valuesets 0.3.1__py3-none-any.whl

valuesets/schema/bio/cell_cycle.yaml

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+name: cell_cycle
+title: Cell Cycle Value Sets
+description: Value sets for cell cycle phases, checkpoints, and related concepts
+id: https://w3id.org/linkml/valuesets/bio/cell_cycle
+imports:
+- linkml:types
+prefixes:
+  valuesets: https://w3id.org/valuesets/
+  GO: http://purl.obolibrary.org/obo/GO_
+default_prefix: valuesets
+slots:
+  cell_cycle_phase:
+    description: Major phases of the eukaryotic cell cycle
+    range: CellCyclePhase
+  mitotic_phase:
+    description: Stages of mitosis (M phase)
+    range: MitoticPhase
+  cell_cycle_checkpoint:
+    description: Cell cycle checkpoints that regulate progression
+    range: CellCycleCheckpoint
+  meiotic_phase:
+    description: Phases specific to meiotic cell division
+    range: MeioticPhase
+  cell_cycle_regulator:
+    description: Types of cell cycle regulatory molecules
+    range: CellCycleRegulator
+  cell_proliferation_state:
+    description: Cell proliferation and growth states
+    range: CellProliferationState
+  dna_damage_response:
+    description: DNA damage response pathways during cell cycle
+    range: DNADamageResponse
+enums:
+  CellCyclePhase:
+    description: Major phases of the eukaryotic cell cycle
+    permissible_values:
+      G0:
+        description: G0 phase (quiescent/resting phase)
+        meaning: GO:0044838
+        title: cell quiescence
+        annotations:
+          aliases: quiescent phase, resting phase
+      G1:
+        description: G1 phase (Gap 1)
+        meaning: GO:0051318
+        title: G1 phase
+        annotations:
+          aliases: Gap 1, first gap phase
+          duration: variable (hours to years)
+      S:
+        description: S phase (DNA synthesis)
+        meaning: GO:0051320
+        title: S phase
+        annotations:
+          aliases: synthesis phase, DNA replication phase
+          duration: 6-8 hours
+      G2:
+        description: G2 phase (Gap 2)
+        meaning: GO:0051319
+        title: G2 phase
+        annotations:
+          aliases: Gap 2, second gap phase
+          duration: 3-4 hours
+      M:
+        description: M phase (mitosis and cytokinesis)
+        meaning: GO:0000279
+        title: M phase
+        annotations:
+          aliases: mitotic phase, division phase
+          duration: ~1 hour
+      INTERPHASE:
+        description: Interphase (G1, S, and G2 phases combined)
+        meaning: GO:0051325
+        annotations:
+          includes: G1, S, G2
+  MitoticPhase:
+    description: Stages of mitosis (M phase)
+    permissible_values:
+      PROPHASE:
+        description: Prophase
+        meaning: GO:0051324
+        annotations:
+          order: 1
+          features: chromatin condensation, spindle formation begins
+      PROMETAPHASE:
+        description: Prometaphase
+        meaning: GO:0007080
+        title: mitotic metaphase chromosome alignment
+        annotations:
+          order: 2
+          features: nuclear envelope breakdown, kinetochore attachment
+      METAPHASE:
+        description: Metaphase
+        meaning: GO:0051323
+        annotations:
+          order: 3
+          features: chromosomes aligned at metaphase plate
+      ANAPHASE:
+        description: Anaphase
+        meaning: GO:0051322
+        annotations:
+          order: 4
+          features: sister chromatid separation
+      TELOPHASE:
+        description: Telophase
+        meaning: GO:0051326
+        annotations:
+          order: 5
+          features: nuclear envelope reformation
+      CYTOKINESIS:
+        description: Cytokinesis
+        meaning: GO:0000910
+        annotations:
+          order: 6
+          features: cytoplasmic division
+  CellCycleCheckpoint:
+    description: Cell cycle checkpoints that regulate progression
+    permissible_values:
+      G1_S_CHECKPOINT:
+        description: G1/S checkpoint (Restriction point)
+        meaning: GO:0000082
+        title: G1/S transition of mitotic cell cycle
+        annotations:
+          aliases: Start checkpoint, Restriction point, R point
+          regulator: p53, Rb
+      INTRA_S_CHECKPOINT:
+        description: Intra-S checkpoint
+        meaning: GO:0031573
+        title: mitotic intra-S DNA damage checkpoint signaling
+        annotations:
+          function: monitors DNA replication
+          regulator: ATR, CHK1
+      G2_M_CHECKPOINT:
+        description: G2/M checkpoint
+        meaning: GO:0031571
+        title: mitotic G1 DNA damage checkpoint signaling
+        annotations:
+          function: ensures DNA properly replicated
+          regulator: p53, CHK1, CHK2
+      SPINDLE_CHECKPOINT:
+        description: Spindle checkpoint (M checkpoint)
+        meaning: GO:0031577
+        title: spindle checkpoint signaling
+        annotations:
+          aliases: SAC, spindle assembly checkpoint
+          function: ensures proper chromosome attachment
+          regulator: MAD2, BubR1
+  MeioticPhase:
+    description: Phases specific to meiotic cell division
+    permissible_values:
+      MEIOSIS_I:
+        description: Meiosis I (reductional division)
+        meaning: GO:0007127
+        annotations:
+          result: reduction from diploid to haploid
+      PROPHASE_I:
+        description: Prophase I
+        meaning: GO:0007128
+        title: meiotic prophase I
+        annotations:
+          substages: leptotene, zygotene, pachytene, diplotene, diakinesis
+      METAPHASE_I:
+        description: Metaphase I
+        meaning: GO:0007132
+        title: meiotic metaphase I
+        annotations:
+          feature: homologous pairs align
+      ANAPHASE_I:
+        description: Anaphase I
+        meaning: GO:0007133
+        title: meiotic anaphase I
+        annotations:
+          feature: homologous chromosomes separate
+      TELOPHASE_I:
+        description: Telophase I
+        meaning: GO:0007134
+        title: meiotic telophase I
+      MEIOSIS_II:
+        description: Meiosis II (equational division)
+        meaning: GO:0007135
+        annotations:
+          similarity: similar to mitosis
+      PROPHASE_II:
+        description: Prophase II
+        meaning: GO:0007136
+        title: meiotic prophase II
+      METAPHASE_II:
+        description: Metaphase II
+        meaning: GO:0007137
+        title: meiotic metaphase II
+      ANAPHASE_II:
+        description: Anaphase II
+        meaning: GO:0007138
+        title: meiotic anaphase II
+        annotations:
+          feature: sister chromatids separate
+      TELOPHASE_II:
+        description: Telophase II
+        meaning: GO:0007139
+        title: meiotic telophase II
+  CellCycleRegulator:
+    description: Types of cell cycle regulatory molecules
+    permissible_values:
+      CYCLIN:
+        description: Cyclin proteins
+        meaning: GO:0016538
+        title: cyclin-dependent protein serine/threonine kinase regulator activity
+        annotations:
+          examples: Cyclin A, B, D, E
+      CDK:
+        description: Cyclin-dependent kinase
+        meaning: GO:0004693
+        title: cyclin-dependent protein serine/threonine kinase activity
+        annotations:
+          examples: CDK1, CDK2, CDK4, CDK6
+      CDK_INHIBITOR:
+        description: CDK inhibitor
+        meaning: GO:0004861
+        title: cyclin-dependent protein serine/threonine kinase inhibitor activity
+        annotations:
+          examples: p21, p27, p57
+      CHECKPOINT_KINASE:
+        description: Checkpoint kinase
+        meaning: GO:0000077
+        title: DNA damage checkpoint signaling
+        annotations:
+          examples: CHK1, CHK2, ATR, ATM
+      TUMOR_SUPPRESSOR:
+        description: Tumor suppressor involved in cell cycle
+        meaning: GO:0051726
+        title: regulation of cell cycle
+        annotations:
+          examples: p53, Rb, BRCA1, BRCA2
+      E3_UBIQUITIN_LIGASE:
+        description: E3 ubiquitin ligase (cell cycle)
+        meaning: GO:0051437
+        title: obsolete positive regulation of ubiquitin-protein ligase activity involved in regulation of mitotic cell cycle
+          transition
+        annotations:
+          examples: APC/C, SCF
+      PHOSPHATASE:
+        description: Cell cycle phosphatase
+        meaning: GO:0004721
+        title: phosphoprotein phosphatase activity
+        annotations:
+          examples: CDC25A, CDC25B, CDC25C
+  CellProliferationState:
+    description: Cell proliferation and growth states
+    permissible_values:
+      PROLIFERATING:
+        description: Actively proliferating cells
+        meaning: GO:0008283
+        title: cell population proliferation
+      QUIESCENT:
+        description: Quiescent cells (reversibly non-dividing)
+        meaning: GO:0044838
+        title: cell quiescence
+        annotations:
+          phase: G0
+          reversible: true
+      SENESCENT:
+        description: Senescent cells (permanently non-dividing)
+        meaning: GO:0090398
+        title: cellular senescence
+        annotations:
+          reversible: false
+          markers: SA-β-gal, p16
+      DIFFERENTIATED:
+        description: Terminally differentiated cells
+        meaning: GO:0030154
+        title: cell differentiation
+        annotations:
+          examples: neurons, cardiomyocytes
+      APOPTOTIC:
+        description: Cells undergoing apoptosis
+        meaning: GO:0006915
+        title: apoptotic process
+        annotations:
+          aliases: programmed cell death
+      NECROTIC:
+        description: Cells undergoing necrosis
+        meaning: GO:0070265
+        title: obsolete necrotic cell death
+        annotations:
+          type: uncontrolled cell death
+  DNADamageResponse:
+    description: DNA damage response pathways during cell cycle
+    permissible_values:
+      CELL_CYCLE_ARREST:
+        description: Cell cycle arrest
+        meaning: GO:0051726
+        aliases:
+        - regulation of cell cycle
+      DNA_REPAIR:
+        description: DNA repair
+        meaning: GO:0006281
+      APOPTOSIS_INDUCTION:
+        description: Induction of apoptosis
+        meaning: GO:0043065
+        aliases:
+        - positive regulation of apoptotic process
+      SENESCENCE_INDUCTION:
+        description: Induction of senescence
+        meaning: GO:0090400
+        title: stress-induced premature senescence
+      CHECKPOINT_ADAPTATION:
+        description: Checkpoint adaptation
+        annotations:
+          description: override of checkpoint despite damage

valuesets/schema/bio/currency_chemicals.yaml

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+name: currency_chemicals
+title: Currency Chemicals Value Sets
+description: Value sets for metabolic currency molecules and cofactors used in energy transfer and redox reactions
+id: https://w3id.org/common-value-sets/currency_chemicals
+imports:
+- linkml:types
+prefixes:
+  CVS: https://w3id.org/common-value-sets/
+  linkml: https://w3id.org/linkml/
+  CHEBI: http://purl.obolibrary.org/obo/CHEBI_
+  valuesets: https://w3id.org/valuesets/
+default_prefix: valuesets
+slots:
+  currency_chemical:
+    description: Common metabolic currency molecules and cofactors that serve as energy carriers, electron donors/acceptors,
+      and group transfer agents in cellular metabolism
+    range: CurrencyChemical
+enums:
+  CurrencyChemical:
+    description: Common metabolic currency molecules and cofactors that serve as energy carriers, electron donors/acceptors,
+      and group transfer agents in cellular metabolism.
+    permissible_values:
+      ATP:
+        description: Adenosine triphosphate - primary energy currency molecule in cells
+        meaning: CHEBI:15422
+      ADP:
+        description: Adenosine diphosphate - product of ATP hydrolysis, energy acceptor
+        meaning: CHEBI:16761
+      AMP:
+        description: Adenosine monophosphate - nucleotide, product of ADP hydrolysis
+        meaning: CHEBI:16027
+        aliases:
+        - adenosine 5'-monophosphate
+      GTP:
+        description: Guanosine triphosphate - energy molecule, protein synthesis and signaling
+        meaning: CHEBI:15996
+      GDP:
+        description: Guanosine diphosphate - product of GTP hydrolysis
+        meaning: CHEBI:17552
+      NAD_PLUS:
+        description: Nicotinamide adenine dinucleotide (oxidized) - electron acceptor in catabolism
+        meaning: CHEBI:15846
+        title: NAD+
+      NADH:
+        description: Nicotinamide adenine dinucleotide (reduced) - electron donor, reducing agent
+        meaning: CHEBI:16908
+      NADP_PLUS:
+        description: Nicotinamide adenine dinucleotide phosphate (oxidized) - electron acceptor
+        meaning: CHEBI:18009
+        title: NADP+
+      NADPH:
+        description: Nicotinamide adenine dinucleotide phosphate (reduced) - anabolic reducing agent
+        meaning: CHEBI:16474
+      FAD:
+        description: Flavin adenine dinucleotide (oxidized) - electron acceptor in oxidation reactions
+        meaning: CHEBI:16238
+      FADH2:
+        description: Flavin adenine dinucleotide (reduced) - electron donor in electron transport chain
+        meaning: CHEBI:17877
+      COA:
+        description: Coenzyme A - acyl group carrier in fatty acid metabolism
+        meaning: CHEBI:15346
+        title: CoA
+        aliases:
+        - coenzyme A
+      ACETYL_COA:
+        description: Acetyl coenzyme A - central metabolic intermediate, links glycolysis to citric acid cycle
+        meaning: CHEBI:15351
+        title: Acetyl-CoA
+default_range: string

valuesets/schema/bio/developmental_stages.yaml

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+name: developmental_stages
+title: Developmental Stages Value Sets
+description: Ontology-mapped developmental stages for human and mouse organisms. Human stages use HsapDv (Human Developmental
+  Stages) ontology. Mouse stages use MmusDv (Mouse Developmental Stages) ontology.
+id: https://w3id.org/valuesets/bio/developmental_stages
+imports:
+- linkml:types
+prefixes:
+  linkml: https://w3id.org/linkml/
+  HsapDv: http://purl.obolibrary.org/obo/HsapDv_
+  MmusDv: http://purl.obolibrary.org/obo/MmusDv_
+  UBERON: http://purl.obolibrary.org/obo/UBERON_
+  valuesets: https://w3id.org/valuesets/
+default_prefix: valuesets
+slots:
+  human_developmental_stage:
+    description: The human developmental stage classification
+    range: HumanDevelopmentalStage
+  mouse_developmental_stage:
+    description: The mouse developmental stage classification
+    range: MouseDevelopmentalStage
+enums:
+  HumanDevelopmentalStage:
+    permissible_values:
+      ZYGOTE_STAGE:
+        text: ZYGOTE_STAGE
+        title: Carnegie stage 01
+        meaning: HsapDv:0000003
+        description: Embryonic stage defined by a fertilized oocyte and presence of pronuclei. Starts at day 1 post-fertilization.
+      CLEAVAGE_STAGE:
+        text: CLEAVAGE_STAGE
+        title: Carnegie stage 02
+        meaning: HsapDv:0000005
+        description: Embryonic stage during which cell division occurs with reduction in cytoplasmic volume, and formation
+          of inner and outer cell mass. 2-8 cells. Usually starts between day 2-3 post-fertilization.
+      MORULA_STAGE:
+        text: MORULA_STAGE
+        title: morula stage
+        meaning: HsapDv:0000205
+        description: The later part of Carnegie stage 02 when the cells have coalesced into a mass but the blastocystic cavity
+          has not formed.
+      BLASTOCYST_STAGE:
+        text: BLASTOCYST_STAGE
+        title: Carnegie stage 03
+        meaning: HsapDv:0000007
+        description: Blastula stage with the loss of the zona pellucida and the definition of a free blastocyst. Usually starts
+          between day 4-5 post-fertilization.
+      GASTRULA_STAGE:
+        text: GASTRULA_STAGE
+        title: gastrula stage
+        meaning: HsapDv:0000010
+        description: Embryonic stage defined by a complex and coordinated series of cellular movements that occurs at the
+          end of cleavage.
+      NEURULA_STAGE:
+        text: NEURULA_STAGE
+        title: neurula stage
+        meaning: HsapDv:0000012
+        description: Embryonic stage defined by the formation of a tube from the flat layer of ectodermal cells known as the
+          neural plate. This stage starts the emergence of the central nervous system.
+      ORGANOGENESIS_STAGE:
+        text: ORGANOGENESIS_STAGE
+        title: organogenesis stage
+        meaning: HsapDv:0000015
+        description: Embryonic stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the
+          organism.
+      FETAL_STAGE:
+        text: FETAL_STAGE
+        title: fetal stage
+        meaning: HsapDv:0000037
+        description: Prenatal stage that starts with the fully formed embryo and ends at birth. Generally from 8 weeks post-fertilization
+          until birth.
+      NEONATAL_STAGE:
+        text: NEONATAL_STAGE
+        title: newborn stage (0-28 days)
+        meaning: HsapDv:0000262
+        description: Immature stage that refers to a human newborn within the first 28 days of life.
+      INFANT_STAGE:
+        text: INFANT_STAGE
+        title: infant stage
+        meaning: HsapDv:0000261
+        description: Immature stage that refers to an infant who is over 28 days and is under 12 months old.
+      TODDLER_STAGE:
+        text: TODDLER_STAGE
+        title: child stage (1-4 yo)
+        meaning: HsapDv:0000265
+        description: Human stage that refers to a child who is over 12 months and under 5 years old. Often divided into early
+          toddler (1-2 years) and late toddler (2-3 years).
+      CHILD_STAGE:
+        text: CHILD_STAGE
+        title: juvenile stage (5-14 yo)
+        meaning: HsapDv:0000271
+        description: Pediatric stage that refers to a human who is over 5 and under 15 years old. Covers elementary and middle
+          school ages.
+      ADOLESCENT_STAGE:
+        text: ADOLESCENT_STAGE
+        title: 15-19 year-old
+        meaning: HsapDv:0000268
+        description: A young adult stage that refers to an individual who is over 15 and under 20 years old. Period of transition
+          from childhood to adulthood.
+      ADULT_STAGE:
+        text: ADULT_STAGE
+        title: adult stage
+        meaning: HsapDv:0000258
+        description: Human developmental stage that refers to a sexually mature human. Starts at approximately 15 years according
+          to HPO definitions.
+      AGED_STAGE:
+        text: AGED_STAGE
+        title: late adult stage
+        meaning: HsapDv:0000227
+        description: Late adult stage that refers to an individual who is over 60 and starts to have some age-related impairments.
+          Often subdivided into young-old (60-79) and old-old (80+).
+      EMBRYONIC_STAGE:
+        text: EMBRYONIC_STAGE
+        title: embryonic stage
+        meaning: HsapDv:0000002
+        description: Prenatal stage that starts with fertilization and ends with a fully formed embryo, before undergoing
+          last development during the fetal stage. Up to 8 weeks post-fertilization.
+      PRENATAL_STAGE:
+        text: PRENATAL_STAGE
+        title: prenatal stage
+        meaning: HsapDv:0000045
+        description: Prenatal stage that starts with fertilization and ends at birth. Encompasses both embryonic and fetal
+          stages.
+      POSTNATAL_STAGE:
+        text: POSTNATAL_STAGE
+        title: postnatal stage
+        meaning: HsapDv:0010000
+        description: Human developmental stage that covers the whole of human life post birth.
+  MouseDevelopmentalStage:
+    permissible_values:
+      ZYGOTE_STAGE:
+        text: ZYGOTE_STAGE
+        title: Theiler stage 01
+        meaning: MmusDv:0000003
+        description: Embryonic stage defined by a one-cell embryo (fertilised egg) with zona pellucida present. Embryonic
+          age 0-0.9 dpc (days post coitum).
+      TWO_CELL_STAGE:
+        text: TWO_CELL_STAGE
+        title: Theiler stage 02
+        meaning: MmusDv:0000005
+        description: Embryonic cleavage stage defined by a dividing 2-4 cells egg. Embryonic age 1 dpc.
+      FOUR_CELL_STAGE:
+        text: FOUR_CELL_STAGE
+        title: Theiler stage 02
+        meaning: MmusDv:0000005
+        description: Part of Theiler stage 02 - dividing egg with 4 cells. Embryonic age approximately 1 dpc.
+      EIGHT_CELL_STAGE:
+        text: EIGHT_CELL_STAGE
+        title: Theiler stage 03
+        meaning: MmusDv:0000006
+        description: Part of early morula stage - dividing egg with 8 cells. Embryonic age approximately 2 dpc.
+      MORULA_STAGE:
+        text: MORULA_STAGE
+        title: Theiler stage 03
+        meaning: MmusDv:0000006
+        description: Embryonic cleavage stage defined by a dividing 4-16 cells egg, early to fully compacted morula. Embryonic
+          age 2 dpc.
+      BLASTOCYST_STAGE:
+        text: BLASTOCYST_STAGE
+        title: Theiler stage 05
+        meaning: MmusDv:0000009
+        description: Embryonic blastula stage defined by a zona free blastocyst (zona pellucida absent). Embryonic age 4 dpc.
+      GASTRULA_STAGE:
+        text: GASTRULA_STAGE
+        title: gastrula stage
+        meaning: MmusDv:0000013
+        description: Embryonic stage defined by complex and coordinated series of cellular movements that occurs at the end
+          of cleavage.
+      NEURULA_STAGE:
+        text: NEURULA_STAGE
+        title: Theiler stage 11
+        meaning: MmusDv:0000017
+        description: Embryonic stage called presomite stage and defined by the formation of the neural plate. This stage starts
+          the emergence of the central nervous system at embryonic age 7.5 dpc.
+      ORGANOGENESIS_STAGE:
+        text: ORGANOGENESIS_STAGE
+        title: organogenesis stage
+        meaning: MmusDv:0000018
+        description: Embryonic stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the
+          organism.
+      E0_5:
+        text: E0_5
+        title: Theiler stage 01
+        meaning: MmusDv:0000003
+        description: Embryonic day 0.5 - one-cell embryo stage. Corresponds to Theiler stage 01.
+      E9_5:
+        text: E9_5
+        title: Theiler stage 16
+        meaning: MmusDv:0000023
+        description: Embryonic day 9.5 - organogenesis stage with visible hind limb buds. Between Theiler stages 15 and 16.
+      E14_5:
+        text: E14_5
+        title: Theiler stage 22
+        meaning: MmusDv:0000029
+        description: Embryonic day 14.5 - late organogenesis with clearly visible fingers and long bones of the limbs present.
+      P0_NEWBORN:
+        text: P0_NEWBORN
+        title: Theiler stage 27
+        meaning: MmusDv:0000036
+        description: Stage that refers to the newborn mouse, aged E19-20, P0. Used for postnatal days 0 through 3.
+      P21_WEANING:
+        text: P21_WEANING
+        title: 2-week-old stage
+        meaning: MmusDv:0000141
+        description: Weaning stage at approximately 21-22 days old. Transition from nursing to independent feeding.
+      P42_JUVENILE:
+        text: P42_JUVENILE
+        title: 6-week-old stage
+        meaning: MmusDv:0000151
+        description: Prime adult stage at 6 weeks (42 days) old. Commonly considered the milestone for sexual maturity.
+      P56_ADULT:
+        text: P56_ADULT
+        title: 8-week-old stage
+        meaning: MmusDv:0000154
+        description: Adult stage at 8 weeks (56 days) old. Fully mature adult mouse.
+      AGED_12_MONTHS:
+        text: AGED_12_MONTHS
+        title: middle aged stage
+        meaning: MmusDv:0000135
+        description: Middle aged stage for mice over 10 and under 18 months old. Shows progressive age-related changes.
+      THEILER_STAGE:
+        text: THEILER_STAGE
+        description: Reference to any Theiler stage (TS1-TS28) which provides standardized morphological staging for mouse
+          development.
+license: Apache-2.0
+default_range: string