In Vitro Biospecimen Metadata Template
A template outlining metadata to be collected for biospecimen used for an in vitro experiment.
| Attribute | Description | Required | Valid Values |
|---|---|---|---|
| individualID | Unique identifier assigned to each study participant. For multi-specimen data files provide all IDs in a comma-separated list. | FALSE | |
| treatment | A short descriptive label indicating what experimental treatments have been applied to a biospecimen before data capture. Please include the word 'control' to indicate specific treatments that are intended to serve as a control group. | True | |
| altSampleID | An alternate identifier for a sample. With some assays there can be default or alternate sample identifiers entered into the data collection software. If you will be uploading data collected with an alternate identifier please provide that here. In some cases, the ARK BDM team will use this field to capture original but out-dated identifiers for samples. | False | |
| project | A sub-level attribute of `program` specifying a research initiative working to investigate particular hypotheses. | True | AIM for RA, ELLIPSS, LOCKIT, RA, SLE, STAMP, V-CoRT |
| notes | Please use this attribute to captured pertinent details not otherwise captured. This is an unstructured text entry, please be concise. | False | |
| biospecimenID | A unique identifier assigned to specimens collected from study participants. For multi-specimen data files provide all IDs in a comma-separated list. | True | |
| program | Name of the funding program that supported the generation of data and associated files | True | AMP AIM, AMP RA/SLE, Community Contribution |
| Component | A high-level attribute for grouping attributes into templates. | True | |
| parentBiospecimenID | The biospecimenID associated with the originating biospecimen for derived or child biospecimens. | False | |
| biospecimenType | A label indicating the biological material collected for experimentation and data collection. Where applicable, provide all types in a comma-separated list. | True | PBMCs, cell line, fibroblast-like synoviocyte, kidney biopsy, none, plasma, primary cell culture, saliva, salivary gland, serum, skin biopsy, skin swab, stool, suction blister cells, suction blister fluid, synovial fluid, synovial tissue, total leukocytes, urine, uvea, whole blood |
| biospecimenSubtype | Biospecimen status before sample is processed into a scRNA-seq library. Several scRNA-seq technologies support a variety of sample processing methods which can introduces sources of technical variation. | False | FFPE tissue, PFA-fixed tissue, cell or tissue lysate, cell suspension, flow-sorted cells, fresh tissue, frozen tissue, nuclei suspension, supernatant |
| treatmentTimepoint | Where applicable, specify the timepoint relative to treatment to distinguish different sets of samples that have undergone the same treatment but for different lengths of time. REQUIRED: please specify the unit of time, e.g., secs, mins, hrs, days, etc. | False | |
| plateID | An identifier corresponding to a multi-well plate. Certain data types and assays (e.g., Olink) profile samples using multi-well plates. Knowing which samples were profiled on each plate is important for establishing sample provenance, finding the right data files for a specific set of samples, as well as downstream exploratory data analysis and QC work particularly regarding identification and correction of batch effects. This attribute is required. Please enter 'Not Applicable' if your biospecimen were not profiled in plated batches. | TRUE | |
| visitID | Ordinal ID distinguishing different patient visits. | True | |
| anatomicalSite | The anatomical site, i.e., location on or within the body, from which the biospecimen was collected. This attribute is required depending on the value selected for biospecimenType. | True | left 2nd MCP joint, left ankle joint, left hip joint, left knee joint, left wrist joint, other site, right 1st MTP joint, right 2nd MCP joint, right 2nd MTP joint, right 3rd MCP joint, right ankle joint, right hip joint, right knee joint, right wrist joint, unknown |
| skinSiteStatus | Disease manifestation status of skin biospecimen. | True | healthy control, lesional, lesional proximal, non-lesional |
| cellOntologyID | Cell Ontology CL identifier that best describes a biopsecimen used to generate data, e.g., CL:0000084 for T cell. | False | |
| cellType | The cell type name from Cell Ontology for the corresponding CL identifier. | False | |
| krennLining | A standardized, semi-quantitative measure of the degree of hyperplasia/enlargement of the synovial lining layer of synovial specimen. This is one of three measures used to derive the Krenn Synovitis Score (KSS) which is a histological scoring system used to quantify inflammation in synovial tissue biopsies, particularly in the context of inflammatory arthritis like rheumatoid arthritis. If value unknown, use '-1'. | False | |
| krennSynovitisScore | The Krenn Synovitis Score (KSS) is a histological scoring system used to quantify inflammation in synovial tissue biopsies, particularly in the context of inflammatory arthritis like rheumatoid arthritis. If value unknown, use '-1'. | False | |
| krennStroma | A standardized, semi-quantitative measure of stromal cell density of synovial specimen. This is one of three measures used to derive the Krenn Synovitis Score (KSS) which is a histological scoring system used to quantify inflammation in synovial tissue biopsies, particularly in the context of inflammatory arthritis like rheumatoid arthritis. If value unknown, use '-1'. | False | |
| synovialCollectionProcedure | Classification of procedure for synovial tissue collection. | True | arthroplasty, biopsy, synovectomy, unknown |
| krennInflammatory | A standardized, semi-quantitative measure of the degree of inflammatory infiltrate in synovial specimen. This is one of three measures used to derive the Krenn Synovitis Score (KSS) which is a histological scoring system used to quantify inflammation in synovial tissue biopsies, particularly in the context of inflammatory arthritis like rheumatoid arthritis. If value unknown, use '-1'. | False | |
| salivaCollectionProcedure | Classification of saliva collection procedure. This is a conditionally dependent attribute triggered for saliva `biospecimenType`. | True | stimulated, unstimulated |
| primaryCellSource | A label indicating the biological source material from which a primary cell culture was derived. | True | PBMCs, kidney, pannus-derived dermis, pannus-derived epidermis, salivary gland, synovial tissue, total leukocytes, urine, uvea, whole blood |
| userDefinedCellType | User-defined label of a cell type. Contributors are provided this option to use preferred or custom cell type labels that may vary from options and standards set by Cell Ontology. | False | |
| FACSPopulation | A description of the marker gating strategy used to derive the population cells with FACS. | True |