Maxsibilla/murine port (#1311)

* Porting over murine source spec * Updating murine spec with datetime support * Phillips/murine port suggested (#1310) * suggested updates to murine-port * changes to make testing happy --------- Co-authored-by: Gesina Phillips <[email protected]> * Rolling back field-descriptions changes * Rolling back field-descriptions changes * Rolling back field-entities changes * Rolling back remainder of doc changes * Rolling back remainder of doc changes * General: Update changelog * General: Add field-* changes back. * General: Add field-* changes back. --------- Co-authored-by: Gesina Phillips <[email protected]> Co-authored-by: Juan Puerto <=>
hubmapconsortium · Mar 20, 2024 · 29eff6d · 29eff6d
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -20,6 +20,7 @@
 - Update Histology to include description on OME-TIFFs
 - Update Histology with links
 - Update GeoMx NGS directory schema
+- Ported murine from SenNet
 
 ## v0.0.17
 

diff --git a/docs/field-descriptions.yaml b/docs/field-descriptions.yaml
@@ -40,6 +40,7 @@ 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.
 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:
@@ -52,6 +53,7 @@ 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."
 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
@@ -106,11 +108,16 @@ 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
@@ -125,6 +132,7 @@ 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
@@ -170,6 +178,8 @@ 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?
@@ -225,6 +235,14 @@ 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)"
@@ -334,6 +352,7 @@ 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.
 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
@@ -355,6 +374,10 @@ 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
@@ -389,13 +412,15 @@ 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.
 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
@@ -430,6 +455,13 @@ 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.
@@ -468,6 +500,8 @@ 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)'

diff --git a/docs/field-entities.yaml b/docs/field-entities.yaml
@@ -48,6 +48,8 @@ bead_barcode_read:
 - dataset
 bead_barcode_size:
 - dataset
+bedding:
+- murine
 bulk_atac_cell_isolation_protocols_io_doi:
 - dataset
 bulk_rna_isolation_protocols_io_doi:
@@ -60,6 +62,8 @@ bulk_rna_yield_value:
 - dataset
 bulk_transposition_input_number_nuclei:
 - dataset
+cage_enhancements:
+- murine
 ce_background_electrolyte:
 - dataset
 ce_capillary_coating:
@@ -124,6 +128,10 @@ data_path:
 - dataset
 data_precision_bytes:
 - dataset
+date_of_birth_or_fertilization:
+- murine
+date_of_death:
+- murine
 description:
 - dataset
 desi_solvent:
@@ -132,6 +140,8 @@ desi_solvent_flow_rate:
 - dataset
 desi_solvent_flow_rate_unit:
 - dataset
+diet:
+- murine
 dilution:
 - antibodies
 dms:
@@ -152,6 +162,8 @@ echo_train_length:
 - dataset
 end_datetime:
 - dataset
+euthanization_method:
+- murine
 execution_datetime:
 - dataset
 expected_cell_count:
@@ -201,6 +213,10 @@ is_cedar:
 - sample
 is_contact:
 - contributors
+is_deceased:
+- murine
+is_embryo:
+- murine
 is_targeted:
 - dataset
 is_technical_replicate:
@@ -277,6 +293,10 @@ library_pcr_cycles_for_sample_index:
 - dataset
 library_preparation_kit:
 - dataset
+light_cycle:
+- murine
+local_lifespan_data:
+- murine
 lot_number:
 - antibodies
 mass_resolving_power:
@@ -435,6 +455,8 @@ quality_criteria:
 - sample
 quality_view:
 - dataset
+rack_setup:
+- murine
 range_z_unit:
 - dataset
 range_z_value:
@@ -467,6 +489,10 @@ roi_description:
 - dataset
 roi_id:
 - dataset
+room_health_status:
+- murine
+room_temperature:
+- murine
 rr_id:
 - antibodies
 sample_id:
@@ -507,6 +533,8 @@ sequencing_read_percent_q30:
 - dataset
 sequencing_reagent_kit:
 - dataset
+sex:
+- murine
 signal_type:
 - dataset
 single_file_export_format:
@@ -515,6 +543,8 @@ sn_quality:
 - dataset
 sn_quality_unit:
 - dataset
+source_id:
+- murine
 source_project:
 - dataset
 source_storage_time_unit:
@@ -547,6 +577,10 @@ storage_media:
 - sample
 storage_method:
 - sample
+strain:
+- murine
+strain_rrid:
+- murine
 suspension_enriched:
 - sample
 suspension_enriched_target:
@@ -608,6 +642,8 @@ warm_ischemic_time_unit:
 - organ
 warm_ischemic_time_value:
 - organ
+water_source:
+- murine
 wavelength_unit:
 - dataset
 wavelength_value:

diff --git a/docs/field-schemas.xlsx b/docs/field-schemas.xlsx
diff --git a/docs/field-schemas.yaml b/docs/field-schemas.yaml
@@ -250,6 +250,8 @@ bead_barcode_read:
 - slideseq
 bead_barcode_size:
 - slideseq
+bedding:
+- murine-source
 bulk_atac_cell_isolation_protocols_io_doi:
 - bulkatacseq
 bulk_rna_isolation_protocols_io_doi:
@@ -262,6 +264,8 @@ bulk_rna_yield_value:
 - bulkrnaseq
 bulk_transposition_input_number_nuclei:
 - bulkatacseq
+cage_enhancements:
+- murine-source
 ce_background_electrolyte:
 - cems
 ce_capillary_coating:
@@ -389,6 +393,10 @@ data_path:
 data_precision_bytes:
 - imc
 - mibi
+date_of_birth_or_fertilization:
+- murine-source
+date_of_death:
+- murine-source
 description:
 - af
 - bodyct
@@ -422,6 +430,8 @@ desi_solvent_flow_rate:
 - ims
 desi_solvent_flow_rate_unit:
 - ims
+diet:
+- murine-source
 dilution:
 - antibodies
 dms:
@@ -470,6 +480,8 @@ echo_train_length:
 end_datetime:
 - imc
 - mibi
+euthanization_method:
+- murine-source
 execution_datetime:
 - af
 - bodyct
@@ -598,6 +610,10 @@ is_cedar:
 - xenium
 is_contact:
 - contributors
+is_deceased:
+- murine-source
+is_embryo:
+- murine-source
 is_targeted:
 - af
 - bulkatacseq
@@ -747,6 +763,10 @@ library_pcr_cycles_for_sample_index:
 - slideseq
 library_preparation_kit:
 - bulkatacseq
+light_cycle:
+- murine-source
+local_lifespan_data:
+- murine-source
 lot_number:
 - antibodies
 mass_resolving_power:
@@ -1181,6 +1201,8 @@ quality_criteria:
 - sample-suspension
 quality_view:
 - ultrasound
+rack_setup:
+- murine-source
 range_z_unit:
 - lightsheet
 range_z_value:
@@ -1322,6 +1344,10 @@ roi_id:
 - mri
 - oct
 - ultrasound
+room_health_status:
+- murine-source
+room_temperature:
+- murine-source
 rr_id:
 - antibodies
 sample_id:
@@ -1413,6 +1439,8 @@ sequencing_reagent_kit:
 - scrnaseq-hca
 - slideseq
 - wgs
+sex:
+- murine-source
 signal_type:
 - imc
 - imc3d
@@ -1427,6 +1455,8 @@ sn_quality:
 - oct
 sn_quality_unit:
 - oct
+source_id:
+- murine-source
 source_project:
 - scrnaseq-hca
 source_storage_time_unit:
@@ -1474,6 +1504,10 @@ storage_method:
 - sample-block
 - sample-section
 - sample-suspension
+strain:
+- murine-source
+strain_rrid:
+- murine-source
 suspension_enriched:
 - sample-suspension
 suspension_enriched_target:
@@ -1595,6 +1629,8 @@ warm_ischemic_time_unit:
 - organ
 warm_ischemic_time_value:
 - organ
+water_source:
+- murine-source
 wavelength_unit:
 - oct
 wavelength_value: