diff --git a/docs/schema/valuesets.yaml b/docs/schema/valuesets.yaml index 2cd1dd4c..0265c911 100644 --- a/docs/schema/valuesets.yaml +++ b/docs/schema/valuesets.yaml @@ -29,6 +29,7 @@ imports: - bio/relationship_to_oxygen - bio/trophic_levels - bio/developmental_stages +- bio/cell_free_expression - time/temporal - academic/research - academic/organizations @@ -88,6 +89,7 @@ imports: - materials_science/pigments_dyes - visual/colors - bio/biological_colors +- bio/pato - bio/sequence_alphabets - bio/sequence_chemistry - bio/sequencing_platforms @@ -7570,6 +7572,509 @@ enums: value: 12+ months aliases: - P365+ Aged + CellFreeExpressionSystemEnum: + name: CellFreeExpressionSystemEnum + definition_uri: https://w3id.org/valuesets/CellFreeExpressionSystemEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition + description: Source extracts and reconstituted systems used for cell-free protein + synthesis. Crude lysate systems are derived from cell extracts, while reconstituted + systems (e.g. PURE) are assembled from purified components. + title: Cell-Free Expression Systems + from_schema: https://w3id.org/valuesets/bio/cell_free_expression + see_also: + - https://en.wikipedia.org/wiki/Cell-free_protein_synthesis + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT + permissible_values: + ECOLI_EXTRACT: + text: ECOLI_EXTRACT + description: Escherichia coli crude cell extract (e.g. S30, S12), the most + widely used prokaryotic cell-free system for high-yield protein production + annotations: + source_taxon: + tag: source_taxon + value: NCBITaxon:562 + extract_type: + tag: extract_type + value: crude lysate + domain: + tag: domain + value: prokaryotic + aliases: + - E. coli extract + - E. coli lysate + - S30 extract + - ECE + broad_mappings: + - BAO:0000366 + PURE_SYSTEM: + text: PURE_SYSTEM + description: Protein synthesis Using Recombinant Elements - a reconstituted + system assembled from individually purified E. coli translation factors, + ribosomes, and enzymes + annotations: + extract_type: + tag: extract_type + value: reconstituted + domain: + tag: domain + value: prokaryotic + advantage: + tag: advantage + value: defined composition, low nuclease/protease activity + aliases: + - PURE + - PURExpress + - reconstituted system + broad_mappings: + - BAO:0000366 + WHEAT_GERM_EXTRACT: + text: WHEAT_GERM_EXTRACT + description: Wheat germ (Triticum aestivum) extract, a eukaryotic system favored + for expression of complex and difficult eukaryotic proteins + annotations: + source_taxon: + tag: source_taxon + value: NCBITaxon:4565 + extract_type: + tag: extract_type + value: crude lysate + domain: + tag: domain + value: eukaryotic + aliases: + - WGE + - wheat germ system + broad_mappings: + - BAO:0000366 + RABBIT_RETICULOCYTE_LYSATE: + text: RABBIT_RETICULOCYTE_LYSATE + description: Rabbit (Oryctolagus cuniculus) reticulocyte lysate, a classic + mammalian system for in vitro translation and protein labeling + meaning: BAO:0000255 + annotations: + source_taxon: + tag: source_taxon + value: NCBITaxon:9986 + extract_type: + tag: extract_type + value: crude lysate + domain: + tag: domain + value: eukaryotic + aliases: + - RRL + - reticulocyte lysate + - rabbit reticulocyte lysate format + INSECT_CELL_EXTRACT: + text: INSECT_CELL_EXTRACT + description: Insect cell extract, typically from Spodoptera frugiperda (Sf21), + supporting eukaryotic post-translational modifications + annotations: + source_taxon: + tag: source_taxon + value: NCBITaxon:7108 + extract_type: + tag: extract_type + value: crude lysate + domain: + tag: domain + value: eukaryotic + aliases: + - ICE + - Sf21 extract + - insect lysate + broad_mappings: + - BAO:0000366 + HELA_EXTRACT: + text: HELA_EXTRACT + description: Human HeLa cell extract used for mammalian cell-free expression + with authentic human translation machinery + annotations: + source_taxon: + tag: source_taxon + value: NCBITaxon:9606 + extract_type: + tag: extract_type + value: crude lysate + domain: + tag: domain + value: eukaryotic + aliases: + - HeLa lysate + - human cell extract + broad_mappings: + - BAO:0000366 + CHO_EXTRACT: + text: CHO_EXTRACT + description: Chinese hamster ovary (Cricetulus griseus) cell extract supporting + glycosylation and disulfide bond formation + annotations: + source_taxon: + tag: source_taxon + value: NCBITaxon:10029 + extract_type: + tag: extract_type + value: crude lysate + domain: + tag: domain + value: eukaryotic + aliases: + - CHO lysate + broad_mappings: + - BAO:0000366 + YEAST_EXTRACT: + text: YEAST_EXTRACT + description: Yeast (Saccharomyces cerevisiae) cell extract for eukaryotic + cell-free protein synthesis + annotations: + source_taxon: + tag: source_taxon + value: NCBITaxon:4932 + extract_type: + tag: extract_type + value: crude lysate + domain: + tag: domain + value: eukaryotic + aliases: + - S. cerevisiae extract + - yeast lysate + broad_mappings: + - BAO:0000366 + LEISHMANIA_EXTRACT: + text: LEISHMANIA_EXTRACT + description: Leishmania tarentolae cell extract, a eukaryotic system supporting + high yields and post-translational modifications + annotations: + source_taxon: + tag: source_taxon + value: NCBITaxon:5689 + extract_type: + tag: extract_type + value: crude lysate + domain: + tag: domain + value: eukaryotic + aliases: + - Leishmania tarentolae extract + - LTE + broad_mappings: + - BAO:0000366 + VIBRIO_NATRIEGENS_EXTRACT: + text: VIBRIO_NATRIEGENS_EXTRACT + description: Vibrio natriegens cell extract, an emerging fast-growing prokaryotic + chassis for rapid, high-yield cell-free expression + annotations: + source_taxon: + tag: source_taxon + value: NCBITaxon:691 + extract_type: + tag: extract_type + value: crude lysate + domain: + tag: domain + value: prokaryotic + aliases: + - V. natriegens extract + - Vmax extract + broad_mappings: + - BAO:0000366 + TOBACCO_BY2_EXTRACT: + text: TOBACCO_BY2_EXTRACT + description: Tobacco BY-2 (Nicotiana tabacum bright yellow-2) cell lysate, + a plant eukaryotic cell-free system + annotations: + extract_type: + tag: extract_type + value: crude lysate + domain: + tag: domain + value: eukaryotic + aliases: + - BY-2 lysate + - BYL + broad_mappings: + - BAO:0000366 + CellFreeReactionFormatEnum: + name: CellFreeReactionFormatEnum + definition_uri: https://w3id.org/valuesets/CellFreeReactionFormatEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition + description: Physical configurations of cell-free expression reactions, differing + in how substrates are supplied and byproducts removed, which affects reaction + duration and protein yield. + title: Cell-Free Reaction Formats + from_schema: https://w3id.org/valuesets/bio/cell_free_expression + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT + permissible_values: + BATCH: + text: BATCH + description: Single closed reaction with all components mixed at the start; + simplest format but limited by substrate depletion and byproduct accumulation + annotations: + duration: + tag: duration + value: short (hours) + aliases: + - batch mode + CONTINUOUS_EXCHANGE: + text: CONTINUOUS_EXCHANGE + description: Continuous-exchange cell-free (CECF) format with a semipermeable + membrane separating a reaction chamber from a feeding chamber, allowing + diffusion of substrates in and byproducts out + annotations: + duration: + tag: duration + value: extended (up to ~24 h) + aliases: + - CECF + - continuous exchange + - dialysis mode + related_mappings: + - OBI:0600052 + CONTINUOUS_FLOW: + text: CONTINUOUS_FLOW + description: Continuous-flow cell-free (CFCF) format in which fresh substrates + are continuously pumped through the reaction while product is collected + annotations: + duration: + tag: duration + value: extended + aliases: + - CFCF + - continuous flow + BILAYER: + text: BILAYER + description: Bilayer format where a feeding solution is layered over the reaction + mixture without a membrane, prolonging reaction by passive diffusion + aliases: + - bilayer mode + LYOPHILIZED: + text: LYOPHILIZED + description: Freeze-dried (lyophilized) cell-free reaction that is shelf-stable + and activated by rehydration; basis of freeze-dried cell-free (FD-CF) diagnostics + and portable biomanufacturing + annotations: + advantage: + tag: advantage + value: cold-chain-free storage and distribution + aliases: + - freeze-dried + - FD-CF + - lyophilised + related_mappings: + - NCIT:C28150 + EnergyRegenerationSubstrateEnum: + name: EnergyRegenerationSubstrateEnum + definition_uri: https://w3id.org/valuesets/EnergyRegenerationSubstrateEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition + description: Secondary energy substrates added to cell-free reactions to regenerate + ATP and GTP consumed during transcription and translation. Choice of substrate + affects cost, reaction longevity, and inorganic phosphate accumulation. + title: Energy Regeneration Substrates + from_schema: https://w3id.org/valuesets/bio/cell_free_expression + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT + permissible_values: + PHOSPHOCREATINE: + text: PHOSPHOCREATINE + description: Creatine phosphate (N-phosphocreatine) regenerated with creatine + kinase; a classic high-energy phosphate donor + meaning: CHEBI:17287 + annotations: + enzyme: + tag: enzyme + value: creatine kinase + aliases: + - creatine phosphate + - phosphocreatine + - N-phosphocreatine + PHOSPHOENOLPYRUVATE: + text: PHOSPHOENOLPYRUVATE + description: Phosphoenolpyruvate (PEP) regenerated with pyruvate kinase; a + common high-energy phosphate donor + meaning: CHEBI:18021 + annotations: + enzyme: + tag: enzyme + value: pyruvate kinase + aliases: + - PEP + ACETYL_PHOSPHATE: + text: ACETYL_PHOSPHATE + description: Acetyl phosphate regenerated with acetate kinase; an inexpensive + energy source + meaning: CHEBI:15350 + annotations: + enzyme: + tag: enzyme + value: acetate kinase + aliases: + - AcP + - acetyl dihydrogen phosphate + THREE_PGA: + text: THREE_PGA + description: 3-phosphoglycerate (3-PGA), a glycolytic intermediate widely + used as a low-cost energy substrate in E. coli cell-free systems + meaning: CHEBI:17794 + aliases: + - 3-PGA + - 3-phosphoglycerate + - 3-phospho-D-glycerate + - 3-phospho-D-glyceric acid + GLUCOSE: + text: GLUCOSE + description: Glucose feeding glycolysis for ATP regeneration; a very low-cost + energy source that requires phosphate buffering + meaning: CHEBI:17634 + aliases: + - D-glucose + GLUCOSE_6_PHOSPHATE: + text: GLUCOSE_6_PHOSPHATE + description: Glucose 6-phosphate fed into glycolysis for energy regeneration + meaning: CHEBI:14314 + aliases: + - G6P + - glucose-6-phosphate + - D-glucose 6-phosphate + MALTOSE: + text: MALTOSE + description: Maltose used as a low-cost energy substrate that limits inorganic + phosphate accumulation + meaning: CHEBI:17306 + PYRUVATE: + text: PYRUVATE + description: Pyruvate used as an energy source, oxidized via the central metabolism + of the extract + meaning: CHEBI:15361 + MALTODEXTRIN: + text: MALTODEXTRIN + description: Maltodextrin (glucose polymer) energy substrate providing slow + glucose release and minimal phosphate buildup + aliases: + - polymeric glucose + CellFreeApplicationEnum: + name: CellFreeApplicationEnum + definition_uri: https://w3id.org/valuesets/CellFreeApplicationEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition + description: Common applications and use cases for cell-free protein synthesis + across research, synthetic biology, and biomanufacturing. + title: Cell-Free Expression Applications + from_schema: https://w3id.org/valuesets/bio/cell_free_expression + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT + permissible_values: + RECOMBINANT_PROTEIN_PRODUCTION: + text: RECOMBINANT_PROTEIN_PRODUCTION + description: General production of recombinant proteins in vitro + aliases: + - protein production + MEMBRANE_PROTEIN_EXPRESSION: + text: MEMBRANE_PROTEIN_EXPRESSION + description: Expression of membrane proteins, often co-translationally inserted + into liposomes, nanodiscs, or detergent micelles + aliases: + - membrane protein synthesis + DIFFICULT_PROTEIN_EXPRESSION: + text: DIFFICULT_PROTEIN_EXPRESSION + description: Expression of toxic, unstable, or otherwise difficult-to-express + proteins that are problematic in living cells + aliases: + - toxic protein expression + GENETIC_CIRCUIT_PROTOTYPING: + text: GENETIC_CIRCUIT_PROTOTYPING + description: Rapid prototyping and characterization of genetic parts and circuits + using in vitro transcription-translation (TX-TL) + aliases: + - TX-TL prototyping + - circuit prototyping + METABOLIC_PATHWAY_PROTOTYPING: + text: METABOLIC_PATHWAY_PROTOTYPING + description: Building and testing enzymatic and metabolic pathways in vitro + for cell-free biosynthesis + aliases: + - cell-free metabolic engineering + - pathway prototyping + BIOSENSOR: + text: BIOSENSOR + description: Cell-free biosensors, including freeze-dried paper-based sensors + for detecting nucleic acids, small molecules, or contaminants + meaning: NCIT:C16350 + aliases: + - cell-free biosensor + - Biosensors + exact_mappings: + - BAO:0010264 + DIAGNOSTICS: + text: DIAGNOSTICS + description: Point-of-care and field-deployable diagnostics, often freeze-dried + cell-free reactions coupled to toehold switches or CRISPR readouts + aliases: + - point-of-care diagnostics + related_mappings: + - NCIT:C209465 + UNNATURAL_AMINO_ACID_INCORPORATION: + text: UNNATURAL_AMINO_ACID_INCORPORATION + description: Site-specific incorporation of non-canonical/unnatural amino + acids via orthogonal translation components + aliases: + - ncAA incorporation + - non-canonical amino acid incorporation + PROTEIN_LABELING: + text: PROTEIN_LABELING + description: Incorporation of radioactive, fluorescent, or isotopic labels + for detection and structural studies + aliases: + - isotopic labeling + - radiolabeling + STRUCTURAL_BIOLOGY: + text: STRUCTURAL_BIOLOGY + description: Production of selectively or uniformly isotope-labeled proteins + for NMR and other structural studies + aliases: + - NMR labeling + HIGH_THROUGHPUT_SCREENING: + text: HIGH_THROUGHPUT_SCREENING + description: Parallelized small-volume expression for protein screening, directed + evolution, and library characterization + meaning: NCIT:C18472 + aliases: + - HTS + exact_mappings: + - BAO:0010074 + VACCINE_PRODUCTION: + text: VACCINE_PRODUCTION + description: On-demand cell-free production of protein subunit and conjugate + vaccine antigens + meaning: OBI:0000719 + aliases: + - on-demand vaccine production + exact_mappings: + - NCIT:C26030 + ANTIBODY_PRODUCTION: + text: ANTIBODY_PRODUCTION + description: Cell-free synthesis of antibodies and antibody fragments + aliases: + - antibody synthesis + EDUCATION: + text: EDUCATION + description: Use of cell-free kits for teaching and outreach in synthetic + biology + aliases: + - teaching DayOfWeek: name: DayOfWeek definition_uri: https://w3id.org/valuesets/DayOfWeek @@ -33679,6 +34184,737 @@ enums: condition: tag: condition value: senescent or dead + ColorEnum: + name: ColorEnum + definition_uri: https://w3id.org/valuesets/ColorEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition + description: A composite chromatic quality composed of hue, saturation and intensity + parts. Derived from PATO color (PATO:0000014) child values. + title: Color + from_schema: https://w3id.org/valuesets/bio/pato + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT + permissible_values: + BLACK: + text: BLACK + description: A color that lacks any hues as parts + meaning: PATO:0000317 + title: black + WHITE: + text: WHITE + description: An achromatic color of maximum brightness + meaning: PATO:0000323 + title: white + GREY: + text: GREY + description: A color between white and black colors + meaning: PATO:0000950 + title: grey + aliases: + - gray + RED: + text: RED + description: A color hue with high wavelength of the long-wave end of the + visible spectrum (630-750 nm) + meaning: PATO:0000322 + title: red + ORANGE: + text: ORANGE + description: A color hue with high-medium wavelength lying between red and + yellow (585-620 nm) + meaning: PATO:0000953 + title: orange + YELLOW: + text: YELLOW + description: A color hue with medium wavelength lying between orange and green + (570-590 nm) + meaning: PATO:0000324 + title: yellow + GREEN: + text: GREEN + description: A color hue with medium-low wavelength lying between yellow and + blue (490-570 nm) + meaning: PATO:0000320 + title: green + CYAN: + text: CYAN + description: A color consisting of green and blue hue + meaning: PATO:0000319 + title: cyan + BLUE: + text: BLUE + description: A color hue with low wavelength lying between green and indigo + (420-490 nm) + meaning: PATO:0000318 + title: blue + VIOLET: + text: VIOLET + description: A color hue with very low wavelength lying between reddish blue + and bluish purple (380-420 nm) + meaning: PATO:0001424 + title: violet + PURPLE: + text: PURPLE + description: A color that falls about midway between red and blue in hue + meaning: PATO:0000951 + title: purple + MAGENTA: + text: MAGENTA + description: A color consisting of red and blue hues + meaning: PATO:0000321 + title: magenta + BROWN: + text: BROWN + description: A color consisting of dark orange, red, of very low intensity + meaning: PATO:0000952 + title: brown + MAROON: + text: MAROON + description: A color consisting of purple and brown hue + meaning: PATO:0001426 + title: maroon + ROSY: + text: ROSY + description: A color hue consisting of red and yellow hue with high brightness + meaning: PATO:0001425 + title: rosy + aliases: + - pink + VERMILION: + text: VERMILION + description: A color consisting of red and orange hue with a slight amount + of gray + meaning: PATO:0001302 + title: vermilion + COLORED: + text: COLORED + description: A color quality inhering in a bearer by virtue of having color + meaning: PATO:0000336 + title: colored + ShapeEnum: + name: ShapeEnum + definition_uri: https://w3id.org/valuesets/ShapeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition + description: A morphological quality inhering in a bearer by virtue of the bearer's + ratios of distances between its features. Derived from PATO shape (PATO:0000052) + child values. + title: Shape + from_schema: https://w3id.org/valuesets/bio/pato + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT + permissible_values: + CIRCULAR: + text: CIRCULAR + description: A shape where every part of the surface or circumference is equidistant + from the center + meaning: PATO:0000411 + title: circular + ELLIPTIC: + text: ELLIPTIC + description: Oval with two axes of symmetry, as produced by a conical section + meaning: PATO:0000947 + title: elliptic + aliases: + - oval + SPHEROID: + text: SPHEROID + description: A convex 3-D shape obtained by rotating an ellipse about one + of its principal axes + meaning: PATO:0001865 + title: spheroid + CONICAL: + text: CONICAL + description: A convex 3-D shape resembling a cone with a round cross section + that tapers + meaning: PATO:0002021 + title: conical + COLUMNAR: + text: COLUMNAR + description: Elongated and cylindrical in shape + meaning: PATO:0002063 + title: columnar + aliases: + - cylindrical + TUBULAR: + text: TUBULAR + description: A cylindrical shape that is hollow + meaning: PATO:0002299 + title: tubular + FLAT: + text: FLAT + description: Having a horizontal surface without a slope, tilt, or curvature + meaning: PATO:0000407 + title: flat + ELONGATED: + text: ELONGATED + description: Length being notably higher relative to width + meaning: PATO:0001154 + title: elongated + LINEAR: + text: LINEAR + description: Narrow, with approximately parallel sides + meaning: PATO:0001199 + title: linear + FILAMENTOUS: + text: FILAMENTOUS + description: Having thin filaments or thread-like structures + meaning: PATO:0001360 + title: filamentous + SLENDER: + text: SLENDER + description: Being small or narrow in circumference or width in proportion + to length or height + meaning: PATO:0002212 + title: slender + BROAD: + text: BROAD + description: Width being notably higher relative to comparable entities + meaning: PATO:0002359 + title: broad + ROBUST: + text: ROBUST + description: Being strong, thick, or stout in form + meaning: PATO:0002310 + title: robust + STRAIGHT: + text: STRAIGHT + description: Free of curves, bends, or angles + meaning: PATO:0002180 + title: straight + BENT: + text: BENT + description: Having one or more fixed curves, folds, or angles + meaning: PATO:0000617 + title: bent + ANGULAR: + text: ANGULAR + description: Having at least one angle formed by two planes + meaning: PATO:0001977 + title: angular + LOBED: + text: LOBED + description: Being partly divided into a determinate number of segments + meaning: PATO:0001979 + title: lobed + TRUNCATED: + text: TRUNCATED + description: Terminating abruptly by a transverse line or plane + meaning: PATO:0000936 + title: truncated + PYRAMIDAL: + text: PYRAMIDAL + description: Having triangular faces meeting at a common point + meaning: PATO:0002336 + title: pyramidal + STAR_SHAPED: + text: STAR_SHAPED + description: Being arranged like a star with radiating points + meaning: PATO:0002065 + title: star shaped + aliases: + - stellate + SIGMOID: + text: SIGMOID + description: Consisting of two curves in opposite directions like the letter + S + meaning: PATO:0001878 + title: sigmoid + UNDULATE: + text: UNDULATE + description: Having a sinuate margin that moves smoothly and regularly up + and down + meaning: PATO:0000967 + title: undulate + aliases: + - wavy + PINNATE: + text: PINNATE + description: Having leaflets or branches on each side of a common axis + meaning: PATO:0000410 + title: pinnate + PLEOMORPHIC: + text: PLEOMORPHIC + description: Having the ability to take on multiple forms + meaning: PATO:0001356 + title: pleomorphic + COILING: + text: COILING + description: Being wound in a spiral or helix + meaning: PATO:0001794 + title: coiling + aliases: + - coiled + - helical + RelativeChangeEnum: + name: RelativeChangeEnum + definition_uri: https://w3id.org/valuesets/RelativeChangeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition + description: Direction of change of any quality relative to normal or baseline. + This is PATO's general-purpose deviation-from-normal axis (PATO:0000069) that + crosscuts all specific quality attributes (size, rate, amount, etc.). + title: Relative Change + from_schema: https://w3id.org/valuesets/bio/pato + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT + permissible_values: + NORMAL: + text: NORMAL + description: Exhibiting no deviation from normal or average + meaning: PATO:0000461 + title: normal + ABNORMAL: + text: ABNORMAL + description: Deviating from normal or average + meaning: PATO:0000460 + title: abnormal + INCREASED: + text: INCREASED + description: A value that is increased compared to normal or average + meaning: PATO:0002300 + title: increased quality + aliases: + - elevated + - high + DECREASED: + text: DECREASED + description: A value that is decreased compared to normal or average + meaning: PATO:0002301 + title: decreased quality + aliases: + - reduced + - low + INCREASED_MAGNITUDE: + text: INCREASED_MAGNITUDE + description: An increased magnitude of a quality + meaning: PATO:0002017 + title: increased magnitude + DECREASED_MAGNITUDE: + text: DECREASED_MAGNITUDE + description: A decreased magnitude of a quality + meaning: PATO:0002018 + title: decreased magnitude + IntensityEnum: + name: IntensityEnum + definition_uri: https://w3id.org/valuesets/IntensityEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition + description: A quality inhering in a bearer by virtue of the bearer's possessing + or displaying a distinctive feature in type or degree or effect or force. Derived + from PATO intensity (PATO:0000049) child values. + title: Intensity + from_schema: https://w3id.org/valuesets/bio/pato + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT + permissible_values: + BORDERLINE: + text: BORDERLINE + description: Borderline in effect or force compared to baseline or normal + meaning: PATO:0002628 + title: borderline intensity + MILD: + text: MILD + description: Less than moderate in type or degree or effect or force + meaning: PATO:0000394 + title: mild intensity + MODERATE: + text: MODERATE + description: Less than extreme in type or degree or effect or force + meaning: PATO:0000395 + title: moderate intensity + SEVERE: + text: SEVERE + description: Extremely bad or unpleasant in type or degree or effect or force + meaning: PATO:0000396 + title: severe intensity + PROFOUND: + text: PROFOUND + description: Very severe in intensity + meaning: PATO:0002629 + title: profound intensity + INCREASED_INTENSITY: + text: INCREASED_INTENSITY + description: Intensity which is relatively high + meaning: PATO:0001782 + title: increased intensity + DECREASED_INTENSITY: + text: DECREASED_INTENSITY + description: Intensity which is relatively low + meaning: PATO:0001783 + title: decreased intensity + REMITTENT: + text: REMITTENT + description: Characterised by temporary abatement in severity + meaning: PATO:0001841 + title: remittent intensity + TextureEnum: + name: TextureEnum + definition_uri: https://w3id.org/valuesets/TextureEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition + description: A morphological quality inhering in a bearer by virtue of the bearer's + surface characteristics. Derived from PATO texture (PATO:0000150) child values. + title: Texture + from_schema: https://w3id.org/valuesets/bio/pato + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT + permissible_values: + SMOOTH: + text: SMOOTH + description: Having a surface free of roughness or irregularities + meaning: PATO:0000701 + title: smooth + ROUGH: + text: ROUGH + description: Having an irregular surface + meaning: PATO:0000700 + title: rough + SCALY: + text: SCALY + description: Being covered or partially covered with scales + meaning: PATO:0001804 + title: scaly + FLAKY: + text: FLAKY + description: Formed or tending to form flakes or thin, crisp fragments + meaning: PATO:0001805 + title: flaky + GROOVED: + text: GROOVED + description: Being marked with one or more channels + meaning: PATO:0002255 + title: grooved + BLISTERED: + text: BLISTERED + description: Having a local accumulation of fluid underneath the surface + meaning: PATO:0001928 + title: blistered + HAIRY: + text: HAIRY + description: Having hair or bristles + meaning: PATO:0000066 + title: pilose + aliases: + - pilose + - hairy + ABRASED: + text: ABRASED + description: Having a portion of the surface scraped away + meaning: PATO:0001849 + title: abrased + RUSTY: + text: RUSTY + description: Being covered by iron oxide as a result of oxidation + meaning: PATO:0070059 + title: rusty + FOVEATE: + text: FOVEATE + description: Being marked by the presence of small, shallow, regular depressions + meaning: PATO:0002296 + title: foveate + PATOBiologicalSexEnum: + name: PATOBiologicalSexEnum + definition_uri: https://w3id.org/valuesets/PATOBiologicalSexEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition + description: An organismal quality inhering in a bearer by virtue of the bearer's + ability to undergo sexual reproduction. Derived from PATO biological sex (PATO:0000047) + and phenotypic sex (PATO:0001894) child values. + title: Biological Sex (PATO) + from_schema: https://w3id.org/valuesets/bio/pato + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT + permissible_values: + FEMALE: + text: FEMALE + description: A biological sex quality inhering in an individual or population + that only produces gametes that can be fertilised by male gametes + meaning: PATO:0000383 + title: female + MALE: + text: MALE + description: A biological sex quality inhering in an individual or population + whose sex organs contain only male gametes + meaning: PATO:0000384 + title: male + HERMAPHRODITE: + text: HERMAPHRODITE + description: A biological sex quality inhering in an organism or population + with both male and female sexual organs in one individual + meaning: PATO:0001340 + title: hermaphrodite + MALE_WITH_DSD: + text: MALE_WITH_DSD + description: A male of a non-hermaphroditic species with ambiguous or atypical + congenital development of the reproductive system + meaning: PATO:0040049 + title: male with DSD + comments: + - DSD = disorders/differences of sexual development/differentiation + FEMALE_WITH_DSD: + text: FEMALE_WITH_DSD + description: A female of a non-hermaphroditic species with ambiguous or atypical + congenital development of the reproductive system + meaning: PATO:0040056 + title: female with DSD + comments: + - DSD = disorders/differences of sexual development/differentiation + PSEUDOHERMAPHRODITE: + text: PSEUDOHERMAPHRODITE + description: Having internal reproductive organs of one sex and external sexual + characteristics of the other sex + meaning: PATO:0001827 + title: pseudohermaphrodite + MaturityEnum: + name: MaturityEnum + definition_uri: https://w3id.org/valuesets/MaturityEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition + description: A quality of a single physical entity held by a bearer when it exhibits + a state of growth, differentiation, or development. Derived from PATO maturity + (PATO:0000261) child values. + title: Maturity + from_schema: https://w3id.org/valuesets/bio/pato + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT + permissible_values: + NEONATAL: + text: NEONATAL + description: Being at the point or shortly after birth + meaning: PATO:0002206 + title: neonatal + LARVAL: + text: LARVAL + description: Undergoing indirect development and metamorphosis + meaning: PATO:0001185 + title: larval + PREPUBESCENT: + text: PREPUBESCENT + description: Being at the age immediately before puberty + meaning: PATO:0001186 + title: prepubescent + PUPAL: + text: PUPAL + description: Being in the chrysalis (cocoon) or post-larval stage + meaning: PATO:0001187 + title: pupal + PREPUPAL: + text: PREPUPAL + description: Being in an inactive stage between the larval and the pupal stages + meaning: PATO:0001188 + title: prepupal + PUBESCENT: + text: PUBESCENT + description: Having arrived at the onset of puberty but not yet fully mature + meaning: PATO:0000455 + title: pubescent + ADOLESCENT: + text: ADOLESCENT + description: Being between the onset of puberty and maturity + meaning: PATO:0001189 + title: adolescent + JUVENILE: + text: JUVENILE + description: Not fully grown or developed + meaning: PATO:0001190 + title: juvenile + IMMATURE: + text: IMMATURE + description: Lacking complete growth, differentiation, or development + meaning: PATO:0001501 + title: immature + MATURE: + text: MATURE + description: Exhibiting complete growth, differentiation, or development + meaning: PATO:0001701 + title: mature + aliases: + - adult + ViabilityEnum: + name: ViabilityEnum + definition_uri: https://w3id.org/valuesets/ViabilityEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition + description: An organismal quality inhering in a bearer by virtue of the bearer's + disposition to survive and develop normally. Derived from PATO viability (PATO:0000169) + child values. + title: Viability + from_schema: https://w3id.org/valuesets/bio/pato + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT + permissible_values: + ALIVE: + text: ALIVE + description: The bearer's condition before death + meaning: PATO:0001421 + title: alive + DEAD: + text: DEAD + description: The cessation of the bearer's life + meaning: PATO:0001422 + title: dead + VIABLE: + text: VIABLE + description: The bearer's ability to survive or the long term survival ability + of a given population + meaning: PATO:0000719 + title: viable + LETHAL: + text: LETHAL + description: The bearer's long term survival inability + meaning: PATO:0000718 + title: lethal (sensu genetics) + SEMI_VIABLE: + text: SEMI_VIABLE + description: Some of the population members' ability to survive + meaning: PATO:0001770 + title: semi-viable + SEMI_LETHAL: + text: SEMI_LETHAL + description: Some of the population members' inability to survive to reproduce + meaning: PATO:0001768 + title: semi-lethal (sensu genetics) + IMMORTAL: + text: IMMORTAL + description: Being capable of indefinite growth or division + meaning: PATO:0001991 + title: immortal + DECAYED: + text: DECAYED + description: Decomposition into component parts + meaning: PATO:0001432 + title: decayed + CellularityEnum: + name: CellularityEnum + definition_uri: https://w3id.org/valuesets/CellularityEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition + description: An organismal quality inhering in a bearer by virtue of the bearer's + consisting of cells. Derived from PATO cellularity (PATO:0001992) child values. + title: Cellularity + from_schema: https://w3id.org/valuesets/bio/pato + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT + permissible_values: + UNICELLULAR: + text: UNICELLULAR + description: Consisting of exactly one cell + meaning: PATO:0001994 + title: unicellular + MULTICELLULAR: + text: MULTICELLULAR + description: Consisting of more than one cell + meaning: PATO:0001993 + title: multicellular + SpatialPatternEnum: + name: SpatialPatternEnum + definition_uri: https://w3id.org/valuesets/SpatialPatternEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition + description: A spatial quality inhering in a bearer by virtue of the bearer's + exhibiting repetition of placement of its parts. Derived from PATO spatial pattern + (PATO:0000060) child values. + title: Spatial Pattern + from_schema: https://w3id.org/valuesets/bio/pato + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT + permissible_values: + LOCALIZED: + text: LOCALIZED + description: Being confined or restricted to a particular location + meaning: PATO:0000627 + title: localized + UNLOCALISED: + text: UNLOCALISED + description: Not being confined or restricted to a particular location + meaning: PATO:0000635 + title: unlocalised + aliases: + - diffuse + MULTI_LOCALISED: + text: MULTI_LOCALISED + description: Being confined or restricted to multiple locations + meaning: PATO:0001791 + title: multi-localised + DISTRIBUTED: + text: DISTRIBUTED + description: Being spread out or scattered about or divided up + meaning: PATO:0001566 + title: distributed + UNDISTRIBUTED: + text: UNDISTRIBUTED + description: Not being spread out or scattered about or divided up + meaning: PATO:0001567 + title: undistributed + SPARSE: + text: SPARSE + description: Being scattered and spread irregularly at a distance from each + other + meaning: PATO:0001609 + title: sparse + UNILATERAL: + text: UNILATERAL + description: Involving only one part or side + meaning: PATO:0000634 + title: unilateral + VERTICAL: + text: VERTICAL + description: Being situated at right angles to the horizon + meaning: PATO:0001854 + title: vertical + REGULAR_SPATIAL_PATTERN: + text: REGULAR_SPATIAL_PATTERN + description: Having a repeatable or predictable placement + meaning: PATO:0000440 + title: regular spatial pattern + IRREGULAR_SPATIAL_PATTERN: + text: IRREGULAR_SPATIAL_PATTERN + description: Magnitude or relationships between repeated parts lack consistency + meaning: PATO:0000330 + title: irregular spatial pattern + GENERALIZED: + text: GENERALIZED + description: Affecting all regions without specificity of distribution + meaning: PATO:0002403 + title: generalized + SEGMENTAL: + text: SEGMENTAL + description: Affecting a segment or segments + meaning: PATO:0002404 + title: segmental + RANDOM_PATTERN: + text: RANDOM_PATTERN + description: Characterised by an unidentifiable pattern + meaning: PATO:0002401 + title: random pattern + SYMMETRICAL: + text: SYMMETRICAL + description: Correspondence in size, shape, and relative position of parts + on opposite sides of a dividing line or about a center or axis + meaning: PATO:0000965 + title: symmetry DNABaseEnum: name: DNABaseEnum definition_uri: https://w3id.org/valuesets/DNABaseEnum @@ -72199,6 +73435,34 @@ slots: from_schema: https://w3id.org/valuesets/bio/developmental_stages slot_uri: valuesets:mouse_postnatal_age_group range: MousePostnatalAgeGroupEnum + cell_free_system: + name: cell_free_system + definition_uri: https://w3id.org/valuesets/cell_free_system + description: The source extract or reconstituted system used for cell-free expression + from_schema: https://w3id.org/valuesets/bio/cell_free_expression + slot_uri: valuesets:cell_free_system + range: CellFreeExpressionSystemEnum + cell_free_reaction_format: + name: cell_free_reaction_format + definition_uri: https://w3id.org/valuesets/cell_free_reaction_format + description: The physical configuration of the cell-free reaction + from_schema: https://w3id.org/valuesets/bio/cell_free_expression + slot_uri: valuesets:cell_free_reaction_format + range: CellFreeReactionFormatEnum + energy_regeneration_substrate: + name: energy_regeneration_substrate + definition_uri: https://w3id.org/valuesets/energy_regeneration_substrate + description: Secondary energy substrate used to regenerate ATP/GTP in the reaction + from_schema: https://w3id.org/valuesets/bio/cell_free_expression + slot_uri: valuesets:energy_regeneration_substrate + range: EnergyRegenerationSubstrateEnum + cell_free_application: + name: cell_free_application + definition_uri: https://w3id.org/valuesets/cell_free_application + description: Application or use case for the cell-free expression reaction + from_schema: https://w3id.org/valuesets/bio/cell_free_expression + slot_uri: valuesets:cell_free_application + range: CellFreeApplicationEnum day_of_week: name: day_of_week definition_uri: https://w3id.org/valuesets/day_of_week @@ -73922,6 +75186,76 @@ slots: from_schema: https://w3id.org/valuesets/bio/biological_colors slot_uri: valuesets:plant_leaf_color range: PlantLeafColorEnum + pato_color: + name: pato_color + definition_uri: https://w3id.org/valuesets/pato_color + description: Color quality of an entity + from_schema: https://w3id.org/valuesets/bio/pato + slot_uri: valuesets:pato_color + range: ColorEnum + pato_shape: + name: pato_shape + definition_uri: https://w3id.org/valuesets/pato_shape + description: Shape quality of an entity + from_schema: https://w3id.org/valuesets/bio/pato + slot_uri: valuesets:pato_shape + range: ShapeEnum + pato_relative_change: + name: pato_relative_change + definition_uri: https://w3id.org/valuesets/pato_relative_change + description: Direction of change of a quality relative to normal or baseline + from_schema: https://w3id.org/valuesets/bio/pato + slot_uri: valuesets:pato_relative_change + range: RelativeChangeEnum + pato_intensity: + name: pato_intensity + definition_uri: https://w3id.org/valuesets/pato_intensity + description: Intensity or severity of a quality + from_schema: https://w3id.org/valuesets/bio/pato + slot_uri: valuesets:pato_intensity + range: IntensityEnum + pato_texture: + name: pato_texture + definition_uri: https://w3id.org/valuesets/pato_texture + description: Surface texture quality of an entity + from_schema: https://w3id.org/valuesets/bio/pato + slot_uri: valuesets:pato_texture + range: TextureEnum + pato_biological_sex: + name: pato_biological_sex + definition_uri: https://w3id.org/valuesets/pato_biological_sex + description: Biological sex quality of an organism (PATO phenotypic sex) + from_schema: https://w3id.org/valuesets/bio/pato + slot_uri: valuesets:pato_biological_sex + range: PATOBiologicalSexEnum + pato_maturity: + name: pato_maturity + definition_uri: https://w3id.org/valuesets/pato_maturity + description: Maturity or developmental stage quality of an organism + from_schema: https://w3id.org/valuesets/bio/pato + slot_uri: valuesets:pato_maturity + range: MaturityEnum + pato_viability: + name: pato_viability + definition_uri: https://w3id.org/valuesets/pato_viability + description: Viability quality of an organism or cell + from_schema: https://w3id.org/valuesets/bio/pato + slot_uri: valuesets:pato_viability + range: ViabilityEnum + pato_cellularity: + name: pato_cellularity + definition_uri: https://w3id.org/valuesets/pato_cellularity + description: Cellularity quality of an organism + from_schema: https://w3id.org/valuesets/bio/pato + slot_uri: valuesets:pato_cellularity + range: CellularityEnum + pato_spatial_pattern: + name: pato_spatial_pattern + definition_uri: https://w3id.org/valuesets/pato_spatial_pattern + description: Spatial pattern quality of an entity + from_schema: https://w3id.org/valuesets/bio/pato + slot_uri: valuesets:pato_spatial_pattern + range: SpatialPatternEnum dna_base: name: dna_base definition_uri: https://w3id.org/valuesets/dna_base @@ -75821,7 +77155,7 @@ classes: class_uri: valuesets:Fake metamodel_version: 1.7.0 source_file: valuesets.yaml -source_file_date: '2026-06-12T22:51:09' -source_file_size: 4266 -generation_date: '2026-06-12T22:52:34' +source_file_date: '2026-06-23T14:42:19' +source_file_size: 4304 +generation_date: '2026-06-23T14:43:49' diff --git a/project/jsonschema/valuesets.schema.json b/project/jsonschema/valuesets.schema.json index fc927d3e..08ddb4d6 100644 --- a/project/jsonschema/valuesets.schema.json +++ b/project/jsonschema/valuesets.schema.json @@ -1502,6 +1502,57 @@ "title": "CellCycleRegulator", "type": "string" }, + "CellFreeApplicationEnum": { + "description": "Common applications and use cases for cell-free protein synthesis across research, synthetic biology, and biomanufacturing.", + "enum": [ + "RECOMBINANT_PROTEIN_PRODUCTION", + "MEMBRANE_PROTEIN_EXPRESSION", + "DIFFICULT_PROTEIN_EXPRESSION", + "GENETIC_CIRCUIT_PROTOTYPING", + "METABOLIC_PATHWAY_PROTOTYPING", + "BIOSENSOR", + "DIAGNOSTICS", + "UNNATURAL_AMINO_ACID_INCORPORATION", + "PROTEIN_LABELING", + "STRUCTURAL_BIOLOGY", + "HIGH_THROUGHPUT_SCREENING", + "VACCINE_PRODUCTION", + "ANTIBODY_PRODUCTION", + "EDUCATION" + ], + "title": "CellFreeApplicationEnum", + "type": "string" + }, + "CellFreeExpressionSystemEnum": { + "description": "Source extracts and reconstituted systems used for cell-free protein synthesis. Crude lysate systems are derived from cell extracts, while reconstituted systems (e.g. PURE) are assembled from purified components.", + "enum": [ + "ECOLI_EXTRACT", + "PURE_SYSTEM", + "WHEAT_GERM_EXTRACT", + "RABBIT_RETICULOCYTE_LYSATE", + "INSECT_CELL_EXTRACT", + "HELA_EXTRACT", + "CHO_EXTRACT", + "YEAST_EXTRACT", + "LEISHMANIA_EXTRACT", + "VIBRIO_NATRIEGENS_EXTRACT", + "TOBACCO_BY2_EXTRACT" + ], + "title": "CellFreeExpressionSystemEnum", + "type": "string" + }, + "CellFreeReactionFormatEnum": { + "description": "Physical configurations of cell-free expression reactions, differing in how substrates are supplied and byproducts removed, which affects reaction duration and protein yield.", + "enum": [ + "BATCH", + "CONTINUOUS_EXCHANGE", + "CONTINUOUS_FLOW", + "BILAYER", + "LYOPHILIZED" + ], + "title": "CellFreeReactionFormatEnum", + "type": "string" + }, "CellPolarity": { "description": "Spatial polarity in cells and tissues", "enum": [ @@ -1541,6 +1592,15 @@ "title": "CellularComponent", "type": "string" }, + "CellularityEnum": { + "description": "An organismal quality inhering in a bearer by virtue of the bearer's consisting of cells. Derived from PATO cellularity (PATO:0001992) child values.", + "enum": [ + "UNICELLULAR", + "MULTICELLULAR" + ], + "title": "CellularityEnum", + "type": "string" + }, "ChemicalEntity": { "description": "Any chemical entity from ChEBI ontology", "title": "ChemicalEntity", @@ -1834,6 +1894,30 @@ "title": "CodonEnum", "type": "string" }, + "ColorEnum": { + "description": "A composite chromatic quality composed of hue, saturation and intensity parts. Derived from PATO color (PATO:0000014) child values.", + "enum": [ + "BLACK", + "WHITE", + "GREY", + "RED", + "ORANGE", + "YELLOW", + "GREEN", + "CYAN", + "BLUE", + "VIOLET", + "PURPLE", + "MAGENTA", + "BROWN", + "MAROON", + "ROSY", + "VERMILION", + "COLORED" + ], + "title": "ColorEnum", + "type": "string" + }, "ColorSpaceEnum": { "description": "Color space and model types", "enum": [ @@ -3360,6 +3444,22 @@ "title": "EnergyEfficiencyRating", "type": "string" }, + "EnergyRegenerationSubstrateEnum": { + "description": "Secondary energy substrates added to cell-free reactions to regenerate ATP and GTP consumed during transcription and translation. Choice of substrate affects cost, reaction longevity, and inorganic phosphate accumulation.", + "enum": [ + "PHOSPHOCREATINE", + "PHOSPHOENOLPYRUVATE", + "ACETYL_PHOSPHATE", + "THREE_PGA", + "GLUCOSE", + "GLUCOSE_6_PHOSPHATE", + "MALTOSE", + "PYRUVATE", + "MALTODEXTRIN" + ], + "title": "EnergyRegenerationSubstrateEnum", + "type": "string" + }, "EnergySource": { "description": "Types of energy sources and generation methods", "enum": [ @@ -5622,6 +5722,21 @@ "title": "IntegrationSystemEnum", "type": "string" }, + "IntensityEnum": { + "description": "A quality inhering in a bearer by virtue of the bearer's possessing or displaying a distinctive feature in type or degree or effect or force. Derived from PATO intensity (PATO:0000049) child values.", + "enum": [ + "BORDERLINE", + "MILD", + "MODERATE", + "SEVERE", + "PROFOUND", + "INCREASED_INTENSITY", + "DECREASED_INTENSITY", + "REMITTENT" + ], + "title": "IntensityEnum", + "type": "string" + }, "IntentClassificationEnum": { "description": "Common chatbot/NLU intent categories", "enum": [ @@ -6545,6 +6660,23 @@ "title": "MaterialsSimulationType", "type": "string" }, + "MaturityEnum": { + "description": "A quality of a single physical entity held by a bearer when it exhibits a state of growth, differentiation, or development. Derived from PATO maturity (PATO:0000261) child values.", + "enum": [ + "NEONATAL", + "LARVAL", + "PREPUBESCENT", + "PUPAL", + "PREPUPAL", + "PUBESCENT", + "ADOLESCENT", + "JUVENILE", + "IMMATURE", + "MATURE" + ], + "title": "MaturityEnum", + "type": "string" + }, "MechanicalBehaviorEnum": { "description": "Mechanical behavior of materials under stress", "enum": [ @@ -7732,6 +7864,19 @@ "title": "OxygenationStrategyEnum", "type": "string" }, + "PATOBiologicalSexEnum": { + "description": "An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction. Derived from PATO biological sex (PATO:0000047) and phenotypic sex (PATO:0001894) child values.", + "enum": [ + "FEMALE", + "MALE", + "HERMAPHRODITE", + "MALE_WITH_DSD", + "FEMALE_WITH_DSD", + "PSEUDOHERMAPHRODITE" + ], + "title": "PATOBiologicalSexEnum", + "type": "string" + }, "PCROperationTypeEnum": { "description": "Types of PCR operations and techniques", "enum": [ @@ -9125,6 +9270,19 @@ "title": "RelToOxygenEnum", "type": "string" }, + "RelativeChangeEnum": { + "description": "Direction of change of any quality relative to normal or baseline. This is PATO's general-purpose deviation-from-normal axis (PATO:0000069) that crosscuts all specific quality attributes (size, rate, amount, etc.).", + "enum": [ + "NORMAL", + "ABNORMAL", + "INCREASED", + "DECREASED", + "INCREASED_MAGNITUDE", + "DECREASED_MAGNITUDE" + ], + "title": "RelativeChangeEnum", + "type": "string" + }, "RelativeDirection": { "description": "Relative directional terms", "enum": [ @@ -9708,6 +9866,38 @@ "title": "SeverityLevelEnum", "type": "string" }, + "ShapeEnum": { + "description": "A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features. Derived from PATO shape (PATO:0000052) child values.", + "enum": [ + "CIRCULAR", + "ELLIPTIC", + "SPHEROID", + "CONICAL", + "COLUMNAR", + "TUBULAR", + "FLAT", + "ELONGATED", + "LINEAR", + "FILAMENTOUS", + "SLENDER", + "BROAD", + "ROBUST", + "STRAIGHT", + "BENT", + "ANGULAR", + "LOBED", + "TRUNCATED", + "PYRAMIDAL", + "STAR_SHAPED", + "SIGMOID", + "UNDULATE", + "PINNATE", + "PLEOMORPHIC", + "COILING" + ], + "title": "ShapeEnum", + "type": "string" + }, "SimpleSpatialDirection": { "description": "Basic spatial directional terms for general use", "enum": [ @@ -9851,6 +10041,27 @@ "title": "SpamClassificationEnum", "type": "string" }, + "SpatialPatternEnum": { + "description": "A spatial quality inhering in a bearer by virtue of the bearer's exhibiting repetition of placement of its parts. Derived from PATO spatial pattern (PATO:0000060) child values.", + "enum": [ + "LOCALIZED", + "UNLOCALISED", + "MULTI_LOCALISED", + "DISTRIBUTED", + "UNDISTRIBUTED", + "SPARSE", + "UNILATERAL", + "VERTICAL", + "REGULAR_SPATIAL_PATTERN", + "IRREGULAR_SPATIAL_PATTERN", + "GENERALIZED", + "SEGMENTAL", + "RANDOM_PATTERN", + "SYMMETRICAL" + ], + "title": "SpatialPatternEnum", + "type": "string" + }, "SpatialRelationship": { "description": "Spatial relationships between anatomical structures", "enum": [ @@ -10429,6 +10640,23 @@ "title": "TextCharset", "type": "string" }, + "TextureEnum": { + "description": "A morphological quality inhering in a bearer by virtue of the bearer's surface characteristics. Derived from PATO texture (PATO:0000150) child values.", + "enum": [ + "SMOOTH", + "ROUGH", + "SCALY", + "FLAKY", + "GROOVED", + "BLISTERED", + "HAIRY", + "ABRASED", + "RUSTY", + "FOVEATE" + ], + "title": "TextureEnum", + "type": "string" + }, "TherapeuticActionabilityEnum": { "description": "Clinical actionability of a genetic finding for treatment decisions", "enum": [ @@ -11309,6 +11537,21 @@ "title": "VendorCategoryEnum", "type": "string" }, + "ViabilityEnum": { + "description": "An organismal quality inhering in a bearer by virtue of the bearer's disposition to survive and develop normally. Derived from PATO viability (PATO:0000169) child values.", + "enum": [ + "ALIVE", + "DEAD", + "VIABLE", + "LETHAL", + "SEMI_VIABLE", + "SEMI_LETHAL", + "IMMORTAL", + "DECAYED" + ], + "title": "ViabilityEnum", + "type": "string" + }, "VideoFormatEnum": { "description": "Video file formats", "enum": [ diff --git a/src/valuesets/datamodel/valuesets.py b/src/valuesets/datamodel/valuesets.py index b07b8c3e..0a5f640a 100644 --- a/src/valuesets/datamodel/valuesets.py +++ b/src/valuesets/datamodel/valuesets.py @@ -2557,6 +2557,124 @@ class MousePostnatalAgeGroupEnum(RichEnum): "P365_PLUS_AGED": {'description': 'Aged stage from postnatal day 365 onwards (12+ months)', 'annotations': {'postnatal_days': 'P365+', 'approximate_age': '12+ months'}, 'aliases': ['P365+ Aged']}, } +class CellFreeExpressionSystemEnum(RichEnum): + """ + Source extracts and reconstituted systems used for cell-free protein synthesis. Crude lysate systems are derived from cell extracts, while reconstituted systems (e.g. PURE) are assembled from purified components. + """ + # Enum members + ECOLI_EXTRACT = "ECOLI_EXTRACT" + PURE_SYSTEM = "PURE_SYSTEM" + WHEAT_GERM_EXTRACT = "WHEAT_GERM_EXTRACT" + RABBIT_RETICULOCYTE_LYSATE = "RABBIT_RETICULOCYTE_LYSATE" + INSECT_CELL_EXTRACT = "INSECT_CELL_EXTRACT" + HELA_EXTRACT = "HELA_EXTRACT" + CHO_EXTRACT = "CHO_EXTRACT" + YEAST_EXTRACT = "YEAST_EXTRACT" + LEISHMANIA_EXTRACT = "LEISHMANIA_EXTRACT" + VIBRIO_NATRIEGENS_EXTRACT = "VIBRIO_NATRIEGENS_EXTRACT" + TOBACCO_BY2_EXTRACT = "TOBACCO_BY2_EXTRACT" + +# Set metadata after class creation to avoid it becoming an enum member +CellFreeExpressionSystemEnum._metadata = { + "ECOLI_EXTRACT": {'description': 'Escherichia coli crude cell extract (e.g. S30, S12), the most widely used prokaryotic cell-free system for high-yield protein production', 'annotations': {'source_taxon': 'NCBITaxon:562', 'extract_type': 'crude lysate', 'domain': 'prokaryotic'}, 'aliases': ['E. coli extract', 'E. coli lysate', 'S30 extract', 'ECE']}, + "PURE_SYSTEM": {'description': 'Protein synthesis Using Recombinant Elements - a reconstituted system assembled from individually purified E. coli translation factors, ribosomes, and enzymes', 'annotations': {'extract_type': 'reconstituted', 'domain': 'prokaryotic', 'advantage': 'defined composition, low nuclease/protease activity'}, 'aliases': ['PURE', 'PURExpress', 'reconstituted system']}, + "WHEAT_GERM_EXTRACT": {'description': 'Wheat germ (Triticum aestivum) extract, a eukaryotic system favored for expression of complex and difficult eukaryotic proteins', 'annotations': {'source_taxon': 'NCBITaxon:4565', 'extract_type': 'crude lysate', 'domain': 'eukaryotic'}, 'aliases': ['WGE', 'wheat germ system']}, + "RABBIT_RETICULOCYTE_LYSATE": {'description': 'Rabbit (Oryctolagus cuniculus) reticulocyte lysate, a classic mammalian system for in vitro translation and protein labeling', 'meaning': 'BAO:0000255', 'annotations': {'source_taxon': 'NCBITaxon:9986', 'extract_type': 'crude lysate', 'domain': 'eukaryotic'}, 'aliases': ['RRL', 'reticulocyte lysate', 'rabbit reticulocyte lysate format']}, + "INSECT_CELL_EXTRACT": {'description': 'Insect cell extract, typically from Spodoptera frugiperda (Sf21), supporting eukaryotic post-translational modifications', 'annotations': {'source_taxon': 'NCBITaxon:7108', 'extract_type': 'crude lysate', 'domain': 'eukaryotic'}, 'aliases': ['ICE', 'Sf21 extract', 'insect lysate']}, + "HELA_EXTRACT": {'description': 'Human HeLa cell extract used for mammalian cell-free expression with authentic human translation machinery', 'annotations': {'source_taxon': 'NCBITaxon:9606', 'extract_type': 'crude lysate', 'domain': 'eukaryotic'}, 'aliases': ['HeLa lysate', 'human cell extract']}, + "CHO_EXTRACT": {'description': 'Chinese hamster ovary (Cricetulus griseus) cell extract supporting glycosylation and disulfide bond formation', 'annotations': {'source_taxon': 'NCBITaxon:10029', 'extract_type': 'crude lysate', 'domain': 'eukaryotic'}, 'aliases': ['CHO lysate']}, + "YEAST_EXTRACT": {'description': 'Yeast (Saccharomyces cerevisiae) cell extract for eukaryotic cell-free protein synthesis', 'annotations': {'source_taxon': 'NCBITaxon:4932', 'extract_type': 'crude lysate', 'domain': 'eukaryotic'}, 'aliases': ['S. cerevisiae extract', 'yeast lysate']}, + "LEISHMANIA_EXTRACT": {'description': 'Leishmania tarentolae cell extract, a eukaryotic system supporting high yields and post-translational modifications', 'annotations': {'source_taxon': 'NCBITaxon:5689', 'extract_type': 'crude lysate', 'domain': 'eukaryotic'}, 'aliases': ['Leishmania tarentolae extract', 'LTE']}, + "VIBRIO_NATRIEGENS_EXTRACT": {'description': 'Vibrio natriegens cell extract, an emerging fast-growing prokaryotic chassis for rapid, high-yield cell-free expression', 'annotations': {'source_taxon': 'NCBITaxon:691', 'extract_type': 'crude lysate', 'domain': 'prokaryotic'}, 'aliases': ['V. natriegens extract', 'Vmax extract']}, + "TOBACCO_BY2_EXTRACT": {'description': 'Tobacco BY-2 (Nicotiana tabacum bright yellow-2) cell lysate, a plant eukaryotic cell-free system', 'annotations': {'extract_type': 'crude lysate', 'domain': 'eukaryotic'}, 'aliases': ['BY-2 lysate', 'BYL']}, +} + +class CellFreeReactionFormatEnum(RichEnum): + """ + Physical configurations of cell-free expression reactions, differing in how substrates are supplied and byproducts removed, which affects reaction duration and protein yield. + """ + # Enum members + BATCH = "BATCH" + CONTINUOUS_EXCHANGE = "CONTINUOUS_EXCHANGE" + CONTINUOUS_FLOW = "CONTINUOUS_FLOW" + BILAYER = "BILAYER" + LYOPHILIZED = "LYOPHILIZED" + +# Set metadata after class creation to avoid it becoming an enum member +CellFreeReactionFormatEnum._metadata = { + "BATCH": {'description': 'Single closed reaction with all components mixed at the start; simplest format but limited by substrate depletion and byproduct accumulation', 'annotations': {'duration': 'short (hours)'}, 'aliases': ['batch mode']}, + "CONTINUOUS_EXCHANGE": {'description': 'Continuous-exchange cell-free (CECF) format with a semipermeable membrane separating a reaction chamber from a feeding chamber, allowing diffusion of substrates in and byproducts out', 'annotations': {'duration': 'extended (up to ~24 h)'}, 'aliases': ['CECF', 'continuous exchange', 'dialysis mode']}, + "CONTINUOUS_FLOW": {'description': 'Continuous-flow cell-free (CFCF) format in which fresh substrates are continuously pumped through the reaction while product is collected', 'annotations': {'duration': 'extended'}, 'aliases': ['CFCF', 'continuous flow']}, + "BILAYER": {'description': 'Bilayer format where a feeding solution is layered over the reaction mixture without a membrane, prolonging reaction by passive diffusion', 'aliases': ['bilayer mode']}, + "LYOPHILIZED": {'description': 'Freeze-dried (lyophilized) cell-free reaction that is shelf-stable and activated by rehydration; basis of freeze-dried cell-free (FD-CF) diagnostics and portable biomanufacturing', 'annotations': {'advantage': 'cold-chain-free storage and distribution'}, 'aliases': ['freeze-dried', 'FD-CF', 'lyophilised']}, +} + +class EnergyRegenerationSubstrateEnum(RichEnum): + """ + Secondary energy substrates added to cell-free reactions to regenerate ATP and GTP consumed during transcription and translation. Choice of substrate affects cost, reaction longevity, and inorganic phosphate accumulation. + """ + # Enum members + PHOSPHOCREATINE = "PHOSPHOCREATINE" + PHOSPHOENOLPYRUVATE = "PHOSPHOENOLPYRUVATE" + ACETYL_PHOSPHATE = "ACETYL_PHOSPHATE" + THREE_PGA = "THREE_PGA" + GLUCOSE = "GLUCOSE" + GLUCOSE_6_PHOSPHATE = "GLUCOSE_6_PHOSPHATE" + MALTOSE = "MALTOSE" + PYRUVATE = "PYRUVATE" + MALTODEXTRIN = "MALTODEXTRIN" + +# Set metadata after class creation to avoid it becoming an enum member +EnergyRegenerationSubstrateEnum._metadata = { + "PHOSPHOCREATINE": {'description': 'Creatine phosphate (N-phosphocreatine) regenerated with creatine kinase; a classic high-energy phosphate donor', 'meaning': 'CHEBI:17287', 'annotations': {'enzyme': 'creatine kinase'}, 'aliases': ['creatine phosphate', 'phosphocreatine', 'N-phosphocreatine']}, + "PHOSPHOENOLPYRUVATE": {'description': 'Phosphoenolpyruvate (PEP) regenerated with pyruvate kinase; a common high-energy phosphate donor', 'meaning': 'CHEBI:18021', 'annotations': {'enzyme': 'pyruvate kinase'}, 'aliases': ['PEP']}, + "ACETYL_PHOSPHATE": {'description': 'Acetyl phosphate regenerated with acetate kinase; an inexpensive energy source', 'meaning': 'CHEBI:15350', 'annotations': {'enzyme': 'acetate kinase'}, 'aliases': ['AcP', 'acetyl dihydrogen phosphate']}, + "THREE_PGA": {'description': '3-phosphoglycerate (3-PGA), a glycolytic intermediate widely used as a low-cost energy substrate in E. coli cell-free systems', 'meaning': 'CHEBI:17794', 'aliases': ['3-PGA', '3-phosphoglycerate', '3-phospho-D-glycerate', '3-phospho-D-glyceric acid']}, + "GLUCOSE": {'description': 'Glucose feeding glycolysis for ATP regeneration; a very low-cost energy source that requires phosphate buffering', 'meaning': 'CHEBI:17634', 'aliases': ['D-glucose']}, + "GLUCOSE_6_PHOSPHATE": {'description': 'Glucose 6-phosphate fed into glycolysis for energy regeneration', 'meaning': 'CHEBI:14314', 'aliases': ['G6P', 'glucose-6-phosphate', 'D-glucose 6-phosphate']}, + "MALTOSE": {'description': 'Maltose used as a low-cost energy substrate that limits inorganic phosphate accumulation', 'meaning': 'CHEBI:17306'}, + "PYRUVATE": {'description': 'Pyruvate used as an energy source, oxidized via the central metabolism of the extract', 'meaning': 'CHEBI:15361'}, + "MALTODEXTRIN": {'description': 'Maltodextrin (glucose polymer) energy substrate providing slow glucose release and minimal phosphate buildup', 'aliases': ['polymeric glucose']}, +} + +class CellFreeApplicationEnum(RichEnum): + """ + Common applications and use cases for cell-free protein synthesis across research, synthetic biology, and biomanufacturing. + """ + # Enum members + RECOMBINANT_PROTEIN_PRODUCTION = "RECOMBINANT_PROTEIN_PRODUCTION" + MEMBRANE_PROTEIN_EXPRESSION = "MEMBRANE_PROTEIN_EXPRESSION" + DIFFICULT_PROTEIN_EXPRESSION = "DIFFICULT_PROTEIN_EXPRESSION" + GENETIC_CIRCUIT_PROTOTYPING = "GENETIC_CIRCUIT_PROTOTYPING" + METABOLIC_PATHWAY_PROTOTYPING = "METABOLIC_PATHWAY_PROTOTYPING" + BIOSENSOR = "BIOSENSOR" + DIAGNOSTICS = "DIAGNOSTICS" + UNNATURAL_AMINO_ACID_INCORPORATION = "UNNATURAL_AMINO_ACID_INCORPORATION" + PROTEIN_LABELING = "PROTEIN_LABELING" + STRUCTURAL_BIOLOGY = "STRUCTURAL_BIOLOGY" + HIGH_THROUGHPUT_SCREENING = "HIGH_THROUGHPUT_SCREENING" + VACCINE_PRODUCTION = "VACCINE_PRODUCTION" + ANTIBODY_PRODUCTION = "ANTIBODY_PRODUCTION" + EDUCATION = "EDUCATION" + +# Set metadata after class creation to avoid it becoming an enum member +CellFreeApplicationEnum._metadata = { + "RECOMBINANT_PROTEIN_PRODUCTION": {'description': 'General production of recombinant proteins in vitro', 'aliases': ['protein production']}, + "MEMBRANE_PROTEIN_EXPRESSION": {'description': 'Expression of membrane proteins, often co-translationally inserted into liposomes, nanodiscs, or detergent micelles', 'aliases': ['membrane protein synthesis']}, + "DIFFICULT_PROTEIN_EXPRESSION": {'description': 'Expression of toxic, unstable, or otherwise difficult-to-express proteins that are problematic in living cells', 'aliases': ['toxic protein expression']}, + "GENETIC_CIRCUIT_PROTOTYPING": {'description': 'Rapid prototyping and characterization of genetic parts and circuits using in vitro transcription-translation (TX-TL)', 'aliases': ['TX-TL prototyping', 'circuit prototyping']}, + "METABOLIC_PATHWAY_PROTOTYPING": {'description': 'Building and testing enzymatic and metabolic pathways in vitro for cell-free biosynthesis', 'aliases': ['cell-free metabolic engineering', 'pathway prototyping']}, + "BIOSENSOR": {'description': 'Cell-free biosensors, including freeze-dried paper-based sensors for detecting nucleic acids, small molecules, or contaminants', 'meaning': 'NCIT:C16350', 'aliases': ['cell-free biosensor', 'Biosensors']}, + "DIAGNOSTICS": {'description': 'Point-of-care and field-deployable diagnostics, often freeze-dried cell-free reactions coupled to toehold switches or CRISPR readouts', 'aliases': ['point-of-care diagnostics']}, + "UNNATURAL_AMINO_ACID_INCORPORATION": {'description': 'Site-specific incorporation of non-canonical/unnatural amino acids via orthogonal translation components', 'aliases': ['ncAA incorporation', 'non-canonical amino acid incorporation']}, + "PROTEIN_LABELING": {'description': 'Incorporation of radioactive, fluorescent, or isotopic labels for detection and structural studies', 'aliases': ['isotopic labeling', 'radiolabeling']}, + "STRUCTURAL_BIOLOGY": {'description': 'Production of selectively or uniformly isotope-labeled proteins for NMR and other structural studies', 'aliases': ['NMR labeling']}, + "HIGH_THROUGHPUT_SCREENING": {'description': 'Parallelized small-volume expression for protein screening, directed evolution, and library characterization', 'meaning': 'NCIT:C18472', 'aliases': ['HTS']}, + "VACCINE_PRODUCTION": {'description': 'On-demand cell-free production of protein subunit and conjugate vaccine antigens', 'meaning': 'OBI:0000719', 'aliases': ['on-demand vaccine production']}, + "ANTIBODY_PRODUCTION": {'description': 'Cell-free synthesis of antibodies and antibody fragments', 'aliases': ['antibody synthesis']}, + "EDUCATION": {'description': 'Use of cell-free kits for teaching and outreach in synthetic biology', 'aliases': ['teaching']}, +} + class DayOfWeek(RichEnum): """ Days of the week following ISO 8601 standard (Monday = 1) @@ -10775,6 +10893,318 @@ class PlantLeafColorEnum(RichEnum): "BROWN": {'description': 'Brown leaves (dead/dying)', 'annotations': {'hex': '964B00', 'condition': 'senescent or dead'}}, } +class ColorEnum(RichEnum): + """ + A composite chromatic quality composed of hue, saturation and intensity parts. Derived from PATO color (PATO:0000014) child values. + """ + # Enum members + BLACK = "BLACK" + WHITE = "WHITE" + GREY = "GREY" + RED = "RED" + ORANGE = "ORANGE" + YELLOW = "YELLOW" + GREEN = "GREEN" + CYAN = "CYAN" + BLUE = "BLUE" + VIOLET = "VIOLET" + PURPLE = "PURPLE" + MAGENTA = "MAGENTA" + BROWN = "BROWN" + MAROON = "MAROON" + ROSY = "ROSY" + VERMILION = "VERMILION" + COLORED = "COLORED" + +# Set metadata after class creation to avoid it becoming an enum member +ColorEnum._metadata = { + "BLACK": {'description': 'A color that lacks any hues as parts', 'meaning': 'PATO:0000317'}, + "WHITE": {'description': 'An achromatic color of maximum brightness', 'meaning': 'PATO:0000323'}, + "GREY": {'description': 'A color between white and black colors', 'meaning': 'PATO:0000950', 'aliases': ['gray']}, + "RED": {'description': 'A color hue with high wavelength of the long-wave end of the visible spectrum (630-750 nm)', 'meaning': 'PATO:0000322'}, + "ORANGE": {'description': 'A color hue with high-medium wavelength lying between red and yellow (585-620 nm)', 'meaning': 'PATO:0000953'}, + "YELLOW": {'description': 'A color hue with medium wavelength lying between orange and green (570-590 nm)', 'meaning': 'PATO:0000324'}, + "GREEN": {'description': 'A color hue with medium-low wavelength lying between yellow and blue (490-570 nm)', 'meaning': 'PATO:0000320'}, + "CYAN": {'description': 'A color consisting of green and blue hue', 'meaning': 'PATO:0000319'}, + "BLUE": {'description': 'A color hue with low wavelength lying between green and indigo (420-490 nm)', 'meaning': 'PATO:0000318'}, + "VIOLET": {'description': 'A color hue with very low wavelength lying between reddish blue and bluish purple (380-420 nm)', 'meaning': 'PATO:0001424'}, + "PURPLE": {'description': 'A color that falls about midway between red and blue in hue', 'meaning': 'PATO:0000951'}, + "MAGENTA": {'description': 'A color consisting of red and blue hues', 'meaning': 'PATO:0000321'}, + "BROWN": {'description': 'A color consisting of dark orange, red, of very low intensity', 'meaning': 'PATO:0000952'}, + "MAROON": {'description': 'A color consisting of purple and brown hue', 'meaning': 'PATO:0001426'}, + "ROSY": {'description': 'A color hue consisting of red and yellow hue with high brightness', 'meaning': 'PATO:0001425', 'aliases': ['pink']}, + "VERMILION": {'description': 'A color consisting of red and orange hue with a slight amount of gray', 'meaning': 'PATO:0001302'}, + "COLORED": {'description': 'A color quality inhering in a bearer by virtue of having color', 'meaning': 'PATO:0000336'}, +} + +class ShapeEnum(RichEnum): + """ + A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features. Derived from PATO shape (PATO:0000052) child values. + """ + # Enum members + CIRCULAR = "CIRCULAR" + ELLIPTIC = "ELLIPTIC" + SPHEROID = "SPHEROID" + CONICAL = "CONICAL" + COLUMNAR = "COLUMNAR" + TUBULAR = "TUBULAR" + FLAT = "FLAT" + ELONGATED = "ELONGATED" + LINEAR = "LINEAR" + FILAMENTOUS = "FILAMENTOUS" + SLENDER = "SLENDER" + BROAD = "BROAD" + ROBUST = "ROBUST" + STRAIGHT = "STRAIGHT" + BENT = "BENT" + ANGULAR = "ANGULAR" + LOBED = "LOBED" + TRUNCATED = "TRUNCATED" + PYRAMIDAL = "PYRAMIDAL" + STAR_SHAPED = "STAR_SHAPED" + SIGMOID = "SIGMOID" + UNDULATE = "UNDULATE" + PINNATE = "PINNATE" + PLEOMORPHIC = "PLEOMORPHIC" + COILING = "COILING" + +# Set metadata after class creation to avoid it becoming an enum member +ShapeEnum._metadata = { + "CIRCULAR": {'description': 'A shape where every part of the surface or circumference is equidistant from the center', 'meaning': 'PATO:0000411'}, + "ELLIPTIC": {'description': 'Oval with two axes of symmetry, as produced by a conical section', 'meaning': 'PATO:0000947', 'aliases': ['oval']}, + "SPHEROID": {'description': 'A convex 3-D shape obtained by rotating an ellipse about one of its principal axes', 'meaning': 'PATO:0001865'}, + "CONICAL": {'description': 'A convex 3-D shape resembling a cone with a round cross section that tapers', 'meaning': 'PATO:0002021'}, + "COLUMNAR": {'description': 'Elongated and cylindrical in shape', 'meaning': 'PATO:0002063', 'aliases': ['cylindrical']}, + "TUBULAR": {'description': 'A cylindrical shape that is hollow', 'meaning': 'PATO:0002299'}, + "FLAT": {'description': 'Having a horizontal surface without a slope, tilt, or curvature', 'meaning': 'PATO:0000407'}, + "ELONGATED": {'description': 'Length being notably higher relative to width', 'meaning': 'PATO:0001154'}, + "LINEAR": {'description': 'Narrow, with approximately parallel sides', 'meaning': 'PATO:0001199'}, + "FILAMENTOUS": {'description': 'Having thin filaments or thread-like structures', 'meaning': 'PATO:0001360'}, + "SLENDER": {'description': 'Being small or narrow in circumference or width in proportion to length or height', 'meaning': 'PATO:0002212'}, + "BROAD": {'description': 'Width being notably higher relative to comparable entities', 'meaning': 'PATO:0002359'}, + "ROBUST": {'description': 'Being strong, thick, or stout in form', 'meaning': 'PATO:0002310'}, + "STRAIGHT": {'description': 'Free of curves, bends, or angles', 'meaning': 'PATO:0002180'}, + "BENT": {'description': 'Having one or more fixed curves, folds, or angles', 'meaning': 'PATO:0000617'}, + "ANGULAR": {'description': 'Having at least one angle formed by two planes', 'meaning': 'PATO:0001977'}, + "LOBED": {'description': 'Being partly divided into a determinate number of segments', 'meaning': 'PATO:0001979'}, + "TRUNCATED": {'description': 'Terminating abruptly by a transverse line or plane', 'meaning': 'PATO:0000936'}, + "PYRAMIDAL": {'description': 'Having triangular faces meeting at a common point', 'meaning': 'PATO:0002336'}, + "STAR_SHAPED": {'description': 'Being arranged like a star with radiating points', 'meaning': 'PATO:0002065', 'aliases': ['stellate']}, + "SIGMOID": {'description': 'Consisting of two curves in opposite directions like the letter S', 'meaning': 'PATO:0001878'}, + "UNDULATE": {'description': 'Having a sinuate margin that moves smoothly and regularly up and down', 'meaning': 'PATO:0000967', 'aliases': ['wavy']}, + "PINNATE": {'description': 'Having leaflets or branches on each side of a common axis', 'meaning': 'PATO:0000410'}, + "PLEOMORPHIC": {'description': 'Having the ability to take on multiple forms', 'meaning': 'PATO:0001356'}, + "COILING": {'description': 'Being wound in a spiral or helix', 'meaning': 'PATO:0001794', 'aliases': ['coiled', 'helical']}, +} + +class RelativeChangeEnum(RichEnum): + """ + Direction of change of any quality relative to normal or baseline. This is PATO's general-purpose deviation-from-normal axis (PATO:0000069) that crosscuts all specific quality attributes (size, rate, amount, etc.). + """ + # Enum members + NORMAL = "NORMAL" + ABNORMAL = "ABNORMAL" + INCREASED = "INCREASED" + DECREASED = "DECREASED" + INCREASED_MAGNITUDE = "INCREASED_MAGNITUDE" + DECREASED_MAGNITUDE = "DECREASED_MAGNITUDE" + +# Set metadata after class creation to avoid it becoming an enum member +RelativeChangeEnum._metadata = { + "NORMAL": {'description': 'Exhibiting no deviation from normal or average', 'meaning': 'PATO:0000461'}, + "ABNORMAL": {'description': 'Deviating from normal or average', 'meaning': 'PATO:0000460'}, + "INCREASED": {'description': 'A value that is increased compared to normal or average', 'meaning': 'PATO:0002300', 'aliases': ['elevated', 'high']}, + "DECREASED": {'description': 'A value that is decreased compared to normal or average', 'meaning': 'PATO:0002301', 'aliases': ['reduced', 'low']}, + "INCREASED_MAGNITUDE": {'description': 'An increased magnitude of a quality', 'meaning': 'PATO:0002017'}, + "DECREASED_MAGNITUDE": {'description': 'A decreased magnitude of a quality', 'meaning': 'PATO:0002018'}, +} + +class IntensityEnum(RichEnum): + """ + A quality inhering in a bearer by virtue of the bearer's possessing or displaying a distinctive feature in type or degree or effect or force. Derived from PATO intensity (PATO:0000049) child values. + """ + # Enum members + BORDERLINE = "BORDERLINE" + MILD = "MILD" + MODERATE = "MODERATE" + SEVERE = "SEVERE" + PROFOUND = "PROFOUND" + INCREASED_INTENSITY = "INCREASED_INTENSITY" + DECREASED_INTENSITY = "DECREASED_INTENSITY" + REMITTENT = "REMITTENT" + +# Set metadata after class creation to avoid it becoming an enum member +IntensityEnum._metadata = { + "BORDERLINE": {'description': 'Borderline in effect or force compared to baseline or normal', 'meaning': 'PATO:0002628'}, + "MILD": {'description': 'Less than moderate in type or degree or effect or force', 'meaning': 'PATO:0000394'}, + "MODERATE": {'description': 'Less than extreme in type or degree or effect or force', 'meaning': 'PATO:0000395'}, + "SEVERE": {'description': 'Extremely bad or unpleasant in type or degree or effect or force', 'meaning': 'PATO:0000396'}, + "PROFOUND": {'description': 'Very severe in intensity', 'meaning': 'PATO:0002629'}, + "INCREASED_INTENSITY": {'description': 'Intensity which is relatively high', 'meaning': 'PATO:0001782'}, + "DECREASED_INTENSITY": {'description': 'Intensity which is relatively low', 'meaning': 'PATO:0001783'}, + "REMITTENT": {'description': 'Characterised by temporary abatement in severity', 'meaning': 'PATO:0001841'}, +} + +class TextureEnum(RichEnum): + """ + A morphological quality inhering in a bearer by virtue of the bearer's surface characteristics. Derived from PATO texture (PATO:0000150) child values. + """ + # Enum members + SMOOTH = "SMOOTH" + ROUGH = "ROUGH" + SCALY = "SCALY" + FLAKY = "FLAKY" + GROOVED = "GROOVED" + BLISTERED = "BLISTERED" + HAIRY = "HAIRY" + ABRASED = "ABRASED" + RUSTY = "RUSTY" + FOVEATE = "FOVEATE" + +# Set metadata after class creation to avoid it becoming an enum member +TextureEnum._metadata = { + "SMOOTH": {'description': 'Having a surface free of roughness or irregularities', 'meaning': 'PATO:0000701'}, + "ROUGH": {'description': 'Having an irregular surface', 'meaning': 'PATO:0000700'}, + "SCALY": {'description': 'Being covered or partially covered with scales', 'meaning': 'PATO:0001804'}, + "FLAKY": {'description': 'Formed or tending to form flakes or thin, crisp fragments', 'meaning': 'PATO:0001805'}, + "GROOVED": {'description': 'Being marked with one or more channels', 'meaning': 'PATO:0002255'}, + "BLISTERED": {'description': 'Having a local accumulation of fluid underneath the surface', 'meaning': 'PATO:0001928'}, + "HAIRY": {'description': 'Having hair or bristles', 'meaning': 'PATO:0000066', 'aliases': ['pilose', 'hairy']}, + "ABRASED": {'description': 'Having a portion of the surface scraped away', 'meaning': 'PATO:0001849'}, + "RUSTY": {'description': 'Being covered by iron oxide as a result of oxidation', 'meaning': 'PATO:0070059'}, + "FOVEATE": {'description': 'Being marked by the presence of small, shallow, regular depressions', 'meaning': 'PATO:0002296'}, +} + +class PATOBiologicalSexEnum(RichEnum): + """ + An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction. Derived from PATO biological sex (PATO:0000047) and phenotypic sex (PATO:0001894) child values. + """ + # Enum members + FEMALE = "FEMALE" + MALE = "MALE" + HERMAPHRODITE = "HERMAPHRODITE" + MALE_WITH_DSD = "MALE_WITH_DSD" + FEMALE_WITH_DSD = "FEMALE_WITH_DSD" + PSEUDOHERMAPHRODITE = "PSEUDOHERMAPHRODITE" + +# Set metadata after class creation to avoid it becoming an enum member +PATOBiologicalSexEnum._metadata = { + "FEMALE": {'description': 'A biological sex quality inhering in an individual or population that only produces gametes that can be fertilised by male gametes', 'meaning': 'PATO:0000383'}, + "MALE": {'description': 'A biological sex quality inhering in an individual or population whose sex organs contain only male gametes', 'meaning': 'PATO:0000384'}, + "HERMAPHRODITE": {'description': 'A biological sex quality inhering in an organism or population with both male and female sexual organs in one individual', 'meaning': 'PATO:0001340'}, + "MALE_WITH_DSD": {'description': 'A male of a non-hermaphroditic species with ambiguous or atypical congenital development of the reproductive system', 'meaning': 'PATO:0040049'}, + "FEMALE_WITH_DSD": {'description': 'A female of a non-hermaphroditic species with ambiguous or atypical congenital development of the reproductive system', 'meaning': 'PATO:0040056'}, + "PSEUDOHERMAPHRODITE": {'description': 'Having internal reproductive organs of one sex and external sexual characteristics of the other sex', 'meaning': 'PATO:0001827'}, +} + +class MaturityEnum(RichEnum): + """ + A quality of a single physical entity held by a bearer when it exhibits a state of growth, differentiation, or development. Derived from PATO maturity (PATO:0000261) child values. + """ + # Enum members + NEONATAL = "NEONATAL" + LARVAL = "LARVAL" + PREPUBESCENT = "PREPUBESCENT" + PUPAL = "PUPAL" + PREPUPAL = "PREPUPAL" + PUBESCENT = "PUBESCENT" + ADOLESCENT = "ADOLESCENT" + JUVENILE = "JUVENILE" + IMMATURE = "IMMATURE" + MATURE = "MATURE" + +# Set metadata after class creation to avoid it becoming an enum member +MaturityEnum._metadata = { + "NEONATAL": {'description': 'Being at the point or shortly after birth', 'meaning': 'PATO:0002206'}, + "LARVAL": {'description': 'Undergoing indirect development and metamorphosis', 'meaning': 'PATO:0001185'}, + "PREPUBESCENT": {'description': 'Being at the age immediately before puberty', 'meaning': 'PATO:0001186'}, + "PUPAL": {'description': 'Being in the chrysalis (cocoon) or post-larval stage', 'meaning': 'PATO:0001187'}, + "PREPUPAL": {'description': 'Being in an inactive stage between the larval and the pupal stages', 'meaning': 'PATO:0001188'}, + "PUBESCENT": {'description': 'Having arrived at the onset of puberty but not yet fully mature', 'meaning': 'PATO:0000455'}, + "ADOLESCENT": {'description': 'Being between the onset of puberty and maturity', 'meaning': 'PATO:0001189'}, + "JUVENILE": {'description': 'Not fully grown or developed', 'meaning': 'PATO:0001190'}, + "IMMATURE": {'description': 'Lacking complete growth, differentiation, or development', 'meaning': 'PATO:0001501'}, + "MATURE": {'description': 'Exhibiting complete growth, differentiation, or development', 'meaning': 'PATO:0001701', 'aliases': ['adult']}, +} + +class ViabilityEnum(RichEnum): + """ + An organismal quality inhering in a bearer by virtue of the bearer's disposition to survive and develop normally. Derived from PATO viability (PATO:0000169) child values. + """ + # Enum members + ALIVE = "ALIVE" + DEAD = "DEAD" + VIABLE = "VIABLE" + LETHAL = "LETHAL" + SEMI_VIABLE = "SEMI_VIABLE" + SEMI_LETHAL = "SEMI_LETHAL" + IMMORTAL = "IMMORTAL" + DECAYED = "DECAYED" + +# Set metadata after class creation to avoid it becoming an enum member +ViabilityEnum._metadata = { + "ALIVE": {'description': "The bearer's condition before death", 'meaning': 'PATO:0001421'}, + "DEAD": {'description': "The cessation of the bearer's life", 'meaning': 'PATO:0001422'}, + "VIABLE": {'description': "The bearer's ability to survive or the long term survival ability of a given population", 'meaning': 'PATO:0000719'}, + "LETHAL": {'description': "The bearer's long term survival inability", 'meaning': 'PATO:0000718'}, + "SEMI_VIABLE": {'description': "Some of the population members' ability to survive", 'meaning': 'PATO:0001770'}, + "SEMI_LETHAL": {'description': "Some of the population members' inability to survive to reproduce", 'meaning': 'PATO:0001768'}, + "IMMORTAL": {'description': 'Being capable of indefinite growth or division', 'meaning': 'PATO:0001991'}, + "DECAYED": {'description': 'Decomposition into component parts', 'meaning': 'PATO:0001432'}, +} + +class CellularityEnum(RichEnum): + """ + An organismal quality inhering in a bearer by virtue of the bearer's consisting of cells. Derived from PATO cellularity (PATO:0001992) child values. + """ + # Enum members + UNICELLULAR = "UNICELLULAR" + MULTICELLULAR = "MULTICELLULAR" + +# Set metadata after class creation to avoid it becoming an enum member +CellularityEnum._metadata = { + "UNICELLULAR": {'description': 'Consisting of exactly one cell', 'meaning': 'PATO:0001994'}, + "MULTICELLULAR": {'description': 'Consisting of more than one cell', 'meaning': 'PATO:0001993'}, +} + +class SpatialPatternEnum(RichEnum): + """ + A spatial quality inhering in a bearer by virtue of the bearer's exhibiting repetition of placement of its parts. Derived from PATO spatial pattern (PATO:0000060) child values. + """ + # Enum members + LOCALIZED = "LOCALIZED" + UNLOCALISED = "UNLOCALISED" + MULTI_LOCALISED = "MULTI_LOCALISED" + DISTRIBUTED = "DISTRIBUTED" + UNDISTRIBUTED = "UNDISTRIBUTED" + SPARSE = "SPARSE" + UNILATERAL = "UNILATERAL" + VERTICAL = "VERTICAL" + REGULAR_SPATIAL_PATTERN = "REGULAR_SPATIAL_PATTERN" + IRREGULAR_SPATIAL_PATTERN = "IRREGULAR_SPATIAL_PATTERN" + GENERALIZED = "GENERALIZED" + SEGMENTAL = "SEGMENTAL" + RANDOM_PATTERN = "RANDOM_PATTERN" + SYMMETRICAL = "SYMMETRICAL" + +# Set metadata after class creation to avoid it becoming an enum member +SpatialPatternEnum._metadata = { + "LOCALIZED": {'description': 'Being confined or restricted to a particular location', 'meaning': 'PATO:0000627'}, + "UNLOCALISED": {'description': 'Not being confined or restricted to a particular location', 'meaning': 'PATO:0000635', 'aliases': ['diffuse']}, + "MULTI_LOCALISED": {'description': 'Being confined or restricted to multiple locations', 'meaning': 'PATO:0001791'}, + "DISTRIBUTED": {'description': 'Being spread out or scattered about or divided up', 'meaning': 'PATO:0001566'}, + "UNDISTRIBUTED": {'description': 'Not being spread out or scattered about or divided up', 'meaning': 'PATO:0001567'}, + "SPARSE": {'description': 'Being scattered and spread irregularly at a distance from each other', 'meaning': 'PATO:0001609'}, + "UNILATERAL": {'description': 'Involving only one part or side', 'meaning': 'PATO:0000634'}, + "VERTICAL": {'description': 'Being situated at right angles to the horizon', 'meaning': 'PATO:0001854'}, + "REGULAR_SPATIAL_PATTERN": {'description': 'Having a repeatable or predictable placement', 'meaning': 'PATO:0000440'}, + "IRREGULAR_SPATIAL_PATTERN": {'description': 'Magnitude or relationships between repeated parts lack consistency', 'meaning': 'PATO:0000330'}, + "GENERALIZED": {'description': 'Affecting all regions without specificity of distribution', 'meaning': 'PATO:0002403'}, + "SEGMENTAL": {'description': 'Affecting a segment or segments', 'meaning': 'PATO:0002404'}, + "RANDOM_PATTERN": {'description': 'Characterised by an unidentifiable pattern', 'meaning': 'PATO:0002401'}, + "SYMMETRICAL": {'description': 'Correspondence in size, shape, and relative position of parts on opposite sides of a dividing line or about a center or axis', 'meaning': 'PATO:0000965'}, +} + class DNABaseEnum(RichEnum): """ Standard DNA nucleotide bases (canonical) diff --git a/src/valuesets/datamodel/valuesets_pydantic.py b/src/valuesets/datamodel/valuesets_pydantic.py index b07b8c3e..0a5f640a 100644 --- a/src/valuesets/datamodel/valuesets_pydantic.py +++ b/src/valuesets/datamodel/valuesets_pydantic.py @@ -2557,6 +2557,124 @@ class MousePostnatalAgeGroupEnum(RichEnum): "P365_PLUS_AGED": {'description': 'Aged stage from postnatal day 365 onwards (12+ months)', 'annotations': {'postnatal_days': 'P365+', 'approximate_age': '12+ months'}, 'aliases': ['P365+ Aged']}, } +class CellFreeExpressionSystemEnum(RichEnum): + """ + Source extracts and reconstituted systems used for cell-free protein synthesis. Crude lysate systems are derived from cell extracts, while reconstituted systems (e.g. PURE) are assembled from purified components. + """ + # Enum members + ECOLI_EXTRACT = "ECOLI_EXTRACT" + PURE_SYSTEM = "PURE_SYSTEM" + WHEAT_GERM_EXTRACT = "WHEAT_GERM_EXTRACT" + RABBIT_RETICULOCYTE_LYSATE = "RABBIT_RETICULOCYTE_LYSATE" + INSECT_CELL_EXTRACT = "INSECT_CELL_EXTRACT" + HELA_EXTRACT = "HELA_EXTRACT" + CHO_EXTRACT = "CHO_EXTRACT" + YEAST_EXTRACT = "YEAST_EXTRACT" + LEISHMANIA_EXTRACT = "LEISHMANIA_EXTRACT" + VIBRIO_NATRIEGENS_EXTRACT = "VIBRIO_NATRIEGENS_EXTRACT" + TOBACCO_BY2_EXTRACT = "TOBACCO_BY2_EXTRACT" + +# Set metadata after class creation to avoid it becoming an enum member +CellFreeExpressionSystemEnum._metadata = { + "ECOLI_EXTRACT": {'description': 'Escherichia coli crude cell extract (e.g. S30, S12), the most widely used prokaryotic cell-free system for high-yield protein production', 'annotations': {'source_taxon': 'NCBITaxon:562', 'extract_type': 'crude lysate', 'domain': 'prokaryotic'}, 'aliases': ['E. coli extract', 'E. coli lysate', 'S30 extract', 'ECE']}, + "PURE_SYSTEM": {'description': 'Protein synthesis Using Recombinant Elements - a reconstituted system assembled from individually purified E. coli translation factors, ribosomes, and enzymes', 'annotations': {'extract_type': 'reconstituted', 'domain': 'prokaryotic', 'advantage': 'defined composition, low nuclease/protease activity'}, 'aliases': ['PURE', 'PURExpress', 'reconstituted system']}, + "WHEAT_GERM_EXTRACT": {'description': 'Wheat germ (Triticum aestivum) extract, a eukaryotic system favored for expression of complex and difficult eukaryotic proteins', 'annotations': {'source_taxon': 'NCBITaxon:4565', 'extract_type': 'crude lysate', 'domain': 'eukaryotic'}, 'aliases': ['WGE', 'wheat germ system']}, + "RABBIT_RETICULOCYTE_LYSATE": {'description': 'Rabbit (Oryctolagus cuniculus) reticulocyte lysate, a classic mammalian system for in vitro translation and protein labeling', 'meaning': 'BAO:0000255', 'annotations': {'source_taxon': 'NCBITaxon:9986', 'extract_type': 'crude lysate', 'domain': 'eukaryotic'}, 'aliases': ['RRL', 'reticulocyte lysate', 'rabbit reticulocyte lysate format']}, + "INSECT_CELL_EXTRACT": {'description': 'Insect cell extract, typically from Spodoptera frugiperda (Sf21), supporting eukaryotic post-translational modifications', 'annotations': {'source_taxon': 'NCBITaxon:7108', 'extract_type': 'crude lysate', 'domain': 'eukaryotic'}, 'aliases': ['ICE', 'Sf21 extract', 'insect lysate']}, + "HELA_EXTRACT": {'description': 'Human HeLa cell extract used for mammalian cell-free expression with authentic human translation machinery', 'annotations': {'source_taxon': 'NCBITaxon:9606', 'extract_type': 'crude lysate', 'domain': 'eukaryotic'}, 'aliases': ['HeLa lysate', 'human cell extract']}, + "CHO_EXTRACT": {'description': 'Chinese hamster ovary (Cricetulus griseus) cell extract supporting glycosylation and disulfide bond formation', 'annotations': {'source_taxon': 'NCBITaxon:10029', 'extract_type': 'crude lysate', 'domain': 'eukaryotic'}, 'aliases': ['CHO lysate']}, + "YEAST_EXTRACT": {'description': 'Yeast (Saccharomyces cerevisiae) cell extract for eukaryotic cell-free protein synthesis', 'annotations': {'source_taxon': 'NCBITaxon:4932', 'extract_type': 'crude lysate', 'domain': 'eukaryotic'}, 'aliases': ['S. cerevisiae extract', 'yeast lysate']}, + "LEISHMANIA_EXTRACT": {'description': 'Leishmania tarentolae cell extract, a eukaryotic system supporting high yields and post-translational modifications', 'annotations': {'source_taxon': 'NCBITaxon:5689', 'extract_type': 'crude lysate', 'domain': 'eukaryotic'}, 'aliases': ['Leishmania tarentolae extract', 'LTE']}, + "VIBRIO_NATRIEGENS_EXTRACT": {'description': 'Vibrio natriegens cell extract, an emerging fast-growing prokaryotic chassis for rapid, high-yield cell-free expression', 'annotations': {'source_taxon': 'NCBITaxon:691', 'extract_type': 'crude lysate', 'domain': 'prokaryotic'}, 'aliases': ['V. natriegens extract', 'Vmax extract']}, + "TOBACCO_BY2_EXTRACT": {'description': 'Tobacco BY-2 (Nicotiana tabacum bright yellow-2) cell lysate, a plant eukaryotic cell-free system', 'annotations': {'extract_type': 'crude lysate', 'domain': 'eukaryotic'}, 'aliases': ['BY-2 lysate', 'BYL']}, +} + +class CellFreeReactionFormatEnum(RichEnum): + """ + Physical configurations of cell-free expression reactions, differing in how substrates are supplied and byproducts removed, which affects reaction duration and protein yield. + """ + # Enum members + BATCH = "BATCH" + CONTINUOUS_EXCHANGE = "CONTINUOUS_EXCHANGE" + CONTINUOUS_FLOW = "CONTINUOUS_FLOW" + BILAYER = "BILAYER" + LYOPHILIZED = "LYOPHILIZED" + +# Set metadata after class creation to avoid it becoming an enum member +CellFreeReactionFormatEnum._metadata = { + "BATCH": {'description': 'Single closed reaction with all components mixed at the start; simplest format but limited by substrate depletion and byproduct accumulation', 'annotations': {'duration': 'short (hours)'}, 'aliases': ['batch mode']}, + "CONTINUOUS_EXCHANGE": {'description': 'Continuous-exchange cell-free (CECF) format with a semipermeable membrane separating a reaction chamber from a feeding chamber, allowing diffusion of substrates in and byproducts out', 'annotations': {'duration': 'extended (up to ~24 h)'}, 'aliases': ['CECF', 'continuous exchange', 'dialysis mode']}, + "CONTINUOUS_FLOW": {'description': 'Continuous-flow cell-free (CFCF) format in which fresh substrates are continuously pumped through the reaction while product is collected', 'annotations': {'duration': 'extended'}, 'aliases': ['CFCF', 'continuous flow']}, + "BILAYER": {'description': 'Bilayer format where a feeding solution is layered over the reaction mixture without a membrane, prolonging reaction by passive diffusion', 'aliases': ['bilayer mode']}, + "LYOPHILIZED": {'description': 'Freeze-dried (lyophilized) cell-free reaction that is shelf-stable and activated by rehydration; basis of freeze-dried cell-free (FD-CF) diagnostics and portable biomanufacturing', 'annotations': {'advantage': 'cold-chain-free storage and distribution'}, 'aliases': ['freeze-dried', 'FD-CF', 'lyophilised']}, +} + +class EnergyRegenerationSubstrateEnum(RichEnum): + """ + Secondary energy substrates added to cell-free reactions to regenerate ATP and GTP consumed during transcription and translation. Choice of substrate affects cost, reaction longevity, and inorganic phosphate accumulation. + """ + # Enum members + PHOSPHOCREATINE = "PHOSPHOCREATINE" + PHOSPHOENOLPYRUVATE = "PHOSPHOENOLPYRUVATE" + ACETYL_PHOSPHATE = "ACETYL_PHOSPHATE" + THREE_PGA = "THREE_PGA" + GLUCOSE = "GLUCOSE" + GLUCOSE_6_PHOSPHATE = "GLUCOSE_6_PHOSPHATE" + MALTOSE = "MALTOSE" + PYRUVATE = "PYRUVATE" + MALTODEXTRIN = "MALTODEXTRIN" + +# Set metadata after class creation to avoid it becoming an enum member +EnergyRegenerationSubstrateEnum._metadata = { + "PHOSPHOCREATINE": {'description': 'Creatine phosphate (N-phosphocreatine) regenerated with creatine kinase; a classic high-energy phosphate donor', 'meaning': 'CHEBI:17287', 'annotations': {'enzyme': 'creatine kinase'}, 'aliases': ['creatine phosphate', 'phosphocreatine', 'N-phosphocreatine']}, + "PHOSPHOENOLPYRUVATE": {'description': 'Phosphoenolpyruvate (PEP) regenerated with pyruvate kinase; a common high-energy phosphate donor', 'meaning': 'CHEBI:18021', 'annotations': {'enzyme': 'pyruvate kinase'}, 'aliases': ['PEP']}, + "ACETYL_PHOSPHATE": {'description': 'Acetyl phosphate regenerated with acetate kinase; an inexpensive energy source', 'meaning': 'CHEBI:15350', 'annotations': {'enzyme': 'acetate kinase'}, 'aliases': ['AcP', 'acetyl dihydrogen phosphate']}, + "THREE_PGA": {'description': '3-phosphoglycerate (3-PGA), a glycolytic intermediate widely used as a low-cost energy substrate in E. coli cell-free systems', 'meaning': 'CHEBI:17794', 'aliases': ['3-PGA', '3-phosphoglycerate', '3-phospho-D-glycerate', '3-phospho-D-glyceric acid']}, + "GLUCOSE": {'description': 'Glucose feeding glycolysis for ATP regeneration; a very low-cost energy source that requires phosphate buffering', 'meaning': 'CHEBI:17634', 'aliases': ['D-glucose']}, + "GLUCOSE_6_PHOSPHATE": {'description': 'Glucose 6-phosphate fed into glycolysis for energy regeneration', 'meaning': 'CHEBI:14314', 'aliases': ['G6P', 'glucose-6-phosphate', 'D-glucose 6-phosphate']}, + "MALTOSE": {'description': 'Maltose used as a low-cost energy substrate that limits inorganic phosphate accumulation', 'meaning': 'CHEBI:17306'}, + "PYRUVATE": {'description': 'Pyruvate used as an energy source, oxidized via the central metabolism of the extract', 'meaning': 'CHEBI:15361'}, + "MALTODEXTRIN": {'description': 'Maltodextrin (glucose polymer) energy substrate providing slow glucose release and minimal phosphate buildup', 'aliases': ['polymeric glucose']}, +} + +class CellFreeApplicationEnum(RichEnum): + """ + Common applications and use cases for cell-free protein synthesis across research, synthetic biology, and biomanufacturing. + """ + # Enum members + RECOMBINANT_PROTEIN_PRODUCTION = "RECOMBINANT_PROTEIN_PRODUCTION" + MEMBRANE_PROTEIN_EXPRESSION = "MEMBRANE_PROTEIN_EXPRESSION" + DIFFICULT_PROTEIN_EXPRESSION = "DIFFICULT_PROTEIN_EXPRESSION" + GENETIC_CIRCUIT_PROTOTYPING = "GENETIC_CIRCUIT_PROTOTYPING" + METABOLIC_PATHWAY_PROTOTYPING = "METABOLIC_PATHWAY_PROTOTYPING" + BIOSENSOR = "BIOSENSOR" + DIAGNOSTICS = "DIAGNOSTICS" + UNNATURAL_AMINO_ACID_INCORPORATION = "UNNATURAL_AMINO_ACID_INCORPORATION" + PROTEIN_LABELING = "PROTEIN_LABELING" + STRUCTURAL_BIOLOGY = "STRUCTURAL_BIOLOGY" + HIGH_THROUGHPUT_SCREENING = "HIGH_THROUGHPUT_SCREENING" + VACCINE_PRODUCTION = "VACCINE_PRODUCTION" + ANTIBODY_PRODUCTION = "ANTIBODY_PRODUCTION" + EDUCATION = "EDUCATION" + +# Set metadata after class creation to avoid it becoming an enum member +CellFreeApplicationEnum._metadata = { + "RECOMBINANT_PROTEIN_PRODUCTION": {'description': 'General production of recombinant proteins in vitro', 'aliases': ['protein production']}, + "MEMBRANE_PROTEIN_EXPRESSION": {'description': 'Expression of membrane proteins, often co-translationally inserted into liposomes, nanodiscs, or detergent micelles', 'aliases': ['membrane protein synthesis']}, + "DIFFICULT_PROTEIN_EXPRESSION": {'description': 'Expression of toxic, unstable, or otherwise difficult-to-express proteins that are problematic in living cells', 'aliases': ['toxic protein expression']}, + "GENETIC_CIRCUIT_PROTOTYPING": {'description': 'Rapid prototyping and characterization of genetic parts and circuits using in vitro transcription-translation (TX-TL)', 'aliases': ['TX-TL prototyping', 'circuit prototyping']}, + "METABOLIC_PATHWAY_PROTOTYPING": {'description': 'Building and testing enzymatic and metabolic pathways in vitro for cell-free biosynthesis', 'aliases': ['cell-free metabolic engineering', 'pathway prototyping']}, + "BIOSENSOR": {'description': 'Cell-free biosensors, including freeze-dried paper-based sensors for detecting nucleic acids, small molecules, or contaminants', 'meaning': 'NCIT:C16350', 'aliases': ['cell-free biosensor', 'Biosensors']}, + "DIAGNOSTICS": {'description': 'Point-of-care and field-deployable diagnostics, often freeze-dried cell-free reactions coupled to toehold switches or CRISPR readouts', 'aliases': ['point-of-care diagnostics']}, + "UNNATURAL_AMINO_ACID_INCORPORATION": {'description': 'Site-specific incorporation of non-canonical/unnatural amino acids via orthogonal translation components', 'aliases': ['ncAA incorporation', 'non-canonical amino acid incorporation']}, + "PROTEIN_LABELING": {'description': 'Incorporation of radioactive, fluorescent, or isotopic labels for detection and structural studies', 'aliases': ['isotopic labeling', 'radiolabeling']}, + "STRUCTURAL_BIOLOGY": {'description': 'Production of selectively or uniformly isotope-labeled proteins for NMR and other structural studies', 'aliases': ['NMR labeling']}, + "HIGH_THROUGHPUT_SCREENING": {'description': 'Parallelized small-volume expression for protein screening, directed evolution, and library characterization', 'meaning': 'NCIT:C18472', 'aliases': ['HTS']}, + "VACCINE_PRODUCTION": {'description': 'On-demand cell-free production of protein subunit and conjugate vaccine antigens', 'meaning': 'OBI:0000719', 'aliases': ['on-demand vaccine production']}, + "ANTIBODY_PRODUCTION": {'description': 'Cell-free synthesis of antibodies and antibody fragments', 'aliases': ['antibody synthesis']}, + "EDUCATION": {'description': 'Use of cell-free kits for teaching and outreach in synthetic biology', 'aliases': ['teaching']}, +} + class DayOfWeek(RichEnum): """ Days of the week following ISO 8601 standard (Monday = 1) @@ -10775,6 +10893,318 @@ class PlantLeafColorEnum(RichEnum): "BROWN": {'description': 'Brown leaves (dead/dying)', 'annotations': {'hex': '964B00', 'condition': 'senescent or dead'}}, } +class ColorEnum(RichEnum): + """ + A composite chromatic quality composed of hue, saturation and intensity parts. Derived from PATO color (PATO:0000014) child values. + """ + # Enum members + BLACK = "BLACK" + WHITE = "WHITE" + GREY = "GREY" + RED = "RED" + ORANGE = "ORANGE" + YELLOW = "YELLOW" + GREEN = "GREEN" + CYAN = "CYAN" + BLUE = "BLUE" + VIOLET = "VIOLET" + PURPLE = "PURPLE" + MAGENTA = "MAGENTA" + BROWN = "BROWN" + MAROON = "MAROON" + ROSY = "ROSY" + VERMILION = "VERMILION" + COLORED = "COLORED" + +# Set metadata after class creation to avoid it becoming an enum member +ColorEnum._metadata = { + "BLACK": {'description': 'A color that lacks any hues as parts', 'meaning': 'PATO:0000317'}, + "WHITE": {'description': 'An achromatic color of maximum brightness', 'meaning': 'PATO:0000323'}, + "GREY": {'description': 'A color between white and black colors', 'meaning': 'PATO:0000950', 'aliases': ['gray']}, + "RED": {'description': 'A color hue with high wavelength of the long-wave end of the visible spectrum (630-750 nm)', 'meaning': 'PATO:0000322'}, + "ORANGE": {'description': 'A color hue with high-medium wavelength lying between red and yellow (585-620 nm)', 'meaning': 'PATO:0000953'}, + "YELLOW": {'description': 'A color hue with medium wavelength lying between orange and green (570-590 nm)', 'meaning': 'PATO:0000324'}, + "GREEN": {'description': 'A color hue with medium-low wavelength lying between yellow and blue (490-570 nm)', 'meaning': 'PATO:0000320'}, + "CYAN": {'description': 'A color consisting of green and blue hue', 'meaning': 'PATO:0000319'}, + "BLUE": {'description': 'A color hue with low wavelength lying between green and indigo (420-490 nm)', 'meaning': 'PATO:0000318'}, + "VIOLET": {'description': 'A color hue with very low wavelength lying between reddish blue and bluish purple (380-420 nm)', 'meaning': 'PATO:0001424'}, + "PURPLE": {'description': 'A color that falls about midway between red and blue in hue', 'meaning': 'PATO:0000951'}, + "MAGENTA": {'description': 'A color consisting of red and blue hues', 'meaning': 'PATO:0000321'}, + "BROWN": {'description': 'A color consisting of dark orange, red, of very low intensity', 'meaning': 'PATO:0000952'}, + "MAROON": {'description': 'A color consisting of purple and brown hue', 'meaning': 'PATO:0001426'}, + "ROSY": {'description': 'A color hue consisting of red and yellow hue with high brightness', 'meaning': 'PATO:0001425', 'aliases': ['pink']}, + "VERMILION": {'description': 'A color consisting of red and orange hue with a slight amount of gray', 'meaning': 'PATO:0001302'}, + "COLORED": {'description': 'A color quality inhering in a bearer by virtue of having color', 'meaning': 'PATO:0000336'}, +} + +class ShapeEnum(RichEnum): + """ + A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features. Derived from PATO shape (PATO:0000052) child values. + """ + # Enum members + CIRCULAR = "CIRCULAR" + ELLIPTIC = "ELLIPTIC" + SPHEROID = "SPHEROID" + CONICAL = "CONICAL" + COLUMNAR = "COLUMNAR" + TUBULAR = "TUBULAR" + FLAT = "FLAT" + ELONGATED = "ELONGATED" + LINEAR = "LINEAR" + FILAMENTOUS = "FILAMENTOUS" + SLENDER = "SLENDER" + BROAD = "BROAD" + ROBUST = "ROBUST" + STRAIGHT = "STRAIGHT" + BENT = "BENT" + ANGULAR = "ANGULAR" + LOBED = "LOBED" + TRUNCATED = "TRUNCATED" + PYRAMIDAL = "PYRAMIDAL" + STAR_SHAPED = "STAR_SHAPED" + SIGMOID = "SIGMOID" + UNDULATE = "UNDULATE" + PINNATE = "PINNATE" + PLEOMORPHIC = "PLEOMORPHIC" + COILING = "COILING" + +# Set metadata after class creation to avoid it becoming an enum member +ShapeEnum._metadata = { + "CIRCULAR": {'description': 'A shape where every part of the surface or circumference is equidistant from the center', 'meaning': 'PATO:0000411'}, + "ELLIPTIC": {'description': 'Oval with two axes of symmetry, as produced by a conical section', 'meaning': 'PATO:0000947', 'aliases': ['oval']}, + "SPHEROID": {'description': 'A convex 3-D shape obtained by rotating an ellipse about one of its principal axes', 'meaning': 'PATO:0001865'}, + "CONICAL": {'description': 'A convex 3-D shape resembling a cone with a round cross section that tapers', 'meaning': 'PATO:0002021'}, + "COLUMNAR": {'description': 'Elongated and cylindrical in shape', 'meaning': 'PATO:0002063', 'aliases': ['cylindrical']}, + "TUBULAR": {'description': 'A cylindrical shape that is hollow', 'meaning': 'PATO:0002299'}, + "FLAT": {'description': 'Having a horizontal surface without a slope, tilt, or curvature', 'meaning': 'PATO:0000407'}, + "ELONGATED": {'description': 'Length being notably higher relative to width', 'meaning': 'PATO:0001154'}, + "LINEAR": {'description': 'Narrow, with approximately parallel sides', 'meaning': 'PATO:0001199'}, + "FILAMENTOUS": {'description': 'Having thin filaments or thread-like structures', 'meaning': 'PATO:0001360'}, + "SLENDER": {'description': 'Being small or narrow in circumference or width in proportion to length or height', 'meaning': 'PATO:0002212'}, + "BROAD": {'description': 'Width being notably higher relative to comparable entities', 'meaning': 'PATO:0002359'}, + "ROBUST": {'description': 'Being strong, thick, or stout in form', 'meaning': 'PATO:0002310'}, + "STRAIGHT": {'description': 'Free of curves, bends, or angles', 'meaning': 'PATO:0002180'}, + "BENT": {'description': 'Having one or more fixed curves, folds, or angles', 'meaning': 'PATO:0000617'}, + "ANGULAR": {'description': 'Having at least one angle formed by two planes', 'meaning': 'PATO:0001977'}, + "LOBED": {'description': 'Being partly divided into a determinate number of segments', 'meaning': 'PATO:0001979'}, + "TRUNCATED": {'description': 'Terminating abruptly by a transverse line or plane', 'meaning': 'PATO:0000936'}, + "PYRAMIDAL": {'description': 'Having triangular faces meeting at a common point', 'meaning': 'PATO:0002336'}, + "STAR_SHAPED": {'description': 'Being arranged like a star with radiating points', 'meaning': 'PATO:0002065', 'aliases': ['stellate']}, + "SIGMOID": {'description': 'Consisting of two curves in opposite directions like the letter S', 'meaning': 'PATO:0001878'}, + "UNDULATE": {'description': 'Having a sinuate margin that moves smoothly and regularly up and down', 'meaning': 'PATO:0000967', 'aliases': ['wavy']}, + "PINNATE": {'description': 'Having leaflets or branches on each side of a common axis', 'meaning': 'PATO:0000410'}, + "PLEOMORPHIC": {'description': 'Having the ability to take on multiple forms', 'meaning': 'PATO:0001356'}, + "COILING": {'description': 'Being wound in a spiral or helix', 'meaning': 'PATO:0001794', 'aliases': ['coiled', 'helical']}, +} + +class RelativeChangeEnum(RichEnum): + """ + Direction of change of any quality relative to normal or baseline. This is PATO's general-purpose deviation-from-normal axis (PATO:0000069) that crosscuts all specific quality attributes (size, rate, amount, etc.). + """ + # Enum members + NORMAL = "NORMAL" + ABNORMAL = "ABNORMAL" + INCREASED = "INCREASED" + DECREASED = "DECREASED" + INCREASED_MAGNITUDE = "INCREASED_MAGNITUDE" + DECREASED_MAGNITUDE = "DECREASED_MAGNITUDE" + +# Set metadata after class creation to avoid it becoming an enum member +RelativeChangeEnum._metadata = { + "NORMAL": {'description': 'Exhibiting no deviation from normal or average', 'meaning': 'PATO:0000461'}, + "ABNORMAL": {'description': 'Deviating from normal or average', 'meaning': 'PATO:0000460'}, + "INCREASED": {'description': 'A value that is increased compared to normal or average', 'meaning': 'PATO:0002300', 'aliases': ['elevated', 'high']}, + "DECREASED": {'description': 'A value that is decreased compared to normal or average', 'meaning': 'PATO:0002301', 'aliases': ['reduced', 'low']}, + "INCREASED_MAGNITUDE": {'description': 'An increased magnitude of a quality', 'meaning': 'PATO:0002017'}, + "DECREASED_MAGNITUDE": {'description': 'A decreased magnitude of a quality', 'meaning': 'PATO:0002018'}, +} + +class IntensityEnum(RichEnum): + """ + A quality inhering in a bearer by virtue of the bearer's possessing or displaying a distinctive feature in type or degree or effect or force. Derived from PATO intensity (PATO:0000049) child values. + """ + # Enum members + BORDERLINE = "BORDERLINE" + MILD = "MILD" + MODERATE = "MODERATE" + SEVERE = "SEVERE" + PROFOUND = "PROFOUND" + INCREASED_INTENSITY = "INCREASED_INTENSITY" + DECREASED_INTENSITY = "DECREASED_INTENSITY" + REMITTENT = "REMITTENT" + +# Set metadata after class creation to avoid it becoming an enum member +IntensityEnum._metadata = { + "BORDERLINE": {'description': 'Borderline in effect or force compared to baseline or normal', 'meaning': 'PATO:0002628'}, + "MILD": {'description': 'Less than moderate in type or degree or effect or force', 'meaning': 'PATO:0000394'}, + "MODERATE": {'description': 'Less than extreme in type or degree or effect or force', 'meaning': 'PATO:0000395'}, + "SEVERE": {'description': 'Extremely bad or unpleasant in type or degree or effect or force', 'meaning': 'PATO:0000396'}, + "PROFOUND": {'description': 'Very severe in intensity', 'meaning': 'PATO:0002629'}, + "INCREASED_INTENSITY": {'description': 'Intensity which is relatively high', 'meaning': 'PATO:0001782'}, + "DECREASED_INTENSITY": {'description': 'Intensity which is relatively low', 'meaning': 'PATO:0001783'}, + "REMITTENT": {'description': 'Characterised by temporary abatement in severity', 'meaning': 'PATO:0001841'}, +} + +class TextureEnum(RichEnum): + """ + A morphological quality inhering in a bearer by virtue of the bearer's surface characteristics. Derived from PATO texture (PATO:0000150) child values. + """ + # Enum members + SMOOTH = "SMOOTH" + ROUGH = "ROUGH" + SCALY = "SCALY" + FLAKY = "FLAKY" + GROOVED = "GROOVED" + BLISTERED = "BLISTERED" + HAIRY = "HAIRY" + ABRASED = "ABRASED" + RUSTY = "RUSTY" + FOVEATE = "FOVEATE" + +# Set metadata after class creation to avoid it becoming an enum member +TextureEnum._metadata = { + "SMOOTH": {'description': 'Having a surface free of roughness or irregularities', 'meaning': 'PATO:0000701'}, + "ROUGH": {'description': 'Having an irregular surface', 'meaning': 'PATO:0000700'}, + "SCALY": {'description': 'Being covered or partially covered with scales', 'meaning': 'PATO:0001804'}, + "FLAKY": {'description': 'Formed or tending to form flakes or thin, crisp fragments', 'meaning': 'PATO:0001805'}, + "GROOVED": {'description': 'Being marked with one or more channels', 'meaning': 'PATO:0002255'}, + "BLISTERED": {'description': 'Having a local accumulation of fluid underneath the surface', 'meaning': 'PATO:0001928'}, + "HAIRY": {'description': 'Having hair or bristles', 'meaning': 'PATO:0000066', 'aliases': ['pilose', 'hairy']}, + "ABRASED": {'description': 'Having a portion of the surface scraped away', 'meaning': 'PATO:0001849'}, + "RUSTY": {'description': 'Being covered by iron oxide as a result of oxidation', 'meaning': 'PATO:0070059'}, + "FOVEATE": {'description': 'Being marked by the presence of small, shallow, regular depressions', 'meaning': 'PATO:0002296'}, +} + +class PATOBiologicalSexEnum(RichEnum): + """ + An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction. Derived from PATO biological sex (PATO:0000047) and phenotypic sex (PATO:0001894) child values. + """ + # Enum members + FEMALE = "FEMALE" + MALE = "MALE" + HERMAPHRODITE = "HERMAPHRODITE" + MALE_WITH_DSD = "MALE_WITH_DSD" + FEMALE_WITH_DSD = "FEMALE_WITH_DSD" + PSEUDOHERMAPHRODITE = "PSEUDOHERMAPHRODITE" + +# Set metadata after class creation to avoid it becoming an enum member +PATOBiologicalSexEnum._metadata = { + "FEMALE": {'description': 'A biological sex quality inhering in an individual or population that only produces gametes that can be fertilised by male gametes', 'meaning': 'PATO:0000383'}, + "MALE": {'description': 'A biological sex quality inhering in an individual or population whose sex organs contain only male gametes', 'meaning': 'PATO:0000384'}, + "HERMAPHRODITE": {'description': 'A biological sex quality inhering in an organism or population with both male and female sexual organs in one individual', 'meaning': 'PATO:0001340'}, + "MALE_WITH_DSD": {'description': 'A male of a non-hermaphroditic species with ambiguous or atypical congenital development of the reproductive system', 'meaning': 'PATO:0040049'}, + "FEMALE_WITH_DSD": {'description': 'A female of a non-hermaphroditic species with ambiguous or atypical congenital development of the reproductive system', 'meaning': 'PATO:0040056'}, + "PSEUDOHERMAPHRODITE": {'description': 'Having internal reproductive organs of one sex and external sexual characteristics of the other sex', 'meaning': 'PATO:0001827'}, +} + +class MaturityEnum(RichEnum): + """ + A quality of a single physical entity held by a bearer when it exhibits a state of growth, differentiation, or development. Derived from PATO maturity (PATO:0000261) child values. + """ + # Enum members + NEONATAL = "NEONATAL" + LARVAL = "LARVAL" + PREPUBESCENT = "PREPUBESCENT" + PUPAL = "PUPAL" + PREPUPAL = "PREPUPAL" + PUBESCENT = "PUBESCENT" + ADOLESCENT = "ADOLESCENT" + JUVENILE = "JUVENILE" + IMMATURE = "IMMATURE" + MATURE = "MATURE" + +# Set metadata after class creation to avoid it becoming an enum member +MaturityEnum._metadata = { + "NEONATAL": {'description': 'Being at the point or shortly after birth', 'meaning': 'PATO:0002206'}, + "LARVAL": {'description': 'Undergoing indirect development and metamorphosis', 'meaning': 'PATO:0001185'}, + "PREPUBESCENT": {'description': 'Being at the age immediately before puberty', 'meaning': 'PATO:0001186'}, + "PUPAL": {'description': 'Being in the chrysalis (cocoon) or post-larval stage', 'meaning': 'PATO:0001187'}, + "PREPUPAL": {'description': 'Being in an inactive stage between the larval and the pupal stages', 'meaning': 'PATO:0001188'}, + "PUBESCENT": {'description': 'Having arrived at the onset of puberty but not yet fully mature', 'meaning': 'PATO:0000455'}, + "ADOLESCENT": {'description': 'Being between the onset of puberty and maturity', 'meaning': 'PATO:0001189'}, + "JUVENILE": {'description': 'Not fully grown or developed', 'meaning': 'PATO:0001190'}, + "IMMATURE": {'description': 'Lacking complete growth, differentiation, or development', 'meaning': 'PATO:0001501'}, + "MATURE": {'description': 'Exhibiting complete growth, differentiation, or development', 'meaning': 'PATO:0001701', 'aliases': ['adult']}, +} + +class ViabilityEnum(RichEnum): + """ + An organismal quality inhering in a bearer by virtue of the bearer's disposition to survive and develop normally. Derived from PATO viability (PATO:0000169) child values. + """ + # Enum members + ALIVE = "ALIVE" + DEAD = "DEAD" + VIABLE = "VIABLE" + LETHAL = "LETHAL" + SEMI_VIABLE = "SEMI_VIABLE" + SEMI_LETHAL = "SEMI_LETHAL" + IMMORTAL = "IMMORTAL" + DECAYED = "DECAYED" + +# Set metadata after class creation to avoid it becoming an enum member +ViabilityEnum._metadata = { + "ALIVE": {'description': "The bearer's condition before death", 'meaning': 'PATO:0001421'}, + "DEAD": {'description': "The cessation of the bearer's life", 'meaning': 'PATO:0001422'}, + "VIABLE": {'description': "The bearer's ability to survive or the long term survival ability of a given population", 'meaning': 'PATO:0000719'}, + "LETHAL": {'description': "The bearer's long term survival inability", 'meaning': 'PATO:0000718'}, + "SEMI_VIABLE": {'description': "Some of the population members' ability to survive", 'meaning': 'PATO:0001770'}, + "SEMI_LETHAL": {'description': "Some of the population members' inability to survive to reproduce", 'meaning': 'PATO:0001768'}, + "IMMORTAL": {'description': 'Being capable of indefinite growth or division', 'meaning': 'PATO:0001991'}, + "DECAYED": {'description': 'Decomposition into component parts', 'meaning': 'PATO:0001432'}, +} + +class CellularityEnum(RichEnum): + """ + An organismal quality inhering in a bearer by virtue of the bearer's consisting of cells. Derived from PATO cellularity (PATO:0001992) child values. + """ + # Enum members + UNICELLULAR = "UNICELLULAR" + MULTICELLULAR = "MULTICELLULAR" + +# Set metadata after class creation to avoid it becoming an enum member +CellularityEnum._metadata = { + "UNICELLULAR": {'description': 'Consisting of exactly one cell', 'meaning': 'PATO:0001994'}, + "MULTICELLULAR": {'description': 'Consisting of more than one cell', 'meaning': 'PATO:0001993'}, +} + +class SpatialPatternEnum(RichEnum): + """ + A spatial quality inhering in a bearer by virtue of the bearer's exhibiting repetition of placement of its parts. Derived from PATO spatial pattern (PATO:0000060) child values. + """ + # Enum members + LOCALIZED = "LOCALIZED" + UNLOCALISED = "UNLOCALISED" + MULTI_LOCALISED = "MULTI_LOCALISED" + DISTRIBUTED = "DISTRIBUTED" + UNDISTRIBUTED = "UNDISTRIBUTED" + SPARSE = "SPARSE" + UNILATERAL = "UNILATERAL" + VERTICAL = "VERTICAL" + REGULAR_SPATIAL_PATTERN = "REGULAR_SPATIAL_PATTERN" + IRREGULAR_SPATIAL_PATTERN = "IRREGULAR_SPATIAL_PATTERN" + GENERALIZED = "GENERALIZED" + SEGMENTAL = "SEGMENTAL" + RANDOM_PATTERN = "RANDOM_PATTERN" + SYMMETRICAL = "SYMMETRICAL" + +# Set metadata after class creation to avoid it becoming an enum member +SpatialPatternEnum._metadata = { + "LOCALIZED": {'description': 'Being confined or restricted to a particular location', 'meaning': 'PATO:0000627'}, + "UNLOCALISED": {'description': 'Not being confined or restricted to a particular location', 'meaning': 'PATO:0000635', 'aliases': ['diffuse']}, + "MULTI_LOCALISED": {'description': 'Being confined or restricted to multiple locations', 'meaning': 'PATO:0001791'}, + "DISTRIBUTED": {'description': 'Being spread out or scattered about or divided up', 'meaning': 'PATO:0001566'}, + "UNDISTRIBUTED": {'description': 'Not being spread out or scattered about or divided up', 'meaning': 'PATO:0001567'}, + "SPARSE": {'description': 'Being scattered and spread irregularly at a distance from each other', 'meaning': 'PATO:0001609'}, + "UNILATERAL": {'description': 'Involving only one part or side', 'meaning': 'PATO:0000634'}, + "VERTICAL": {'description': 'Being situated at right angles to the horizon', 'meaning': 'PATO:0001854'}, + "REGULAR_SPATIAL_PATTERN": {'description': 'Having a repeatable or predictable placement', 'meaning': 'PATO:0000440'}, + "IRREGULAR_SPATIAL_PATTERN": {'description': 'Magnitude or relationships between repeated parts lack consistency', 'meaning': 'PATO:0000330'}, + "GENERALIZED": {'description': 'Affecting all regions without specificity of distribution', 'meaning': 'PATO:0002403'}, + "SEGMENTAL": {'description': 'Affecting a segment or segments', 'meaning': 'PATO:0002404'}, + "RANDOM_PATTERN": {'description': 'Characterised by an unidentifiable pattern', 'meaning': 'PATO:0002401'}, + "SYMMETRICAL": {'description': 'Correspondence in size, shape, and relative position of parts on opposite sides of a dividing line or about a center or axis', 'meaning': 'PATO:0000965'}, +} + class DNABaseEnum(RichEnum): """ Standard DNA nucleotide bases (canonical) diff --git a/src/valuesets/enums/__init__.py b/src/valuesets/enums/__init__.py index 3c31e97c..29c32a2d 100644 --- a/src/valuesets/enums/__init__.py +++ b/src/valuesets/enums/__init__.py @@ -31,6 +31,7 @@ from .bio.biological_colors import EyeColorEnum, HairColorEnum, FlowerColorEnum, AnimalCoatColorEnum, SkinToneEnum, PlantLeafColorEnum from .bio.biosafety import BiosafetyLevelEnum from .bio.cell_cycle import CellCyclePhase, MitoticPhase, CellCycleCheckpoint, MeioticPhase, CellCycleRegulator, CellProliferationState, DNADamageResponse +from .bio.cell_free_expression import CellFreeExpressionSystemEnum, CellFreeReactionFormatEnum, EnergyRegenerationSubstrateEnum, CellFreeApplicationEnum from .bio.currency_chemicals import CurrencyChemical from .bio.developmental_stages import HumanDevelopmentalStage, MouseDevelopmentalStage, HumanAgeGroupEnum, MousePostnatalAgeGroupEnum from .bio.expression_units import ExpressionUnitEnum, ConcentrationUnitEnum, TimeUnitEnum @@ -43,6 +44,7 @@ from .bio.insdc_geographic_locations import InsdcGeographicLocationEnum from .bio.insdc_missing_values import InsdcMissingValueEnum from .bio.lipid_categories import RelativeTimeEnum, PresenceEnum, LipidCategory +from .bio.pato import ColorEnum, ShapeEnum, RelativeChangeEnum, IntensityEnum, TextureEnum, PATOBiologicalSexEnum, MaturityEnum, ViabilityEnum, CellularityEnum, SpatialPatternEnum from .bio.plant_biology import PlantSexualSystem from .bio.plant_developmental_stages import PlantDevelopmentalStage from .bio.plant_experimental_conditions import PlantStudyConditionEnum, SeasonalEnvironmentExposureEnum, EcologicalEnvironmentExposureEnum, PlantGrowthMediumExposureEnum @@ -326,8 +328,12 @@ "CellCycleCheckpoint", "CellCyclePhase", "CellCycleRegulator", + "CellFreeApplicationEnum", + "CellFreeExpressionSystemEnum", + "CellFreeReactionFormatEnum", "CellPolarity", "CellProliferationState", + "CellularityEnum", "ChipFabricationNodeType", "ChiralityEnum", "ChromatographyType", @@ -336,6 +342,7 @@ "ClinicalBehavioralAssayEnum", "CloudLabExperimentEnum", "CodonEnum", + "ColorEnum", "ColorSpaceEnum", "CommonMineral", "CommonOrganismTaxaEnum", @@ -423,6 +430,7 @@ "EmploymentTypeEnum", "EndocrineDisruptorEnum", "EnergyEfficiencyRating", + "EnergyRegenerationSubstrateEnum", "EnergySource", "EnergyStorageType", "EnergyUnit", @@ -544,6 +552,7 @@ "InspectionTypeEnum", "IntegrationFeatureEnum", "IntegrationSystemEnum", + "IntensityEnum", "IntentClassificationEnum", "InteractionDetectionMethod", "InteractionType", @@ -595,6 +604,7 @@ "MaterialClassEnum", "MaterialPropertyPredictionType", "MaterialsSimulationType", + "MaturityEnum", "MechanicalBehaviorEnum", "MechanicalTestingMethodEnum", "MedicalSpecialtyEnum", @@ -670,6 +680,7 @@ "OutcomeTypeEnum", "OxidationStateEnum", "OxygenationStrategyEnum", + "PATOBiologicalSexEnum", "PCROperationTypeEnum", "PCRPlateTypeEnum", "PVCellType", @@ -758,6 +769,7 @@ "RegulatoryConstraint", "RegulatoryFrameworkEnum", "RelToOxygenEnum", + "RelativeChangeEnum", "RelativeDirection", "RelativeTimeEnum", "RemoteSensingDataType", @@ -798,6 +810,7 @@ "SequencingChemistry", "SequencingPlatform", "SeverityLevelEnum", + "ShapeEnum", "SimpleSpatialDirection", "SkinToneEnum", "SmartManufacturingTechnologyType", @@ -807,6 +820,7 @@ "SourceMaterialTypeEnum", "SourcingStrategyEnum", "SpamClassificationEnum", + "SpatialPatternEnum", "SpatialRelationship", "SpatialResolutionEnum", "SpecimenCollectionMethodEnum", @@ -844,6 +858,7 @@ "TemperatureUnitEnum", "TemporalAggregationEnum", "TextCharset", + "TextureEnum", "TherapeuticActionabilityEnum", "ThermalAnalysisMethodEnum", "ThermalConductivityEnum", @@ -883,6 +898,7 @@ "ValueSetStewardEnum", "VectorTypeEnum", "VendorCategoryEnum", + "ViabilityEnum", "VideoFormatEnum", "ViralGenomeTypeEnum", "VisitProvenanceEnum", diff --git a/src/valuesets/enums/bio/cell_free_expression.py b/src/valuesets/enums/bio/cell_free_expression.py new file mode 100644 index 00000000..1a592b46 --- /dev/null +++ b/src/valuesets/enums/bio/cell_free_expression.py @@ -0,0 +1,136 @@ +""" +Cell-Free Expression Value Sets + +Value sets for cell-free protein synthesis (CFPS), also known as cell-free expression or in vitro transcription-translation (TX-TL). Covers the source extracts/systems, reaction formats, energy regeneration substrates, and common applications used in synthetic biology, structural biology, and biomanufacturing. + +Generated from: bio/cell_free_expression.yaml +""" + +from __future__ import annotations + +from valuesets.generators.rich_enum import RichEnum + +class CellFreeExpressionSystemEnum(RichEnum): + """ + Source extracts and reconstituted systems used for cell-free protein synthesis. Crude lysate systems are derived from cell extracts, while reconstituted systems (e.g. PURE) are assembled from purified components. + """ + # Enum members + ECOLI_EXTRACT = "ECOLI_EXTRACT" + PURE_SYSTEM = "PURE_SYSTEM" + WHEAT_GERM_EXTRACT = "WHEAT_GERM_EXTRACT" + RABBIT_RETICULOCYTE_LYSATE = "RABBIT_RETICULOCYTE_LYSATE" + INSECT_CELL_EXTRACT = "INSECT_CELL_EXTRACT" + HELA_EXTRACT = "HELA_EXTRACT" + CHO_EXTRACT = "CHO_EXTRACT" + YEAST_EXTRACT = "YEAST_EXTRACT" + LEISHMANIA_EXTRACT = "LEISHMANIA_EXTRACT" + VIBRIO_NATRIEGENS_EXTRACT = "VIBRIO_NATRIEGENS_EXTRACT" + TOBACCO_BY2_EXTRACT = "TOBACCO_BY2_EXTRACT" + +# Set metadata after class creation +CellFreeExpressionSystemEnum._metadata = { + "ECOLI_EXTRACT": {'description': 'Escherichia coli crude cell extract (e.g. S30, S12), the most widely used prokaryotic cell-free system for high-yield protein production', 'annotations': {'source_taxon': 'NCBITaxon:562', 'extract_type': 'crude lysate', 'domain': 'prokaryotic'}, 'aliases': ['E. coli extract', 'E. coli lysate', 'S30 extract', 'ECE']}, + "PURE_SYSTEM": {'description': 'Protein synthesis Using Recombinant Elements - a reconstituted system assembled from individually purified E. coli translation factors, ribosomes, and enzymes', 'annotations': {'extract_type': 'reconstituted', 'domain': 'prokaryotic', 'advantage': 'defined composition, low nuclease/protease activity'}, 'aliases': ['PURE', 'PURExpress', 'reconstituted system']}, + "WHEAT_GERM_EXTRACT": {'description': 'Wheat germ (Triticum aestivum) extract, a eukaryotic system favored for expression of complex and difficult eukaryotic proteins', 'annotations': {'source_taxon': 'NCBITaxon:4565', 'extract_type': 'crude lysate', 'domain': 'eukaryotic'}, 'aliases': ['WGE', 'wheat germ system']}, + "RABBIT_RETICULOCYTE_LYSATE": {'description': 'Rabbit (Oryctolagus cuniculus) reticulocyte lysate, a classic mammalian system for in vitro translation and protein labeling', 'meaning': 'BAO:0000255', 'annotations': {'source_taxon': 'NCBITaxon:9986', 'extract_type': 'crude lysate', 'domain': 'eukaryotic'}, 'aliases': ['RRL', 'reticulocyte lysate', 'rabbit reticulocyte lysate format']}, + "INSECT_CELL_EXTRACT": {'description': 'Insect cell extract, typically from Spodoptera frugiperda (Sf21), supporting eukaryotic post-translational modifications', 'annotations': {'source_taxon': 'NCBITaxon:7108', 'extract_type': 'crude lysate', 'domain': 'eukaryotic'}, 'aliases': ['ICE', 'Sf21 extract', 'insect lysate']}, + "HELA_EXTRACT": {'description': 'Human HeLa cell extract used for mammalian cell-free expression with authentic human translation machinery', 'annotations': {'source_taxon': 'NCBITaxon:9606', 'extract_type': 'crude lysate', 'domain': 'eukaryotic'}, 'aliases': ['HeLa lysate', 'human cell extract']}, + "CHO_EXTRACT": {'description': 'Chinese hamster ovary (Cricetulus griseus) cell extract supporting glycosylation and disulfide bond formation', 'annotations': {'source_taxon': 'NCBITaxon:10029', 'extract_type': 'crude lysate', 'domain': 'eukaryotic'}, 'aliases': ['CHO lysate']}, + "YEAST_EXTRACT": {'description': 'Yeast (Saccharomyces cerevisiae) cell extract for eukaryotic cell-free protein synthesis', 'annotations': {'source_taxon': 'NCBITaxon:4932', 'extract_type': 'crude lysate', 'domain': 'eukaryotic'}, 'aliases': ['S. cerevisiae extract', 'yeast lysate']}, + "LEISHMANIA_EXTRACT": {'description': 'Leishmania tarentolae cell extract, a eukaryotic system supporting high yields and post-translational modifications', 'annotations': {'source_taxon': 'NCBITaxon:5689', 'extract_type': 'crude lysate', 'domain': 'eukaryotic'}, 'aliases': ['Leishmania tarentolae extract', 'LTE']}, + "VIBRIO_NATRIEGENS_EXTRACT": {'description': 'Vibrio natriegens cell extract, an emerging fast-growing prokaryotic chassis for rapid, high-yield cell-free expression', 'annotations': {'source_taxon': 'NCBITaxon:691', 'extract_type': 'crude lysate', 'domain': 'prokaryotic'}, 'aliases': ['V. natriegens extract', 'Vmax extract']}, + "TOBACCO_BY2_EXTRACT": {'description': 'Tobacco BY-2 (Nicotiana tabacum bright yellow-2) cell lysate, a plant eukaryotic cell-free system', 'annotations': {'extract_type': 'crude lysate', 'domain': 'eukaryotic'}, 'aliases': ['BY-2 lysate', 'BYL']}, +} + +class CellFreeReactionFormatEnum(RichEnum): + """ + Physical configurations of cell-free expression reactions, differing in how substrates are supplied and byproducts removed, which affects reaction duration and protein yield. + """ + # Enum members + BATCH = "BATCH" + CONTINUOUS_EXCHANGE = "CONTINUOUS_EXCHANGE" + CONTINUOUS_FLOW = "CONTINUOUS_FLOW" + BILAYER = "BILAYER" + LYOPHILIZED = "LYOPHILIZED" + +# Set metadata after class creation +CellFreeReactionFormatEnum._metadata = { + "BATCH": {'description': 'Single closed reaction with all components mixed at the start; simplest format but limited by substrate depletion and byproduct accumulation', 'annotations': {'duration': 'short (hours)'}, 'aliases': ['batch mode']}, + "CONTINUOUS_EXCHANGE": {'description': 'Continuous-exchange cell-free (CECF) format with a semipermeable membrane separating a reaction chamber from a feeding chamber, allowing diffusion of substrates in and byproducts out', 'annotations': {'duration': 'extended (up to ~24 h)'}, 'aliases': ['CECF', 'continuous exchange', 'dialysis mode']}, + "CONTINUOUS_FLOW": {'description': 'Continuous-flow cell-free (CFCF) format in which fresh substrates are continuously pumped through the reaction while product is collected', 'annotations': {'duration': 'extended'}, 'aliases': ['CFCF', 'continuous flow']}, + "BILAYER": {'description': 'Bilayer format where a feeding solution is layered over the reaction mixture without a membrane, prolonging reaction by passive diffusion', 'aliases': ['bilayer mode']}, + "LYOPHILIZED": {'description': 'Freeze-dried (lyophilized) cell-free reaction that is shelf-stable and activated by rehydration; basis of freeze-dried cell-free (FD-CF) diagnostics and portable biomanufacturing', 'annotations': {'advantage': 'cold-chain-free storage and distribution'}, 'aliases': ['freeze-dried', 'FD-CF', 'lyophilised']}, +} + +class EnergyRegenerationSubstrateEnum(RichEnum): + """ + Secondary energy substrates added to cell-free reactions to regenerate ATP and GTP consumed during transcription and translation. Choice of substrate affects cost, reaction longevity, and inorganic phosphate accumulation. + """ + # Enum members + PHOSPHOCREATINE = "PHOSPHOCREATINE" + PHOSPHOENOLPYRUVATE = "PHOSPHOENOLPYRUVATE" + ACETYL_PHOSPHATE = "ACETYL_PHOSPHATE" + THREE_PGA = "THREE_PGA" + GLUCOSE = "GLUCOSE" + GLUCOSE_6_PHOSPHATE = "GLUCOSE_6_PHOSPHATE" + MALTOSE = "MALTOSE" + PYRUVATE = "PYRUVATE" + MALTODEXTRIN = "MALTODEXTRIN" + +# Set metadata after class creation +EnergyRegenerationSubstrateEnum._metadata = { + "PHOSPHOCREATINE": {'description': 'Creatine phosphate (N-phosphocreatine) regenerated with creatine kinase; a classic high-energy phosphate donor', 'meaning': 'CHEBI:17287', 'annotations': {'enzyme': 'creatine kinase'}, 'aliases': ['creatine phosphate', 'phosphocreatine', 'N-phosphocreatine']}, + "PHOSPHOENOLPYRUVATE": {'description': 'Phosphoenolpyruvate (PEP) regenerated with pyruvate kinase; a common high-energy phosphate donor', 'meaning': 'CHEBI:18021', 'annotations': {'enzyme': 'pyruvate kinase'}, 'aliases': ['PEP']}, + "ACETYL_PHOSPHATE": {'description': 'Acetyl phosphate regenerated with acetate kinase; an inexpensive energy source', 'meaning': 'CHEBI:15350', 'annotations': {'enzyme': 'acetate kinase'}, 'aliases': ['AcP', 'acetyl dihydrogen phosphate']}, + "THREE_PGA": {'description': '3-phosphoglycerate (3-PGA), a glycolytic intermediate widely used as a low-cost energy substrate in E. coli cell-free systems', 'meaning': 'CHEBI:17794', 'aliases': ['3-PGA', '3-phosphoglycerate', '3-phospho-D-glycerate', '3-phospho-D-glyceric acid']}, + "GLUCOSE": {'description': 'Glucose feeding glycolysis for ATP regeneration; a very low-cost energy source that requires phosphate buffering', 'meaning': 'CHEBI:17634', 'aliases': ['D-glucose']}, + "GLUCOSE_6_PHOSPHATE": {'description': 'Glucose 6-phosphate fed into glycolysis for energy regeneration', 'meaning': 'CHEBI:14314', 'aliases': ['G6P', 'glucose-6-phosphate', 'D-glucose 6-phosphate']}, + "MALTOSE": {'description': 'Maltose used as a low-cost energy substrate that limits inorganic phosphate accumulation', 'meaning': 'CHEBI:17306'}, + "PYRUVATE": {'description': 'Pyruvate used as an energy source, oxidized via the central metabolism of the extract', 'meaning': 'CHEBI:15361'}, + "MALTODEXTRIN": {'description': 'Maltodextrin (glucose polymer) energy substrate providing slow glucose release and minimal phosphate buildup', 'aliases': ['polymeric glucose']}, +} + +class CellFreeApplicationEnum(RichEnum): + """ + Common applications and use cases for cell-free protein synthesis across research, synthetic biology, and biomanufacturing. + """ + # Enum members + RECOMBINANT_PROTEIN_PRODUCTION = "RECOMBINANT_PROTEIN_PRODUCTION" + MEMBRANE_PROTEIN_EXPRESSION = "MEMBRANE_PROTEIN_EXPRESSION" + DIFFICULT_PROTEIN_EXPRESSION = "DIFFICULT_PROTEIN_EXPRESSION" + GENETIC_CIRCUIT_PROTOTYPING = "GENETIC_CIRCUIT_PROTOTYPING" + METABOLIC_PATHWAY_PROTOTYPING = "METABOLIC_PATHWAY_PROTOTYPING" + BIOSENSOR = "BIOSENSOR" + DIAGNOSTICS = "DIAGNOSTICS" + UNNATURAL_AMINO_ACID_INCORPORATION = "UNNATURAL_AMINO_ACID_INCORPORATION" + PROTEIN_LABELING = "PROTEIN_LABELING" + STRUCTURAL_BIOLOGY = "STRUCTURAL_BIOLOGY" + HIGH_THROUGHPUT_SCREENING = "HIGH_THROUGHPUT_SCREENING" + VACCINE_PRODUCTION = "VACCINE_PRODUCTION" + ANTIBODY_PRODUCTION = "ANTIBODY_PRODUCTION" + EDUCATION = "EDUCATION" + +# Set metadata after class creation +CellFreeApplicationEnum._metadata = { + "RECOMBINANT_PROTEIN_PRODUCTION": {'description': 'General production of recombinant proteins in vitro', 'aliases': ['protein production']}, + "MEMBRANE_PROTEIN_EXPRESSION": {'description': 'Expression of membrane proteins, often co-translationally inserted into liposomes, nanodiscs, or detergent micelles', 'aliases': ['membrane protein synthesis']}, + "DIFFICULT_PROTEIN_EXPRESSION": {'description': 'Expression of toxic, unstable, or otherwise difficult-to-express proteins that are problematic in living cells', 'aliases': ['toxic protein expression']}, + "GENETIC_CIRCUIT_PROTOTYPING": {'description': 'Rapid prototyping and characterization of genetic parts and circuits using in vitro transcription-translation (TX-TL)', 'aliases': ['TX-TL prototyping', 'circuit prototyping']}, + "METABOLIC_PATHWAY_PROTOTYPING": {'description': 'Building and testing enzymatic and metabolic pathways in vitro for cell-free biosynthesis', 'aliases': ['cell-free metabolic engineering', 'pathway prototyping']}, + "BIOSENSOR": {'description': 'Cell-free biosensors, including freeze-dried paper-based sensors for detecting nucleic acids, small molecules, or contaminants', 'meaning': 'NCIT:C16350', 'aliases': ['cell-free biosensor', 'Biosensors']}, + "DIAGNOSTICS": {'description': 'Point-of-care and field-deployable diagnostics, often freeze-dried cell-free reactions coupled to toehold switches or CRISPR readouts', 'aliases': ['point-of-care diagnostics']}, + "UNNATURAL_AMINO_ACID_INCORPORATION": {'description': 'Site-specific incorporation of non-canonical/unnatural amino acids via orthogonal translation components', 'aliases': ['ncAA incorporation', 'non-canonical amino acid incorporation']}, + "PROTEIN_LABELING": {'description': 'Incorporation of radioactive, fluorescent, or isotopic labels for detection and structural studies', 'aliases': ['isotopic labeling', 'radiolabeling']}, + "STRUCTURAL_BIOLOGY": {'description': 'Production of selectively or uniformly isotope-labeled proteins for NMR and other structural studies', 'aliases': ['NMR labeling']}, + "HIGH_THROUGHPUT_SCREENING": {'description': 'Parallelized small-volume expression for protein screening, directed evolution, and library characterization', 'meaning': 'NCIT:C18472', 'aliases': ['HTS']}, + "VACCINE_PRODUCTION": {'description': 'On-demand cell-free production of protein subunit and conjugate vaccine antigens', 'meaning': 'OBI:0000719', 'aliases': ['on-demand vaccine production']}, + "ANTIBODY_PRODUCTION": {'description': 'Cell-free synthesis of antibodies and antibody fragments', 'aliases': ['antibody synthesis']}, + "EDUCATION": {'description': 'Use of cell-free kits for teaching and outreach in synthetic biology', 'aliases': ['teaching']}, +} + +__all__ = [ + "CellFreeExpressionSystemEnum", + "CellFreeReactionFormatEnum", + "EnergyRegenerationSubstrateEnum", + "CellFreeApplicationEnum", +] \ No newline at end of file diff --git a/src/valuesets/enums/bio/pato.py b/src/valuesets/enums/bio/pato.py new file mode 100644 index 00000000..90dda2c9 --- /dev/null +++ b/src/valuesets/enums/bio/pato.py @@ -0,0 +1,336 @@ +""" +PATO Phenotypic Quality Value Sets + +Value sets derived from the Phenotype And Trait Ontology (PATO). Each enum corresponds to a leaf attribute in the PATO hierarchy, with child quality values as permissible values. + +Generated from: bio/pato.yaml +""" + +from __future__ import annotations + +from valuesets.generators.rich_enum import RichEnum + +class ColorEnum(RichEnum): + """ + A composite chromatic quality composed of hue, saturation and intensity parts. Derived from PATO color (PATO:0000014) child values. + """ + # Enum members + BLACK = "BLACK" + WHITE = "WHITE" + GREY = "GREY" + RED = "RED" + ORANGE = "ORANGE" + YELLOW = "YELLOW" + GREEN = "GREEN" + CYAN = "CYAN" + BLUE = "BLUE" + VIOLET = "VIOLET" + PURPLE = "PURPLE" + MAGENTA = "MAGENTA" + BROWN = "BROWN" + MAROON = "MAROON" + ROSY = "ROSY" + VERMILION = "VERMILION" + COLORED = "COLORED" + +# Set metadata after class creation +ColorEnum._metadata = { + "BLACK": {'description': 'A color that lacks any hues as parts', 'meaning': 'PATO:0000317'}, + "WHITE": {'description': 'An achromatic color of maximum brightness', 'meaning': 'PATO:0000323'}, + "GREY": {'description': 'A color between white and black colors', 'meaning': 'PATO:0000950', 'aliases': ['gray']}, + "RED": {'description': 'A color hue with high wavelength of the long-wave end of the visible spectrum (630-750 nm)', 'meaning': 'PATO:0000322'}, + "ORANGE": {'description': 'A color hue with high-medium wavelength lying between red and yellow (585-620 nm)', 'meaning': 'PATO:0000953'}, + "YELLOW": {'description': 'A color hue with medium wavelength lying between orange and green (570-590 nm)', 'meaning': 'PATO:0000324'}, + "GREEN": {'description': 'A color hue with medium-low wavelength lying between yellow and blue (490-570 nm)', 'meaning': 'PATO:0000320'}, + "CYAN": {'description': 'A color consisting of green and blue hue', 'meaning': 'PATO:0000319'}, + "BLUE": {'description': 'A color hue with low wavelength lying between green and indigo (420-490 nm)', 'meaning': 'PATO:0000318'}, + "VIOLET": {'description': 'A color hue with very low wavelength lying between reddish blue and bluish purple (380-420 nm)', 'meaning': 'PATO:0001424'}, + "PURPLE": {'description': 'A color that falls about midway between red and blue in hue', 'meaning': 'PATO:0000951'}, + "MAGENTA": {'description': 'A color consisting of red and blue hues', 'meaning': 'PATO:0000321'}, + "BROWN": {'description': 'A color consisting of dark orange, red, of very low intensity', 'meaning': 'PATO:0000952'}, + "MAROON": {'description': 'A color consisting of purple and brown hue', 'meaning': 'PATO:0001426'}, + "ROSY": {'description': 'A color hue consisting of red and yellow hue with high brightness', 'meaning': 'PATO:0001425', 'aliases': ['pink']}, + "VERMILION": {'description': 'A color consisting of red and orange hue with a slight amount of gray', 'meaning': 'PATO:0001302'}, + "COLORED": {'description': 'A color quality inhering in a bearer by virtue of having color', 'meaning': 'PATO:0000336'}, +} + +class ShapeEnum(RichEnum): + """ + A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features. Derived from PATO shape (PATO:0000052) child values. + """ + # Enum members + CIRCULAR = "CIRCULAR" + ELLIPTIC = "ELLIPTIC" + SPHEROID = "SPHEROID" + CONICAL = "CONICAL" + COLUMNAR = "COLUMNAR" + TUBULAR = "TUBULAR" + FLAT = "FLAT" + ELONGATED = "ELONGATED" + LINEAR = "LINEAR" + FILAMENTOUS = "FILAMENTOUS" + SLENDER = "SLENDER" + BROAD = "BROAD" + ROBUST = "ROBUST" + STRAIGHT = "STRAIGHT" + BENT = "BENT" + ANGULAR = "ANGULAR" + LOBED = "LOBED" + TRUNCATED = "TRUNCATED" + PYRAMIDAL = "PYRAMIDAL" + STAR_SHAPED = "STAR_SHAPED" + SIGMOID = "SIGMOID" + UNDULATE = "UNDULATE" + PINNATE = "PINNATE" + PLEOMORPHIC = "PLEOMORPHIC" + COILING = "COILING" + +# Set metadata after class creation +ShapeEnum._metadata = { + "CIRCULAR": {'description': 'A shape where every part of the surface or circumference is equidistant from the center', 'meaning': 'PATO:0000411'}, + "ELLIPTIC": {'description': 'Oval with two axes of symmetry, as produced by a conical section', 'meaning': 'PATO:0000947', 'aliases': ['oval']}, + "SPHEROID": {'description': 'A convex 3-D shape obtained by rotating an ellipse about one of its principal axes', 'meaning': 'PATO:0001865'}, + "CONICAL": {'description': 'A convex 3-D shape resembling a cone with a round cross section that tapers', 'meaning': 'PATO:0002021'}, + "COLUMNAR": {'description': 'Elongated and cylindrical in shape', 'meaning': 'PATO:0002063', 'aliases': ['cylindrical']}, + "TUBULAR": {'description': 'A cylindrical shape that is hollow', 'meaning': 'PATO:0002299'}, + "FLAT": {'description': 'Having a horizontal surface without a slope, tilt, or curvature', 'meaning': 'PATO:0000407'}, + "ELONGATED": {'description': 'Length being notably higher relative to width', 'meaning': 'PATO:0001154'}, + "LINEAR": {'description': 'Narrow, with approximately parallel sides', 'meaning': 'PATO:0001199'}, + "FILAMENTOUS": {'description': 'Having thin filaments or thread-like structures', 'meaning': 'PATO:0001360'}, + "SLENDER": {'description': 'Being small or narrow in circumference or width in proportion to length or height', 'meaning': 'PATO:0002212'}, + "BROAD": {'description': 'Width being notably higher relative to comparable entities', 'meaning': 'PATO:0002359'}, + "ROBUST": {'description': 'Being strong, thick, or stout in form', 'meaning': 'PATO:0002310'}, + "STRAIGHT": {'description': 'Free of curves, bends, or angles', 'meaning': 'PATO:0002180'}, + "BENT": {'description': 'Having one or more fixed curves, folds, or angles', 'meaning': 'PATO:0000617'}, + "ANGULAR": {'description': 'Having at least one angle formed by two planes', 'meaning': 'PATO:0001977'}, + "LOBED": {'description': 'Being partly divided into a determinate number of segments', 'meaning': 'PATO:0001979'}, + "TRUNCATED": {'description': 'Terminating abruptly by a transverse line or plane', 'meaning': 'PATO:0000936'}, + "PYRAMIDAL": {'description': 'Having triangular faces meeting at a common point', 'meaning': 'PATO:0002336'}, + "STAR_SHAPED": {'description': 'Being arranged like a star with radiating points', 'meaning': 'PATO:0002065', 'aliases': ['stellate']}, + "SIGMOID": {'description': 'Consisting of two curves in opposite directions like the letter S', 'meaning': 'PATO:0001878'}, + "UNDULATE": {'description': 'Having a sinuate margin that moves smoothly and regularly up and down', 'meaning': 'PATO:0000967', 'aliases': ['wavy']}, + "PINNATE": {'description': 'Having leaflets or branches on each side of a common axis', 'meaning': 'PATO:0000410'}, + "PLEOMORPHIC": {'description': 'Having the ability to take on multiple forms', 'meaning': 'PATO:0001356'}, + "COILING": {'description': 'Being wound in a spiral or helix', 'meaning': 'PATO:0001794', 'aliases': ['coiled', 'helical']}, +} + +class RelativeChangeEnum(RichEnum): + """ + Direction of change of any quality relative to normal or baseline. This is PATO's general-purpose deviation-from-normal axis (PATO:0000069) that crosscuts all specific quality attributes (size, rate, amount, etc.). + """ + # Enum members + NORMAL = "NORMAL" + ABNORMAL = "ABNORMAL" + INCREASED = "INCREASED" + DECREASED = "DECREASED" + INCREASED_MAGNITUDE = "INCREASED_MAGNITUDE" + DECREASED_MAGNITUDE = "DECREASED_MAGNITUDE" + +# Set metadata after class creation +RelativeChangeEnum._metadata = { + "NORMAL": {'description': 'Exhibiting no deviation from normal or average', 'meaning': 'PATO:0000461'}, + "ABNORMAL": {'description': 'Deviating from normal or average', 'meaning': 'PATO:0000460'}, + "INCREASED": {'description': 'A value that is increased compared to normal or average', 'meaning': 'PATO:0002300', 'aliases': ['elevated', 'high']}, + "DECREASED": {'description': 'A value that is decreased compared to normal or average', 'meaning': 'PATO:0002301', 'aliases': ['reduced', 'low']}, + "INCREASED_MAGNITUDE": {'description': 'An increased magnitude of a quality', 'meaning': 'PATO:0002017'}, + "DECREASED_MAGNITUDE": {'description': 'A decreased magnitude of a quality', 'meaning': 'PATO:0002018'}, +} + +class IntensityEnum(RichEnum): + """ + A quality inhering in a bearer by virtue of the bearer's possessing or displaying a distinctive feature in type or degree or effect or force. Derived from PATO intensity (PATO:0000049) child values. + """ + # Enum members + BORDERLINE = "BORDERLINE" + MILD = "MILD" + MODERATE = "MODERATE" + SEVERE = "SEVERE" + PROFOUND = "PROFOUND" + INCREASED_INTENSITY = "INCREASED_INTENSITY" + DECREASED_INTENSITY = "DECREASED_INTENSITY" + REMITTENT = "REMITTENT" + +# Set metadata after class creation +IntensityEnum._metadata = { + "BORDERLINE": {'description': 'Borderline in effect or force compared to baseline or normal', 'meaning': 'PATO:0002628'}, + "MILD": {'description': 'Less than moderate in type or degree or effect or force', 'meaning': 'PATO:0000394'}, + "MODERATE": {'description': 'Less than extreme in type or degree or effect or force', 'meaning': 'PATO:0000395'}, + "SEVERE": {'description': 'Extremely bad or unpleasant in type or degree or effect or force', 'meaning': 'PATO:0000396'}, + "PROFOUND": {'description': 'Very severe in intensity', 'meaning': 'PATO:0002629'}, + "INCREASED_INTENSITY": {'description': 'Intensity which is relatively high', 'meaning': 'PATO:0001782'}, + "DECREASED_INTENSITY": {'description': 'Intensity which is relatively low', 'meaning': 'PATO:0001783'}, + "REMITTENT": {'description': 'Characterised by temporary abatement in severity', 'meaning': 'PATO:0001841'}, +} + +class TextureEnum(RichEnum): + """ + A morphological quality inhering in a bearer by virtue of the bearer's surface characteristics. Derived from PATO texture (PATO:0000150) child values. + """ + # Enum members + SMOOTH = "SMOOTH" + ROUGH = "ROUGH" + SCALY = "SCALY" + FLAKY = "FLAKY" + GROOVED = "GROOVED" + BLISTERED = "BLISTERED" + HAIRY = "HAIRY" + ABRASED = "ABRASED" + RUSTY = "RUSTY" + FOVEATE = "FOVEATE" + +# Set metadata after class creation +TextureEnum._metadata = { + "SMOOTH": {'description': 'Having a surface free of roughness or irregularities', 'meaning': 'PATO:0000701'}, + "ROUGH": {'description': 'Having an irregular surface', 'meaning': 'PATO:0000700'}, + "SCALY": {'description': 'Being covered or partially covered with scales', 'meaning': 'PATO:0001804'}, + "FLAKY": {'description': 'Formed or tending to form flakes or thin, crisp fragments', 'meaning': 'PATO:0001805'}, + "GROOVED": {'description': 'Being marked with one or more channels', 'meaning': 'PATO:0002255'}, + "BLISTERED": {'description': 'Having a local accumulation of fluid underneath the surface', 'meaning': 'PATO:0001928'}, + "HAIRY": {'description': 'Having hair or bristles', 'meaning': 'PATO:0000066', 'aliases': ['pilose', 'hairy']}, + "ABRASED": {'description': 'Having a portion of the surface scraped away', 'meaning': 'PATO:0001849'}, + "RUSTY": {'description': 'Being covered by iron oxide as a result of oxidation', 'meaning': 'PATO:0070059'}, + "FOVEATE": {'description': 'Being marked by the presence of small, shallow, regular depressions', 'meaning': 'PATO:0002296'}, +} + +class PATOBiologicalSexEnum(RichEnum): + """ + An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction. Derived from PATO biological sex (PATO:0000047) and phenotypic sex (PATO:0001894) child values. + """ + # Enum members + FEMALE = "FEMALE" + MALE = "MALE" + HERMAPHRODITE = "HERMAPHRODITE" + MALE_WITH_DSD = "MALE_WITH_DSD" + FEMALE_WITH_DSD = "FEMALE_WITH_DSD" + PSEUDOHERMAPHRODITE = "PSEUDOHERMAPHRODITE" + +# Set metadata after class creation +PATOBiologicalSexEnum._metadata = { + "FEMALE": {'description': 'A biological sex quality inhering in an individual or population that only produces gametes that can be fertilised by male gametes', 'meaning': 'PATO:0000383'}, + "MALE": {'description': 'A biological sex quality inhering in an individual or population whose sex organs contain only male gametes', 'meaning': 'PATO:0000384'}, + "HERMAPHRODITE": {'description': 'A biological sex quality inhering in an organism or population with both male and female sexual organs in one individual', 'meaning': 'PATO:0001340'}, + "MALE_WITH_DSD": {'description': 'A male of a non-hermaphroditic species with ambiguous or atypical congenital development of the reproductive system', 'meaning': 'PATO:0040049'}, + "FEMALE_WITH_DSD": {'description': 'A female of a non-hermaphroditic species with ambiguous or atypical congenital development of the reproductive system', 'meaning': 'PATO:0040056'}, + "PSEUDOHERMAPHRODITE": {'description': 'Having internal reproductive organs of one sex and external sexual characteristics of the other sex', 'meaning': 'PATO:0001827'}, +} + +class MaturityEnum(RichEnum): + """ + A quality of a single physical entity held by a bearer when it exhibits a state of growth, differentiation, or development. Derived from PATO maturity (PATO:0000261) child values. + """ + # Enum members + NEONATAL = "NEONATAL" + LARVAL = "LARVAL" + PREPUBESCENT = "PREPUBESCENT" + PUPAL = "PUPAL" + PREPUPAL = "PREPUPAL" + PUBESCENT = "PUBESCENT" + ADOLESCENT = "ADOLESCENT" + JUVENILE = "JUVENILE" + IMMATURE = "IMMATURE" + MATURE = "MATURE" + +# Set metadata after class creation +MaturityEnum._metadata = { + "NEONATAL": {'description': 'Being at the point or shortly after birth', 'meaning': 'PATO:0002206'}, + "LARVAL": {'description': 'Undergoing indirect development and metamorphosis', 'meaning': 'PATO:0001185'}, + "PREPUBESCENT": {'description': 'Being at the age immediately before puberty', 'meaning': 'PATO:0001186'}, + "PUPAL": {'description': 'Being in the chrysalis (cocoon) or post-larval stage', 'meaning': 'PATO:0001187'}, + "PREPUPAL": {'description': 'Being in an inactive stage between the larval and the pupal stages', 'meaning': 'PATO:0001188'}, + "PUBESCENT": {'description': 'Having arrived at the onset of puberty but not yet fully mature', 'meaning': 'PATO:0000455'}, + "ADOLESCENT": {'description': 'Being between the onset of puberty and maturity', 'meaning': 'PATO:0001189'}, + "JUVENILE": {'description': 'Not fully grown or developed', 'meaning': 'PATO:0001190'}, + "IMMATURE": {'description': 'Lacking complete growth, differentiation, or development', 'meaning': 'PATO:0001501'}, + "MATURE": {'description': 'Exhibiting complete growth, differentiation, or development', 'meaning': 'PATO:0001701', 'aliases': ['adult']}, +} + +class ViabilityEnum(RichEnum): + """ + An organismal quality inhering in a bearer by virtue of the bearer's disposition to survive and develop normally. Derived from PATO viability (PATO:0000169) child values. + """ + # Enum members + ALIVE = "ALIVE" + DEAD = "DEAD" + VIABLE = "VIABLE" + LETHAL = "LETHAL" + SEMI_VIABLE = "SEMI_VIABLE" + SEMI_LETHAL = "SEMI_LETHAL" + IMMORTAL = "IMMORTAL" + DECAYED = "DECAYED" + +# Set metadata after class creation +ViabilityEnum._metadata = { + "ALIVE": {'description': "The bearer's condition before death", 'meaning': 'PATO:0001421'}, + "DEAD": {'description': "The cessation of the bearer's life", 'meaning': 'PATO:0001422'}, + "VIABLE": {'description': "The bearer's ability to survive or the long term survival ability of a given population", 'meaning': 'PATO:0000719'}, + "LETHAL": {'description': "The bearer's long term survival inability", 'meaning': 'PATO:0000718'}, + "SEMI_VIABLE": {'description': "Some of the population members' ability to survive", 'meaning': 'PATO:0001770'}, + "SEMI_LETHAL": {'description': "Some of the population members' inability to survive to reproduce", 'meaning': 'PATO:0001768'}, + "IMMORTAL": {'description': 'Being capable of indefinite growth or division', 'meaning': 'PATO:0001991'}, + "DECAYED": {'description': 'Decomposition into component parts', 'meaning': 'PATO:0001432'}, +} + +class CellularityEnum(RichEnum): + """ + An organismal quality inhering in a bearer by virtue of the bearer's consisting of cells. Derived from PATO cellularity (PATO:0001992) child values. + """ + # Enum members + UNICELLULAR = "UNICELLULAR" + MULTICELLULAR = "MULTICELLULAR" + +# Set metadata after class creation +CellularityEnum._metadata = { + "UNICELLULAR": {'description': 'Consisting of exactly one cell', 'meaning': 'PATO:0001994'}, + "MULTICELLULAR": {'description': 'Consisting of more than one cell', 'meaning': 'PATO:0001993'}, +} + +class SpatialPatternEnum(RichEnum): + """ + A spatial quality inhering in a bearer by virtue of the bearer's exhibiting repetition of placement of its parts. Derived from PATO spatial pattern (PATO:0000060) child values. + """ + # Enum members + LOCALIZED = "LOCALIZED" + UNLOCALISED = "UNLOCALISED" + MULTI_LOCALISED = "MULTI_LOCALISED" + DISTRIBUTED = "DISTRIBUTED" + UNDISTRIBUTED = "UNDISTRIBUTED" + SPARSE = "SPARSE" + UNILATERAL = "UNILATERAL" + VERTICAL = "VERTICAL" + REGULAR_SPATIAL_PATTERN = "REGULAR_SPATIAL_PATTERN" + IRREGULAR_SPATIAL_PATTERN = "IRREGULAR_SPATIAL_PATTERN" + GENERALIZED = "GENERALIZED" + SEGMENTAL = "SEGMENTAL" + RANDOM_PATTERN = "RANDOM_PATTERN" + SYMMETRICAL = "SYMMETRICAL" + +# Set metadata after class creation +SpatialPatternEnum._metadata = { + "LOCALIZED": {'description': 'Being confined or restricted to a particular location', 'meaning': 'PATO:0000627'}, + "UNLOCALISED": {'description': 'Not being confined or restricted to a particular location', 'meaning': 'PATO:0000635', 'aliases': ['diffuse']}, + "MULTI_LOCALISED": {'description': 'Being confined or restricted to multiple locations', 'meaning': 'PATO:0001791'}, + "DISTRIBUTED": {'description': 'Being spread out or scattered about or divided up', 'meaning': 'PATO:0001566'}, + "UNDISTRIBUTED": {'description': 'Not being spread out or scattered about or divided up', 'meaning': 'PATO:0001567'}, + "SPARSE": {'description': 'Being scattered and spread irregularly at a distance from each other', 'meaning': 'PATO:0001609'}, + "UNILATERAL": {'description': 'Involving only one part or side', 'meaning': 'PATO:0000634'}, + "VERTICAL": {'description': 'Being situated at right angles to the horizon', 'meaning': 'PATO:0001854'}, + "REGULAR_SPATIAL_PATTERN": {'description': 'Having a repeatable or predictable placement', 'meaning': 'PATO:0000440'}, + "IRREGULAR_SPATIAL_PATTERN": {'description': 'Magnitude or relationships between repeated parts lack consistency', 'meaning': 'PATO:0000330'}, + "GENERALIZED": {'description': 'Affecting all regions without specificity of distribution', 'meaning': 'PATO:0002403'}, + "SEGMENTAL": {'description': 'Affecting a segment or segments', 'meaning': 'PATO:0002404'}, + "RANDOM_PATTERN": {'description': 'Characterised by an unidentifiable pattern', 'meaning': 'PATO:0002401'}, + "SYMMETRICAL": {'description': 'Correspondence in size, shape, and relative position of parts on opposite sides of a dividing line or about a center or axis', 'meaning': 'PATO:0000965'}, +} + +__all__ = [ + "ColorEnum", + "ShapeEnum", + "RelativeChangeEnum", + "IntensityEnum", + "TextureEnum", + "PATOBiologicalSexEnum", + "MaturityEnum", + "ViabilityEnum", + "CellularityEnum", + "SpatialPatternEnum", +] \ No newline at end of file