OSDR Metadata Curation Guidelines Summary
For GEO-sourced data:
Only list “contributors” in the people section.
Use the author ontology if there’s an associated publication.
If the publication is too broad or lists multiple GSEs, opt for the GEO summary as the description.
Enter full funding statements in the funding field, not just grant numbers.
General Rules:
Maintain the same sample order as in NCBI.
Exclude special characters from factor levels; use only letters, numbers, and spaces.
Retype any special characters from publications, substituting mu (μ) with “u”.
For associated publications, use keywords as study design descriptors.
Excel Handling:
If editing outside GEODE, remove blank columns at the end before re-importing.
Formatting:
Prioritize characteristics, then factors, then protocols and parameters in column order in the sample table. Comments positioning is flexible.
Metadata normalization:
Investigation file level - all
Correct all date formats to dd-mmm-yyyy (i.e. 01-Jan-2018)
Examples of study design types: MESH: Space Flight, EFO: transcription profiling by array
Update the following Study Factors to below terms and ontologies:
Factor terms to avoid |
New Study Factor Name |
New Study Factor Type (search for ontology term) |
Ontology term |
|---|---|---|---|
~~microgravity~~, space flight, ~~gravity, treatment, weightlessness,~~ extraterrestrial environment, environmental stress, ~~gravitation~~ |
Spaceflight |
Space Flight |
|
treatment protocol, plant treatment, bleomycin treatment, clinical treatment, |
Treatment |
treatment |
EFO: |
timepoint, sampling time, time |
Time |
Time |
EFO: |
Radiation Ionizing, irradiation, response to ionizing radiation, radiation, irradiate, radiation type |
Ionizing Radiation |
ionizing radiation |
|
dose, treatment dose (not radiation related) |
dose |
dose |
OBI: |
dose related to radiation: dose, radiation dose absorbed radiation dose |
Absorbed Radiation Dose |
Absorbed Radiation Dose |
NCIT: |
cell culture, cell line, |
Cell Line |
cell line |
|
uG condition (For ground studies report the simulated gravity hardware or device in the same cell as g) |
Microgravity Simulation |
Weightlessness simulation |
MESH: http://bioportal.bioontology.org/ontologies/MESH?p=classes&conceptid=D018474 |
tail suspension |
Hindlimb Unloading |
hindlimb suspension |
MESH: |
Partial Weight Bearing* |
Partial Weight Bearing |
free text |
|
growth time |
Growth Time |
Time |
EFO: |
Root Zone |
Root Zone |
**root |
|
simulated gravity (g level),simulated microgravity (for studies simulating various gravity levels. If uG and 1G are the only two conditions use ‘Microgravity Simulation’ instead of ‘Altered Gravity’) (For ground studies report the simulated gravity hardware or device in the same cell as g) |
Altered Gravity |
Gravity, Altered |
|
genotype |
Genotype |
Genotype |
|
ecotype |
Ecotype |
ecotype |
EFO: https://www.ebi.ac.uk/ols/ontologies/efo/terms?short_form=EFO_0000434 |
tissue |
***Tissue |
Tissue |
NCIT: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C12801 |
To differentiate from “Time” in the case that samples are not collected right after the treatment exposure duration |
Time of Sample Collection After Treatment |
Time of Sample Collection After Treatment (free text) |
|
organism part |
Organism Part |
Organism Part |
EFO: https://www.ebi.ac.uk/ols/ontologies/efo/terms?short_form=EFO_0000635 |
*Partial Weight Bearing is referring to the quadrupedal unloading model in rats developed by Marie Morteux et al., described in this manuscript. The values of this column would be normal loading with full harness (PWB100) for controls, 40% of normal loading (PWB40) for Mars gravity simulation, 2_0% of normal loading (PWB40)_ for Moon gravity simulation, or 7_0% of normal loading (PWB40)._
\
**In GLDS-208 the author uses Root Zone to refer to distinct sections of the primary root. In plant studies, the ‘Root Zone’ is also commonly used to describe the entire rhizosphere, which would include the soil (or agar) around the roots as well as the root tissue itself.
***Tissue is considered as a factor only if it was an intended factor and direct comparisons like DGE are done with tissue types. If they don’t meet this criteria, the dataset should be split into separate studies by tissue type (even if they are from the same accession number from an outside repository).
\