Musculoskeletal - Tier 2

[arschat]

We have received a very well organised recommendations template.
We need to study and provide feedback.

• investigate overlap with Tier 1 or other Tier 2
• investigate potential mapping with DCP fields
• investigate suggested ontologies (!), enums & data types

[arschat]

Some preliminary feedback.

mapping	number	percent
new	10	28.57
dcp	14	40
tier1	4	11.43
tier2	7	20

detailed table

Field name	mapping	existing field
smoking_status	tier2	donor_organism.medical_history.smoking_status
smoking_pack_years	tier2	donor_organism.medical_history.smoking_pack_years
years_since_smoking_cessation	tier2	donor_organism.medical_history.years_since_smoking_cessation
bmi	dcp	donor_organism.human_specific.body_mass_index
tissue_dissociation_method	tier2	dissociation_protocol.method
height	dcp	donor_organism.height
weight	dcp	donor_organism.weight
age	dcp	donor_organism.organism_age
age_unit	dcp	donor_organism.organism_age_unit.text
comorbidities	tier2	donor_organism.comorbidities.ontology_label
alcohol history	dcp	donor_organism.medical_history.alcohol_history
nutritional state	dcp	donor_organism.medical_history.nutritional_state
medications	dcp	donor_organism.medical_history.medication
medical test results	dcp	donor_organism.medical_history.test_results
treatments	dcp	donor_organism.medical_history.treatment
self reported ethnicity	dcp	donor_organism.human_specific.ethnicity.text
time to laboratory receipt	new
date of sample storage	new
date of sample dissociation	new
How long were dissociated cells or nuclei stored prior to library preparation	dcp	?? specimen_from_organism.preservation_storage.storage_time
date of library preparation	new
occupation	tier2	donor_organism.occupation
tissue acquistion method from donor	tier1	sample_collection_method
history of injury to sampled joint or previous surgeries	new	MONDO
anatomical name of collected tissue	tier1	tissue_ontology_term_id
microanatomical_region_of collected tissue	new
side_of_tissue_collected	new	uberon usually allows such distinction (i.e. left forelimb)
library_preparation_method	tier1	assay_ontology_term_id
handedness of patient	new
method of tissue storage prior to sequencing	dcp	storage method
ancstral DNA sequencing result	tier2
sample dissociation method	new	is this separate from tissue dissociation?
sequencing information	tier1	sequencing_platform
tissue processing prior to dissociation	dcp	preservation method
tissue transportation	new	what the options could be here

[arschat]

We replied with some feedback and followed-up with answers about the procedure.

[arschat]

We are having a meeting tomorrow 16/10 with Sarah and team, to discuss. Here are the main points:

• free text requires labour to extract consistent info
  • what MSK wish to get from free text fields (occupation, tissue_dissociation, physical_activity_physical_exposure etc.)
• tissue dissociation
  • how order of dissociation protocols is going to be used downstream.
  • it there is no need for
• occupation related fields
  • occupation -> free text that matches to ontology SNOMED:14679004
  • physical_activity -> enum [sedentary, moderate (<60 minutes per day), Active (>60 minutes per day)]
  • physical_activity_type -> free text (i.e. ballet, football, hiking, boxing, yoga etc.)

[idazucchi]

Key points from the meeting:

• the free text field for activity and microanatomical location can't be standardised at the moment because there is no shared standard in the field and the aim is to capture as much metadata as possible so that it can be analysed later on
• fields required by MSK for dissociation protocol: tempreature, dissociation type, description and doi/protocol link

Post meeting action points:

• find ontology for occupation that could record physical exposure & activity and share with them
• agree internally on dissociation protocol fields, so that they work for lung too
• add catch-all free text field

Future actions:

• review free-text fields to standardise their content
• review microanataomical location, discuss how to integrate terms into UBERON ?

[arschat]

About tissue dissociation, we decided to introduce 4 new fields:
time, time_unit, temperature, solution [array]
MSK will use the dissociation_protocol.protocol_core.protocols_io_doi, dissociation_protocol.protocol_core.protocol_description and temperature while for Lung tier 2 #1235 we will map the enum options to values in those 4 fields (see here). For the solution, we will use this list.

#1313 ticket to describe the modelling before creating PR.

[arschat]

An ontology that could be appropriate for recording the occupation is the OccO ontology. Specifically as childOf OCCO:00000001.

It contains hierarchical data with a lot of grouping, and 1603 different occupations. I will reply to MSK with this suggestion to see if it fits their needs.

We can suggest a free-text field for that that a curator will map to an ontologised field afterwards.