Merge pull request #60 from HEAL/update_slmd0324

update_slmd0324: Updating SLMD files to align with CEDAR changes

study-level-metadata-schema/schema-clean/cedar_subset/study-metadata-schema-for-humans_cedar_subset.md

@@ -11,7 +11,7 @@
   - **`alternative_study_description`** *(string)*: An alternative description of or abstract for the study. - Generally, for studies with an NIH appl id, if this field is filled out, the text will be searchable on the Platform, but the NIH appl id abstract text will be the study description displayed for the study in the Platform study table entry.
 - **`metadata_location`** *(object)*
   - **`nih_application_id`** *(string)*: NIH application ID; only applicable if study is funded by NIH.
-  - **`other_study_websites`** *(array)*: any other websites officially associated with this study that provide additional information about the study.
+  - **`other_study_websites`** *(array)*: Other websites officially associated with this study that provide additional information about the study.
     - **Items** *(string)*: Refer to *#/definitions/saneUrl*.
 - **`data_availability`** *(object)*
   - **`produce_data`** *(boolean)*: Indicate whether or not the study will collect/produce (primary or secondary) data.
@@ -37,6 +37,19 @@
     - **Items** *(string)*: Must be one of: `['Human', 'Animal', 'Human cell/tissue/tissue model', 'Animal cell/tissue/tissue model', 'Molecule (e.g. chemical/protein engineering, protein crystallization)']`.
   - **`study_type_design`** *(array)*: The overarching study type and more granular study design. Choose as many as apply.
     - **Items** *(string)*: Must be one of: `['Basic Research - Theory/Modeling', 'Basic Research - Applied', 'Basic Research - Method/Protocol development', 'Basic Research - Animal study', 'Basic Research - Cell study', 'Basic Research - Genetic study', 'Basic Research - Biochemistry study', 'Basic Research - Biophysical study', 'Basic Research - Gene sequencing', 'Basic Research - Genetic Engineering', 'Basic Research - Material Development', 'Basic Research - Device Development', 'Basic Research - Small molecule screen', 'Basic Research - High throughput screen', 'Basic Research - Screen, other', 'Clinical Research - Phase I', 'Clinical Research - Phase II', 'Clinical Research - Phase III', 'Clinical Research - Phase IV', 'Clinical Research - Therapy/drug study without intervention', 'Clinical Research - Case Report or Series', 'Preclinical Research', 'Randomized Control Trial', 'Pre/Post', 'Stepped Wedge', 'Regression Discontinuity', 'Difference in Differences', 'Cross-over', 'Natural Experiment', 'Cohort, prospective', 'Cohort, retrospective', 'Cohort - panel, longitudinal', 'Cohort - cross-sectional, longitudinal', 'Cohort - cross-sectional, single time-point', 'Case control', 'Ecological', 'Monitoring/surveillance', 'Inventory', 'Curation', 'Meta-analysis', 'Review', 'Review, Systematic', 'Review, Simple (narrative)']`.
+- **`human_subject_applicability`** *(object)*
+  - **`gender_applicability`** *(array)*: Considering the study in a translational context, to humans of which gender identity(ies) are the study results intended to apply and/or likely to generalize to.
+    - **Items** *(string)*: Must be one of: `['Female', 'Transgender woman/trans woman/male-to-female (MTF)', 'Male', 'Transgender man/trans man/female-to-male (FTM)', 'Genderqueer/gender nonconforming/neither exclusively male nor female', 'Other']`.
+  - **`sexual_identity_applicability`** *(array)*: Considering the study in a translational context, to humans of which sexual identity(ies) are the study results intended to apply and/or likely to generalize to.
+    - **Items** *(string)*: Must be one of: `['Heterosexual', 'Homosexual (gay/lesbian)', 'Bisexual', 'Asexual', 'Other']`.
+  - **`biological_sex_applicability`** *(array)*: Considering the study in a translational context, to humans of which biological sexes are the study results intended to apply and/or likely to generalize to.
+    - **Items** *(string)*: Must be one of: `['Ambiguous', 'Female', 'Male']`.
+  - **`age_applicability`** *(array)*: Considering the study in a translational context, to humans of which age or developmental stage are the study results intended to apply and/or likely to generalize to.
+    - **Items** *(string)*: Must be one of: `['Fetus', 'Infant, newborn (Birth to 1 month)', 'Infant (1 to 23 months)', 'Child, preschool (2 to 5 years)', 'Child (6 to 12 years)', 'Adolescent (13 to 18 years)', 'Adult (19 to 44 years)', 'Middle aged adult (45 to 64 years)', 'Aged adult (65 to 79 years)', 'Aged, 80 and over (80 years and over)']`.
+  - **`irb_vulnerability_conditions_applicability`** *(array)*: Considering the study in a translational context, which special IRB human vulnerability conditions are the study results intended to address or apply to?
+    - **Items** *(string)*: Must be one of: `['Pregnant women', 'Human fetuses', 'Neonates', 'Prisoners', 'Children', 'Individuals with physical disabilities', 'Individuals with mental disabilities or cognitive impairments', 'Economically disadvantaged', 'Socially disadvantaged', 'Terminally ill or very sick', 'Racial or ethnic minorities', 'Institutionalized persons (for example, persons in correctional facilities, nursing homes or mental health facilities)']`.
+  - **`geographic_applicability`** *(array)*: For studies with human subjects, from which geographic location(s) are subjects recruited. If subjects are recruited in the US nationally, choose only US - national. If subject are recruited in the US only in specific state(s), choose US - Specific States, then please also select the abbreviation of each of the specific states from which subjects are recruited. If subjects are recruited in the US from specific county(ies) within specific state(s), please choose US - Specific States and US - Specific Counties, and choose the abbreviation of each specific state from which subjects are recruited.
+    - **Items** *(string)*: Must be one of: `['Non US', 'US - National', 'US - Specific States', 'US - Specific Counties', 'AK', 'AL', 'AR', 'AZ', 'CA', 'CO', 'CT', 'DE', 'FL', 'GA', 'HI', 'IA', 'ID', 'IL', 'IN', 'KS', 'KY', 'LA', 'MA', 'MD', 'ME', 'MI', 'MN', 'MO', 'MS', 'MT', 'NC', 'ND', 'NE', 'NH', 'NJ', 'NM', 'NV', 'NY', 'OH', 'OK', 'OR', 'PA', 'RI', 'SC', 'SD', 'TN', 'TX', 'UT', 'VA', 'VT', 'WA', 'WI', 'WV', 'WY']`.
 - **`human_treatment_applicability`** *(object)*
   - **`treatment_investigation_stage_or_type`** *(array)*: If the study is investigating a treatment, intervention, or solution to a human opioid or pain condition, what type of investigation is the study undertaking? at what stage in the treatment investigation process does this study lie?
     - **Items** *(string)*: Must be one of: `['target discovery', 'target mechanism', 'treatment discovery', 'treatment mechanism', 'treatment efficacy', 'differential treatment efficacy', 'treatment implementation', 'treatment availability or accessibility']`.
@@ -63,19 +76,6 @@
     - **Items** *(string)*
   - **`all_other_condition`** *(array)*: If the study is measuring or tracking other human health conditions besides the treatment or study target condition and outcome condition, please indicate the other tracked/measured condition(s) here. Choose as many as apply - Values will be restricted to NLM MeSH Diseases - see Branch 'C' here: https://meshb-prev.nlm.nih.gov/treeView.
     - **Items** *(string)*
-- **`human_subject_applicability`** *(object)*
-  - **`gender_applicability`** *(array)*: Considering the study in a translational context, to humans of which gender identity(ies) are the study results intended to apply and/or likely to generalize to.
-    - **Items** *(string)*: Must be one of: `['Female', 'Female-to-male transsexual', 'Intersexed', 'Male', 'Male-to-female transsexual', 'Other']`.
-  - **`sexual_identity_applicability`** *(array)*: Considering the study in a translational context, to humans of which sexual identity(ies) are the study results intended to apply and/or likely to generalize to.
-    - **Items** *(string)*: Must be one of: `['Heterosexual', 'Homosexual (gay/lesbian)', 'Bisexual', 'Asexual', 'Other']`.
-  - **`biological_sex_applicability`** *(array)*: Considering the study in a translational context, to humans of which biological sexes are the study results intended to apply and/or likely to generalize to.
-    - **Items** *(string)*: Must be one of: `['Ambiguous', 'Female', 'Male']`.
-  - **`age_applicability`** *(array)*: Considering the study in a translational context, to humans of which age or developmental stage are the study results intended to apply and/or likely to generalize to.
-    - **Items** *(string)*: Must be one of: `['Fetus', 'Infant, newborn (Birth to 1 month)', 'Infant (1 to 23 months)', 'Child, preschool (2 to 5 years)', 'Child (6 to 12 years)', 'Adolescent (13 to 18 years)', 'Adult (19 to 44 years)', 'Middle aged adult (45 to 64 years)', 'Aged adult (65 to 79 years)', 'Aged, 80 and over (80 years and over)']`.
-  - **`irb_vulnerability_conditions_applicability`** *(array)*: Considering the study in a translational context, which special IRB human vulnerability conditions are the study results intended to address or apply to?
-    - **Items** *(string)*: Must be one of: `['Pregnant women', 'Human fetuses', 'Neonates', 'Prisoners', 'Children', 'Individuals with physical disabilities', 'Individuals with mental disabilities or cognitive impairments', 'Economically disadvantaged', 'Socially disadvantaged', 'Terminally ill or very sick', 'Racial or ethnic minorities', 'Institutionalized persons (for example, persons in correctional facilities, nursing homes or mental health facilities)']`.
-  - **`geographic_applicability`** *(array)*: For studies with human subjects, from which geographic location(s) are subjects recruited. If subjects are recruited in the US nationally, choose only US - national. If subject are recruited in the US only in specific state(s), choose US - Specific States, then please also select the abbreviation of each of the specific states from which subjects are recruited. If subjects are recruited in the US from specific county(ies) within specific state(s), please choose US - Specific States and US - Specific Counties, and choose the abbreviation of each specific state from which subjects are recruited.
-    - **Items** *(string)*: Must be one of: `['Non US', 'US - National', 'US - Specific States', 'US - Specific Counties', 'AK', 'AL', 'AR', 'AZ', 'CA', 'CO', 'CT', 'DE', 'FL', 'GA', 'HI', 'IA', 'ID', 'IL', 'IN', 'KS', 'KY', 'LA', 'MA', 'MD', 'ME', 'MI', 'MN', 'MO', 'MS', 'MT', 'NC', 'ND', 'NE', 'NH', 'NJ', 'NM', 'NV', 'NY', 'OH', 'OK', 'OR', 'PA', 'RI', 'SC', 'SD', 'TN', 'TX', 'UT', 'VA', 'VT', 'WA', 'WI', 'WV', 'WY']`.
 - **`data`** *(object)*
   - **`data_orientation`** *(array)*: Does the study produce/collect quantitative data?, qualitative data? Choose as many as apply.
     - **Items** *(string)*: Must be one of: `['Quantitative', 'Qualitative']`.