add Protocol-definition.yml #8
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| 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 | ||
|
There was a problem hiding this comment. @ishitasati11 format for storing a URL |
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| 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 | ||
|
There was a problem hiding this comment. @ishitasati11 This property stores the description of the attribute and not the value it stores. So the description could be something like |
||
| 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 | ||
|
There was a problem hiding this comment. @ishitasati11 Same as above |
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| 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" | ||
|
There was a problem hiding this comment. @ishitasati11 If a given attribute is encoded please specify the type in an additional There was a problem hiding this comment. @ishitasati11 What i understand is that if you are using the format property then it should specify the format of the value it stores and not the unit of measurement. Generally, for this you can store it in a property simply called |
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| 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" | ||
|
There was a problem hiding this comment. @ishitasati11 Same as above |
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| 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: | ||
|
There was a problem hiding this comment. @ishitasati11 Use There was a problem hiding this comment. Also values should be without quotes |
||
| - '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 | ||
|
There was a problem hiding this comment. @ishitasati11 |
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| 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 | ||
|
There was a problem hiding this comment. @ishitasati11 Let's separate format from unit of measurement wherever applicable |
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| 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' | ||
|
There was a problem hiding this comment. @ishitasati11 Remove single quotes |
||
| 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: | ||
|
There was a problem hiding this comment. @ishitasati11 Use |
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| - '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 | ||
|
There was a problem hiding this comment. This ontology link redirects to the label |
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| probe: | ||
| description: Information about each probe in the imaging experiment | ||
| type: array | ||
| format: text | ||
| type: object | ||
| version: 1.0.0 | ||
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@ishitasati11 Are we only storing URL here?
A suggestion would be to store the URL as a subproperty of this attribute in
url.