From e94f83c6801a95177290259acf96d514a0155361 Mon Sep 17 00:00:00 2001 From: Ishita Sati <64841420+esheetah@users.noreply.github.com> Date: Wed, 22 May 2024 16:37:21 +0530 Subject: [PATCH] add Protocol-definition.yml --- DataModel/Protocol/Protocol-definition.yml | 285 +++++++++++++++++++++ 1 file changed, 285 insertions(+) create mode 100644 DataModel/Protocol/Protocol-definition.yml diff --git a/DataModel/Protocol/Protocol-definition.yml b/DataModel/Protocol/Protocol-definition.yml new file mode 100644 index 0000000..66dfcde --- /dev/null +++ b/DataModel/Protocol/Protocol-definition.yml @@ -0,0 +1,285 @@ +Protocol: + description: Describes the protocols followed in a study, including details such + as the cell capture system, library protocol, the chemistry kit and sampling technique + used, as well as sequencing related information. + properties: + donor_id: + description: Foreign key to map to donor ID + type: string + format: alphanumeric + pattern: '"^DO-[0-9]{4}$"' + project_id: + description: Foreign key to map a project + type: string + format: alphanumeric + pattern: '"^P[0-9]{3}$"' + protocol_id: + description: Primary key for the protocol ID + type: string + format: alphanumeric + pattern: '"^PRT[0-9]{3}$"' + protocol_name: + description: Name given to the protocol such as single cell sequencing protocol, + Cytokine staining Protocol + type: string + format: text + protocol_description: + description: Description that provides enough information about the protocol + type: string + format: text + protocol_core: + description: Core protocol-level information + type: string + format: text + computational_method: + description: A URL to a versioned workflow and versioned execution environment + type: string + format: text + ontology_link: https://bioportal.bioontology.org/ontologies/MMO?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMMO_0000575 + matrix_transformation: + description: Information related to protocols that transforms a matrix + type: string + format: text + ontology_link: https://bioportal.bioontology.org/ontologies/ATOM?p=classes&conceptid=http%3A%2F%2Furi.interlex.org%2Ftgbugs%2Furis%2Freadable%2Fatlas%2FTransformationMatrix + bioinformatics_software: + description: Name of software used + type: string + format: text + ontology_link: https://bioportal.bioontology.org/ontologies/NGBO?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FNGBO_6000410 + bioinformatics_software_version: + description: Version of software used + type: string + format: alphanumeric + ontology_link: https://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C111093 + gene_annotation_version: + description: Ensembl release version accession number or NCBI RefSeq assembly + version used for gene annotation + type: string + format: alphanumeric + chemistry_kit: + description: Chemistry/Reagent kit used in the protocol + type: string + format: text + ontology_link: https://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C42793 + library_protocol: + description: Specifies the protocol for preparing sequencing libraries from + single-cell RNA or DNA, outlining the steps for library construction and amplification. + type: string + format: text + ontology_link: https://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C41111 + sampling_technique: + description: The method/procedure used for collecting samples + type: string + format: text + ontology_link: https://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C71492 + sequencer: + description: The sequencing platform used to generate single-cell sequencing + data. + type: string + format: text + ontology_link: https://bioportal.bioontology.org/ontologies/BIRNLEX?p=classes&conceptid=http%3A%2F%2Fbioontology.org%2Fprojects%2Fontologies%2Fbirnlex%23birnlex_2408 + sequencing_technology: + description: Describes the methodology employed for sequencing, such as single + cell RNA-seq, ATAC-seq, or DNA sequencing. + type: string + format: text + ontology_link: https://bioportal.bioontology.org/ontologies/GFVO?p=classes&conceptid=https%3A%2F%2Fwww.codamono.com%2Fbiointerchange%2Fgfvo%23SequencingTechnologyPlatform + formation_method: + description: Method used to form cell aggregates + type: string + format: text + ontology_link: https://bioportal.bioontology.org/ontologies/ENM?p=classes&conceptid=http%3A%2F%2Fpurl.enanomapper.org%2Fonto%2FENM_9000002 + cell_uniformity: + description: Description of the cell aggregates uniformity after formation + type: string + format: text + ontology_link: https://bioportal.bioontology.org/ontologies/IOBC?p=classes&conceptid=http%3A%2F%2Fpurl.jp%2Fbio%2F4%2Fid%2F201106089792994038 + method_collection: + description: Method used to collect the biomaterial + type: string + format: text + ontology_link: https://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C70700 + reagents: + description: A list of purchased reagents used in this protocol + type: array + format: text + ontology_link: https://bioportal.bioontology.org/ontologies/SNOMEDCT?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F337340002 + method_differentiation: + description: Method applied to cell culture to induce a specific differentiation + response + type: string + format: text + media_differentiation: + description: Culture media used to induce a specific differentiation response + type: string + format: text + ontology_link: https://bioportal.bioontology.org/ontologies/EFO?p=classes&conceptid=http%3A%2F%2Fwww.ebi.ac.uk%2Fefo%2FEFO_0000579 + small_molecules: + description: Small molecules added to stem cell medium to induce a specific + differentiation response + type: string + format: text + ontology_link: https://bioportal.bioontology.org/ontologies/EDAM?p=classes&conceptid=http%3A%2F%2Fedamontology.org%2Ftopic_0154 + target_cell_yield: + description: Percent of target cells obtained after directed differentiation + of origin cell + type: float + format: float + target_pathway: + description: Targeted pathway for specific differentiation response + type: string + format: text + ontology_link: https://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C20633 + validation_method: + description: Method used to validate origin cell successfully differentiated + to target cell + type: string + format: text + ontology_link: https://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C115542 + validation_result: + description: Result confirming successful differentiation to target cell type + type: string + format: text + ontology_link: https://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C16237 + markers: + description: A list of markers used to enrich for or against certain cells + type: string + format: alphanumerical + ontology_link: https://bioportal.bioontology.org/ontologies/LOINC?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FLNC%2FLP7783-6 + minimum_size: + description: Minimum cell or organelle size passing selection, in microns + type: integer + format: "\xB5m" + upper_value: 10000.0 + lower_value: 0.01 + ontology_link: https://bioportal.bioontology.org/ontologies/ONTODT?p=classes&conceptid=http%3A%2F%2Fontodm.com%2FOntoDT%23OntoDT_844136 + maximum_size: + description: Maximum cell or organelle size passing selection, in microns + type: integer + format: "\xB5m" + upper_value: 10000.0 + lower_value: 0.01 + ontology_link: https://bioportal.bioontology.org/ontologies/ONTODT?p=classes&conceptid=http%3A%2F%2Fontodm.com%2FOntoDT%23OntoDT_844136 + method_induction: + description: Induction method applied to primary cell culture to induce pluripotent + stem cell generation + type: string + format: text + ontology_link: https://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C61367 + reprogramming_factors: + description: Reprogramming factors added to primary cell culture to induce pluripotency + type: string + format: text + ontology_link: https://bioportal.bioontology.org/ontologies/MESH?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMESH%2FD065150 + ipsc_induction_kit: + description: Kit used to induce pluripotent stem cell generation + type: string + format: text + pluripotency_test: + description: Description of how pluripotency was tested in induced pluripotent + stem cells + type: string + format: text + ontology_link: https://bioportal.bioontology.org/ontologies/PLOSTHES?p=classes&conceptid=http%3A%2F%2Flocalhost%2Fplosthes.2017-1%236180 + percent_pluripotency: + description: Percent of iPSCs that passed the pluripotency test + type: integer + format: text + pluripotency_vector_removed: + description: Whether a viral vector was removed after induction + type: boolean + format: boolean + options: + - 'True' + - 'False' + slice_thickness: + description: Thickness of the imaged slice in micrometres + type: string + format: um + ontology_link: https://bioportal.bioontology.org/ontologies/DCM?p=classes&conceptid=http%3A%2F%2Fdicom.nema.org%2Fresources%2Fontology%2FDCM%2F112225 + internal_anatomical_structures: + description: Internal (landmark) structures visible in the overview image that + are informative about the broader anatomical context/location of the sample + type: string + format: text + ontology_link: https://bioportal.bioontology.org/ontologies/OCHV?p=classes&conceptid=http%3A%2F%2Fsbmi.uth.tmc.edu%2Fontology%2Fochv%2325102 + fiducial_marker: + description: Fiducial markers for the alignment of images taken across multiple + rounds of imaging + type: string + format: text + ontology_link: https://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C82602 + expansion_factor: + description: Factor by which the imaged tissue was expanded in one dimension + type: integer + format: number + ontology_link: https://bioportal.bioontology.org/ontologies/AGRO?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FIAO_0000101 + microscope_setup_description: + description: Description of the microscope setup + type: string + format: text + ontology_link: https://bioportal.bioontology.org/ontologies/OBI?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBI_0400169 + microscopy_technique: + description: The type of microscopy + type: string + format: text + ontology_link: https://bioportal.bioontology.org/ontologies/SNOMEDCT?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F278289002 + magnification: + description: Magnification of the objective used for imaging + type: string + format: text + numerical_aperture: + description: Numerical aperture of the objective + type: integer + format: number + ontology_link: https://bioportal.bioontology.org/ontologies/PLOSTHES?p=classes&conceptid=http%3A%2F%2Flocalhost%2Fplosthes.2017-1%2310222 + immersion_medium_type: + description: Immersion medium used for imaging + type: string + format: text + ontology_link: https://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C182013 + immersion_medium_refractive_index: + description: Refractive index of the immersion medium used for imaging + type: integer + format: number + ontology_link: https://bioportal.bioontology.org/ontologies/FBbi?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FFBbi_00000311 + pixel_size: + description: Pixel size in nanometers + type: integer + format: nm + ontology_link: https://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C94953 + number_of_tiles: + description: Number of XY tiles in the experiment + type: integer + format: number + tile_size_y: + description: ' Y size of the tile in micrometers' + type: integer + format: um + tile_size_x: + description: X size of the tile in micrometers + type: integer + format: um + z_stack_step_size: + description: Z-stack step size in nanometers + type: integer + format: nm + ontology_link: https://bioportal.bioontology.org/ontologies/DCM?p=classes&conceptid=http%3A%2F%2Fdicom.nema.org%2Fresources%2Fontology%2FDCM%2F110903 + overlapping_tiles: + description: Whether tiles were collected with overlap + type: boolean + format: boolean + options: + - 'True' + - 'False' + channel: + description: Information about each channel used in the imaging protocol + type: array + format: text + ontology_link: https://bioportal.bioontology.org/ontologies/BAO?p=classes&conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23BAO_0000459 + probe: + description: Information about each probe in the imaging experiment + type: array + format: text + type: object + version: 1.0.0