diff --git a/cache/chmo/terms.csv b/cache/chmo/terms.csv index e9c0345d..9af679d0 100644 --- a/cache/chmo/terms.csv +++ b/cache/chmo/terms.csv @@ -70,3 +70,25 @@ CHMO:0000230,alpha-particle spectroscopy,2026-02-14T13:13:05.886238 CHMO:0000782,neutron activation analysis,2026-02-14T13:13:05.886825 CHMO:0000068,electron microscopy,2026-02-14T13:13:05.887378 CHMO:0002119,granulometry,2026-02-15T15:45:57.306305 +CHMO:0001685,mixing,2026-06-11T16:05:44.304992 +CHMO:0002772,degassing,2026-06-11T16:06:05.532497 +CHMO:0001553,freeze drying,2026-06-11T16:06:20.032530 +CHMO:0001652,grinding,2026-06-11T16:06:27.004201 +CHMO:0002582,flash chromatography,2026-06-11T16:06:55.637038 +CHMO:0001002,gas chromatography,2026-06-11T16:07:02.864406 +CHMO:0002874,ion chromatography,2026-06-11T16:07:12.622374 +CHMO:0001600,liquid–liquid extraction,2026-06-11T16:07:19.850639 +CHMO:0001522,dialysis,2026-06-11T16:07:26.698916 +CHMO:0001022,agarose gel electrophoresis,2026-06-11T16:07:34.167416 +CHMO:0001023,polyacrylamide gel electrophoresis,2026-06-11T16:07:41.819445 +CHMO:0001033,capillary isoelectric focusing,2026-06-11T16:07:54.977323 +CHMO:0000598,two-dimensional nuclear magnetic resonance spectroscopy,2026-06-11T16:08:20.455125 +CHMO:0000287,fluorescence spectroscopy,2026-06-11T16:08:29.342121 +CHMO:0002415,luminescence spectroscopy,2026-06-11T16:08:37.365158 +CHMO:0000630,infrared absorption spectroscopy,2026-06-11T16:08:44.426791 +CHMO:0000167,dynamic light scattering,2026-06-11T16:09:00.370478 +CHMO:0000538,inductively coupled plasma mass spectrometry,2026-06-11T16:09:32.102434 +CHMO:0001477,crystallisation,2026-06-11T16:10:14.320283 +CHMO:0000158,powder X-ray diffraction,2026-06-11T16:10:21.908188 +CHMO:0000025,cyclic voltammetry,2026-06-11T16:10:31.974523 +CHMO:0002535,Karl–Fischer titration,2026-06-11T16:10:40.306624 diff --git a/cache/obi/terms.csv b/cache/obi/terms.csv index 7fdb8292..e227aa15 100644 --- a/cache/obi/terms.csv +++ b/cache/obi/terms.csv @@ -78,3 +78,6 @@ OBI:0000659,specimen collection process,2025-12-22T08:16:54.248591 OBI:0000094,material processing,2025-12-22T08:16:54.249148 OBI:0000854,western blot assay,2026-02-22T14:59:00.342925 OBI:0302736,comet assay,2026-02-22T14:59:17.858350 +OBI:0302886,centrifugation,2026-06-11T16:05:52.111915 +OBI:0000626,DNA sequencing assay,2026-06-11T16:09:55.501188 +OBI:0002107,bio-layer interferometry assay,2026-06-11T16:12:09.434877 diff --git a/src/valuesets/schema/lab_automation/cloud_lab.yaml b/src/valuesets/schema/lab_automation/cloud_lab.yaml new file mode 100644 index 00000000..52a6fd03 --- /dev/null +++ b/src/valuesets/schema/lab_automation/cloud_lab.yaml @@ -0,0 +1,519 @@ +name: cloud_lab +id: https://w3id.org/valuesets/lab_automation/cloud_lab +title: Cloud Laboratory Protocol Value Sets +description: >- + Controlled vocabularies for cloud-laboratory research protocols, modeled on the + operational taxonomy exposed by remote/cloud labs such as Emerald Cloud Lab (ECL) + and its Symbolic Lab Language (SLL). Two complementary layers are captured: + (1) LabUnitOperationEnum -- the composable sample-manipulation primitives ("unit + operations") that make up a sample-preparation protocol; and + (2) CloudLabExperimentEnum -- the higher-level experiment/assay functions that a + protocol invokes. The experiment layer is cross-referenced to the assay value sets + under bio/assays/ (OBIAssayEnum, BAOBioassayEnum) and to analytical-chemistry + vocabularies; OBI/CHMO/MMO terms are used for `meaning:` where an equivalent + ontology class exists. These vocabularies use neutral ontology mappings rather than + vendor-specific identifiers; ECL function names are used only as an input checklist + for completeness. +license: https://creativecommons.org/publicdomain/zero/1.0/ +version: 0.1.0 +prefixes: + valuesets: https://w3id.org/valuesets/ + linkml: https://w3id.org/linkml/ + OBI: http://purl.obolibrary.org/obo/OBI_ + CHMO: http://purl.obolibrary.org/obo/CHMO_ + MMO: http://purl.obolibrary.org/obo/MMO_ + EFO: http://www.ebi.ac.uk/efo/EFO_ + NCIT: http://purl.obolibrary.org/obo/NCIT_ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ +default_prefix: valuesets +imports: +- linkml:types +- ../core + +slots: + lab_unit_operation: + description: A sample-manipulation unit operation in a cloud-laboratory protocol + range: LabUnitOperationEnum + cloud_lab_experiment: + description: A cloud-laboratory experiment or assay function + range: CloudLabExperimentEnum + +enums: + LabUnitOperationEnum: + title: Lab Unit Operation + description: >- + Composable sample-manipulation primitives ("unit operations") used to build + sample-preparation protocols in a cloud laboratory. Modeled on the ECL Symbolic + Lab Language sample-preparation unit operations (Transfer, Aliquot, Mix, + Incubate, Filter, Centrifuge, Pellet, Resuspend, etc.). Complements the lower + level LiquidHandlingOperationEnum and SampleProcessingOperationEnum in + lab_automation/operations. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + see_also: + - https://w3id.org/valuesets/lab_automation/operations + - https://www.emeraldcloudlab.com/guides/runningexperiments + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + # --- Labeling / definition --- + DEFINE: + title: define + description: Declare a new sample, container, or model and assign it a label for later reference in the protocol + LABEL_SAMPLE: + title: label sample + description: Assign a human-readable label to a sample so it can be referenced by later unit operations + LABEL_CONTAINER: + title: label container + description: Assign a human-readable label to a container so it can be referenced by later unit operations + # --- Liquid handling / volumetric --- + TRANSFER: + title: transfer + description: Move a specified amount of sample from one source to one or more destinations + ALIQUOT: + title: aliquot + description: Distribute a sample into multiple equal portions in separate containers + CONSOLIDATE: + title: consolidate + description: Combine multiple source samples into a single destination container + DILUTE: + title: dilute + description: Reduce the concentration of a sample by adding diluent to a target volume or concentration + SERIAL_DILUTE: + title: serial dilute + description: Create a stepwise series of dilutions by repeatedly transferring and diluting a sample + FILL_TO_VOLUME: + title: fill to volume + description: Add solvent to a sample until a specified total volume is reached + RESUSPEND: + title: resuspend + description: Dissolve or re-disperse a solid or pellet in a specified volume of solvent + PREPARE_STOCK_SOLUTION: + title: prepare stock solution + description: Prepare a solution of defined composition from components and solvent + ADJUST_PH: + title: adjust pH + description: Add titrant to bring a sample to a target pH + # --- Mixing / incubation / timing --- + MIX: + title: mix + description: Homogenize a sample by pipetting, inversion, vortexing, stirring, sonication, or related agitation + meaning: CHMO:0001685 # mixing + aliases: + - mixing + INCUBATE: + title: incubate + description: Hold a sample at controlled temperature (and optionally mixing) for a specified duration + WAIT: + title: wait + description: Pause the protocol for a specified duration without other manipulation + # --- Separation / clarification --- + CENTRIFUGE: + title: centrifuge + description: Apply centrifugal force to a sample to separate components by density + meaning: OBI:0302886 # centrifugation + aliases: + - centrifugation + PELLET: + title: pellet + description: Centrifuge to precipitate solids, optionally aspirate the supernatant, and optionally resuspend the pellet + FILTER: + title: filter + description: Pass a sample through a filter to separate particulates or to sterilize + meaning: CHMO:0001640 # filtration + aliases: + - filtration + MAGNETIC_BEAD_SEPARATION: + title: magnetic bead separation + description: Isolate target analytes bound to magnetic beads using a magnetic field + MOVE_TO_MAGNET: + title: move to magnet + description: Place a container on a magnetic rack to immobilize magnetic beads + REMOVE_FROM_MAGNET: + title: remove from magnet + description: Remove a container from a magnetic rack to release magnetic beads + # --- Conditioning / state change --- + COVER: + title: cover + description: Apply a lid, cap, or seal to a container + UNCOVER: + title: uncover + description: Remove a lid, cap, or seal from a container + DEGAS: + title: degas + description: Remove dissolved gases from a liquid sample + meaning: CHMO:0002772 # degassing + aliases: + - degassing + DESICCATE: + title: desiccate + description: Remove moisture from a sample using a desiccant or controlled-humidity chamber + EVAPORATE: + title: evaporate + description: Remove solvent from a sample by evaporation, optionally under reduced pressure + meaning: CHMO:0001574 # evaporation + aliases: + - evaporation + LYOPHILIZE: + title: lyophilize + description: Freeze-dry a sample to remove solvent by sublimation under vacuum + meaning: CHMO:0001553 # freeze drying + aliases: + - freeze drying + FLASH_FREEZE: + title: flash freeze + description: Rapidly freeze a sample, typically in liquid nitrogen + AUTOCLAVE: + title: autoclave + description: Sterilize a sample or labware using pressurized saturated steam + GRIND: + title: grind + description: Mechanically reduce a solid sample to smaller particles or powder + meaning: CHMO:0001652 # grinding + aliases: + - grinding + MICROWAVE_DIGESTION: + title: microwave digestion + description: Digest a sample in acid under microwave heating to bring analytes into solution + + CloudLabExperimentEnum: + title: Cloud Lab Experiment + description: >- + Higher-level experiment and assay functions offered as protocols by a cloud + laboratory, modeled on the ECL Symbolic Lab Language experiment functions and + grouped by category (synthesis, separations/chromatography, spectroscopy, mass + spectrometry, bioassays, crystallography, property measurement, cellular). + Cross-referenced to the assay value sets in bio/assays/ (OBIAssayEnum, + BAOBioassayEnum) and to analytical_chemistry vocabularies; `meaning:` maps to + OBI/CHMO classes where an equivalent assay or analytical method exists. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + see_also: + - https://w3id.org/valuesets/bio/assays/bio_assay + - https://www.emeraldcloudlab.com/guides/runningexperiments + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + # --- Organic / biomolecular synthesis --- + DNA_SYNTHESIS: + title: DNA synthesis + description: Solid-phase chemical synthesis of DNA oligonucleotides + RNA_SYNTHESIS: + title: RNA synthesis + description: Solid-phase chemical synthesis of RNA oligonucleotides + PNA_SYNTHESIS: + title: PNA synthesis + description: Solid-phase chemical synthesis of peptide nucleic acid oligomers + PEPTIDE_SYNTHESIS: + title: peptide synthesis + description: Solid-phase chemical synthesis of peptides + PCR: + title: PCR + description: Polymerase chain reaction amplification of nucleic acids + meaning: OBI:0000415 # polymerase chain reaction + aliases: + - polymerase chain reaction + BIOCONJUGATION: + title: bioconjugation + description: Covalent coupling of biomolecules or labels to a target molecule + # --- Separations / chromatography / electrophoresis --- + HPLC: + title: HPLC + description: High-performance liquid chromatography separation + meaning: CHMO:0001009 # high-performance liquid chromatography + aliases: + - high-performance liquid chromatography + FPLC: + title: FPLC + description: Fast protein liquid chromatography separation + FLASH_CHROMATOGRAPHY: + title: flash chromatography + description: Medium-pressure flash column chromatography separation + meaning: CHMO:0002582 # flash chromatography + GAS_CHROMATOGRAPHY: + title: gas chromatography + description: Gas chromatography separation of volatile analytes + meaning: CHMO:0001002 # gas chromatography + ION_CHROMATOGRAPHY: + title: ion chromatography + description: Chromatographic separation of ionic species + meaning: CHMO:0002874 # ion chromatography + SUPERCRITICAL_FLUID_CHROMATOGRAPHY: + title: supercritical fluid chromatography + description: Chromatographic separation using a supercritical fluid mobile phase + SOLID_PHASE_EXTRACTION: + title: solid phase extraction + description: Sample cleanup or enrichment by selective retention on a solid sorbent + LIQUID_LIQUID_EXTRACTION: + title: liquid-liquid extraction + description: Separation of analytes between two immiscible liquid phases + meaning: CHMO:0001600 # liquid–liquid extraction + aliases: + - liquid–liquid extraction + CROSS_FLOW_FILTRATION: + title: cross-flow filtration + description: Tangential-flow filtration for concentration or buffer exchange + DIALYSIS: + title: dialysis + description: Separation of molecules by size across a semipermeable membrane + meaning: CHMO:0001522 # dialysis + AGAROSE_GEL_ELECTROPHORESIS: + title: agarose gel electrophoresis + description: Size-based separation of nucleic acids in an agarose gel + meaning: CHMO:0001022 # agarose gel electrophoresis + PAGE: + title: PAGE + description: Polyacrylamide gel electrophoresis separation of biomolecules + meaning: CHMO:0001023 # polyacrylamide gel electrophoresis + aliases: + - polyacrylamide gel electrophoresis + CAPILLARY_GEL_ELECTROPHORESIS_SDS: + title: capillary gel electrophoresis SDS + description: SDS capillary gel electrophoresis sizing of proteins + CAPILLARY_ISOELECTRIC_FOCUSING: + title: capillary isoelectric focusing + description: Separation of proteins by isoelectric point in a capillary + meaning: CHMO:0001033 # capillary isoelectric focusing + WESTERN_BLOT: + title: Western blot + description: Immunodetection of proteins separated by electrophoresis + meaning: OBI:0000854 # western blot assay + aliases: + - western blot assay + # --- Spectroscopy --- + NMR: + title: NMR + description: One-dimensional nuclear magnetic resonance spectroscopy + meaning: CHMO:0000591 # nuclear magnetic resonance spectroscopy + aliases: + - nuclear magnetic resonance spectroscopy + NMR_2D: + title: 2D NMR + description: Two-dimensional nuclear magnetic resonance spectroscopy + meaning: CHMO:0000598 # two-dimensional nuclear magnetic resonance spectroscopy + aliases: + - two-dimensional nuclear magnetic resonance spectroscopy + ABSORBANCE_SPECTROSCOPY: + title: absorbance spectroscopy + description: Measurement of absorbance across a wavelength range + ABSORBANCE_INTENSITY: + title: absorbance intensity + description: Measurement of absorbance at one or more discrete wavelengths + ABSORBANCE_KINETICS: + title: absorbance kinetics + description: Time-resolved measurement of absorbance + FLUORESCENCE_SPECTROSCOPY: + title: fluorescence spectroscopy + description: Measurement of fluorescence emission across a wavelength range + meaning: CHMO:0000287 # fluorescence spectroscopy + FLUORESCENCE_INTENSITY: + title: fluorescence intensity + description: Measurement of fluorescence intensity at discrete wavelengths + FLUORESCENCE_KINETICS: + title: fluorescence kinetics + description: Time-resolved measurement of fluorescence intensity + FLUORESCENCE_POLARIZATION: + title: fluorescence polarization + description: Measurement of fluorescence polarization/anisotropy + LUMINESCENCE_SPECTROSCOPY: + title: luminescence spectroscopy + description: Measurement of luminescence emission across a wavelength range + meaning: CHMO:0002415 # luminescence spectroscopy + LUMINESCENCE_INTENSITY: + title: luminescence intensity + description: Measurement of luminescence intensity at discrete wavelengths + LUMINESCENCE_KINETICS: + title: luminescence kinetics + description: Time-resolved measurement of luminescence intensity + IR_SPECTROSCOPY: + title: IR spectroscopy + description: Infrared absorption spectroscopy + meaning: CHMO:0000630 # infrared absorption spectroscopy + aliases: + - infrared absorption spectroscopy + RAMAN_SPECTROSCOPY: + title: Raman spectroscopy + description: Raman scattering spectroscopy + meaning: CHMO:0000656 # Raman spectroscopy + CIRCULAR_DICHROISM: + title: circular dichroism + description: Measurement of differential absorption of circularly polarized light + DYNAMIC_LIGHT_SCATTERING: + title: dynamic light scattering + description: Measurement of particle size distribution from scattered-light fluctuations + meaning: CHMO:0000167 # dynamic light scattering + NEPHELOMETRY: + title: nephelometry + description: Measurement of turbidity by scattered light + THERMAL_SHIFT: + title: thermal shift + description: Measurement of protein thermal stability via a fluorescent thermal shift assay + UV_MELTING: + title: UV melting + description: Measurement of nucleic acid or protein melting curves by UV absorbance + # --- Mass spectrometry --- + MASS_SPECTROMETRY: + title: mass spectrometry + description: Determination of mass-to-charge ratios of ionized analytes + meaning: CHMO:0000470 # mass spectrometry + LCMS: + title: LC-MS + description: Liquid chromatography coupled to mass spectrometry + meaning: CHMO:0000524 # liquid chromatography-mass spectrometry + aliases: + - liquid chromatography-mass spectrometry + GCMS: + title: GC-MS + description: Gas chromatography coupled to mass spectrometry + meaning: CHMO:0000497 # gas chromatography-mass spectrometry + aliases: + - gas chromatography-mass spectrometry + ICPMS: + title: ICP-MS + description: Inductively coupled plasma mass spectrometry for elemental analysis + meaning: CHMO:0000538 # inductively coupled plasma mass spectrometry + aliases: + - inductively coupled plasma mass spectrometry + # --- Bioassays / immunoassays --- + ELISA: + title: ELISA + description: Enzyme-linked immunosorbent assay + meaning: OBI:0000661 # enzyme-linked immunosorbent assay + aliases: + - enzyme-linked immunosorbent assay + CAPILLARY_ELISA: + title: capillary ELISA + description: Automated capillary-based enzyme-linked immunosorbent assay + ALPHASCREEN: + title: AlphaScreen + description: Bead-based amplified luminescent proximity homogeneous assay + BIOLAYER_INTERFEROMETRY: + title: biolayer interferometry + description: Label-free measurement of biomolecular binding kinetics by interferometry + meaning: OBI:0002107 # bio-layer interferometry assay + aliases: + - bio-layer interferometry assay + QPCR: + title: qPCR + description: Quantitative real-time polymerase chain reaction + meaning: OBI:0000893 # real time polymerase chain reaction assay + aliases: + - real time polymerase chain reaction assay + DNA_SEQUENCING: + title: DNA sequencing + description: Determination of nucleotide sequence of DNA (Sanger/capillary) + meaning: OBI:0000626 # DNA sequencing assay + aliases: + - DNA sequencing assay + TOTAL_PROTEIN_QUANTIFICATION: + title: total protein quantification + description: Colorimetric or fluorometric quantification of total protein + TOTAL_PROTEIN_DETECTION: + title: total protein detection + description: Capillary-based detection and sizing of total protein + DIFFERENTIAL_SCANNING_CALORIMETRY: + title: differential scanning calorimetry + description: Measurement of heat flow associated with thermal transitions + meaning: CHMO:0000684 # differential scanning calorimetry + # --- Crystallography / solid-state --- + GROW_CRYSTAL: + title: grow crystal + description: Crystallization of a compound or macromolecule for structural analysis + meaning: CHMO:0001477 # crystallisation + aliases: + - crystallisation + POWDER_XRD: + title: powder XRD + description: Powder X-ray diffraction analysis of crystalline solids + meaning: CHMO:0000158 # powder X-ray diffraction + aliases: + - powder X-ray diffraction + # --- Physical property measurement --- + MEASURE_PH: + title: measure pH + description: Measurement of sample pH + MEASURE_CONDUCTIVITY: + title: measure conductivity + description: Measurement of electrical conductivity of a solution + MEASURE_DENSITY: + title: measure density + description: Measurement of sample density + MEASURE_VISCOSITY: + title: measure viscosity + description: Measurement of sample viscosity + MEASURE_OSMOLALITY: + title: measure osmolality + description: Measurement of solute concentration as osmolality + MEASURE_REFRACTIVE_INDEX: + title: measure refractive index + description: Measurement of the refractive index of a sample + MEASURE_SURFACE_TENSION: + title: measure surface tension + description: Measurement of liquid surface tension + MEASURE_CONTACT_ANGLE: + title: measure contact angle + description: Measurement of the contact angle of a liquid on a surface + MEASURE_DISSOLVED_OXYGEN: + title: measure dissolved oxygen + description: Measurement of dissolved oxygen concentration in a liquid + MEASURE_MELTING_POINT: + title: measure melting point + description: Determination of the melting point of a solid + MEASURE_WEIGHT: + title: measure weight + description: Gravimetric measurement of sample mass + MEASURE_VOLUME: + title: measure volume + description: Measurement of sample volume + MEASURE_COUNT: + title: measure count + description: Counting of discrete objects (e.g. particles, colonies, cells) + COUNT_LIQUID_PARTICLES: + title: count liquid particles + description: Counting and sizing of particles suspended in a liquid + COULTER_COUNT: + title: Coulter count + description: Counting and sizing of particles or cells by electrical impedance + CYCLIC_VOLTAMMETRY: + title: cyclic voltammetry + description: Electrochemical measurement of current versus swept potential + meaning: CHMO:0000025 # cyclic voltammetry + KARL_FISCHER_TITRATION: + title: Karl Fischer titration + description: Titrimetric determination of water content + meaning: CHMO:0002535 # Karl–Fischer titration + aliases: + - Karl–Fischer titration + DISSOLUTION: + title: dissolution + description: Measurement of the rate and extent of dissolution of a solid + DYNAMIC_FOAM_ANALYSIS: + title: dynamic foam analysis + description: Measurement of foam formation and decay + VISUAL_INSPECTION: + title: visual inspection + description: Operator or imaging-based visual assessment of a sample + IMAGE_SAMPLE: + title: image sample + description: Acquisition of a photographic image of a sample + # --- Cellular / microbiology --- + IMAGE_CELLS: + title: image cells + description: Microscopic imaging of cells + IMAGE_COLONIES: + title: image colonies + description: Imaging of microbial colonies on solid media + QUANTIFY_COLONIES: + title: quantify colonies + description: Counting and quantification of microbial colonies + LYSE_CELLS: + title: lyse cells + description: Disruption of cells to release intracellular contents + FREEZE_CELLS: + title: freeze cells + description: Controlled-rate freezing of cells for storage diff --git a/src/valuesets/schema/valuesets.yaml b/src/valuesets/schema/valuesets.yaml index fddac088..0859ea47 100644 --- a/src/valuesets/schema/valuesets.yaml +++ b/src/valuesets/schema/valuesets.yaml @@ -132,6 +132,7 @@ imports: - analytical_chemistry/mass_spectrometry - lab_automation/devices - lab_automation/operations +- lab_automation/cloud_lab - lab_automation/labware - lab_automation/protocols - lab_automation/standards