolysisType +## 22.2. hemolysis.hemolysisType HemolysisType `Required` Description: @@ -45,7 +45,7 @@ Enum: gamma --- -## 24.3. hemolysis.source +## 22.3. hemolysis.source Source `Required` Description: diff --git a/docs/schema/25. cultivationMedia.md b/docs/schema/23. cultivationMedia.md similarity index 62% rename from docs/schema/25. cultivationMedia.md rename to docs/schema/23. cultivationMedia.md index 6bfe743..17bd8af 100644 --- a/docs/schema/25. cultivationMedia.md +++ b/docs/schema/23. cultivationMedia.md @@ -1,29 +1,29 @@ --- -## 25. cultivationMedia +## 23. cultivationMedia Cultivation Media **array[object]** --- -## 25.1. cultivationMedia.name +## 23.1. cultivationMedia.name Name `Required` **string** --- -## 25.2. cultivationMedia.url +## 23.2. cultivationMedia.url URL **string, null** --- -## 25.3. cultivationMedia.reagentUsed +## 23.3. cultivationMedia.reagentUsed Reagent Used **array[string]** --- -## 25.4. cultivationMedia.source +## 23.4. cultivationMedia.source Source `Required` Description: @@ -32,7 +32,7 @@ Description: **array[string]** --- -## 25.5. cultivationMedia.relatedData +## 23.5. cultivationMedia.relatedData Related Data Description: diff --git a/docs/schema/26. halophily.md b/docs/schema/24. halophily.md similarity index 64% rename from docs/schema/26. halophily.md rename to docs/schema/24. halophily.md index 634130f..90d9362 100644 --- a/docs/schema/26. halophily.md +++ b/docs/schema/24. halophily.md @@ -1,11 +1,11 @@ --- -## 26. halophily +## 24. halophily Halophily **array[object]** --- -## 26.1. halophily.name +## 24.1. halophily.name Name of Chemical Substance Description: @@ -14,7 +14,7 @@ Description: **string, null** --- -## 26.2. halophily.identifier +## 24.2. halophily.identifier Identifier Description: @@ -23,7 +23,7 @@ Description: **array[object]** --- -## 26.2.1. halophily.identifier.name +## 24.2.1. halophily.identifier.name Name `Required` Description: @@ -32,7 +32,7 @@ Description: **string** --- -## 26.2.2. halophily.identifier.value +## 24.2.2. halophily.identifier.value Value `Required` Description: @@ -41,7 +41,7 @@ Description: **string** --- -## 26.2.3. halophily.identifier.propertyID +## 24.2.3. halophily.identifier.propertyID Property ID Description: @@ -50,7 +50,7 @@ Description: **string, null** --- -## 26.2.4. halophily.identifier.url +## 24.2.4. halophily.identifier.url URL Description: @@ -59,7 +59,7 @@ Description: **string, null** --- -## 26.2.5. halophily.identifier.logo +## 24.2.5. halophily.identifier.logo Logo Description: @@ -68,7 +68,7 @@ Description: **string, null** --- -## 26.3. halophily.alternateName +## 24.3. halophily.alternateName Alternate Name Description: @@ -77,7 +77,7 @@ Description: **array[string]** --- -## 26.4. halophily.optimal +## 24.4. halophily.minimal Optimal Description: @@ -86,25 +86,25 @@ Description: **number, null** --- -## 26.5. halophily.minimal -Minimal +## 24.5. halophily.maximal +Optimal Description: -> Known minimal growth value +> Single optimal growth value **number, null** --- -## 26.6. halophily.maximal -Maximal +## 24.6. halophily.optimal +Optimal Description: -> Known maximal growth value +> Single optimal growth value **number, null** --- -## 26.7. halophily.unit +## 24.7. halophily.unit ConcentrationUnit `Required` Description: @@ -127,7 +127,7 @@ Enum: unknown --- -## 26.8. halophily.tests +## 24.8. halophily.tests Tests Description: @@ -136,7 +136,7 @@ Description: **array[object]** --- -## 26.8.1. halophily.tests.minimal +## 24.8.1. halophily.tests.minimal Minimal Description: @@ -145,7 +145,7 @@ Description: **number, null** --- -## 26.8.2. halophily.tests.maximal +## 24.8.2. halophily.tests.maximal Maximal Description: @@ -154,30 +154,7 @@ Description: **number, null** --- -## 26.8.3. halophily.tests.unit -ConcentrationUnit `Required` - -Description: -> Valid concentration units for solutions -> -> Attributes: -> gram_per_liter: g/L -> mol_per_liter: mol/L -> mass_percent: g/g% -> volume_percent: v/v% - -**string** - -Enum: - - g/L - mol/L - g/g% - v/v% - unknown - ---- -## 26.8.4. halophily.tests.growth +## 24.8.3. halophily.tests.growth Growth `Required` Description: @@ -186,7 +163,7 @@ Description: **boolean** --- -## 26.8.5. halophily.tests.relatedData +## 24.8.4. halophily.tests.relatedData Related Data Description: @@ -195,7 +172,7 @@ Description: **array[string]** --- -## 26.9. halophily.source +## 24.9. halophily.source Source `Required` Description: diff --git a/docs/schema/27. tolerances.md b/docs/schema/25. tolerances.md similarity index 76% rename from docs/schema/27. tolerances.md rename to docs/schema/25. tolerances.md index 373b561..76eb5f5 100644 --- a/docs/schema/27. tolerances.md +++ b/docs/schema/25. tolerances.md @@ -1,11 +1,11 @@ --- -## 27. tolerances +## 25. tolerances Tolerances **array[object]** --- -## 27.1. tolerances.name +## 25.1. tolerances.name Name of Chemical Substance Description: @@ -14,7 +14,7 @@ Description: **string, null** --- -## 27.2. tolerances.identifier +## 25.2. tolerances.identifier Identifier Description: @@ -23,7 +23,7 @@ Description: **array[object]** --- -## 27.2.1. tolerances.identifier.name +## 25.2.1. tolerances.identifier.name Name `Required` Description: @@ -32,7 +32,7 @@ Description: **string** --- -## 27.2.2. tolerances.identifier.value +## 25.2.2. tolerances.identifier.value Value `Required` Description: @@ -41,7 +41,7 @@ Description: **string** --- -## 27.2.3. tolerances.identifier.propertyID +## 25.2.3. tolerances.identifier.propertyID Property ID Description: @@ -50,7 +50,7 @@ Description: **string, null** --- -## 27.2.4. tolerances.identifier.url +## 25.2.4. tolerances.identifier.url URL Description: @@ -59,7 +59,7 @@ Description: **string, null** --- -## 27.2.5. tolerances.identifier.logo +## 25.2.5. tolerances.identifier.logo Logo Description: @@ -68,7 +68,7 @@ Description: **string, null** --- -## 27.3. tolerances.alternateName +## 25.3. tolerances.alternateName Alternate Name Description: @@ -77,7 +77,7 @@ Description: **array[string]** --- -## 27.4. tolerances.reaction +## 25.4. tolerances.reaction Reaction **string, null** @@ -89,7 +89,7 @@ Enum: intermediate --- -## 27.5. tolerances.mic +## 25.5. tolerances.mic MIC Description: @@ -98,7 +98,7 @@ Description: **string, null** --- -## 27.6. tolerances.unit +## 25.6. tolerances.unit Unit **string, null** @@ -112,7 +112,7 @@ Enum: unknown --- -## 27.7. tolerances.tests +## 25.7. tolerances.tests Tests Description: @@ -121,7 +121,7 @@ Description: **array[object]** --- -## 27.7.1. tolerances.tests.reaction +## 25.7.1. tolerances.tests.reaction ToleranceReaction `Required` Description: @@ -141,7 +141,7 @@ Enum: intermediate --- -## 27.7.2. tolerances.tests.concentration +## 25.7.2. tolerances.tests.concentration Concentration Description: @@ -150,7 +150,7 @@ Description: **number, null** --- -## 27.7.3. tolerances.tests.unit +## 25.7.3. tolerances.tests.unit ConcentrationUnit `Required` Description: @@ -173,7 +173,7 @@ Enum: unknown --- -## 27.7.4. tolerances.tests.relatedData +## 25.7.4. tolerances.tests.relatedData Related Data Description: @@ -182,7 +182,7 @@ Description: **array[string]** --- -## 27.8. tolerances.source +## 25.8. tolerances.source Source `Required` Description: diff --git a/docs/schema/28. enzymes.md b/docs/schema/26. enzymes.md similarity index 73% rename from docs/schema/28. enzymes.md rename to docs/schema/26. enzymes.md index a206f76..e94aa41 100644 --- a/docs/schema/28. enzymes.md +++ b/docs/schema/26. enzymes.md @@ -1,17 +1,17 @@ --- -## 28. enzymes +## 26. enzymes Enzymes **array[object]** --- -## 28.1. enzymes.name +## 26.1. enzymes.name Name **string, null** --- -## 28.2. enzymes.hasECNumber +## 26.2. enzymes.hasECNumber EC Number `Required` Description: @@ -20,7 +20,7 @@ Description: **string** --- -## 28.3. enzymes.identifier +## 26.3. enzymes.identifier Identifier Description: @@ -29,7 +29,7 @@ Description: **array[object]** --- -## 28.3.1. enzymes.identifier.name +## 26.3.1. enzymes.identifier.name Name `Required` Description: @@ -38,7 +38,7 @@ Description: **string** --- -## 28.3.2. enzymes.identifier.value +## 26.3.2. enzymes.identifier.value Value `Required` Description: @@ -47,7 +47,7 @@ Description: **string** --- -## 28.3.3. enzymes.identifier.propertyID +## 26.3.3. enzymes.identifier.propertyID Property ID Description: @@ -56,7 +56,7 @@ Description: **string, null** --- -## 28.3.4. enzymes.identifier.url +## 26.3.4. enzymes.identifier.url URL Description: @@ -65,7 +65,7 @@ Description: **string, null** --- -## 28.3.5. enzymes.identifier.logo +## 26.3.5. enzymes.identifier.logo Logo Description: @@ -74,13 +74,13 @@ Description: **string, null** --- -## 28.4. enzymes.alternateName +## 26.4. enzymes.alternateName Alternate Name **array[string]** --- -## 28.5. enzymes.active +## 26.5. enzymes.active Active Description: @@ -89,7 +89,7 @@ Description: **boolean, null** --- -## 28.6. enzymes.relatedData +## 26.6. enzymes.relatedData Related Data Description: @@ -98,7 +98,7 @@ Description: **array[string]** --- -## 28.7. enzymes.source +## 26.7. enzymes.source Source `Required` Description: diff --git a/docs/schema/29. metabolites.md b/docs/schema/27. metabolites.md similarity index 75% rename from docs/schema/29. metabolites.md rename to docs/schema/27. metabolites.md index 27d6c91..d6676bb 100644 --- a/docs/schema/29. metabolites.md +++ b/docs/schema/27. metabolites.md @@ -1,11 +1,11 @@ --- -## 29. metabolites +## 27. metabolites Metabolites **array[object]** --- -## 29.1. metabolites.name +## 27.1. metabolites.name Name of Chemical Substance Description: @@ -14,7 +14,7 @@ Description: **string, null** --- -## 29.2. metabolites.identifier +## 27.2. metabolites.identifier Identifier Description: @@ -23,7 +23,7 @@ Description: **array[object]** --- -## 29.2.1. metabolites.identifier.name +## 27.2.1. metabolites.identifier.name Name `Required` Description: @@ -32,7 +32,7 @@ Description: **string** --- -## 29.2.2. metabolites.identifier.value +## 27.2.2. metabolites.identifier.value Value `Required` Description: @@ -41,7 +41,7 @@ Description: **string** --- -## 29.2.3. metabolites.identifier.propertyID +## 27.2.3. metabolites.identifier.propertyID Property ID Description: @@ -50,7 +50,7 @@ Description: **string, null** --- -## 29.2.4. metabolites.identifier.url +## 27.2.4. metabolites.identifier.url URL Description: @@ -59,7 +59,7 @@ Description: **string, null** --- -## 29.2.5. metabolites.identifier.logo +## 27.2.5. metabolites.identifier.logo Logo Description: @@ -68,7 +68,7 @@ Description: **string, null** --- -## 29.3. metabolites.alternateName +## 27.3. metabolites.alternateName Alternate Name Description: @@ -77,7 +77,7 @@ Description: **array[string]** --- -## 29.4. metabolites.tests +## 27.4. metabolites.tests Tests Description: @@ -86,7 +86,7 @@ Description: **array[object]** --- -## 29.4.1. metabolites.tests.type +## 27.4.1. metabolites.tests.type MetaboliteTestType `Required` Description: @@ -104,7 +104,7 @@ Enum: production --- -## 29.4.2. metabolites.tests.active +## 27.4.2. metabolites.tests.active Active Description: @@ -113,7 +113,7 @@ Description: **boolean, null** --- -## 29.4.3. metabolites.tests.protocol +## 27.4.3. metabolites.tests.protocol Protocol Description: @@ -122,7 +122,7 @@ Description: **string, null** --- -## 29.4.4. metabolites.tests.kindOfUtilization +## 27.4.4. metabolites.tests.kindOfUtilization Kind Of Utilization Description: @@ -141,7 +141,7 @@ Enum: reduction --- -## 29.4.5. metabolites.tests.relatedData +## 27.4.5. metabolites.tests.relatedData Related Data Description: @@ -150,7 +150,7 @@ Description: **array[string]** --- -## 29.5. metabolites.source +## 27.5. metabolites.source Source `Required` Description: diff --git a/docs/schema/30. knownApplications.md b/docs/schema/28. knownApplications.md similarity index 70% rename from docs/schema/30. knownApplications.md rename to docs/schema/28. knownApplications.md index ffa56c1..2dcfecb 100644 --- a/docs/schema/30. knownApplications.md +++ b/docs/schema/28. knownApplications.md @@ -1,11 +1,11 @@ --- -## 30. knownApplications +## 28. knownApplications Known Applications **array[object]** --- -## 30.1. knownApplications.application +## 28.1. knownApplications.application Application `Required` Description: @@ -14,7 +14,7 @@ Description: **string** --- -## 30.2. knownApplications.source +## 28.2. knownApplications.source Source `Required` Description: diff --git a/docs/schema/31. collections.md b/docs/schema/29. collections.md similarity index 71% rename from docs/schema/31. collections.md rename to docs/schema/29. collections.md index 8d19188..58626b9 100644 --- a/docs/schema/31. collections.md +++ b/docs/schema/29. collections.md @@ -1,11 +1,11 @@ --- -## 31. collections +## 29. collections Collections **array[object]** --- -## 31.1. collections.name +## 29.1. collections.name Name `Required` Description: @@ -14,7 +14,7 @@ Description: **string** --- -## 31.2. collections.identifier +## 29.2. collections.identifier Identifier Description: @@ -23,7 +23,7 @@ Description: **array[object]** --- -## 31.2.1. collections.identifier.name +## 29.2.1. collections.identifier.name Name `Required` Description: @@ -32,7 +32,7 @@ Description: **string** --- -## 31.2.2. collections.identifier.value +## 29.2.2. collections.identifier.value Value `Required` Description: @@ -41,7 +41,7 @@ Description: **string** --- -## 31.2.3. collections.identifier.propertyID +## 29.2.3. collections.identifier.propertyID Property ID Description: @@ -50,7 +50,7 @@ Description: **string, null** --- -## 31.2.4. collections.identifier.url +## 29.2.4. collections.identifier.url URL Description: @@ -59,7 +59,7 @@ Description: **string, null** --- -## 31.2.5. collections.identifier.logo +## 29.2.5. collections.identifier.logo Logo Description: @@ -68,7 +68,7 @@ Description: **string, null** --- -## 31.3. collections.legalName +## 29.3. collections.legalName Legal Name Description: @@ -77,7 +77,7 @@ Description: **string, null** --- -## 31.4. collections.address +## 29.4. collections.address Address Description: @@ -86,7 +86,7 @@ Description: **object, null** --- -## 31.4.1. collections.address.addressCountry +## 29.4.1. collections.address.addressCountry Country Description: @@ -95,7 +95,7 @@ Description: **string, null** --- -## 31.4.2. collections.address.addressRegion +## 29.4.2. collections.address.addressRegion Region Description: @@ -104,7 +104,7 @@ Description: **string, null** --- -## 31.4.3. collections.address.addressLocality +## 29.4.3. collections.address.addressLocality Locality Description: @@ -113,19 +113,19 @@ Description: **string, null** --- -## 31.4.4. collections.address.postOfficeBoxNumber +## 29.4.4. collections.address.postOfficeBoxNumber Post Office Box Number **string, null** --- -## 31.4.5. collections.address.postalCode +## 29.4.5. collections.address.postalCode Postal Code **string, null** --- -## 31.4.6. collections.address.streetAddress +## 29.4.6. collections.address.streetAddress Street Address Description: @@ -134,7 +134,7 @@ Description: **string, null** --- -## 31.5. collections.url +## 29.5. collections.url URL Description: @@ -143,7 +143,7 @@ Description: **string, null** --- -## 31.6. collections.email +## 29.6. collections.email Email Description: @@ -152,7 +152,7 @@ Description: **string, null** --- -## 31.7. collections.logo +## 29.7. collections.logo Logo Description: @@ -161,7 +161,7 @@ Description: **string, null** --- -## 31.8. collections.resourceNumber +## 29.8. collections.resourceNumber Resource Number `Required` Description: @@ -170,7 +170,7 @@ Description: **string** --- -## 31.9. collections.available +## 29.9. collections.available Availability Description: @@ -179,7 +179,7 @@ Description: **boolean, null** --- -## 31.10. collections.catalogUrl +## 29.10. collections.catalogUrl Catalog URL Description: @@ -188,7 +188,7 @@ Description: **string, null** --- -## 31.11. collections.restrictionsOnUse +## 29.11. collections.restrictionsOnUse Restrictions On Use Description: @@ -203,7 +203,7 @@ Enum: For commercial development a special agreement is requested --- -## 31.12. collections.policyUrl +## 29.12. collections.policyUrl Policy URL Description: @@ -212,7 +212,7 @@ Description: **string, null** --- -## 31.13. collections.axenicCulture +## 29.13. collections.axenicCulture Axenic Culture Description: @@ -221,7 +221,7 @@ Description: **boolean, null** --- -## 31.14. collections.supplyForms +## 29.14. collections.supplyForms Supply Forms Description: @@ -230,7 +230,7 @@ Description: **array[string]** --- -## 31.15. collections.history +## 29.15. collections.history History Description: @@ -239,7 +239,7 @@ Description: **string, null** --- -## 31.16. collections.depositionDate +## 29.16. collections.depositionDate Deposition Date Description: @@ -248,7 +248,7 @@ Description: **string, null** --- -## 31.17. collections.depositor +## 29.17. collections.depositor Depositor Description: @@ -257,7 +257,7 @@ Description: **object, null** --- -## 31.17.1. collections.depositor.name +## 29.17.1. collections.depositor.name Name `Required` Description: @@ -266,7 +266,7 @@ Description: **string** --- -## 31.17.2. collections.depositor.identifier +## 29.17.2. collections.depositor.identifier Identifier Description: @@ -275,7 +275,7 @@ Description: **array[object]** --- -## 31.17.2.1. collections.depositor.identifier.name +## 29.17.2.1. collections.depositor.identifier.name Name `Required` Description: @@ -284,7 +284,7 @@ Description: **string** --- -## 31.17.2.2. collections.depositor.identifier.value +## 29.17.2.2. collections.depositor.identifier.value Value `Required` Description: @@ -293,7 +293,7 @@ Description: **string** --- -## 31.17.2.3. collections.depositor.identifier.propertyID +## 29.17.2.3. collections.depositor.identifier.propertyID Property ID Description: @@ -302,7 +302,7 @@ Description: **string, null** --- -## 31.17.2.4. collections.depositor.identifier.url +## 29.17.2.4. collections.depositor.identifier.url URL Description: @@ -311,7 +311,7 @@ Description: **string, null** --- -## 31.17.2.5. collections.depositor.identifier.logo +## 29.17.2.5. collections.depositor.identifier.logo Logo Description: @@ -320,7 +320,7 @@ Description: **string, null** --- -## 31.18. collections.depositedAs +## 29.18. collections.depositedAs Deposited as Description: @@ -329,7 +329,7 @@ Description: **string, null** --- -## 31.19. collections.registeredCollection +## 29.19. collections.registeredCollection Registered Collection Description: @@ -338,7 +338,7 @@ Description: **boolean, null** --- -## 31.20. collections.mtaFile +## 29.20. collections.mtaFile MTA file Description: @@ -347,7 +347,7 @@ Description: **string, null** --- -## 31.21. collections.absFile +## 29.21. collections.absFile ABS related file Description: @@ -356,7 +356,7 @@ Description: **string, null** --- -## 31.22. collections.source +## 29.22. collections.source Source `Required` Description: diff --git a/docs/schema/32. otherMedia.md b/docs/schema/30. otherMedia.md similarity index 71% rename from docs/schema/32. otherMedia.md rename to docs/schema/30. otherMedia.md index c902ab3..93f4617 100644 --- a/docs/schema/32. otherMedia.md +++ b/docs/schema/30. otherMedia.md @@ -1,11 +1,11 @@ --- -## 32. otherMedia +## 30. otherMedia Other Media **array[object]** --- -## 32.1. otherMedia.url +## 30.1. otherMedia.url URL Description: @@ -14,13 +14,13 @@ Description: **string, null** --- -## 32.2. otherMedia.name +## 30.2. otherMedia.name Name **string, null** --- -## 32.3. otherMedia.description +## 30.3. otherMedia.description Description Description: @@ -29,7 +29,7 @@ Description: **string, null** --- -## 32.4. otherMedia.usageInfo +## 30.4. otherMedia.usageInfo Usage Information Description: @@ -38,13 +38,13 @@ Description: **string, null** --- -## 32.5. otherMedia.additionalType +## 30.5. otherMedia.additionalType Additional Type **string, null** --- -## 32.6. otherMedia.source +## 30.6. otherMedia.source Source `Required` Description: diff --git a/docs/schema/33. relatedData.md b/docs/schema/31. relatedData.md similarity index 78% rename from docs/schema/33. relatedData.md rename to docs/schema/31. relatedData.md index 038345c..30e43e1 100644 --- a/docs/schema/33. relatedData.md +++ b/docs/schema/31. relatedData.md @@ -1,11 +1,11 @@ --- -## 33. relatedData +## 31. relatedData Related Data **array[object]** --- -## 33.1. relatedData.relation +## 31.1. relatedData.relation Relation `Required` Description: @@ -14,7 +14,7 @@ Description: **string** --- -## 33.2. relatedData.source +## 31.2. relatedData.source Source `Required` Description: diff --git a/docs/schema/34. sources.md b/docs/schema/32. sources.md similarity index 68% rename from docs/schema/34. sources.md rename to docs/schema/32. sources.md index 8cf3191..7558158 100644 --- a/docs/schema/34. sources.md +++ b/docs/schema/32. sources.md @@ -1,11 +1,11 @@ --- -## 34. sources +## 32. sources Sources `Required` **array[object]** --- -## 34.1. sources.sourceType +## 32.1. sources.sourceType SourceType `Required` Description: @@ -25,7 +25,7 @@ Enum: dataset --- -## 34.2. sources.mode +## 32.2. sources.mode CurationMode `Required` Description: @@ -45,19 +45,19 @@ Enum: unknown --- -## 34.3. sources.name +## 32.3. sources.name Name **string, null** --- -## 34.4. sources.url +## 32.4. sources.url URL **string, null** --- -## 34.5. sources.identifier +## 32.5. sources.identifier Identifier Description: @@ -66,7 +66,7 @@ Description: **array[object]** --- -## 34.5.1. sources.identifier.name +## 32.5.1. sources.identifier.name Name `Required` Description: @@ -75,7 +75,7 @@ Description: **string** --- -## 34.5.2. sources.identifier.value +## 32.5.2. sources.identifier.value Value `Required` Description: @@ -84,7 +84,7 @@ Description: **string** --- -## 34.5.3. sources.identifier.propertyID +## 32.5.3. sources.identifier.propertyID Property ID Description: @@ -93,7 +93,7 @@ Description: **string, null** --- -## 34.5.4. sources.identifier.url +## 32.5.4. sources.identifier.url URL Description: @@ -102,7 +102,7 @@ Description: **string, null** --- -## 34.5.5. sources.identifier.logo +## 32.5.5. sources.identifier.logo Logo Description: @@ -111,13 +111,13 @@ Description: **string, null** --- -## 34.6. sources.datePublished +## 32.6. sources.datePublished Date Published **string, null** --- -## 34.7. sources.dateRecorded +## 32.7. sources.dateRecorded Date Recorded **string** @@ -127,13 +127,13 @@ Format: date --- -## 34.8. sources.lastUpdate +## 32.8. sources.lastUpdate Date of last update **string, null** --- -## 34.9. sources.author +## 32.9. sources.author Author Description: @@ -142,7 +142,7 @@ Description: **array[object]** --- -## 34.9.1. sources.author.name +## 32.9.1. sources.author.name Name `Required` Description: @@ -151,7 +151,7 @@ Description: **string** --- -## 34.9.2. sources.author.identifier +## 32.9.2. sources.author.identifier Identifier Description: @@ -160,7 +160,7 @@ Description: **array[object]** --- -## 34.9.2.1. sources.author.identifier.name +## 32.9.2.1. sources.author.identifier.name Name `Required` Description: @@ -169,7 +169,7 @@ Description: **string** --- -## 34.9.2.2. sources.author.identifier.value +## 32.9.2.2. sources.author.identifier.value Value `Required` Description: @@ -178,7 +178,7 @@ Description: **string** --- -## 34.9.2.3. sources.author.identifier.propertyID +## 32.9.2.3. sources.author.identifier.propertyID Property ID Description: @@ -187,7 +187,7 @@ Description: **string, null** --- -## 34.9.2.4. sources.author.identifier.url +## 32.9.2.4. sources.author.identifier.url URL Description: @@ -196,7 +196,7 @@ Description: **string, null** --- -## 34.9.2.5. sources.author.identifier.logo +## 32.9.2.5. sources.author.identifier.logo Logo Description: @@ -205,7 +205,7 @@ Description: **string, null** --- -## 34.10. sources.publisher +## 32.10. sources.publisher Publisher Description: @@ -214,7 +214,7 @@ Description: **array[object]** --- -## 34.10.1. sources.publisher.name +## 32.10.1. sources.publisher.name Name `Required` Description: @@ -223,7 +223,7 @@ Description: **string** --- -## 34.10.2. sources.publisher.identifier +## 32.10.2. sources.publisher.identifier Identifier Description: @@ -232,7 +232,7 @@ Description: **array[object]** --- -## 34.10.2.1. sources.publisher.identifier.name +## 32.10.2.1. sources.publisher.identifier.name Name `Required` Description: @@ -241,7 +241,7 @@ Description: **string** --- -## 34.10.2.2. sources.publisher.identifier.value +## 32.10.2.2. sources.publisher.identifier.value Value `Required` Description: @@ -250,7 +250,7 @@ Description: **string** --- -## 34.10.2.3. sources.publisher.identifier.propertyID +## 32.10.2.3. sources.publisher.identifier.propertyID Property ID Description: @@ -259,7 +259,7 @@ Description: **string, null** --- -## 34.10.2.4. sources.publisher.identifier.url +## 32.10.2.4. sources.publisher.identifier.url URL Description: @@ -268,7 +268,7 @@ Description: **string, null** --- -## 34.10.2.5. sources.publisher.identifier.logo +## 32.10.2.5. sources.publisher.identifier.logo Logo Description: @@ -277,7 +277,7 @@ Description: **string, null** --- -## 34.10.3. sources.publisher.legalName +## 32.10.3. sources.publisher.legalName Legal Name Description: @@ -286,7 +286,7 @@ Description: **string, null** --- -## 34.10.4. sources.publisher.address +## 32.10.4. sources.publisher.address Address Description: @@ -295,7 +295,7 @@ Description: **object, null** --- -## 34.10.4.1. sources.publisher.address.addressCountry +## 32.10.4.1. sources.publisher.address.addressCountry Country Description: @@ -304,7 +304,7 @@ Description: **string, null** --- -## 34.10.4.2. sources.publisher.address.addressRegion +## 32.10.4.2. sources.publisher.address.addressRegion Region Description: @@ -313,7 +313,7 @@ Description: **string, null** --- -## 34.10.4.3. sources.publisher.address.addressLocality +## 32.10.4.3. sources.publisher.address.addressLocality Locality Description: @@ -322,19 +322,19 @@ Description: **string, null** --- -## 34.10.4.4. sources.publisher.address.postOfficeBoxNumber +## 32.10.4.4. sources.publisher.address.postOfficeBoxNumber Post Office Box Number **string, null** --- -## 34.10.4.5. sources.publisher.address.postalCode +## 32.10.4.5. sources.publisher.address.postalCode Postal Code **string, null** --- -## 34.10.4.6. sources.publisher.address.streetAddress +## 32.10.4.6. sources.publisher.address.streetAddress Street Address Description: @@ -343,7 +343,7 @@ Description: **string, null** --- -## 34.10.5. sources.publisher.url +## 32.10.5. sources.publisher.url URL Description: @@ -352,7 +352,7 @@ Description: **string, null** --- -## 34.10.6. sources.publisher.email +## 32.10.6. sources.publisher.email Email Description: @@ -361,7 +361,7 @@ Description: **string, null** --- -## 34.10.7. sources.publisher.logo +## 32.10.7. sources.publisher.logo Logo Description: diff --git a/schema/microbe_schema.json b/schema/microbe_schema.json index 3025c1a..76bfd4b 100644 --- a/schema/microbe_schema.json +++ b/schema/microbe_schema.json @@ -548,52 +548,6 @@ "title": "ConcentrationUnit", "type": "string" }, - "ConnectedPerson": { - "additionalProperties": false, - "description": "Connected Person = Person + Role", - "properties": { - "identifier": { - "description": "Person identifiers like ORCID", - "items": { - "$ref": "#/$defs/Identifier" - }, - "title": "Identifier", - "type": "array" - }, - "name": { - "description": "Name of the person, preferable: [Last], [First]", - "title": "Name", - "type": "string" - }, - "role": { - "anyOf": [ - { - "$ref": "#/$defs/PersonRole" - }, - { - "type": "null" - } - ], - "default": null, - "title": "Role" - }, - "source": { - "description": "List of JSON paths to source object", - "items": { - "pattern": "^\\/sources\\/\\d+$", - "type": "string" - }, - "title": "Source", - "type": "array" - } - }, - "required": [ - "name", - "source" - ], - "title": "ConnectedPerson", - "type": "object" - }, "Country": { "additionalProperties": false, "description": "Country information, mostly on nagoya protocol", @@ -1041,7 +995,7 @@ "type": "object" }, "GCMethod": { - "description": "Methods for GC measurement\n\nArgs:\n experimental: experimental\n genomeSequence: genome sequence", + "description": "Methods for GC measurement\n\nAttributes:\n experimental: experimental\n genomeSequence: genome sequence", "enum": [ "experimental", "genome sequence" @@ -1113,15 +1067,11 @@ "title": "GeoPoint", "type": "object" }, - "GrowthRange_ConcentrationUnit_": { + "GrowthCondition": { "additionalProperties": false, + "description": "Optimal and tested information about growing a Strain", "properties": { - "growth": { - "description": "Does the strain grow within this range?", - "title": "Growth", - "type": "boolean" - }, - "maximal": { + "maximalPh": { "anyOf": [ { "type": "number" @@ -1131,51 +1081,10 @@ } ], "default": null, - "description": "Maximal value of tested range", + "description": "Known maximal growth pH value", "title": "Maximal" }, - "minimal": { - "anyOf": [ - { - "type": "number" - }, - { - "type": "null" - } - ], - "default": null, - "description": "Minimal value of tested range", - "title": "Minimal" - }, - "relatedData": { - "description": "JSON paths to relation object", - "items": { - "pattern": "^\\/relatedData\\/\\d+$", - "type": "string" - }, - "title": "Related Data", - "type": "array" - }, - "unit": { - "$ref": "#/$defs/ConcentrationUnit" - } - }, - "required": [ - "unit", - "growth" - ], - "title": "GrowthRange[ConcentrationUnit]", - "type": "object" - }, - "GrowthRange_Literal__C___": { - "additionalProperties": false, - "properties": { - "growth": { - "description": "Does the strain grow within this range?", - "title": "Growth", - "type": "boolean" - }, - "maximal": { + "maximalTemperature": { "anyOf": [ { "type": "number" @@ -1185,10 +1094,10 @@ } ], "default": null, - "description": "Maximal value of tested range", + "description": "Known maximal growth temperature value in celsius", "title": "Maximal" }, - "minimal": { + "minimalPh": { "anyOf": [ { "type": "number" @@ -1198,53 +1107,10 @@ } ], "default": null, - "description": "Minimal value of tested range", + "description": "Known minimal growth pH value", "title": "Minimal" }, - "relatedData": { - "description": "JSON paths to relation object", - "items": { - "pattern": "^\\/relatedData\\/\\d+$", - "type": "string" - }, - "title": "Related Data", - "type": "array" - }, - "unit": { - "const": "C", - "title": "Unit", - "type": "string" - } - }, - "required": [ - "unit", - "growth" - ], - "title": "GrowthRange[Literal['C']]", - "type": "object" - }, - "GrowthRange_Literal__pH___": { - "additionalProperties": false, - "properties": { - "growth": { - "description": "Does the strain grow within this range?", - "title": "Growth", - "type": "boolean" - }, - "maximal": { - "anyOf": [ - { - "type": "number" - }, - { - "type": "null" - } - ], - "default": null, - "description": "Maximal value of tested range", - "title": "Maximal" - }, - "minimal": { + "minimalTemperature": { "anyOf": [ { "type": "number" @@ -1254,35 +1120,10 @@ } ], "default": null, - "description": "Minimal value of tested range", + "description": "Known minimal growth temperature value in celsius", "title": "Minimal" }, - "relatedData": { - "description": "JSON paths to relation object", - "items": { - "pattern": "^\\/relatedData\\/\\d+$", - "type": "string" - }, - "title": "Related Data", - "type": "array" - }, - "unit": { - "const": "pH", - "title": "Unit", - "type": "string" - } - }, - "required": [ - "unit", - "growth" - ], - "title": "GrowthRange[Literal['pH']]", - "type": "object" - }, - "Growth_Literal__C___": { - "additionalProperties": false, - "properties": { - "maximal": { + "optimalPh": { "anyOf": [ { "type": "number" @@ -1292,10 +1133,10 @@ } ], "default": null, - "description": "Known maximal growth value", - "title": "Maximal" + "description": "Single optimal growth pH value", + "title": "Optimal" }, - "minimal": { + "optimalTemperature": { "anyOf": [ { "type": "number" @@ -1305,21 +1146,21 @@ } ], "default": null, - "description": "Known minimal growth value", - "title": "Minimal" + "description": "Single optimal growth temperature value in celsius", + "title": "Optimal" }, - "optimal": { + "oxygenRelation": { "anyOf": [ { - "type": "number" + "$ref": "#/$defs/OxygenTolerance" }, { "type": "null" } ], "default": null, - "description": "Single optimal growth value", - "title": "Optimal" + "description": "Aerobic, anaerobic etc.", + "title": "Oxygen Relation" }, "source": { "description": "List of JSON paths to source object", @@ -1330,30 +1171,38 @@ "title": "Source", "type": "array" }, - "tests": { + "testsPh": { "description": "List of tests and if the strain grows in tested ranges", "items": { - "$ref": "#/$defs/GrowthRange_Literal__C___" + "$ref": "#/$defs/GrowthRange" }, "title": "Tests", "type": "array" }, - "unit": { - "const": "C", - "title": "Unit", - "type": "string" + "testsTemperature": { + "description": "List of tests and if the strain grows in tested ranges", + "items": { + "$ref": "#/$defs/GrowthRange" + }, + "title": "Tests", + "type": "array" } }, "required": [ - "unit", "source" ], - "title": "Growth[Literal['C']]", + "title": "GrowthCondition", "type": "object" }, - "Growth_Literal__pH___": { + "GrowthRange": { "additionalProperties": false, + "description": "Single grow condition test", "properties": { + "growth": { + "description": "Does the strain grow within this range?", + "title": "Growth", + "type": "boolean" + }, "maximal": { "anyOf": [ { @@ -1364,7 +1213,7 @@ } ], "default": null, - "description": "Known maximal growth value", + "description": "Maximal value of tested range", "title": "Maximal" }, "minimal": { @@ -1377,50 +1226,23 @@ } ], "default": null, - "description": "Known minimal growth value", + "description": "Minimal value of tested range", "title": "Minimal" }, - "optimal": { - "anyOf": [ - { - "type": "number" - }, - { - "type": "null" - } - ], - "default": null, - "description": "Single optimal growth value", - "title": "Optimal" - }, - "source": { - "description": "List of JSON paths to source object", + "relatedData": { + "description": "JSON paths to relation object", "items": { - "pattern": "^\\/sources\\/\\d+$", + "pattern": "^\\/relatedData\\/\\d+$", "type": "string" }, - "title": "Source", - "type": "array" - }, - "tests": { - "description": "List of tests and if the strain grows in tested ranges", - "items": { - "$ref": "#/$defs/GrowthRange_Literal__pH___" - }, - "title": "Tests", + "title": "Related Data", "type": "array" - }, - "unit": { - "const": "pH", - "title": "Unit", - "type": "string" } }, "required": [ - "unit", - "source" + "growth" ], - "title": "Growth[Literal['pH']]", + "title": "GrowthRange", "type": "object" }, "Halophil": { @@ -1452,8 +1274,8 @@ } ], "default": null, - "description": "Known maximal growth value", - "title": "Maximal" + "description": "Single optimal growth value", + "title": "Optimal" }, "minimal": { "anyOf": [ @@ -1465,8 +1287,8 @@ } ], "default": null, - "description": "Known minimal growth value", - "title": "Minimal" + "description": "Single optimal growth value", + "title": "Optimal" }, "name": { "anyOf": [ @@ -1506,13 +1328,15 @@ "tests": { "description": "List of tests and if the strain grows in tested ranges", "items": { - "$ref": "#/$defs/GrowthRange_ConcentrationUnit_" + "$ref": "#/$defs/GrowthRange" }, "title": "Tests", "type": "array" }, "unit": { - "$ref": "#/$defs/ConcentrationUnit" + "$ref": "#/$defs/ConcentrationUnit", + "description": "", + "title": "Unit" } }, "required": [ @@ -1772,7 +1596,7 @@ "type": "object" }, "KindOfUtilization": { - "description": "Types of utilization\n\nArgs:\n assimilation: assimilation\n buildsAcidFrom: builds acid from\n degradation: degradation\n energySource: energy source\n fermentation: fermentation\n hydrolysis: hydrolysis\n reduction: reduction", + "description": "Types of utilization\n\nAttributes:\n assimilation: assimilation\n buildsAcidFrom: builds acid from\n degradation: degradation\n energySource: energy source\n fermentation: fermentation\n hydrolysis: hydrolysis\n reduction: reduction", "enum": [ "assimilation", "builds acid from", @@ -2249,6 +2073,19 @@ "description": "Are the cells of this strain are motile", "title": "Motile" }, + "multiCellComplexForming": { + "anyOf": [ + { + "type": "boolean" + }, + { + "type": "null" + } + ], + "default": null, + "description": "Do the cells form complexes", + "title": "Multi Cell Complex Forming" + }, "source": { "description": "List of JSON paths to source object", "items": { @@ -2268,41 +2105,6 @@ "title": "Morphology", "type": "object" }, - "MultiCell": { - "additionalProperties": false, - "description": "MultiCell ability of the strain", - "properties": { - "multiCellComplexForming": { - "description": "Do the cells form complexes", - "title": "Multi Cell Complex Forming", - "type": "boolean" - }, - "relatedData": { - "description": "JSON paths to relation object", - "items": { - "pattern": "^\\/relatedData\\/\\d+$", - "type": "string" - }, - "title": "Related Data", - "type": "array" - }, - "source": { - "description": "List of JSON paths to source object", - "items": { - "pattern": "^\\/sources\\/\\d+$", - "type": "string" - }, - "title": "Source", - "type": "array" - } - }, - "required": [ - "multiCellComplexForming", - "source" - ], - "title": "MultiCell", - "type": "object" - }, "NagoyaRestrictions": { "description": "Valid values of Nagoya protocol information\n\nAttributes:\n no_restrictions: No known restrictions under the Nagoya protocol\n documents_available: Documents providing proof of legal access and terms of use available at the collection\n contact_collection: Strain probably in scope, please contact the culture collection", "enum": [ @@ -2640,43 +2442,8 @@ "title": "OtherMedia", "type": "object" }, - "OxygenRelation": { - "additionalProperties": false, - "description": "OxygenRelation of the strain", - "properties": { - "oxygenRelation": { - "$ref": "#/$defs/OxygenTolerance", - "description": "Aerobic, anaerobic etc.", - "title": "Oxygen Relation" - }, - "relatedData": { - "description": "JSON paths to relation object", - "items": { - "pattern": "^\\/relatedData\\/\\d+$", - "type": "string" - }, - "title": "Related Data", - "type": "array" - }, - "source": { - "description": "List of JSON paths to source object", - "items": { - "pattern": "^\\/sources\\/\\d+$", - "type": "string" - }, - "title": "Source", - "type": "array" - } - }, - "required": [ - "oxygenRelation", - "source" - ], - "title": "OxygenRelation", - "type": "object" - }, "OxygenTolerance": { - "description": "How does the strain tolerate Oxygen\n\nArgs:\n aerobe: aerobe\n aerotolerant: aerotolerant\n anaerobe: anaerobe\n facultativeAerobe: facultative aerobe\n facultativeAnaerobe: facultative anaerobe\n microaerophile: microaerophile\n microaerotolerant: microaerotolerant\n obligateAerobe: obligate aerobe\n obligateAnaerobe: obligate anaerobe", + "description": "How does the strain tolerate Oxygen\n\nAttributes:\n aerobe: aerobe\n aerotolerant: aerotolerant\n anaerobe: anaerobe\n facultativeAerobe: facultative aerobe\n facultativeAnaerobe: facultative anaerobe\n microaerophile: microaerophile\n microaerotolerant: microaerotolerant\n obligateAerobe: obligate aerobe\n obligateAnaerobe: obligate anaerobe", "enum": [ "aerobe", "aerotolerant", @@ -2785,16 +2552,6 @@ "title": "Person", "type": "object" }, - "PersonRole": { - "description": "Valid roles for persons related to strain\n\nAttributes:\n sampler: sampler\n isolator: isolator\n other: other", - "enum": [ - "sampler", - "isolator", - "other" - ], - "title": "PersonRole", - "type": "string" - }, "RelatedData": { "additionalProperties": false, "description": "RelatedData", @@ -3663,14 +3420,6 @@ "title": "Collections", "type": "array" }, - "connectedPersons": { - "description": "", - "items": { - "$ref": "#/$defs/ConnectedPerson" - }, - "title": "Connected Persons", - "type": "array" - }, "creation_date": { "format": "date", "title": "Creation Date", @@ -3708,6 +3457,14 @@ "title": "GC Content", "type": "array" }, + "growthConditions": { + "description": "Temperature and pH values", + "items": { + "$ref": "#/$defs/GrowthCondition" + }, + "title": "Growth conditions", + "type": "array" + }, "halophily": { "description": "", "items": { @@ -3785,14 +3542,6 @@ "title": "Morphology", "type": "array" }, - "multiCellComplexForming": { - "description": "", - "items": { - "$ref": "#/$defs/MultiCell" - }, - "title": "Multi Cell Complex Forming", - "type": "array" - }, "organismType": { "$ref": "#/$defs/OrganismType", "description": "", @@ -3814,14 +3563,6 @@ "title": "Other Media", "type": "array" }, - "oxygenRelation": { - "description": "", - "items": { - "$ref": "#/$defs/OxygenRelation" - }, - "title": "Oxygen Relation", - "type": "array" - }, "pathogenicity": { "description": "", "items": { @@ -3830,14 +3571,6 @@ "title": "pathogenicity", "type": "array" }, - "ph": { - "description": "", - "items": { - "$ref": "#/$defs/Growth_Literal__pH___" - }, - "title": "pH", - "type": "array" - }, "relatedData": { "description": "", "items": { @@ -3886,14 +3619,6 @@ "title": "Taxon", "type": "array" }, - "temperature": { - "description": "", - "items": { - "$ref": "#/$defs/Growth_Literal__C___" - }, - "title": "Temperature", - "type": "array" - }, "tolerances": { "description": "", "items": { diff --git a/src/microbial_strain_data_model/classes/enums.py b/src/microbial_strain_data_model/classes/enums.py index c1f3aa0..d4cd32e 100644 --- a/src/microbial_strain_data_model/classes/enums.py +++ b/src/microbial_strain_data_model/classes/enums.py @@ -466,7 +466,7 @@ class KindOfUtilization(str, Enum): """ Types of utilization - Args: + Attributes: assimilation: assimilation buildsAcidFrom: builds acid from degradation: degradation @@ -489,7 +489,7 @@ class GCMethod(str, Enum): """ Methods for GC measurement - Args: + Attributes: experimental: experimental genomeSequence: genome sequence """ @@ -502,7 +502,7 @@ class OxygenTolerance(str, Enum): """ How does the strain tolerate Oxygen - Args: + Attributes: aerobe: aerobe aerotolerant: aerotolerant anaerobe: anaerobe diff --git a/src/microbial_strain_data_model/classes/growthcondition.py b/src/microbial_strain_data_model/classes/growthcondition.py index 83825ce..24659d7 100644 --- a/src/microbial_strain_data_model/classes/growthcondition.py +++ b/src/microbial_strain_data_model/classes/growthcondition.py @@ -1,5 +1,6 @@ from pydantic import BaseModel, ConfigDict, Field +from microbial_strain_data_model.classes.enums import OxygenTolerance from microbial_strain_data_model.classes.links import SourceLink, RelationLink @@ -75,6 +76,10 @@ class GrowthCondition(BaseModel): description="List of tests and if the strain grows in tested ranges", ) + oxygenRelation: OxygenTolerance | None = Field( + default=None, title="Oxygen Relation", description="Aerobic, anaerobic etc." + ) + source: list[SourceLink] = Field( title="Source", description="List of JSON paths to source object" ) diff --git a/src/microbial_strain_data_model/classes/morphology.py b/src/microbial_strain_data_model/classes/morphology.py index 14f9f89..5b8255e 100644 --- a/src/microbial_strain_data_model/classes/morphology.py +++ b/src/microbial_strain_data_model/classes/morphology.py @@ -40,6 +40,11 @@ class Morphology(BaseModel): colonyColor: ColonyColor | None = Field( default=None, title="Color of Colony", description="Color of the colony on the" ) + multiCellComplexForming: bool | None = Field( + default=None, + title="Multi Cell Complex Forming", + description="Do the cells form complexes", + ) source: list[SourceLink] = Field( title="Source", description="List of JSON paths to source object" ) diff --git a/src/microbial_strain_data_model/classes/multicell.py b/src/microbial_strain_data_model/classes/multicell.py deleted file mode 100644 index 5ee48a3..0000000 --- a/src/microbial_strain_data_model/classes/multicell.py +++ /dev/null @@ -1,26 +0,0 @@ -from pydantic import BaseModel, ConfigDict, Field - -from microbial_strain_data_model.classes.links import RelationLink, SourceLink - - -class MultiCell(BaseModel): - """MultiCell ability of the strain""" - - model_config = ConfigDict( - strict=True, - extra="forbid", - revalidate_instances="always", - str_strip_whitespace=True, - ) - - multiCellComplexForming: bool = Field( - title="Multi Cell Complex Forming", description="Do the cells form complexes" - ) - relatedData: list[RelationLink] = Field( - default_factory=list, - title="Related Data", - description="JSON paths to relation object", - ) - source: list[SourceLink] = Field( - title="Source", description="List of JSON paths to source object" - ) diff --git a/src/microbial_strain_data_model/classes/oxygenrelation.py b/src/microbial_strain_data_model/classes/oxygenrelation.py deleted file mode 100644 index 554cdba..0000000 --- a/src/microbial_strain_data_model/classes/oxygenrelation.py +++ /dev/null @@ -1,27 +0,0 @@ -from pydantic import BaseModel, ConfigDict, Field - -from microbial_strain_data_model.classes.enums import OxygenTolerance -from microbial_strain_data_model.classes.links import RelationLink, SourceLink - - -class OxygenRelation(BaseModel): - """OxygenRelation of the strain""" - - model_config = ConfigDict( - strict=True, - extra="forbid", - revalidate_instances="always", - str_strip_whitespace=True, - ) - - oxygenRelation: OxygenTolerance = Field( - title="Oxygen Relation", description="Aerobic, anaerobic etc." - ) - relatedData: list[RelationLink] = Field( - default_factory=list, - title="Related Data", - description="JSON paths to relation object", - ) - source: list[SourceLink] = Field( - title="Source", description="List of JSON paths to source object" - ) diff --git a/src/microbial_strain_data_model/strain.py b/src/microbial_strain_data_model/strain.py index d18c031..3de4524 100644 --- a/src/microbial_strain_data_model/strain.py +++ b/src/microbial_strain_data_model/strain.py @@ -18,10 +18,8 @@ from microbial_strain_data_model.classes.legal import Legal from microbial_strain_data_model.classes.literature import Literature from microbial_strain_data_model.classes.morphology import Morphology -from microbial_strain_data_model.classes.multicell import MultiCell from microbial_strain_data_model.classes.organization import Collection from microbial_strain_data_model.classes.othermedia import OtherMedia -from microbial_strain_data_model.classes.oxygenrelation import OxygenRelation from microbial_strain_data_model.classes.pathogen import Pathogen from microbial_strain_data_model.classes.identifier import IdentifierStrain from microbial_strain_data_model.classes.origin import Origin @@ -66,18 +64,6 @@ class Strain(BaseModel): legal: list[Legal] = Field(default_factory=list, title="Legal", description="") - oxygenRelation: list[OxygenRelation] = Field( - default_factory=list, - title="Oxygen Relation", - description="", - ) - - multiCellComplexForming: list[MultiCell] = Field( - default_factory=list, - title="Multi Cell Complex Forming", - description="", - ) - morphology: list[Morphology] = Field( default_factory=list, title="Morphology", description="Morphology information" ) diff --git a/tests/example_data/bacteria.json b/tests/example_data/bacteria.json index 18da9d3..8240d13 100644 --- a/tests/example_data/bacteria.json +++ b/tests/example_data/bacteria.json @@ -522,6 +522,7 @@ "minimalTemperature": null, "optimalPh": 7.0, "optimalTemperature": 37.0, + "oxygenRelation": "anaerobe", "source": [ "/sources/0" ], @@ -1096,13 +1097,6 @@ "flagellumArrangement": null, "gliding": false, "motile": true, - "source": [ - "/sources/0" - ] - } - ], - "multiCellComplexForming": [ - { "multiCellComplexForming": true, "source": [ "/sources/0" @@ -1165,17 +1159,6 @@ "usageInfo": null } ], - "oxygenRelation": [ - { - "oxygenRelation": "anaerobe", - "relatedData": [ - "/relatedData/0" - ], - "source": [ - "/sources/0" - ] - } - ], "pathogenicity": [ { "classification": "German classification", From d44550de42601f46efd697e37de6113253ad5742 Mon Sep 17 00:00:00 2001 From: juwitte Date: Fri, 29 Aug 2025 09:19:18 +0000 Subject: [PATCH 09/10] refactor(restructure): restructure --- docs/graph.md | 193 +++++++++--------- docs/schema/01. creation_date.md | 9 - ...2. organismType.md => 01. organismType.md} | 2 +- .../{03. morphType.md => 02. morphType.md} | 2 +- .../{04. typeStrain.md => 03. typeStrain.md} | 6 +- docs/schema/{05. taxon.md => 04. taxon.md} | 34 +-- .../{13. identifier.md => 05. identifier.md} | 14 +- docs/schema/08. oxygenRelation.md | 55 ----- ... pathogenicity.md => 08. pathogenicity.md} | 12 +- .../{15. bioSafety.md => 09. bioSafety.md} | 10 +- docs/schema/09. multiCellComplexForming.md | 32 --- docs/schema/10. morphology.md | 11 +- ...onstituents.md => 11. wallConstituents.md} | 22 +- .../{21. staining.md => 12. staining.md} | 8 +- ...poreFormation.md => 13. sporeFormation.md} | 12 +- ...hConditions.md => 14. growthConditions.md} | 57 ++++-- ...vationMedia.md => 15. cultivationMedia.md} | 12 +- ...idProfiles.md => 18. fattyAcidProfiles.md} | 32 +-- .../{22. hemolysis.md => 19. hemolysis.md} | 8 +- .../{24. halophily.md => 20. halophily.md} | 38 ++-- .../{25. tolerances.md => 21. tolerances.md} | 36 ++-- .../schema/{26. enzymes.md => 22. enzymes.md} | 26 +-- ...{27. metabolites.md => 23. metabolites.md} | 32 +-- ...plications.md => 24. knownApplications.md} | 6 +- ...{29. collections.md => 25. collections.md} | 82 ++++---- .../{18. literature.md => 26. literature.md} | 64 +++--- .../{30. otherMedia.md => 27. otherMedia.md} | 14 +- ...{31. relatedData.md => 28. relatedData.md} | 6 +- .../schema/{32. sources.md => 29. sources.md} | 82 ++++---- schema/microbe_schema.json | 7 +- src/microbial_strain_data_model/strain.py | 66 +++--- 31 files changed, 458 insertions(+), 532 deletions(-) delete mode 100644 docs/schema/01. creation_date.md rename docs/schema/{02. organismType.md => 01. organismType.md} (93%) rename docs/schema/{03. morphType.md => 02. morphType.md} (87%) rename docs/schema/{04. typeStrain.md => 03. typeStrain.md} (70%) rename docs/schema/{05. taxon.md => 04. taxon.md} (71%) rename docs/schema/{13. identifier.md => 05. identifier.md} (77%) delete mode 100644 docs/schema/08. oxygenRelation.md rename docs/schema/{14. pathogenicity.md => 08. pathogenicity.md} (84%) rename docs/schema/{15. bioSafety.md => 09. bioSafety.md} (77%) delete mode 100644 docs/schema/09. multiCellComplexForming.md rename docs/schema/{19. wallConstituents.md => 11. wallConstituents.md} (69%) rename docs/schema/{21. staining.md => 12. staining.md} (81%) rename docs/schema/{11. sporeFormation.md => 13. sporeFormation.md} (70%) rename docs/schema/{12. growthConditions.md => 14. growthConditions.md} (60%) rename docs/schema/{23. cultivationMedia.md => 15. cultivationMedia.md} (62%) rename docs/schema/{20. fattyAcidProfiles.md => 18. fattyAcidProfiles.md} (64%) rename docs/schema/{22. hemolysis.md => 19. hemolysis.md} (83%) rename docs/schema/{24. halophily.md => 20. halophily.md} (76%) rename docs/schema/{25. tolerances.md => 21. tolerances.md} (76%) rename docs/schema/{26. enzymes.md => 22. enzymes.md} (73%) rename docs/schema/{27. metabolites.md => 23. metabolites.md} (75%) rename docs/schema/{28. knownApplications.md => 24. knownApplications.md} (70%) rename docs/schema/{29. collections.md => 25. collections.md} (71%) rename docs/schema/{18. literature.md => 26. literature.md} (64%) rename docs/schema/{30. otherMedia.md => 27. otherMedia.md} (71%) rename docs/schema/{31. relatedData.md => 28. relatedData.md} (78%) rename docs/schema/{32. sources.md => 29. sources.md} (68%) diff --git a/docs/graph.md b/docs/graph.md index 778413f..9d2eb6e 100644 --- a/docs/graph.md +++ b/docs/graph.md @@ -83,6 +83,15 @@ parentTaxon: Taxon | null sameAs: string } +class `IdentifierStrain`{ +name: string +value: string +propertyID: string | null +url: string | null +logo: string | null +source: string +} + class `Origin`{ sampleDate: string | null country: Country | null @@ -203,6 +212,40 @@ value: string url: string | null } +class `Pathogen`{ +host: Host +pathogen: PathogenLevel +classification: string | null +url: string | null +source: string +} + +class `Host`{ +<> +plant +animal +invertebrates +vertebrates +mammals +non-human primates +human +fungi +} + +class `PathogenLevel`{ +<> +no pathogen +opportunistic +obligate +} + +class `BioSafety`{ +riskgroup: string +classification: string | null +url: string | null +source: string +} + class `Morphology`{ cellShape: string cellLength: Size @@ -252,6 +295,27 @@ beige brownish } +class `CellWall`{ +name: string | null +identifier: array[Identifier] +alternateName: string +percent: number | null +source: string +} + +class `Staining`{ +name: string +value: StainingValue +source: string +} + +class `StainingValue`{ +<> +positive +negative +variable +} + class `Spore`{ sporeBuilding: boolean | null typeOfSpore: SporeType @@ -299,47 +363,12 @@ obligate aerobe obligate anaerobe } -class `IdentifierStrain`{ +class `CultivationMedia`{ name: string -value: string -propertyID: string | null -url: string | null -logo: string | null -source: string -} - -class `Pathogen`{ -host: Host -pathogen: PathogenLevel -classification: string | null -url: string | null -source: string -} - -class `Host`{ -<> -plant -animal -invertebrates -vertebrates -mammals -non-human primates -human -fungi -} - -class `PathogenLevel`{ -<> -no pathogen -opportunistic -obligate -} - -class `BioSafety`{ -riskgroup: string -classification: string | null url: string | null +reagentUsed: string source: string +relatedData: string } class `Sequence`{ @@ -380,23 +409,6 @@ experimental genome sequence } -class `Literature`{ -name: string | null -url: string | null -datePublished: string | null -author: array[Person] -publisher: array[Organization] -source: string -} - -class `CellWall`{ -name: string | null -identifier: array[Identifier] -alternateName: string -percent: number | null -source: string -} - class `FattyAcidProfile`{ profile: array[FattyAcid] library: string | null @@ -413,19 +425,6 @@ percent: number | null ecl: string | null } -class `Staining`{ -name: string -value: StainingValue -source: string -} - -class `StainingValue`{ -<> -positive -negative -variable -} - class `Hemolysis`{ blood: HemolysisBlood hemolysisType: HemolysisType @@ -446,14 +445,6 @@ beta gamma } -class `CultivationMedia`{ -name: string -url: string | null -reagentUsed: string -source: string -relatedData: string -} - class `Halophil`{ name: string | null identifier: array[Identifier] @@ -592,6 +583,15 @@ Water DNA } +class `Literature`{ +name: string | null +url: string | null +datePublished: string | null +author: array[Person] +publisher: array[Organization] +source: string +} + class `OtherMedia`{ url: string | null name: string | null @@ -634,33 +634,32 @@ unknown } class `Strain`{ -creation_date: string organismType: OrganismType morphType: Morph | null typeStrain: array[TypeStrain] taxon: array[TaxonWithSource] +identifier: array[IdentifierStrain] origin: array[Origin] legal: array[Legal] +pathogenicity: array[Pathogen] +bioSafety: array[BioSafety] morphology: array[Morphology] +wallConstituents: array[CellWall] +staining: array[Staining] sporeFormation: array[Spore] growthConditions: array[GrowthCondition] -identifier: array[IdentifierStrain] -pathogenicity: array[Pathogen] -bioSafety: array[BioSafety] +cultivationMedia: array[CultivationMedia] sequences: array[Sequence] gcContent: array[GCContent] -literature: array[Literature] -wallConstituents: array[CellWall] fattyAcidProfiles: array[FattyAcidProfile] -staining: array[Staining] hemolysis: array[Hemolysis] -cultivationMedia: array[CultivationMedia] halophily: array[Halophil] tolerances: array[Tolerance] enzymes: array[Enzyme] metabolites: array[Metabolite] knownApplications: array[Application] collections: array[Collection] +literature: array[Literature] otherMedia: array[OtherMedia] relatedData: array[RelatedData] sources: array[Source] @@ -680,6 +679,7 @@ sources: array[Source] `Taxon` ..> `Identifier` `Taxon` ..> `ScientificName` `Taxon` ..> `Taxon` +`Strain` ..> `IdentifierStrain` `Strain` ..> `Origin` `Origin` ..> `Country` `Country` ..> `CountryHistoricalAlpha2` @@ -698,6 +698,10 @@ sources: array[Source] `Legal` ..> `NagoyaRestrictions` `Legal` ..> `microbial_strain_data_model__classes__legal__Restriction` `microbial_strain_data_model__classes__legal__Restriction` ..> `Country` +`Strain` ..> `Pathogen` +`Pathogen` ..> `Host` +`Pathogen` ..> `PathogenLevel` +`Strain` ..> `BioSafety` `Strain` ..> `Morphology` `Morphology` ..> `Size` `Size` ..> `SizeUnit` @@ -705,37 +709,29 @@ sources: array[Source] `Morphology` ..> `FlagellumArrangement` `Morphology` ..> `Size` `Morphology` ..> `ColonyColor` +`Strain` ..> `CellWall` +`CellWall` ..> `Identifier` +`Strain` ..> `Staining` +`Staining` ..> `StainingValue` `Strain` ..> `Spore` `Spore` ..> `SporeType` `Strain` ..> `GrowthCondition` `GrowthCondition` ..> `GrowthRange` `GrowthCondition` ..> `GrowthRange` `GrowthCondition` ..> `OxygenTolerance` -`Strain` ..> `IdentifierStrain` -`Strain` ..> `Pathogen` -`Pathogen` ..> `Host` -`Pathogen` ..> `PathogenLevel` -`Strain` ..> `BioSafety` +`Strain` ..> `CultivationMedia` `Strain` ..> `Sequence` `Sequence` ..> `SequenceType` `Sequence` ..> `SequenceLevel` `Sequence` ..> `Identifier` `Strain` ..> `GCContent` `GCContent` ..> `GCMethod` -`Strain` ..> `Literature` -`Literature` ..> `Person` -`Literature` ..> `Organization` -`Strain` ..> `CellWall` -`CellWall` ..> `Identifier` `Strain` ..> `FattyAcidProfile` `FattyAcidProfile` ..> `FattyAcid` `FattyAcid` ..> `Identifier` -`Strain` ..> `Staining` -`Staining` ..> `StainingValue` `Strain` ..> `Hemolysis` `Hemolysis` ..> `HemolysisBlood` `Hemolysis` ..> `HemolysisType` -`Strain` ..> `CultivationMedia` `Strain` ..> `Halophil` `Halophil` ..> `Identifier` `Halophil` ..> `ConcentrationUnit` @@ -761,6 +757,9 @@ sources: array[Source] `Collection` ..> `microbial_strain_data_model__classes__enums__Restriction` `Collection` ..> `SupplyForm` `Collection` ..> `Person` +`Strain` ..> `Literature` +`Literature` ..> `Person` +`Literature` ..> `Organization` `Strain` ..> `OtherMedia` `Strain` ..> `RelatedData` `Strain` ..> `Source` diff --git a/docs/schema/01. creation_date.md b/docs/schema/01. creation_date.md deleted file mode 100644 index cef948b..0000000 --- a/docs/schema/01. creation_date.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -## 01. creation_date -Creation Date - -**string** - -Format: - - date diff --git a/docs/schema/02. organismType.md b/docs/schema/01. organismType.md similarity index 93% rename from docs/schema/02. organismType.md rename to docs/schema/01. organismType.md index 41e7c5c..ebd9d61 100644 --- a/docs/schema/02. organismType.md +++ b/docs/schema/01. organismType.md @@ -1,5 +1,5 @@ --- -## 02. organismType +## 01. organismType OrganismType `Required` Description: diff --git a/docs/schema/03. morphType.md b/docs/schema/02. morphType.md similarity index 87% rename from docs/schema/03. morphType.md rename to docs/schema/02. morphType.md index 8ff4b96..35e3448 100644 --- a/docs/schema/03. morphType.md +++ b/docs/schema/02. morphType.md @@ -1,5 +1,5 @@ --- -## 03. morphType +## 02. morphType Morph Type Description: diff --git a/docs/schema/04. typeStrain.md b/docs/schema/03. typeStrain.md similarity index 70% rename from docs/schema/04. typeStrain.md rename to docs/schema/03. typeStrain.md index 1fc08c8..76d1410 100644 --- a/docs/schema/04. typeStrain.md +++ b/docs/schema/03. typeStrain.md @@ -1,17 +1,17 @@ --- -## 04. typeStrain +## 03. typeStrain Type Strain `Required` **array[object]** --- -## 04.1. typeStrain.typeStrain +## 03.1. typeStrain.typeStrain Type Strain `Required` **boolean** --- -## 04.2. typeStrain.source +## 03.2. typeStrain.source Source `Required` Description: diff --git a/docs/schema/05. taxon.md b/docs/schema/04. taxon.md similarity index 71% rename from docs/schema/05. taxon.md rename to docs/schema/04. taxon.md index 03bb198..38fbfc3 100644 --- a/docs/schema/05. taxon.md +++ b/docs/schema/04. taxon.md @@ -1,17 +1,17 @@ --- -## 05. taxon +## 04. taxon Taxon `Required` **array[object]** --- -## 05.1. taxon.name +## 04.1. taxon.name Name `Required` **string** --- -## 05.2. taxon.taxonRank +## 04.2. taxon.taxonRank Taxon Rank **string, null** @@ -29,7 +29,7 @@ Enum: domain --- -## 05.3. taxon.taxonStatus +## 04.3. taxon.taxonStatus Taxon Status **string, null** @@ -41,7 +41,7 @@ Enum: validly published synonym --- -## 05.4. taxon.identifier +## 04.4. taxon.identifier Identifier Description: @@ -50,7 +50,7 @@ Description: **array[object]** --- -## 05.4.1. taxon.identifier.name +## 04.4.1. taxon.identifier.name Name `Required` Description: @@ -59,7 +59,7 @@ Description: **string** --- -## 05.4.2. taxon.identifier.value +## 04.4.2. taxon.identifier.value Value `Required` Description: @@ -68,7 +68,7 @@ Description: **string** --- -## 05.4.3. taxon.identifier.propertyID +## 04.4.3. taxon.identifier.propertyID Property ID Description: @@ -77,7 +77,7 @@ Description: **string, null** --- -## 05.4.4. taxon.identifier.url +## 04.4.4. taxon.identifier.url URL Description: @@ -86,7 +86,7 @@ Description: **string, null** --- -## 05.4.5. taxon.identifier.logo +## 04.4.5. taxon.identifier.logo Logo Description: @@ -95,43 +95,43 @@ Description: **string, null** --- -## 05.5. taxon.scientificName +## 04.5. taxon.scientificName Scientific Name **object, null** --- -## 05.5.1. taxon.scientificName.name +## 04.5.1. taxon.scientificName.name Name `Required` **string** --- -## 05.5.2. taxon.scientificName.author +## 04.5.2. taxon.scientificName.author Author `Required` **string** --- -## 05.6. taxon.alternateName +## 04.6. taxon.alternateName Alternate Name **array[string]** --- -## 05.7. taxon.parentTaxon +## 04.7. taxon.parentTaxon Parent Taxon **object, null** --- -## 05.8. taxon.sameAs +## 04.8. taxon.sameAs Same As **array[string]** --- -## 05.9. taxon.source +## 04.9. taxon.source Source `Required` Description: diff --git a/docs/schema/13. identifier.md b/docs/schema/05. identifier.md similarity index 77% rename from docs/schema/13. identifier.md rename to docs/schema/05. identifier.md index 66f6cac..2778fc3 100644 --- a/docs/schema/13. identifier.md +++ b/docs/schema/05. identifier.md @@ -1,11 +1,11 @@ --- -## 13. identifier +## 05. identifier Identifier **array[object]** --- -## 13.1. identifier.name +## 05.1. identifier.name Name `Required` Description: @@ -14,7 +14,7 @@ Description: **string** --- -## 13.2. identifier.value +## 05.2. identifier.value Value `Required` Description: @@ -23,7 +23,7 @@ Description: **string** --- -## 13.3. identifier.propertyID +## 05.3. identifier.propertyID Property ID Description: @@ -32,7 +32,7 @@ Description: **string, null** --- -## 13.4. identifier.url +## 05.4. identifier.url URL Description: @@ -41,7 +41,7 @@ Description: **string, null** --- -## 13.5. identifier.logo +## 05.5. identifier.logo Logo Description: @@ -50,7 +50,7 @@ Description: **string, null** --- -## 13.6. identifier.source +## 05.6. identifier.source Source `Required` Description: diff --git a/docs/schema/08. oxygenRelation.md b/docs/schema/08. oxygenRelation.md deleted file mode 100644 index a58a13d..0000000 --- a/docs/schema/08. oxygenRelation.md +++ /dev/null @@ -1,55 +0,0 @@ ---- -## 08. oxygenRelation -Oxygen Relation - -**array[object]** - ---- -## 08.1. oxygenRelation.oxygenRelation -OxygenTolerance `Required` - -Description: -> How does the strain tolerate Oxygen -> -> Attributes: -> aerobe: aerobe -> aerotolerant: aerotolerant -> anaerobe: anaerobe -> facultativeAerobe: facultative aerobe -> facultativeAnaerobe: facultative anaerobe -> microaerophile: microaerophile -> microaerotolerant: microaerotolerant -> obligateAerobe: obligate aerobe -> obligateAnaerobe: obligate anaerobe - -**string** - -Enum: - - aerobe - aerotolerant - anaerobe - facultative aerobe - facultative anaerobe - microaerophile - microaerotolerant - obligate aerobe - obligate anaerobe - ---- -## 08.2. oxygenRelation.relatedData -Related Data - -Description: -> JSON paths to relation object - -**array[string]** - ---- -## 08.3. oxygenRelation.source -Source `Required` - -Description: -> List of JSON paths to source object - -**array[string]** diff --git a/docs/schema/14. pathogenicity.md b/docs/schema/08. pathogenicity.md similarity index 84% rename from docs/schema/14. pathogenicity.md rename to docs/schema/08. pathogenicity.md index 4b6c172..19a0029 100644 --- a/docs/schema/14. pathogenicity.md +++ b/docs/schema/08. pathogenicity.md @@ -1,11 +1,11 @@ --- -## 14. pathogenicity +## 08. pathogenicity pathogenicity **array[object]** --- -## 14.1. pathogenicity.host +## 08.1. pathogenicity.host Host `Required` Description: @@ -35,7 +35,7 @@ Enum: fungi --- -## 14.2. pathogenicity.pathogen +## 08.2. pathogenicity.pathogen PathogenLevel `Required` Description: @@ -55,7 +55,7 @@ Enum: obligate --- -## 14.3. pathogenicity.classification +## 08.3. pathogenicity.classification Classification Description: @@ -64,7 +64,7 @@ Description: **string, null** --- -## 14.4. pathogenicity.url +## 08.4. pathogenicity.url URL Description: @@ -73,7 +73,7 @@ Description: **string, null** --- -## 14.5. pathogenicity.source +## 08.5. pathogenicity.source Source `Required` Description: diff --git a/docs/schema/15. bioSafety.md b/docs/schema/09. bioSafety.md similarity index 77% rename from docs/schema/15. bioSafety.md rename to docs/schema/09. bioSafety.md index 2dc801c..d1654dc 100644 --- a/docs/schema/15. bioSafety.md +++ b/docs/schema/09. bioSafety.md @@ -1,11 +1,11 @@ --- -## 15. bioSafety +## 09. bioSafety Bio Safety **array[object]** --- -## 15.1. bioSafety.riskgroup +## 09.1. bioSafety.riskgroup Riskgroup `Required` Description: @@ -14,7 +14,7 @@ Description: **string** --- -## 15.2. bioSafety.classification +## 09.2. bioSafety.classification Classification Description: @@ -23,7 +23,7 @@ Description: **string, null** --- -## 15.3. bioSafety.url +## 09.3. bioSafety.url URL Description: @@ -32,7 +32,7 @@ Description: **string, null** --- -## 15.4. bioSafety.source +## 09.4. bioSafety.source Source `Required` Description: diff --git a/docs/schema/09. multiCellComplexForming.md b/docs/schema/09. multiCellComplexForming.md deleted file mode 100644 index f063614..0000000 --- a/docs/schema/09. multiCellComplexForming.md +++ /dev/null @@ -1,32 +0,0 @@ ---- -## 09. multiCellComplexForming -Multi Cell Complex Forming - -**array[object]** - ---- -## 09.1. multiCellComplexForming.multiCellComplexForming -Multi Cell Complex Forming `Required` - -Description: -> Do the cells form complexes - -**boolean** - ---- -## 09.2. multiCellComplexForming.relatedData -Related Data - -Description: -> JSON paths to relation object - -**array[string]** - ---- -## 09.3. multiCellComplexForming.source -Source `Required` - -Description: -> List of JSON paths to source object - -**array[string]** diff --git a/docs/schema/10. morphology.md b/docs/schema/10. morphology.md index 78567a5..af565ce 100644 --- a/docs/schema/10. morphology.md +++ b/docs/schema/10. morphology.md @@ -197,7 +197,16 @@ Enum: brownish --- -## 10.10. morphology.source +## 10.10. morphology.multiCellComplexForming +Multi Cell Complex Forming + +Description: +> Do the cells form complexes + +**boolean, null** + +--- +## 10.11. morphology.source Source `Required` Description: diff --git a/docs/schema/19. wallConstituents.md b/docs/schema/11. wallConstituents.md similarity index 69% rename from docs/schema/19. wallConstituents.md rename to docs/schema/11. wallConstituents.md index 56a7d2c..e62e2e3 100644 --- a/docs/schema/19. wallConstituents.md +++ b/docs/schema/11. wallConstituents.md @@ -1,11 +1,11 @@ --- -## 19. wallConstituents +## 11. wallConstituents Wall Constituents **array[object]** --- -## 19.1. wallConstituents.name +## 11.1. wallConstituents.name Name of Chemical Substance Description: @@ -14,7 +14,7 @@ Description: **string, null** --- -## 19.2. wallConstituents.identifier +## 11.2. wallConstituents.identifier Identifier Description: @@ -23,7 +23,7 @@ Description: **array[object]** --- -## 19.2.1. wallConstituents.identifier.name +## 11.2.1. wallConstituents.identifier.name Name `Required` Description: @@ -32,7 +32,7 @@ Description: **string** --- -## 19.2.2. wallConstituents.identifier.value +## 11.2.2. wallConstituents.identifier.value Value `Required` Description: @@ -41,7 +41,7 @@ Description: **string** --- -## 19.2.3. wallConstituents.identifier.propertyID +## 11.2.3. wallConstituents.identifier.propertyID Property ID Description: @@ -50,7 +50,7 @@ Description: **string, null** --- -## 19.2.4. wallConstituents.identifier.url +## 11.2.4. wallConstituents.identifier.url URL Description: @@ -59,7 +59,7 @@ Description: **string, null** --- -## 19.2.5. wallConstituents.identifier.logo +## 11.2.5. wallConstituents.identifier.logo Logo Description: @@ -68,7 +68,7 @@ Description: **string, null** --- -## 19.3. wallConstituents.alternateName +## 11.3. wallConstituents.alternateName Alternate Name Description: @@ -77,13 +77,13 @@ Description: **array[string]** --- -## 19.4. wallConstituents.percent +## 11.4. wallConstituents.percent Percent **number, null** --- -## 19.5. wallConstituents.source +## 11.5. wallConstituents.source Source `Required` Description: diff --git a/docs/schema/21. staining.md b/docs/schema/12. staining.md similarity index 81% rename from docs/schema/21. staining.md rename to docs/schema/12. staining.md index 98e82e2..a3ac6ef 100644 --- a/docs/schema/21. staining.md +++ b/docs/schema/12. staining.md @@ -1,17 +1,17 @@ --- -## 21. staining +## 12. staining Stainings **array[object]** --- -## 21.1. staining.name +## 12.1. staining.name Name `Required` **string** --- -## 21.2. staining.value +## 12.2. staining.value StainingValue `Required` Description: @@ -31,7 +31,7 @@ Enum: variable --- -## 21.3. staining.source +## 12.3. staining.source Source `Required` Description: diff --git a/docs/schema/11. sporeFormation.md b/docs/schema/13. sporeFormation.md similarity index 70% rename from docs/schema/11. sporeFormation.md rename to docs/schema/13. sporeFormation.md index ea75ba6..ff9ab8e 100644 --- a/docs/schema/11. sporeFormation.md +++ b/docs/schema/13. sporeFormation.md @@ -1,17 +1,17 @@ --- -## 11. sporeFormation +## 13. sporeFormation Spore Formation **array[object]** --- -## 11.1. sporeFormation.sporeBuilding +## 13.1. sporeFormation.sporeBuilding sporeBuilding **boolean, null** --- -## 11.2. sporeFormation.typeOfSpore +## 13.2. sporeFormation.typeOfSpore SporeType `Required` Description: @@ -29,13 +29,13 @@ Enum: endospore --- -## 11.3. sporeFormation.sporeEjection +## 13.3. sporeFormation.sporeEjection Spore Ejection **string, null** --- -## 11.4. sporeFormation.relatedData +## 13.4. sporeFormation.relatedData Related Data Description: @@ -44,7 +44,7 @@ Description: **array[string]** --- -## 11.5. sporeFormation.source +## 13.5. sporeFormation.source Source `Required` Description: diff --git a/docs/schema/12. growthConditions.md b/docs/schema/14. growthConditions.md similarity index 60% rename from docs/schema/12. growthConditions.md rename to docs/schema/14. growthConditions.md index 9b2705b..9adf4ff 100644 --- a/docs/schema/12. growthConditions.md +++ b/docs/schema/14. growthConditions.md @@ -1,5 +1,5 @@ --- -## 12. growthConditions +## 14. growthConditions Growth conditions Description: @@ -8,7 +8,7 @@ Description: **array[object]** --- -## 12.1. growthConditions.optimalTemperature +## 14.1. growthConditions.optimalTemperature Optimal Description: @@ -17,7 +17,7 @@ Description: **number, null** --- -## 12.2. growthConditions.minimalTemperature +## 14.2. growthConditions.minimalTemperature Minimal Description: @@ -26,7 +26,7 @@ Description: **number, null** --- -## 12.3. growthConditions.maximalTemperature +## 14.3. growthConditions.maximalTemperature Maximal Description: @@ -35,7 +35,7 @@ Description: **number, null** --- -## 12.4. growthConditions.testsTemperature +## 14.4. growthConditions.testsTemperature Tests Description: @@ -44,7 +44,7 @@ Description: **array[object]** --- -## 12.4.1. growthConditions.testsTemperature.minimal +## 14.4.1. growthConditions.testsTemperature.minimal Minimal Description: @@ -53,7 +53,7 @@ Description: **number, null** --- -## 12.4.2. growthConditions.testsTemperature.maximal +## 14.4.2. growthConditions.testsTemperature.maximal Maximal Description: @@ -62,7 +62,7 @@ Description: **number, null** --- -## 12.4.3. growthConditions.testsTemperature.growth +## 14.4.3. growthConditions.testsTemperature.growth Growth `Required` Description: @@ -71,7 +71,7 @@ Description: **boolean** --- -## 12.4.4. growthConditions.testsTemperature.relatedData +## 14.4.4. growthConditions.testsTemperature.relatedData Related Data Description: @@ -80,7 +80,7 @@ Description: **array[string]** --- -## 12.5. growthConditions.optimalPh +## 14.5. growthConditions.optimalPh Optimal Description: @@ -89,7 +89,7 @@ Description: **number, null** --- -## 12.6. growthConditions.minimalPh +## 14.6. growthConditions.minimalPh Minimal Description: @@ -98,7 +98,7 @@ Description: **number, null** --- -## 12.7. growthConditions.maximalPh +## 14.7. growthConditions.maximalPh Maximal Description: @@ -107,7 +107,7 @@ Description: **number, null** --- -## 12.8. growthConditions.testsPh +## 14.8. growthConditions.testsPh Tests Description: @@ -116,7 +116,7 @@ Description: **array[object]** --- -## 12.8.1. growthConditions.testsPh.minimal +## 14.8.1. growthConditions.testsPh.minimal Minimal Description: @@ -125,7 +125,7 @@ Description: **number, null** --- -## 12.8.2. growthConditions.testsPh.maximal +## 14.8.2. growthConditions.testsPh.maximal Maximal Description: @@ -134,7 +134,7 @@ Description: **number, null** --- -## 12.8.3. growthConditions.testsPh.growth +## 14.8.3. growthConditions.testsPh.growth Growth `Required` Description: @@ -143,7 +143,7 @@ Description: **boolean** --- -## 12.8.4. growthConditions.testsPh.relatedData +## 14.8.4. growthConditions.testsPh.relatedData Related Data Description: @@ -152,7 +152,28 @@ Description: **array[string]** --- -## 12.9. growthConditions.source +## 14.9. growthConditions.oxygenRelation +Oxygen Relation + +Description: +> Aerobic, anaerobic etc. + +**string, null** + +Enum: + + aerobe + aerotolerant + anaerobe + facultative aerobe + facultative anaerobe + microaerophile + microaerotolerant + obligate aerobe + obligate anaerobe + +--- +## 14.10. growthConditions.source Source `Required` Description: diff --git a/docs/schema/23. cultivationMedia.md b/docs/schema/15. cultivationMedia.md similarity index 62% rename from docs/schema/23. cultivationMedia.md rename to docs/schema/15. cultivationMedia.md index 17bd8af..eef0989 100644 --- a/docs/schema/23. cultivationMedia.md +++ b/docs/schema/15. cultivationMedia.md @@ -1,29 +1,29 @@ --- -## 23. cultivationMedia +## 15. cultivationMedia Cultivation Media **array[object]** --- -## 23.1. cultivationMedia.name +## 15.1. cultivationMedia.name Name `Required` **string** --- -## 23.2. cultivationMedia.url +## 15.2. cultivationMedia.url URL **string, null** --- -## 23.3. cultivationMedia.reagentUsed +## 15.3. cultivationMedia.reagentUsed Reagent Used **array[string]** --- -## 23.4. cultivationMedia.source +## 15.4. cultivationMedia.source Source `Required` Description: @@ -32,7 +32,7 @@ Description: **array[string]** --- -## 23.5. cultivationMedia.relatedData +## 15.5. cultivationMedia.relatedData Related Data Description: diff --git a/docs/schema/20. fattyAcidProfiles.md b/docs/schema/18. fattyAcidProfiles.md similarity index 64% rename from docs/schema/20. fattyAcidProfiles.md rename to docs/schema/18. fattyAcidProfiles.md index 057d527..0c6ff9b 100644 --- a/docs/schema/20. fattyAcidProfiles.md +++ b/docs/schema/18. fattyAcidProfiles.md @@ -1,11 +1,11 @@ --- -## 20. fattyAcidProfiles +## 18. fattyAcidProfiles Fatty Acid Profile **array[object]** --- -## 20.1. fattyAcidProfiles.profile +## 18.1. fattyAcidProfiles.profile Profile Description: @@ -14,7 +14,7 @@ Description: **array[object]** --- -## 20.1.1. fattyAcidProfiles.profile.name +## 18.1.1. fattyAcidProfiles.profile.name Name of Chemical Substance Description: @@ -23,7 +23,7 @@ Description: **string, null** --- -## 20.1.2. fattyAcidProfiles.profile.identifier +## 18.1.2. fattyAcidProfiles.profile.identifier Identifier Description: @@ -32,7 +32,7 @@ Description: **array[object]** --- -## 20.1.2.1. fattyAcidProfiles.profile.identifier.name +## 18.1.2.1. fattyAcidProfiles.profile.identifier.name Name `Required` Description: @@ -41,7 +41,7 @@ Description: **string** --- -## 20.1.2.2. fattyAcidProfiles.profile.identifier.value +## 18.1.2.2. fattyAcidProfiles.profile.identifier.value Value `Required` Description: @@ -50,7 +50,7 @@ Description: **string** --- -## 20.1.2.3. fattyAcidProfiles.profile.identifier.propertyID +## 18.1.2.3. fattyAcidProfiles.profile.identifier.propertyID Property ID Description: @@ -59,7 +59,7 @@ Description: **string, null** --- -## 20.1.2.4. fattyAcidProfiles.profile.identifier.url +## 18.1.2.4. fattyAcidProfiles.profile.identifier.url URL Description: @@ -68,7 +68,7 @@ Description: **string, null** --- -## 20.1.2.5. fattyAcidProfiles.profile.identifier.logo +## 18.1.2.5. fattyAcidProfiles.profile.identifier.logo Logo Description: @@ -77,7 +77,7 @@ Description: **string, null** --- -## 20.1.3. fattyAcidProfiles.profile.alternateName +## 18.1.3. fattyAcidProfiles.profile.alternateName Alternate Name Description: @@ -86,19 +86,19 @@ Description: **array[string]** --- -## 20.1.4. fattyAcidProfiles.profile.percent +## 18.1.4. fattyAcidProfiles.profile.percent Percent **number, null** --- -## 20.1.5. fattyAcidProfiles.profile.ecl +## 18.1.5. fattyAcidProfiles.profile.ecl ECL **string, null** --- -## 20.2. fattyAcidProfiles.library +## 18.2. fattyAcidProfiles.library Library Description: @@ -107,7 +107,7 @@ Description: **string, null** --- -## 20.3. fattyAcidProfiles.software +## 18.3. fattyAcidProfiles.software Software Description: @@ -116,7 +116,7 @@ Description: **string, null** --- -## 20.4. fattyAcidProfiles.relatedData +## 18.4. fattyAcidProfiles.relatedData Related Data Description: @@ -125,7 +125,7 @@ Description: **array[string]** --- -## 20.5. fattyAcidProfiles.source +## 18.5. fattyAcidProfiles.source Source `Required` Description: diff --git a/docs/schema/22. hemolysis.md b/docs/schema/19. hemolysis.md similarity index 83% rename from docs/schema/22. hemolysis.md rename to docs/schema/19. hemolysis.md index 1da4ae3..d5d05d9 100644 --- a/docs/schema/22. hemolysis.md +++ b/docs/schema/19. hemolysis.md @@ -1,11 +1,11 @@ --- -## 22. hemolysis +## 19. hemolysis Hemolysis **array[object]** --- -## 22.1. hemolysis.blood +## 19.1. hemolysis.blood HemolysisBlood `Required` Description: @@ -25,7 +25,7 @@ Enum: unknown --- -## 22.2. hemolysis.hemolysisType +## 19.2. hemolysis.hemolysisType HemolysisType `Required` Description: @@ -45,7 +45,7 @@ Enum: gamma --- -## 22.3. hemolysis.source +## 19.3. hemolysis.source Source `Required` Description: diff --git a/docs/schema/24. halophily.md b/docs/schema/20. halophily.md similarity index 76% rename from docs/schema/24. halophily.md rename to docs/schema/20. halophily.md index 90d9362..7257be5 100644 --- a/docs/schema/24. halophily.md +++ b/docs/schema/20. halophily.md @@ -1,11 +1,11 @@ --- -## 24. halophily +## 20. halophily Halophily **array[object]** --- -## 24.1. halophily.name +## 20.1. halophily.name Name of Chemical Substance Description: @@ -14,7 +14,7 @@ Description: **string, null** --- -## 24.2. halophily.identifier +## 20.2. halophily.identifier Identifier Description: @@ -23,7 +23,7 @@ Description: **array[object]** --- -## 24.2.1. halophily.identifier.name +## 20.2.1. halophily.identifier.name Name `Required` Description: @@ -32,7 +32,7 @@ Description: **string** --- -## 24.2.2. halophily.identifier.value +## 20.2.2. halophily.identifier.value Value `Required` Description: @@ -41,7 +41,7 @@ Description: **string** --- -## 24.2.3. halophily.identifier.propertyID +## 20.2.3. halophily.identifier.propertyID Property ID Description: @@ -50,7 +50,7 @@ Description: **string, null** --- -## 24.2.4. halophily.identifier.url +## 20.2.4. halophily.identifier.url URL Description: @@ -59,7 +59,7 @@ Description: **string, null** --- -## 24.2.5. halophily.identifier.logo +## 20.2.5. halophily.identifier.logo Logo Description: @@ -68,7 +68,7 @@ Description: **string, null** --- -## 24.3. halophily.alternateName +## 20.3. halophily.alternateName Alternate Name Description: @@ -77,7 +77,7 @@ Description: **array[string]** --- -## 24.4. halophily.minimal +## 20.4. halophily.minimal Optimal Description: @@ -86,7 +86,7 @@ Description: **number, null** --- -## 24.5. halophily.maximal +## 20.5. halophily.maximal Optimal Description: @@ -95,7 +95,7 @@ Description: **number, null** --- -## 24.6. halophily.optimal +## 20.6. halophily.optimal Optimal Description: @@ -104,7 +104,7 @@ Description: **number, null** --- -## 24.7. halophily.unit +## 20.7. halophily.unit ConcentrationUnit `Required` Description: @@ -127,7 +127,7 @@ Enum: unknown --- -## 24.8. halophily.tests +## 20.8. halophily.tests Tests Description: @@ -136,7 +136,7 @@ Description: **array[object]** --- -## 24.8.1. halophily.tests.minimal +## 20.8.1. halophily.tests.minimal Minimal Description: @@ -145,7 +145,7 @@ Description: **number, null** --- -## 24.8.2. halophily.tests.maximal +## 20.8.2. halophily.tests.maximal Maximal Description: @@ -154,7 +154,7 @@ Description: **number, null** --- -## 24.8.3. halophily.tests.growth +## 20.8.3. halophily.tests.growth Growth `Required` Description: @@ -163,7 +163,7 @@ Description: **boolean** --- -## 24.8.4. halophily.tests.relatedData +## 20.8.4. halophily.tests.relatedData Related Data Description: @@ -172,7 +172,7 @@ Description: **array[string]** --- -## 24.9. halophily.source +## 20.9. halophily.source Source `Required` Description: diff --git a/docs/schema/25. tolerances.md b/docs/schema/21. tolerances.md similarity index 76% rename from docs/schema/25. tolerances.md rename to docs/schema/21. tolerances.md index 76eb5f5..c34891a 100644 --- a/docs/schema/25. tolerances.md +++ b/docs/schema/21. tolerances.md @@ -1,11 +1,11 @@ --- -## 25. tolerances +## 21. tolerances Tolerances **array[object]** --- -## 25.1. tolerances.name +## 21.1. tolerances.name Name of Chemical Substance Description: @@ -14,7 +14,7 @@ Description: **string, null** --- -## 25.2. tolerances.identifier +## 21.2. tolerances.identifier Identifier Description: @@ -23,7 +23,7 @@ Description: **array[object]** --- -## 25.2.1. tolerances.identifier.name +## 21.2.1. tolerances.identifier.name Name `Required` Description: @@ -32,7 +32,7 @@ Description: **string** --- -## 25.2.2. tolerances.identifier.value +## 21.2.2. tolerances.identifier.value Value `Required` Description: @@ -41,7 +41,7 @@ Description: **string** --- -## 25.2.3. tolerances.identifier.propertyID +## 21.2.3. tolerances.identifier.propertyID Property ID Description: @@ -50,7 +50,7 @@ Description: **string, null** --- -## 25.2.4. tolerances.identifier.url +## 21.2.4. tolerances.identifier.url URL Description: @@ -59,7 +59,7 @@ Description: **string, null** --- -## 25.2.5. tolerances.identifier.logo +## 21.2.5. tolerances.identifier.logo Logo Description: @@ -68,7 +68,7 @@ Description: **string, null** --- -## 25.3. tolerances.alternateName +## 21.3. tolerances.alternateName Alternate Name Description: @@ -77,7 +77,7 @@ Description: **array[string]** --- -## 25.4. tolerances.reaction +## 21.4. tolerances.reaction Reaction **string, null** @@ -89,7 +89,7 @@ Enum: intermediate --- -## 25.5. tolerances.mic +## 21.5. tolerances.mic MIC Description: @@ -98,7 +98,7 @@ Description: **string, null** --- -## 25.6. tolerances.unit +## 21.6. tolerances.unit Unit **string, null** @@ -112,7 +112,7 @@ Enum: unknown --- -## 25.7. tolerances.tests +## 21.7. tolerances.tests Tests Description: @@ -121,7 +121,7 @@ Description: **array[object]** --- -## 25.7.1. tolerances.tests.reaction +## 21.7.1. tolerances.tests.reaction ToleranceReaction `Required` Description: @@ -141,7 +141,7 @@ Enum: intermediate --- -## 25.7.2. tolerances.tests.concentration +## 21.7.2. tolerances.tests.concentration Concentration Description: @@ -150,7 +150,7 @@ Description: **number, null** --- -## 25.7.3. tolerances.tests.unit +## 21.7.3. tolerances.tests.unit ConcentrationUnit `Required` Description: @@ -173,7 +173,7 @@ Enum: unknown --- -## 25.7.4. tolerances.tests.relatedData +## 21.7.4. tolerances.tests.relatedData Related Data Description: @@ -182,7 +182,7 @@ Description: **array[string]** --- -## 25.8. tolerances.source +## 21.8. tolerances.source Source `Required` Description: diff --git a/docs/schema/26. enzymes.md b/docs/schema/22. enzymes.md similarity index 73% rename from docs/schema/26. enzymes.md rename to docs/schema/22. enzymes.md index e94aa41..b6271d8 100644 --- a/docs/schema/26. enzymes.md +++ b/docs/schema/22. enzymes.md @@ -1,17 +1,17 @@ --- -## 26. enzymes +## 22. enzymes Enzymes **array[object]** --- -## 26.1. enzymes.name +## 22.1. enzymes.name Name **string, null** --- -## 26.2. enzymes.hasECNumber +## 22.2. enzymes.hasECNumber EC Number `Required` Description: @@ -20,7 +20,7 @@ Description: **string** --- -## 26.3. enzymes.identifier +## 22.3. enzymes.identifier Identifier Description: @@ -29,7 +29,7 @@ Description: **array[object]** --- -## 26.3.1. enzymes.identifier.name +## 22.3.1. enzymes.identifier.name Name `Required` Description: @@ -38,7 +38,7 @@ Description: **string** --- -## 26.3.2. enzymes.identifier.value +## 22.3.2. enzymes.identifier.value Value `Required` Description: @@ -47,7 +47,7 @@ Description: **string** --- -## 26.3.3. enzymes.identifier.propertyID +## 22.3.3. enzymes.identifier.propertyID Property ID Description: @@ -56,7 +56,7 @@ Description: **string, null** --- -## 26.3.4. enzymes.identifier.url +## 22.3.4. enzymes.identifier.url URL Description: @@ -65,7 +65,7 @@ Description: **string, null** --- -## 26.3.5. enzymes.identifier.logo +## 22.3.5. enzymes.identifier.logo Logo Description: @@ -74,13 +74,13 @@ Description: **string, null** --- -## 26.4. enzymes.alternateName +## 22.4. enzymes.alternateName Alternate Name **array[string]** --- -## 26.5. enzymes.active +## 22.5. enzymes.active Active Description: @@ -89,7 +89,7 @@ Description: **boolean, null** --- -## 26.6. enzymes.relatedData +## 22.6. enzymes.relatedData Related Data Description: @@ -98,7 +98,7 @@ Description: **array[string]** --- -## 26.7. enzymes.source +## 22.7. enzymes.source Source `Required` Description: diff --git a/docs/schema/27. metabolites.md b/docs/schema/23. metabolites.md similarity index 75% rename from docs/schema/27. metabolites.md rename to docs/schema/23. metabolites.md index d6676bb..625280a 100644 --- a/docs/schema/27. metabolites.md +++ b/docs/schema/23. metabolites.md @@ -1,11 +1,11 @@ --- -## 27. metabolites +## 23. metabolites Metabolites **array[object]** --- -## 27.1. metabolites.name +## 23.1. metabolites.name Name of Chemical Substance Description: @@ -14,7 +14,7 @@ Description: **string, null** --- -## 27.2. metabolites.identifier +## 23.2. metabolites.identifier Identifier Description: @@ -23,7 +23,7 @@ Description: **array[object]** --- -## 27.2.1. metabolites.identifier.name +## 23.2.1. metabolites.identifier.name Name `Required` Description: @@ -32,7 +32,7 @@ Description: **string** --- -## 27.2.2. metabolites.identifier.value +## 23.2.2. metabolites.identifier.value Value `Required` Description: @@ -41,7 +41,7 @@ Description: **string** --- -## 27.2.3. metabolites.identifier.propertyID +## 23.2.3. metabolites.identifier.propertyID Property ID Description: @@ -50,7 +50,7 @@ Description: **string, null** --- -## 27.2.4. metabolites.identifier.url +## 23.2.4. metabolites.identifier.url URL Description: @@ -59,7 +59,7 @@ Description: **string, null** --- -## 27.2.5. metabolites.identifier.logo +## 23.2.5. metabolites.identifier.logo Logo Description: @@ -68,7 +68,7 @@ Description: **string, null** --- -## 27.3. metabolites.alternateName +## 23.3. metabolites.alternateName Alternate Name Description: @@ -77,7 +77,7 @@ Description: **array[string]** --- -## 27.4. metabolites.tests +## 23.4. metabolites.tests Tests Description: @@ -86,7 +86,7 @@ Description: **array[object]** --- -## 27.4.1. metabolites.tests.type +## 23.4.1. metabolites.tests.type MetaboliteTestType `Required` Description: @@ -104,7 +104,7 @@ Enum: production --- -## 27.4.2. metabolites.tests.active +## 23.4.2. metabolites.tests.active Active Description: @@ -113,7 +113,7 @@ Description: **boolean, null** --- -## 27.4.3. metabolites.tests.protocol +## 23.4.3. metabolites.tests.protocol Protocol Description: @@ -122,7 +122,7 @@ Description: **string, null** --- -## 27.4.4. metabolites.tests.kindOfUtilization +## 23.4.4. metabolites.tests.kindOfUtilization Kind Of Utilization Description: @@ -141,7 +141,7 @@ Enum: reduction --- -## 27.4.5. metabolites.tests.relatedData +## 23.4.5. metabolites.tests.relatedData Related Data Description: @@ -150,7 +150,7 @@ Description: **array[string]** --- -## 27.5. metabolites.source +## 23.5. metabolites.source Source `Required` Description: diff --git a/docs/schema/28. knownApplications.md b/docs/schema/24. knownApplications.md similarity index 70% rename from docs/schema/28. knownApplications.md rename to docs/schema/24. knownApplications.md index 2dcfecb..ae56d13 100644 --- a/docs/schema/28. knownApplications.md +++ b/docs/schema/24. knownApplications.md @@ -1,11 +1,11 @@ --- -## 28. knownApplications +## 24. knownApplications Known Applications **array[object]** --- -## 28.1. knownApplications.application +## 24.1. knownApplications.application Application `Required` Description: @@ -14,7 +14,7 @@ Description: **string** --- -## 28.2. knownApplications.source +## 24.2. knownApplications.source Source `Required` Description: diff --git a/docs/schema/29. collections.md b/docs/schema/25. collections.md similarity index 71% rename from docs/schema/29. collections.md rename to docs/schema/25. collections.md index 58626b9..33f3b0a 100644 --- a/docs/schema/29. collections.md +++ b/docs/schema/25. collections.md @@ -1,11 +1,11 @@ --- -## 29. collections +## 25. collections Collections **array[object]** --- -## 29.1. collections.name +## 25.1. collections.name Name `Required` Description: @@ -14,7 +14,7 @@ Description: **string** --- -## 29.2. collections.identifier +## 25.2. collections.identifier Identifier Description: @@ -23,7 +23,7 @@ Description: **array[object]** --- -## 29.2.1. collections.identifier.name +## 25.2.1. collections.identifier.name Name `Required` Description: @@ -32,7 +32,7 @@ Description: **string** --- -## 29.2.2. collections.identifier.value +## 25.2.2. collections.identifier.value Value `Required` Description: @@ -41,7 +41,7 @@ Description: **string** --- -## 29.2.3. collections.identifier.propertyID +## 25.2.3. collections.identifier.propertyID Property ID Description: @@ -50,7 +50,7 @@ Description: **string, null** --- -## 29.2.4. collections.identifier.url +## 25.2.4. collections.identifier.url URL Description: @@ -59,7 +59,7 @@ Description: **string, null** --- -## 29.2.5. collections.identifier.logo +## 25.2.5. collections.identifier.logo Logo Description: @@ -68,7 +68,7 @@ Description: **string, null** --- -## 29.3. collections.legalName +## 25.3. collections.legalName Legal Name Description: @@ -77,7 +77,7 @@ Description: **string, null** --- -## 29.4. collections.address +## 25.4. collections.address Address Description: @@ -86,7 +86,7 @@ Description: **object, null** --- -## 29.4.1. collections.address.addressCountry +## 25.4.1. collections.address.addressCountry Country Description: @@ -95,7 +95,7 @@ Description: **string, null** --- -## 29.4.2. collections.address.addressRegion +## 25.4.2. collections.address.addressRegion Region Description: @@ -104,7 +104,7 @@ Description: **string, null** --- -## 29.4.3. collections.address.addressLocality +## 25.4.3. collections.address.addressLocality Locality Description: @@ -113,19 +113,19 @@ Description: **string, null** --- -## 29.4.4. collections.address.postOfficeBoxNumber +## 25.4.4. collections.address.postOfficeBoxNumber Post Office Box Number **string, null** --- -## 29.4.5. collections.address.postalCode +## 25.4.5. collections.address.postalCode Postal Code **string, null** --- -## 29.4.6. collections.address.streetAddress +## 25.4.6. collections.address.streetAddress Street Address Description: @@ -134,7 +134,7 @@ Description: **string, null** --- -## 29.5. collections.url +## 25.5. collections.url URL Description: @@ -143,7 +143,7 @@ Description: **string, null** --- -## 29.6. collections.email +## 25.6. collections.email Email Description: @@ -152,7 +152,7 @@ Description: **string, null** --- -## 29.7. collections.logo +## 25.7. collections.logo Logo Description: @@ -161,7 +161,7 @@ Description: **string, null** --- -## 29.8. collections.resourceNumber +## 25.8. collections.resourceNumber Resource Number `Required` Description: @@ -170,7 +170,7 @@ Description: **string** --- -## 29.9. collections.available +## 25.9. collections.available Availability Description: @@ -179,7 +179,7 @@ Description: **boolean, null** --- -## 29.10. collections.catalogUrl +## 25.10. collections.catalogUrl Catalog URL Description: @@ -188,7 +188,7 @@ Description: **string, null** --- -## 29.11. collections.restrictionsOnUse +## 25.11. collections.restrictionsOnUse Restrictions On Use Description: @@ -203,7 +203,7 @@ Enum: For commercial development a special agreement is requested --- -## 29.12. collections.policyUrl +## 25.12. collections.policyUrl Policy URL Description: @@ -212,7 +212,7 @@ Description: **string, null** --- -## 29.13. collections.axenicCulture +## 25.13. collections.axenicCulture Axenic Culture Description: @@ -221,7 +221,7 @@ Description: **boolean, null** --- -## 29.14. collections.supplyForms +## 25.14. collections.supplyForms Supply Forms Description: @@ -230,7 +230,7 @@ Description: **array[string]** --- -## 29.15. collections.history +## 25.15. collections.history History Description: @@ -239,7 +239,7 @@ Description: **string, null** --- -## 29.16. collections.depositionDate +## 25.16. collections.depositionDate Deposition Date Description: @@ -248,7 +248,7 @@ Description: **string, null** --- -## 29.17. collections.depositor +## 25.17. collections.depositor Depositor Description: @@ -257,7 +257,7 @@ Description: **object, null** --- -## 29.17.1. collections.depositor.name +## 25.17.1. collections.depositor.name Name `Required` Description: @@ -266,7 +266,7 @@ Description: **string** --- -## 29.17.2. collections.depositor.identifier +## 25.17.2. collections.depositor.identifier Identifier Description: @@ -275,7 +275,7 @@ Description: **array[object]** --- -## 29.17.2.1. collections.depositor.identifier.name +## 25.17.2.1. collections.depositor.identifier.name Name `Required` Description: @@ -284,7 +284,7 @@ Description: **string** --- -## 29.17.2.2. collections.depositor.identifier.value +## 25.17.2.2. collections.depositor.identifier.value Value `Required` Description: @@ -293,7 +293,7 @@ Description: **string** --- -## 29.17.2.3. collections.depositor.identifier.propertyID +## 25.17.2.3. collections.depositor.identifier.propertyID Property ID Description: @@ -302,7 +302,7 @@ Description: **string, null** --- -## 29.17.2.4. collections.depositor.identifier.url +## 25.17.2.4. collections.depositor.identifier.url URL Description: @@ -311,7 +311,7 @@ Description: **string, null** --- -## 29.17.2.5. collections.depositor.identifier.logo +## 25.17.2.5. collections.depositor.identifier.logo Logo Description: @@ -320,7 +320,7 @@ Description: **string, null** --- -## 29.18. collections.depositedAs +## 25.18. collections.depositedAs Deposited as Description: @@ -329,7 +329,7 @@ Description: **string, null** --- -## 29.19. collections.registeredCollection +## 25.19. collections.registeredCollection Registered Collection Description: @@ -338,7 +338,7 @@ Description: **boolean, null** --- -## 29.20. collections.mtaFile +## 25.20. collections.mtaFile MTA file Description: @@ -347,7 +347,7 @@ Description: **string, null** --- -## 29.21. collections.absFile +## 25.21. collections.absFile ABS related file Description: @@ -356,7 +356,7 @@ Description: **string, null** --- -## 29.22. collections.source +## 25.22. collections.source Source `Required` Description: diff --git a/docs/schema/18. literature.md b/docs/schema/26. literature.md similarity index 64% rename from docs/schema/18. literature.md rename to docs/schema/26. literature.md index 7d481ae..93c2ede 100644 --- a/docs/schema/18. literature.md +++ b/docs/schema/26. literature.md @@ -1,29 +1,29 @@ --- -## 18. literature +## 26. literature Literature **array[object]** --- -## 18.1. literature.name +## 26.1. literature.name Name **string, null** --- -## 18.2. literature.url +## 26.2. literature.url URL **string, null** --- -## 18.3. literature.datePublished +## 26.3. literature.datePublished Date Published **string, null** --- -## 18.4. literature.author +## 26.4. literature.author Author Description: @@ -32,7 +32,7 @@ Description: **array[object]** --- -## 18.4.1. literature.author.name +## 26.4.1. literature.author.name Name `Required` Description: @@ -41,7 +41,7 @@ Description: **string** --- -## 18.4.2. literature.author.identifier +## 26.4.2. literature.author.identifier Identifier Description: @@ -50,7 +50,7 @@ Description: **array[object]** --- -## 18.4.2.1. literature.author.identifier.name +## 26.4.2.1. literature.author.identifier.name Name `Required` Description: @@ -59,7 +59,7 @@ Description: **string** --- -## 18.4.2.2. literature.author.identifier.value +## 26.4.2.2. literature.author.identifier.value Value `Required` Description: @@ -68,7 +68,7 @@ Description: **string** --- -## 18.4.2.3. literature.author.identifier.propertyID +## 26.4.2.3. literature.author.identifier.propertyID Property ID Description: @@ -77,7 +77,7 @@ Description: **string, null** --- -## 18.4.2.4. literature.author.identifier.url +## 26.4.2.4. literature.author.identifier.url URL Description: @@ -86,7 +86,7 @@ Description: **string, null** --- -## 18.4.2.5. literature.author.identifier.logo +## 26.4.2.5. literature.author.identifier.logo Logo Description: @@ -95,7 +95,7 @@ Description: **string, null** --- -## 18.5. literature.publisher +## 26.5. literature.publisher Publisher Description: @@ -104,7 +104,7 @@ Description: **array[object]** --- -## 18.5.1. literature.publisher.name +## 26.5.1. literature.publisher.name Name `Required` Description: @@ -113,7 +113,7 @@ Description: **string** --- -## 18.5.2. literature.publisher.identifier +## 26.5.2. literature.publisher.identifier Identifier Description: @@ -122,7 +122,7 @@ Description: **array[object]** --- -## 18.5.2.1. literature.publisher.identifier.name +## 26.5.2.1. literature.publisher.identifier.name Name `Required` Description: @@ -131,7 +131,7 @@ Description: **string** --- -## 18.5.2.2. literature.publisher.identifier.value +## 26.5.2.2. literature.publisher.identifier.value Value `Required` Description: @@ -140,7 +140,7 @@ Description: **string** --- -## 18.5.2.3. literature.publisher.identifier.propertyID +## 26.5.2.3. literature.publisher.identifier.propertyID Property ID Description: @@ -149,7 +149,7 @@ Description: **string, null** --- -## 18.5.2.4. literature.publisher.identifier.url +## 26.5.2.4. literature.publisher.identifier.url URL Description: @@ -158,7 +158,7 @@ Description: **string, null** --- -## 18.5.2.5. literature.publisher.identifier.logo +## 26.5.2.5. literature.publisher.identifier.logo Logo Description: @@ -167,7 +167,7 @@ Description: **string, null** --- -## 18.5.3. literature.publisher.legalName +## 26.5.3. literature.publisher.legalName Legal Name Description: @@ -176,7 +176,7 @@ Description: **string, null** --- -## 18.5.4. literature.publisher.address +## 26.5.4. literature.publisher.address Address Description: @@ -185,7 +185,7 @@ Description: **object, null** --- -## 18.5.4.1. literature.publisher.address.addressCountry +## 26.5.4.1. literature.publisher.address.addressCountry Country Description: @@ -194,7 +194,7 @@ Description: **string, null** --- -## 18.5.4.2. literature.publisher.address.addressRegion +## 26.5.4.2. literature.publisher.address.addressRegion Region Description: @@ -203,7 +203,7 @@ Description: **string, null** --- -## 18.5.4.3. literature.publisher.address.addressLocality +## 26.5.4.3. literature.publisher.address.addressLocality Locality Description: @@ -212,19 +212,19 @@ Description: **string, null** --- -## 18.5.4.4. literature.publisher.address.postOfficeBoxNumber +## 26.5.4.4. literature.publisher.address.postOfficeBoxNumber Post Office Box Number **string, null** --- -## 18.5.4.5. literature.publisher.address.postalCode +## 26.5.4.5. literature.publisher.address.postalCode Postal Code **string, null** --- -## 18.5.4.6. literature.publisher.address.streetAddress +## 26.5.4.6. literature.publisher.address.streetAddress Street Address Description: @@ -233,7 +233,7 @@ Description: **string, null** --- -## 18.5.5. literature.publisher.url +## 26.5.5. literature.publisher.url URL Description: @@ -242,7 +242,7 @@ Description: **string, null** --- -## 18.5.6. literature.publisher.email +## 26.5.6. literature.publisher.email Email Description: @@ -251,7 +251,7 @@ Description: **string, null** --- -## 18.5.7. literature.publisher.logo +## 26.5.7. literature.publisher.logo Logo Description: @@ -260,7 +260,7 @@ Description: **string, null** --- -## 18.6. literature.source +## 26.6. literature.source Source `Required` Description: diff --git a/docs/schema/30. otherMedia.md b/docs/schema/27. otherMedia.md similarity index 71% rename from docs/schema/30. otherMedia.md rename to docs/schema/27. otherMedia.md index 93f4617..424c28d 100644 --- a/docs/schema/30. otherMedia.md +++ b/docs/schema/27. otherMedia.md @@ -1,11 +1,11 @@ --- -## 30. otherMedia +## 27. otherMedia Other Media **array[object]** --- -## 30.1. otherMedia.url +## 27.1. otherMedia.url URL Description: @@ -14,13 +14,13 @@ Description: **string, null** --- -## 30.2. otherMedia.name +## 27.2. otherMedia.name Name **string, null** --- -## 30.3. otherMedia.description +## 27.3. otherMedia.description Description Description: @@ -29,7 +29,7 @@ Description: **string, null** --- -## 30.4. otherMedia.usageInfo +## 27.4. otherMedia.usageInfo Usage Information Description: @@ -38,13 +38,13 @@ Description: **string, null** --- -## 30.5. otherMedia.additionalType +## 27.5. otherMedia.additionalType Additional Type **string, null** --- -## 30.6. otherMedia.source +## 27.6. otherMedia.source Source `Required` Description: diff --git a/docs/schema/31. relatedData.md b/docs/schema/28. relatedData.md similarity index 78% rename from docs/schema/31. relatedData.md rename to docs/schema/28. relatedData.md index 30e43e1..0c897ab 100644 --- a/docs/schema/31. relatedData.md +++ b/docs/schema/28. relatedData.md @@ -1,11 +1,11 @@ --- -## 31. relatedData +## 28. relatedData Related Data **array[object]** --- -## 31.1. relatedData.relation +## 28.1. relatedData.relation Relation `Required` Description: @@ -14,7 +14,7 @@ Description: **string** --- -## 31.2. relatedData.source +## 28.2. relatedData.source Source `Required` Description: diff --git a/docs/schema/32. sources.md b/docs/schema/29. sources.md similarity index 68% rename from docs/schema/32. sources.md rename to docs/schema/29. sources.md index 7558158..200c86e 100644 --- a/docs/schema/32. sources.md +++ b/docs/schema/29. sources.md @@ -1,11 +1,11 @@ --- -## 32. sources +## 29. sources Sources `Required` **array[object]** --- -## 32.1. sources.sourceType +## 29.1. sources.sourceType SourceType `Required` Description: @@ -25,7 +25,7 @@ Enum: dataset --- -## 32.2. sources.mode +## 29.2. sources.mode CurationMode `Required` Description: @@ -45,19 +45,19 @@ Enum: unknown --- -## 32.3. sources.name +## 29.3. sources.name Name **string, null** --- -## 32.4. sources.url +## 29.4. sources.url URL **string, null** --- -## 32.5. sources.identifier +## 29.5. sources.identifier Identifier Description: @@ -66,7 +66,7 @@ Description: **array[object]** --- -## 32.5.1. sources.identifier.name +## 29.5.1. sources.identifier.name Name `Required` Description: @@ -75,7 +75,7 @@ Description: **string** --- -## 32.5.2. sources.identifier.value +## 29.5.2. sources.identifier.value Value `Required` Description: @@ -84,7 +84,7 @@ Description: **string** --- -## 32.5.3. sources.identifier.propertyID +## 29.5.3. sources.identifier.propertyID Property ID Description: @@ -93,7 +93,7 @@ Description: **string, null** --- -## 32.5.4. sources.identifier.url +## 29.5.4. sources.identifier.url URL Description: @@ -102,7 +102,7 @@ Description: **string, null** --- -## 32.5.5. sources.identifier.logo +## 29.5.5. sources.identifier.logo Logo Description: @@ -111,13 +111,13 @@ Description: **string, null** --- -## 32.6. sources.datePublished +## 29.6. sources.datePublished Date Published **string, null** --- -## 32.7. sources.dateRecorded +## 29.7. sources.dateRecorded Date Recorded **string** @@ -127,13 +127,13 @@ Format: date --- -## 32.8. sources.lastUpdate +## 29.8. sources.lastUpdate Date of last update **string, null** --- -## 32.9. sources.author +## 29.9. sources.author Author Description: @@ -142,7 +142,7 @@ Description: **array[object]** --- -## 32.9.1. sources.author.name +## 29.9.1. sources.author.name Name `Required` Description: @@ -151,7 +151,7 @@ Description: **string** --- -## 32.9.2. sources.author.identifier +## 29.9.2. sources.author.identifier Identifier Description: @@ -160,7 +160,7 @@ Description: **array[object]** --- -## 32.9.2.1. sources.author.identifier.name +## 29.9.2.1. sources.author.identifier.name Name `Required` Description: @@ -169,7 +169,7 @@ Description: **string** --- -## 32.9.2.2. sources.author.identifier.value +## 29.9.2.2. sources.author.identifier.value Value `Required` Description: @@ -178,7 +178,7 @@ Description: **string** --- -## 32.9.2.3. sources.author.identifier.propertyID +## 29.9.2.3. sources.author.identifier.propertyID Property ID Description: @@ -187,7 +187,7 @@ Description: **string, null** --- -## 32.9.2.4. sources.author.identifier.url +## 29.9.2.4. sources.author.identifier.url URL Description: @@ -196,7 +196,7 @@ Description: **string, null** --- -## 32.9.2.5. sources.author.identifier.logo +## 29.9.2.5. sources.author.identifier.logo Logo Description: @@ -205,7 +205,7 @@ Description: **string, null** --- -## 32.10. sources.publisher +## 29.10. sources.publisher Publisher Description: @@ -214,7 +214,7 @@ Description: **array[object]** --- -## 32.10.1. sources.publisher.name +## 29.10.1. sources.publisher.name Name `Required` Description: @@ -223,7 +223,7 @@ Description: **string** --- -## 32.10.2. sources.publisher.identifier +## 29.10.2. sources.publisher.identifier Identifier Description: @@ -232,7 +232,7 @@ Description: **array[object]** --- -## 32.10.2.1. sources.publisher.identifier.name +## 29.10.2.1. sources.publisher.identifier.name Name `Required` Description: @@ -241,7 +241,7 @@ Description: **string** --- -## 32.10.2.2. sources.publisher.identifier.value +## 29.10.2.2. sources.publisher.identifier.value Value `Required` Description: @@ -250,7 +250,7 @@ Description: **string** --- -## 32.10.2.3. sources.publisher.identifier.propertyID +## 29.10.2.3. sources.publisher.identifier.propertyID Property ID Description: @@ -259,7 +259,7 @@ Description: **string, null** --- -## 32.10.2.4. sources.publisher.identifier.url +## 29.10.2.4. sources.publisher.identifier.url URL Description: @@ -268,7 +268,7 @@ Description: **string, null** --- -## 32.10.2.5. sources.publisher.identifier.logo +## 29.10.2.5. sources.publisher.identifier.logo Logo Description: @@ -277,7 +277,7 @@ Description: **string, null** --- -## 32.10.3. sources.publisher.legalName +## 29.10.3. sources.publisher.legalName Legal Name Description: @@ -286,7 +286,7 @@ Description: **string, null** --- -## 32.10.4. sources.publisher.address +## 29.10.4. sources.publisher.address Address Description: @@ -295,7 +295,7 @@ Description: **object, null** --- -## 32.10.4.1. sources.publisher.address.addressCountry +## 29.10.4.1. sources.publisher.address.addressCountry Country Description: @@ -304,7 +304,7 @@ Description: **string, null** --- -## 32.10.4.2. sources.publisher.address.addressRegion +## 29.10.4.2. sources.publisher.address.addressRegion Region Description: @@ -313,7 +313,7 @@ Description: **string, null** --- -## 32.10.4.3. sources.publisher.address.addressLocality +## 29.10.4.3. sources.publisher.address.addressLocality Locality Description: @@ -322,19 +322,19 @@ Description: **string, null** --- -## 32.10.4.4. sources.publisher.address.postOfficeBoxNumber +## 29.10.4.4. sources.publisher.address.postOfficeBoxNumber Post Office Box Number **string, null** --- -## 32.10.4.5. sources.publisher.address.postalCode +## 29.10.4.5. sources.publisher.address.postalCode Postal Code **string, null** --- -## 32.10.4.6. sources.publisher.address.streetAddress +## 29.10.4.6. sources.publisher.address.streetAddress Street Address Description: @@ -343,7 +343,7 @@ Description: **string, null** --- -## 32.10.5. sources.publisher.url +## 29.10.5. sources.publisher.url URL Description: @@ -352,7 +352,7 @@ Description: **string, null** --- -## 32.10.6. sources.publisher.email +## 29.10.6. sources.publisher.email Email Description: @@ -361,7 +361,7 @@ Description: **string, null** --- -## 32.10.7. sources.publisher.logo +## 29.10.7. sources.publisher.logo Logo Description: diff --git a/schema/microbe_schema.json b/schema/microbe_schema.json index 76bfd4b..7bb6557 100644 --- a/schema/microbe_schema.json +++ b/schema/microbe_schema.json @@ -3401,7 +3401,7 @@ "type": "object" } }, - "additionalProperties": false, + "additionalProperties": true, "description": "Microbial Strain - main class of the new microbial strain data standard", "properties": { "bioSafety": { @@ -3420,11 +3420,6 @@ "title": "Collections", "type": "array" }, - "creation_date": { - "format": "date", - "title": "Creation Date", - "type": "string" - }, "cultivationMedia": { "description": "", "items": { diff --git a/src/microbial_strain_data_model/strain.py b/src/microbial_strain_data_model/strain.py index 3de4524..6c81c34 100644 --- a/src/microbial_strain_data_model/strain.py +++ b/src/microbial_strain_data_model/strain.py @@ -1,4 +1,3 @@ -from pydantic_extra_types.pendulum_dt import Date from pydantic import BaseModel, ConfigDict, Field @@ -39,8 +38,6 @@ class Strain(BaseModel): """Microbial Strain - main class of the new microbial strain data standard""" - creation_date: Date = Field(default_factory=Date.today) - # single data points organismType: OrganismType = Field(title="Organism Type", description="", frozen=True) @@ -58,16 +55,38 @@ class Strain(BaseModel): taxon: list[TaxonWithSource] = Field(title="Taxon", description="") + identifier: list[IdentifierStrain] = Field( + default_factory=list, title="Identifier", description="" + ) + origin: list[Origin] = Field( default_factory=list, title="Origin", description="Sample and isolation data" ) legal: list[Legal] = Field(default_factory=list, title="Legal", description="") + pathogenicity: list[Pathogen] = Field( + default_factory=list, title="pathogenicity", description="" + ) + + bioSafety: list[BioSafety] = Field( + default_factory=list, title="Bio Safety", description="" + ) + morphology: list[Morphology] = Field( default_factory=list, title="Morphology", description="Morphology information" ) + wallConstituents: list[CellWall] = Field( + default_factory=list, + title="Wall Constituents", + description="", + ) + + staining: list[Staining] = Field( + default_factory=list, title="Stainings", description="" + ) + sporeFormation: list[Spore] = Field( default_factory=list, title="Spore Formation", @@ -80,16 +99,10 @@ class Strain(BaseModel): description="Temperature and pH values", ) - identifier: list[IdentifierStrain] = Field( - default_factory=list, title="Identifier", description="" - ) - - pathogenicity: list[Pathogen] = Field( - default_factory=list, title="pathogenicity", description="" - ) - - bioSafety: list[BioSafety] = Field( - default_factory=list, title="Bio Safety", description="" + cultivationMedia: list[CultivationMedia] = Field( + default_factory=list, + title="Cultivation Media", + description="", ) sequences: list[Sequence] = Field( @@ -100,36 +113,16 @@ class Strain(BaseModel): default_factory=list, title="GC Content", description="" ) - literature: list[Literature] = Field( - default_factory=list, title="Literature", description="" - ) - - wallConstituents: list[CellWall] = Field( - default_factory=list, - title="Wall Constituents", - description="", - ) - fattyAcidProfiles: list[FattyAcidProfile] = Field( default_factory=list, title="Fatty Acid Profile", description="", ) - staining: list[Staining] = Field( - default_factory=list, title="Stainings", description="" - ) - hemolysis: list[Hemolysis] = Field( default_factory=list, title="Hemolysis", description="" ) - cultivationMedia: list[CultivationMedia] = Field( - default_factory=list, - title="Cultivation Media", - description="", - ) - halophily: list[Halophil] = Field( default_factory=list, title="Halophily", description="" ) @@ -139,6 +132,7 @@ class Strain(BaseModel): ) enzymes: list[Enzyme] = Field(default_factory=list, title="Enzymes", description="") + metabolites: list[Metabolite] = Field( default_factory=list, title="Metabolites", description="" ) @@ -153,6 +147,10 @@ class Strain(BaseModel): default_factory=list, title="Collections", description="" ) + literature: list[Literature] = Field( + default_factory=list, title="Literature", description="" + ) + otherMedia: list[OtherMedia] = Field( default_factory=list, title="Other Media", description="" ) @@ -165,7 +163,7 @@ class Strain(BaseModel): model_config = ConfigDict( strict=True, - extra="forbid", + extra="allow", revalidate_instances="always", str_strip_whitespace=True, ) From 9e91b6141e39daabe29659230a78bb2c5eb0e8cd Mon Sep 17 00:00:00 2001 From: juwitte Date: Fri, 29 Aug 2025 09:26:18 +0000 Subject: [PATCH 10/10] =?UTF-8?q?bump:=20version=200.7.0=20=E2=86=92=200.8?= =?UTF-8?q?.0?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- CHANGELOG.md | 20 ++++++++++++++++++++ README.md | 2 +- pyproject.toml | 2 +- 3 files changed, 22 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3f11592..b6607b2 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,23 @@ +## v0.8.0 (2025-08-29) + +### Feat + +- add OxygenRelation Enum +- add GCMethod enum +- add lastUpdate to source and logo to identifier +- add KindOfUtilization enum + +### Fix + +- change concentration of tolerance test to float value, was string +- changed enzyme url to identifier list + +### Refactor + +- **restructure**: restructure +- **restructure**: restructure data multicallcomplex and oxygenrelation into other classes +- **restructure**: restructure information of origin, morphology and growthcondtion into new classes + ## v0.7.0 (2025-08-14) ### Feat diff --git a/README.md b/README.md index 6741212..ba17655 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -[![release: 0.7.0](https://img.shields.io/badge/rel-0.7.0-blue.svg?style=flat-square)](https://github.com/LeibnizDSMZ/microbial-data-standard) +[![release: 0.8.0](https://img.shields.io/badge/rel-0.8.0-blue.svg?style=flat-square)](https://github.com/LeibnizDSMZ/microbial-data-standard) [![MIT LICENSE](https://img.shields.io/badge/License-MIT-brightgreen.svg?style=flat-square)](https://choosealicense.com/licenses/mit/) [![Documentation Status](https://img.shields.io/badge/docs-GitHub-blue.svg?style=flat-square)](https://LeibnizDSMZ.github.io/microbial-data-standard/) diff --git a/pyproject.toml b/pyproject.toml index 39dbf7a..e804fe1 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [project] name = "microbial_strain_data_model" -version = "0.7.0" +version = "0.8.0" description = """Read strain data from microbiolgy DB and transforms them into JSONs""" readme = "README.md" authors = [{ name = "Julius Witte", email = "julius.witte@dsmz.de" }]