Musculoskeletal - Tier 2

[arschat]

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

• [x] investigate overlap with Tier 1 or other Tier 2
• [x] investigate potential mapping with DCP fields
• [x] 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.