Set up a schema for Dataset for MorPhiC

[gabsie]

For which schema is a change/update being suggested? MorPhiC

What should the change/update be?
I would like to add a new schema for a dataset. The entity will be in hierarchy one level down from Study, i.e. Studies might have multiple datasets. Also, in DB, datasets might exist independently, to attach a Dataset to a Study is optional.

What new field(s) need to be changed/added?

Field name: dataset_name

• Field description: A brief name for the dataset
• Field type: text
• Multiple values: no
• Required: yes
• Examples: Extra-embryonic lineage KO of gene STS
• CV or enum: no

Field name: cell_line_name

• Field description: Name of the cell line studied with this dataset
• Field type: text
• Multiple values: no
• Required: yes
• Examples: KOLF2.2J
• CV or enum: no

Field name: assay_type

• Field description: Name of the assay used in the generation of the dataset.
• Field type: text
• Multiple values: no
• Required: yes
• Examples: scRNAseq
  (Note: should we consider the options for Pooled on this level, as well as Arrayed for the Genes altered... I don't know .. )
• CV or enum: yes, CV

Field name: perturbation_type

• Field description: Type of perturbation introduced by the gene expression alteration assay.
• Field type: text
• Multiple values: no
• Required: yes
• Examples: CRISPR-Cas9 KO
• CV or enum: don't know? please advise :)

Field name: duo_code

• Field description: Data Usage Ontology code that describe the data sharing restrictions for this dataset.
• Field type: text
• Multiple values: no
• Required: yes
• Examples: NRES, or DUO:0000046
• Enum: don't know? please advise :)

Field name: release_date

• Field description: Estimated date of data release to the public.
• Field type: date
• Multiple values: no
• Required: yes
• Examples: 2025-03-03
• CV or enum: no

Field name: other_notes

• Field description: Any notes for the dataset
• Field type: text
• Multiple values: no
• Required: no
• Examples: This dataset is not for processing just yet.
• CV or enum: no

Why is the change requested?

At the moment all existing MorPhiC studies are equal to datasets, but we wish to establish the option to have datasets under Studies in case multiple assay types or DUO codes would be supported.

[ESapenaVentura]

#59

[gabsie]

Enrique
Hold off on all of this, I think with Tony's permission we will just rename the current Study schema to be dataset :-D

Gabs

[ESapenaVentura]

Not needed atm! closing

[gabsie]

I am resurrecting this ticket. We need a schema for dataset. Let's just copy for now from the list above:

• Dataset ID (generated from the system)
• Dataset Type: (single-choice)

raw reads
processed files
analysis

• (if raw reads) Assay technology - only 1 (ontology options)
• (if raw reads) DUO code (can be confirm from Study)
• Release date (can be confirm from Study)
• Accession number (non mandatory - this is not for the user to fill in, we will populate when we accession)

@anu-shiva @dipayan1985 @ESapenaVentura please review or ask questions.

The point of the above is to address any occasions when they might have two technologies for the same study (bulk and single cell), for which they will have to submit two different metadata spreadsheets.

The second point to have the types is to allow for different folder types to be available per study.
I am happy to review this as you guys take a look.

Thanks,
Gabby

[gabsie]

So after we discussed this some time ago, for dataset we will just need:

• Dataset ID (generated from the system)
• Dataset short name/label
• Assay technology - only 1 (ontology options)
• DUO code
• Release date
• Accession number (non mandatory)

Any final remarks? @dipayan1985 @anu-shiva