Jpuerto/donor yaml update (#1329)

* Docs: Add donor files back to YAML

* Docs: Remove murine-source fields

* Docs: Remove murine-source fields

---------

Co-authored-by: Juan Puerto <=>

CHANGELOG.md

@@ -39,6 +39,7 @@
 - Bugfix stripping trailing slash in ingest api url
 - Converted upload `_url_checks` to use `_get_method` for SenNet compatibility
 - Add CEDAR template for murine-source
+- Add donor field descriptions back, remove murine-source descriptions
 
 ## v0.0.17
 

docs/field-descriptions.yaml

@@ -24,6 +24,8 @@ acquisition_matrix_size_in_frequency_encoding_direction: Dimensions of the acqui
 acquisition_matrix_size_in_phase_encoding_direction: Dimensions of the acquired phase
   data before reconstruction, per image.
 affiliation: Institutional affiliation
+age_unit: Unit for age measurement.
+age_value: The time elapsed since birth.
 analyte_class: Analytes are the target molecules being measured with the assay.
 antibodies_path: Relative path to file with antibody information for this dataset.
 antibody_name: Anti-(target name) antibody. Not validated or used down-stream.
@@ -40,7 +42,10 @@ assay_type: The specific type of assay being executed.
 bead_barcode_offset: Position(s) in the read at which the bead barcode starts
 bead_barcode_read: Which read file contains the bead barcode
 bead_barcode_size: Length of the bead barcode in base pairs
-bedding: The type of cage bedding in the cage where the source is housed.
+blood_type: ABO blood type or "serotype" refers to the presence/absence of the either/both
+  A & B blood antigens.
+body_mass_index_value: An individual's weight in kilograms divided by the square of
+  the height in meters.
 bulk_atac_cell_isolation_protocols_io_doi: 'Link to a protocols document answering
   the question: How was tissue stored and processed for cell/nuclei isolation'
 bulk_rna_isolation_protocols_io_doi: 'Link to a protocols document answering the question:
@@ -53,7 +58,7 @@ bulk_rna_yield_value: 'RNA (ng) per Weight of Tissue (mg). Answer the question:
   RNA? Calculate the yield by dividing total RNA isolated by amount of tissue used
   to isolate RNA from (ng/mg).'
 bulk_transposition_input_number_nuclei: A number (no comma separators)
-cage_enhancements: "Environmental enrichments present in the source\u2019s cage."
+cause_of_death: The circumstance or condition that caused death.
 ce_background_electrolyte: Chemical composition of the background electrolyte that
   fills the separation capillary (e.g. "3% acetic acid").
 ce_capillary_coating: Treatment of surface of separation capillary. Capillary coating
@@ -108,16 +113,11 @@ data_collection_mode: Mode of data collection in tandem MS assays. Either DDA (D
 data_path: Relative path to file or directory with instrument data. Downstream processing
   will depend on filename extension conventions.
 data_precision_bytes: Numerical data precision in bytes
-date_of_birth_or_fertilization: The date when the mouse/embryo was born/fertilized.
-  If the hours/minutes are not known, use '00:00'.
-date_of_death: The date when the mouse/embryo died. If the hours/minutes are not known,
-  use '00:00'.
 description: Free-text description of this assay.
 desi_solvent: Solvent composition for conducting nanospray desorption electrospray
   ionization (nanoDESI) or desorption electrospray ionization (DESI).
 desi_solvent_flow_rate: The rate of flow of the solvent into a spray.
 desi_solvent_flow_rate_unit: Units of the rate of solvent flow.
-diet: A free text description of the source's diet.
 dilution: Antibody solutions may be diluted according to the experimental protocol.
 dms: Was differential mobility spectrometry used in this assay?
 dna_assay_input_unit: Units of DNA input into library preparation
@@ -132,7 +132,6 @@ echo_time: 'Time in msec between the middle of the excitation pulse and the peak
   to cover the center of k-space (i.e., -kx=0, ky=0). '
 echo_train_length: 'Number of lines in k-space acquired per excitation per image. '
 end_datetime: Time stamp indicating end of ablation for ROI
-euthanization_method: If the source was euthanized, select the method of euthanization.
 execution_datetime: Start date and time of assay, typically a date-time stamped folder
   generated by the acquisition instrument. YYYY-MM-DD hh:mm, where YYYY is the year,
   MM is the month with leading 0s, and DD is the day with leading 0s, hh is the hour
@@ -160,6 +159,9 @@ health_status: "Patient's baseline physical condition prior to immediate event l
   \ healthy subject may have experienced trauma leading to brain death.  As a result\
   \ of organ donation, a sample is collected.  In this scenario, the subject is deemed\
   \ \u201Crelatively healthy.\u201D"
+height_unit: Unit for height measurement.
+height_value: The vertical measurement or distance from the base to the top of a subject
+  or participant.
 histological_report: histopathological reporting of key variables that are important
   for the tissue (absence of necrosis, comment on composition, significant pathology
   description, high level inflammation/fibrosis assessment etc
@@ -178,11 +180,21 @@ ion_mobility: 'Specifies whether or not ion mobility spectrometry was performed
 ion_source: Specifies the ion source used
 is_cedar: Identifies whether the version is hosted by CEDAR
 is_contact: Is this individual a contact for DOI purposes?
-is_deceased: Is the source deceased? Use either 'True' or 'False'.
-is_embryo: Is the source an embryo? Use either 'True' or 'False'.
 is_targeted: Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement
   by the assay.
 is_technical_replicate: Is this a sequencing replicate?
+kidney_donor_profile_index_value: 'The Kidney Donor Profle Index (KDPI) is a numerical
+  measure that combines ten donor factors, including clinical parameters and demographics,
+  to summarize into a single number the quality of deceased donor kidneys relative
+  to other recovered kidneys. The KDPI is derived by frst calculating the Kidney Donor
+  Risk Index (KDRI) for a deceased donor. Kidneys from a donor with a KDPI of 90%,
+  for example, have a KDRI (which indicates relative risk of graft failure) greater
+  than 90% of recovered kidneys. The KDPI is simply a mapping of the KDRI from a relative
+  risk scale to a cumulative percentage scale. The reference population used for this
+  mapping is all deceased donors in the United States with a kidney recovered for
+  the purpose of transplantation in the prior calendar year. Lower KDPI values are
+  associated with increased donor quality and expected longevity. https://optn.transplant.hrsa.gov/media/1512/guide_to_calculating_interpreting_kdpi.pdf
+  '
 lab_id: "An internal field labs can use it to add whatever ID(s) they want or need\
   \ for dataset validation and tracking. This could be a single ID (e.g., \"Visium_9OLC_A4_S1\"\
   ) or a delimited list of IDs (e.g., \u201C9OL; 9OLC.A2; Visium_9OLC_A4_S1\u201D\
@@ -235,21 +247,17 @@ library_layout: Whether the library was generated for single-end or paired end s
 library_pcr_cycles: Number of PCR cycles to amplify cDNA
 library_pcr_cycles_for_sample_index: Number of PCR cycles performed for library indexing
 library_preparation_kit: Reagent kit used for library preparation
-light_cycle: The light cycle in the room where the source is housed. "Standard/default"
-  refers to 12-hour photoperiods (e.g., lights on at 7:00 AM, lights off at 7:00 PM).
-  "Longer photoperiods" refers to 14-hour photoperiods (e.g., lights on at 7:00 AM,
-  lights off at 9:00 PM). "Reverse lightcycles" means that the the timing of the 12-hour
-  photoperiod is reversed (.e.g, lights on at 7:00 PM, lights off at 7:00 AM).
-local_lifespan_data: A free text description of how long mice live within the local
-  environment. It is recommended to provide the median or maximum values for murine
-  lifespans.
 lot_number: 'The lot# is specific to the vendor. (eg: Abcam lot# GR3238979-1)'
 mass_resolving_power: "The MS1 resolving power defined as m/\u2206m where \u2206m\
   \ is the FWHM for a given peak with a specified m/z (m). (unitless)"
 max_x_width_unit: Units of image width of the ROI acquisition
 max_x_width_value: Image width value of the ROI acquisition
 max_y_height_unit: Units of image height of the ROI acquisition
 max_y_height_value: Image height value of the ROI acquisition
+mechanism_of_injury: 'Mechanism of injury may be, for example: fall, impact (eg: auto
+  accident), weapon (eg: firearm), etc.'
+medical_history: A record of a patient's background regarding health and the occurrence
+  of disease events of the individual.
 middle_name_or_initial: Middle name or initial
 ms_scan_mode: Indicates whether the data were generated using MS, MS/MS or MS3.
 ms_source: The ion source type used for surface sampling.
@@ -352,7 +360,8 @@ quality_criteria: 'For example, RIN: 8.7. For suspensions, measured by visual in
   or no cells. This can be captured at a high level. "OK" or "not OK", or with more
   specificity such as "debris", "clump", "low clump".'
 quality_view: The quality of the acquired ultrasound images.
-rack_setup: The rack setup type in which the source is housed.
+race: A grouping of humans based on shared physical characteristics or social/ethnic
+  identity generally viewed as distinct.
 range_z_unit: The unit of range_z_value.
 range_z_value: The total range of the z axis.
 reagent_prep_protocols_io_doi: DOI for protocols.io referring to the protocol for
@@ -374,10 +383,6 @@ roi_description: A description of the region of interest (ROI) captured in the i
 roi_id: Multiple images (1-n) are acquired from regions of interest (ROI1, ROI2, ROI3,
   etc) on a slide. The roi_id is a number from 1-n representing the ROI captured on
   a slide.
-room_health_status: A description of the pathogen and opportunist exclusion level
-  of the room where the source is housed.
-room_temperature: The temperature value in Celsius of the room where the source is
-  housed. An example is "23".
 rr_id: The rr_id is a unique antibody identifier that comes from the Antibody Registry
   (https://antibodyregistry.org).
 sample_id: UUID or HuBMAP ID of parent
@@ -412,15 +417,14 @@ sequencing_read_format: Slash-delimited list of the number of sequencing cycles
 sequencing_read_percent_q30: 'Q30 is the weighted average of all the reads (e.g. #
   bases UMI * q30 UMI + # bases R2 * q30 R2 + ...)'
 sequencing_reagent_kit: Reagent kit used for sequencing
-sex: The sex of the mouse.
+sex: 'Biological sex at birth: male or female or other.'
 signal_type: Type of signal measured per channel (usually dual counts)
 single_file_export_format: 'The format in which each single imaging file will be exported.
   (Example: DICOM, tiff, avi, etc.)'
 sn_quality: 'An integer describing the signal to noise quality of an OCT image (Example:
   30)'
 sn_quality_unit: 'The unit of the integer describing the signal to noise quality of
   an OCT image (Example: dB)'
-source_id: SenNet ID of the source (whole organism) of the assayed tissue.
 source_project: External source (outside of HuBMAP) of the project, eg. HCA (The Human
   Cell Atlas Consortium).
 source_storage_time_unit: Time unit
@@ -455,13 +459,6 @@ step_z_value: The number of optical sections in z axis range.
 storage_media: What was the sample preserved in.
 storage_method: The method by which the sample was stored, after preparation and before
   the assay was performed.
-strain: Jackson Labs nomenclature. When mutant alleles are part of the strain name,
-  use "<" and ">" to indicate the superscripted alleles. For example, C57BL/6J-KitW-39J
-  should be entered as "C57BL/6J-Kit<W-39J>", where "W-39J" would be the portion of
-  the string displayed as superscripted text. For further information, see the "Quick
-  Guide to Mouse Nomenclature" (https://resources.jax.org/guides/quick-guide-to-mouse-nomenclature).
-strain_rrid: The Research Resource Identifier (RRID) (https://scicrunch.org/resources/data/source/nlx_154697-1/search)
-  for the strain. An example is 'RRID:MGI:3713213'
 suspension_enriched: Was the cell/nuclei population enriched?
 suspension_enriched_target: If the suspension was enriched, then this is the target
   of the enrichment.
@@ -500,8 +497,6 @@ warm_ischemic_time_value: 'Time interval from interruption of blood supply of ti
   to cooling to 4C: For organ donor: cessation of blood flow to perfusion of organ
   (cooled to 4C) For surgical specimen/biopsy: cessation of blood flow to specimen
   (time biopsy taken or blood supply is interrupted) to cooling of specimen to 4C.'
-water_source: A free text description of the source's water supply, including any
-  treatments to the water.
 wavelength_unit: The unit of the wavelength value used to acquire OCT images (nm)
 wavelength_value: 'The value of the wavelength used to acquire OCT images (Example:
   787)'

docs/field-entities.yaml

@@ -22,6 +22,10 @@ acquisition_matrix_size_in_phase_encoding_direction:
 - dataset
 affiliation:
 - contributors
+age_unit:
+- donor
+age_value:
+- donor
 analyte_class:
 - dataset
 antibodies_path:
@@ -48,8 +52,10 @@ bead_barcode_read:
 - dataset
 bead_barcode_size:
 - dataset
-bedding:
-- murine
+blood_type:
+- donor
+body_mass_index_value:
+- donor
 bulk_atac_cell_isolation_protocols_io_doi:
 - dataset
 bulk_rna_isolation_protocols_io_doi:
@@ -62,8 +68,8 @@ bulk_rna_yield_value:
 - dataset
 bulk_transposition_input_number_nuclei:
 - dataset
-cage_enhancements:
-- murine
+cause_of_death:
+- donor
 ce_background_electrolyte:
 - dataset
 ce_capillary_coating:
@@ -128,10 +134,6 @@ data_path:
 - dataset
 data_precision_bytes:
 - dataset
-date_of_birth_or_fertilization:
-- murine
-date_of_death:
-- murine
 description:
 - dataset
 desi_solvent:
@@ -140,8 +142,6 @@ desi_solvent_flow_rate:
 - dataset
 desi_solvent_flow_rate_unit:
 - dataset
-diet:
-- murine
 dilution:
 - antibodies
 dms:
@@ -162,8 +162,6 @@ echo_train_length:
 - dataset
 end_datetime:
 - dataset
-euthanization_method:
-- murine
 execution_datetime:
 - dataset
 expected_cell_count:
@@ -190,6 +188,10 @@ harmonics:
 - dataset
 health_status:
 - sample
+height_unit:
+- donor
+height_value:
+- donor
 histological_report:
 - sample
 imaging_threshold_unit_value:
@@ -213,14 +215,12 @@ is_cedar:
 - sample
 is_contact:
 - contributors
-is_deceased:
-- murine
-is_embryo:
-- murine
 is_targeted:
 - dataset
 is_technical_replicate:
 - dataset
+kidney_donor_profile_index_value:
+- donor
 lab_id:
 - organ
 label_name:
@@ -293,10 +293,6 @@ library_pcr_cycles_for_sample_index:
 - dataset
 library_preparation_kit:
 - dataset
-light_cycle:
-- murine
-local_lifespan_data:
-- murine
 lot_number:
 - antibodies
 mass_resolving_power:
@@ -309,6 +305,10 @@ max_y_height_unit:
 - dataset
 max_y_height_value:
 - dataset
+mechanism_of_injury:
+- donor
+medical_history:
+- donor
 middle_name_or_initial:
 - contributors
 ms_scan_mode:
@@ -455,8 +455,8 @@ quality_criteria:
 - sample
 quality_view:
 - dataset
-rack_setup:
-- murine
+race:
+- donor
 range_z_unit:
 - dataset
 range_z_value:
@@ -489,10 +489,6 @@ roi_description:
 - dataset
 roi_id:
 - dataset
-room_health_status:
-- murine
-room_temperature:
-- murine
 rr_id:
 - antibodies
 sample_id:
@@ -534,7 +530,7 @@ sequencing_read_percent_q30:
 sequencing_reagent_kit:
 - dataset
 sex:
-- murine
+- donor
 signal_type:
 - dataset
 single_file_export_format:
@@ -543,8 +539,6 @@ sn_quality:
 - dataset
 sn_quality_unit:
 - dataset
-source_id:
-- murine
 source_project:
 - dataset
 source_storage_time_unit:
@@ -577,10 +571,6 @@ storage_media:
 - sample
 storage_method:
 - sample
-strain:
-- murine
-strain_rrid:
-- murine
 suspension_enriched:
 - sample
 suspension_enriched_target:
@@ -642,15 +632,15 @@ warm_ischemic_time_unit:
 - organ
 warm_ischemic_time_value:
 - organ
-water_source:
-- murine
 wavelength_unit:
 - dataset
 wavelength_value:
 - dataset
 weight_unit:
+- donor
 - organ
 - sample
 weight_value:
+- donor
 - sample