diff --git a/src/valuesets/schema/bio/pato.yaml b/src/valuesets/schema/bio/pato.yaml new file mode 100644 index 00000000..b55b698c --- /dev/null +++ b/src/valuesets/schema/bio/pato.yaml @@ -0,0 +1,644 @@ +name: pato +title: PATO Phenotypic Quality Value Sets +description: >- + 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. +id: https://w3id.org/valuesets/bio/pato +imports: +- linkml:types +prefixes: + linkml: https://w3id.org/linkml/ + PATO: http://purl.obolibrary.org/obo/PATO_ + valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ +default_prefix: valuesets +slots: + pato_color: + description: Color quality of an entity + range: ColorEnum + pato_shape: + description: Shape quality of an entity + range: ShapeEnum + pato_relative_change: + description: Direction of change of a quality relative to normal or baseline + range: RelativeChangeEnum + pato_intensity: + description: Intensity or severity of a quality + range: IntensityEnum + pato_texture: + description: Surface texture quality of an entity + range: TextureEnum + pato_biological_sex: + description: Biological sex quality of an organism (PATO phenotypic sex) + range: PATOBiologicalSexEnum + pato_maturity: + description: Maturity or developmental stage quality of an organism + range: MaturityEnum + pato_viability: + description: Viability quality of an organism or cell + range: ViabilityEnum + pato_cellularity: + description: Cellularity quality of an organism + range: CellularityEnum + pato_spatial_pattern: + description: Spatial pattern quality of an entity + range: SpatialPatternEnum +enums: + ColorEnum: + title: Color + description: >- + A composite chromatic quality composed of hue, saturation and intensity parts. + Derived from PATO color (PATO:0000014) child values. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + BLACK: + description: A color that lacks any hues as parts + meaning: PATO:0000317 + title: black + WHITE: + description: An achromatic color of maximum brightness + meaning: PATO:0000323 + title: white + GREY: + description: A color between white and black colors + meaning: PATO:0000950 + title: grey + 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 + title: red + ORANGE: + description: A color hue with high-medium wavelength lying between red and yellow (585-620 nm) + meaning: PATO:0000953 + title: orange + YELLOW: + description: A color hue with medium wavelength lying between orange and green (570-590 nm) + meaning: PATO:0000324 + title: yellow + GREEN: + description: A color hue with medium-low wavelength lying between yellow and blue (490-570 nm) + meaning: PATO:0000320 + title: green + CYAN: + description: A color consisting of green and blue hue + meaning: PATO:0000319 + title: cyan + BLUE: + description: A color hue with low wavelength lying between green and indigo (420-490 nm) + meaning: PATO:0000318 + title: blue + 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: + description: A color that falls about midway between red and blue in hue + meaning: PATO:0000951 + title: purple + MAGENTA: + description: A color consisting of red and blue hues + meaning: PATO:0000321 + title: magenta + BROWN: + description: A color consisting of dark orange, red, of very low intensity + meaning: PATO:0000952 + title: brown + MAROON: + description: A color consisting of purple and brown hue + meaning: PATO:0001426 + title: maroon + ROSY: + description: A color hue consisting of red and yellow hue with high brightness + meaning: PATO:0001425 + title: rosy + aliases: + - pink + VERMILION: + description: A color consisting of red and orange hue with a slight amount of gray + meaning: PATO:0001302 + title: vermilion + COLORED: + description: A color quality inhering in a bearer by virtue of having color + meaning: PATO:0000336 + title: colored + + ShapeEnum: + title: Shape + 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. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + CIRCULAR: + description: A shape where every part of the surface or circumference is equidistant from the center + meaning: PATO:0000411 + title: circular + ELLIPTIC: + description: Oval with two axes of symmetry, as produced by a conical section + meaning: PATO:0000947 + title: elliptic + aliases: + - oval + SPHEROID: + description: A convex 3-D shape obtained by rotating an ellipse about one of its principal axes + meaning: PATO:0001865 + title: spheroid + CONICAL: + description: A convex 3-D shape resembling a cone with a round cross section that tapers + meaning: PATO:0002021 + title: conical + COLUMNAR: + description: Elongated and cylindrical in shape + meaning: PATO:0002063 + title: columnar + aliases: + - cylindrical + TUBULAR: + description: A cylindrical shape that is hollow + meaning: PATO:0002299 + title: tubular + FLAT: + description: Having a horizontal surface without a slope, tilt, or curvature + meaning: PATO:0000407 + title: flat + ELONGATED: + description: Length being notably higher relative to width + meaning: PATO:0001154 + title: elongated + LINEAR: + description: Narrow, with approximately parallel sides + meaning: PATO:0001199 + title: linear + FILAMENTOUS: + description: Having thin filaments or thread-like structures + meaning: PATO:0001360 + title: filamentous + SLENDER: + description: Being small or narrow in circumference or width in proportion to length or height + meaning: PATO:0002212 + title: slender + BROAD: + description: Width being notably higher relative to comparable entities + meaning: PATO:0002359 + title: broad + ROBUST: + description: Being strong, thick, or stout in form + meaning: PATO:0002310 + title: robust + STRAIGHT: + description: Free of curves, bends, or angles + meaning: PATO:0002180 + title: straight + BENT: + description: Having one or more fixed curves, folds, or angles + meaning: PATO:0000617 + title: bent + ANGULAR: + description: Having at least one angle formed by two planes + meaning: PATO:0001977 + title: angular + LOBED: + description: Being partly divided into a determinate number of segments + meaning: PATO:0001979 + title: lobed + TRUNCATED: + description: Terminating abruptly by a transverse line or plane + meaning: PATO:0000936 + title: truncated + PYRAMIDAL: + description: Having triangular faces meeting at a common point + meaning: PATO:0002336 + title: pyramidal + STAR_SHAPED: + description: Being arranged like a star with radiating points + meaning: PATO:0002065 + title: star shaped + aliases: + - stellate + SIGMOID: + description: Consisting of two curves in opposite directions like the letter S + meaning: PATO:0001878 + title: sigmoid + UNDULATE: + description: Having a sinuate margin that moves smoothly and regularly up and down + meaning: PATO:0000967 + title: undulate + aliases: + - wavy + PINNATE: + description: Having leaflets or branches on each side of a common axis + meaning: PATO:0000410 + title: pinnate + PLEOMORPHIC: + description: Having the ability to take on multiple forms + meaning: PATO:0001356 + title: pleomorphic + COILING: + description: Being wound in a spiral or helix + meaning: PATO:0001794 + title: coiling + aliases: + - coiled + - helical + + RelativeChangeEnum: + title: Relative Change + 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.). + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + NORMAL: + description: Exhibiting no deviation from normal or average + meaning: PATO:0000461 + title: normal + ABNORMAL: + description: Deviating from normal or average + meaning: PATO:0000460 + title: abnormal + INCREASED: + description: A value that is increased compared to normal or average + meaning: PATO:0002300 + title: increased quality + aliases: + - elevated + - high + DECREASED: + description: A value that is decreased compared to normal or average + meaning: PATO:0002301 + title: decreased quality + aliases: + - reduced + - low + INCREASED_MAGNITUDE: + description: An increased magnitude of a quality + meaning: PATO:0002017 + title: increased magnitude + DECREASED_MAGNITUDE: + description: A decreased magnitude of a quality + meaning: PATO:0002018 + title: decreased magnitude + + IntensityEnum: + title: Intensity + 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. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + BORDERLINE: + description: Borderline in effect or force compared to baseline or normal + meaning: PATO:0002628 + title: borderline intensity + MILD: + description: Less than moderate in type or degree or effect or force + meaning: PATO:0000394 + title: mild intensity + MODERATE: + description: Less than extreme in type or degree or effect or force + meaning: PATO:0000395 + title: moderate intensity + SEVERE: + description: Extremely bad or unpleasant in type or degree or effect or force + meaning: PATO:0000396 + title: severe intensity + PROFOUND: + description: Very severe in intensity + meaning: PATO:0002629 + title: profound intensity + INCREASED_INTENSITY: + description: Intensity which is relatively high + meaning: PATO:0001782 + title: increased intensity + DECREASED_INTENSITY: + description: Intensity which is relatively low + meaning: PATO:0001783 + title: decreased intensity + REMITTENT: + description: Characterised by temporary abatement in severity + meaning: PATO:0001841 + title: remittent intensity + + TextureEnum: + title: Texture + description: >- + A morphological quality inhering in a bearer by virtue of the bearer's surface + characteristics. Derived from PATO texture (PATO:0000150) child values. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + SMOOTH: + description: Having a surface free of roughness or irregularities + meaning: PATO:0000701 + title: smooth + ROUGH: + description: Having an irregular surface + meaning: PATO:0000700 + title: rough + SCALY: + description: Being covered or partially covered with scales + meaning: PATO:0001804 + title: scaly + FLAKY: + description: Formed or tending to form flakes or thin, crisp fragments + meaning: PATO:0001805 + title: flaky + GROOVED: + description: Being marked with one or more channels + meaning: PATO:0002255 + title: grooved + BLISTERED: + description: Having a local accumulation of fluid underneath the surface + meaning: PATO:0001928 + title: blistered + HAIRY: + description: Having hair or bristles + meaning: PATO:0000066 + title: pilose + aliases: + - pilose + - hairy + ABRASED: + description: Having a portion of the surface scraped away + meaning: PATO:0001849 + title: abrased + RUSTY: + description: Being covered by iron oxide as a result of oxidation + meaning: PATO:0070059 + title: rusty + FOVEATE: + description: Being marked by the presence of small, shallow, regular depressions + meaning: PATO:0002296 + title: foveate + + PATOBiologicalSexEnum: + title: Biological Sex (PATO) + 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. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + 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: + description: A biological sex quality inhering in an individual or population whose sex organs + contain only male gametes + meaning: PATO:0000384 + title: male + 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: + 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: + 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: + description: Having internal reproductive organs of one sex and external sexual characteristics + of the other sex + meaning: PATO:0001827 + title: pseudohermaphrodite + + MaturityEnum: + title: Maturity + 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. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + NEONATAL: + description: Being at the point or shortly after birth + meaning: PATO:0002206 + title: neonatal + LARVAL: + description: Undergoing indirect development and metamorphosis + meaning: PATO:0001185 + title: larval + PREPUBESCENT: + description: Being at the age immediately before puberty + meaning: PATO:0001186 + title: prepubescent + PUPAL: + description: Being in the chrysalis (cocoon) or post-larval stage + meaning: PATO:0001187 + title: pupal + PREPUPAL: + description: Being in an inactive stage between the larval and the pupal stages + meaning: PATO:0001188 + title: prepupal + PUBESCENT: + description: Having arrived at the onset of puberty but not yet fully mature + meaning: PATO:0000455 + title: pubescent + ADOLESCENT: + description: Being between the onset of puberty and maturity + meaning: PATO:0001189 + title: adolescent + JUVENILE: + description: Not fully grown or developed + meaning: PATO:0001190 + title: juvenile + IMMATURE: + description: Lacking complete growth, differentiation, or development + meaning: PATO:0001501 + title: immature + MATURE: + description: Exhibiting complete growth, differentiation, or development + meaning: PATO:0001701 + title: mature + aliases: + - adult + + ViabilityEnum: + title: Viability + 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. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + ALIVE: + description: The bearer's condition before death + meaning: PATO:0001421 + title: alive + DEAD: + description: The cessation of the bearer's life + meaning: PATO:0001422 + title: dead + VIABLE: + description: The bearer's ability to survive or the long term survival ability of a given population + meaning: PATO:0000719 + title: viable + LETHAL: + description: The bearer's long term survival inability + meaning: PATO:0000718 + title: lethal (sensu genetics) + SEMI_VIABLE: + description: Some of the population members' ability to survive + meaning: PATO:0001770 + title: semi-viable + SEMI_LETHAL: + description: Some of the population members' inability to survive to reproduce + meaning: PATO:0001768 + title: semi-lethal (sensu genetics) + IMMORTAL: + description: Being capable of indefinite growth or division + meaning: PATO:0001991 + title: immortal + DECAYED: + description: Decomposition into component parts + meaning: PATO:0001432 + title: decayed + + CellularityEnum: + title: Cellularity + 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. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + UNICELLULAR: + description: Consisting of exactly one cell + meaning: PATO:0001994 + title: unicellular + MULTICELLULAR: + description: Consisting of more than one cell + meaning: PATO:0001993 + title: multicellular + + SpatialPatternEnum: + title: Spatial Pattern + 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. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + LOCALIZED: + description: Being confined or restricted to a particular location + meaning: PATO:0000627 + title: localized + UNLOCALISED: + description: Not being confined or restricted to a particular location + meaning: PATO:0000635 + title: unlocalised + aliases: + - diffuse + MULTI_LOCALISED: + description: Being confined or restricted to multiple locations + meaning: PATO:0001791 + title: multi-localised + DISTRIBUTED: + description: Being spread out or scattered about or divided up + meaning: PATO:0001566 + title: distributed + UNDISTRIBUTED: + description: Not being spread out or scattered about or divided up + meaning: PATO:0001567 + title: undistributed + SPARSE: + description: Being scattered and spread irregularly at a distance from each other + meaning: PATO:0001609 + title: sparse + UNILATERAL: + description: Involving only one part or side + meaning: PATO:0000634 + title: unilateral + VERTICAL: + description: Being situated at right angles to the horizon + meaning: PATO:0001854 + title: vertical + REGULAR_SPATIAL_PATTERN: + description: Having a repeatable or predictable placement + meaning: PATO:0000440 + title: regular spatial pattern + IRREGULAR_SPATIAL_PATTERN: + description: Magnitude or relationships between repeated parts lack consistency + meaning: PATO:0000330 + title: irregular spatial pattern + GENERALIZED: + description: Affecting all regions without specificity of distribution + meaning: PATO:0002403 + title: generalized + SEGMENTAL: + description: Affecting a segment or segments + meaning: PATO:0002404 + title: segmental + RANDOM_PATTERN: + description: Characterised by an unidentifiable pattern + meaning: PATO:0002401 + title: random pattern + 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 diff --git a/src/valuesets/schema/valuesets.yaml b/src/valuesets/schema/valuesets.yaml index fddac088..5712647c 100644 --- a/src/valuesets/schema/valuesets.yaml +++ b/src/valuesets/schema/valuesets.yaml @@ -84,6 +84,7 @@ imports: - materials_science/pigments_dyes - visual/colors - bio/biological_colors +- bio/pato - bio/sequence_alphabets - bio/sequence_chemistry - bio/sequencing_platforms