Template Catalog
All templates are documented individually under Template Documentation; this page groups them by role so an agent can quickly identify which ones a given submission needs. See How to Read the Template Documentation for what the Required/Conditional/Optional and Type & Constraints columns mean.
Core templates (used by almost every study)
| Template | Role |
|---|---|
| basic_study_design | Registers the study, arms/cohorts, planned visits (compound template) |
| study_design_edit | Add/edit optional study elements after initial registration — includes arm_2_subject (link an existing subject to another arm/study) |
| protocols | Methods/procedures referenced by studies, samples, experiments |
| subjecthumans / subjectanimals | Define subjects and assign them to an arm/cohort |
| biosamples | Biological samples taken from subjects |
| treatments | In-vitro treatment conditions applied to samples — referenced by nearly every assay workflow |
| interventions | Interventions/co-administered medications |
| adverseevents | Adverse events |
| assessments, assessmentpanel, assessmentcomponent | Non-sample-based results (questionnaires, medical history) |
| labtests, labtestpanels, labtest_results | Clinical lab test results |
| experiments | Describes the experiment/measurement technique, links to protocols |
| immuneexposure | Immune exposure history |
| public_repositories | Pointers to data also housed in external repositories (e.g. GEO, SRA) |
Assay-specific templates (reagents → experiment samples → results)
Every assay has its own reagents / experiment-samples / (optional) results trio, plus sometimes a derived-data file. See Upload Order and the per-assay pages under Workflows → Assay Upload Order for the exact sequencing and same-package bundling rules.
| Assay | Reagents | Experiment Samples | Results / Derived |
|---|---|---|---|
| CyTOF | cytof_reagents | cytof | cytof_derived_data |
| ELISA | elisa_reagents | elisa | elisa_results |
| ELISPOT | elispot_reagents | elispot | elispot_results |
| Flow Cytometry | flow_cytometry_reagents | flow_cytometry | fcm_derived_data |
| Gene Expression Array | array reagents | gene_experession_array | results file + optional public_repositories |
| Genotyping Array | array reagents | genotyping_array | results file + optional public_repositories |
| HAI | hai_reagents | hai | hai_results |
| HLA Typing | hla_typing_reagents | hla | hla_typing (structured, optional) |
| Image Histology | other reagents | image_histology | results file only |
| KIR Typing | kir_typing_reagents | kir | kir_typing (structured, optional) |
| MBAA | mbaa_reagents | mbaa | standardcurves, controlsamples, mbaa_results (each independently optional) |
| Mass Spec — Metabolomics | other reagents | mass_spec_metabolomics | results file only |
| Mass Spec — Proteomics | (none) | mass_spec_proteomics | results file only |
| Neutralizing Antibody Titer | neutralizing_antibody_titer_reagents | neutralizing_antibody_titer | virus_neutralization_results |
| Other (unlisted assay) | other_reagents | other | results file only |
| QRT-PCR | pcr_reagents | qrt-pcr | pcr_results |
| RNA Sequencing | sequencing_reagents | rna_sequencing | rna_seq_results + optional public_repositories |
reagent_sets
reagent_sets is an optional grouping layer used by CyTOF and Flow Cytometry when the same group of reagents is reused across many experiment samples — see those assays' workflow pages for when it applies.
Lookup tables
Controlled-vocabulary fields reference lk_* tables (e.g. lk_species, lk_disease) — browse the full set under Template Documentation → Lookup Tables.