Adding schemas for image-based spatial transcriptomics #48
Conversation
rightbower
added
documentation
There was a problem hiding this comment.
Hi, I am new to the BICAN group, from a SSPsyGene consortium which will also have spatial transciptomics. I was curious about the "light treatment time" field, this isn't one that I've seen in other groups (HuBMAP/HTAN), and also was not considering for our SSPsyGene schema. I am guessing that light treatment came up when gathering input from your generating labs? I see that this field is "if applied" and so it looks great for BICAN. I am more asking in case SSPsyGene should consider this field, or how it was decided it add it.
There was a problem hiding this comment.
One other question, for these fields are there some that are strictly 'required'? -where it appears the "light treatment time" field is optional -only used when applied?
There was a problem hiding this comment.
For "gene name" I was curious what the thoughts were about HGNC identifiers as well? Our group has decided on HGNC identifiers (with the plan to also connect those to Ensembl IDs in the background).
There was a problem hiding this comment.
@rightbower - I left comments for the specific elements of the tables.
I will have to talk to you also about the class description (and relations between them), some value sets that are not included as a separate file, e.g. BICAN-Species/synonym, and if the fields have some exact mapping that we should use, e.g. from NIMP.
| donor age unit,bil:Specimen/Donor/Age unit,,Units for donor age,FALSE,bil_donor_age_units,ValueSet,Days,,,,categorical,, | ||
| donor sex,bil:Specimen/Donor/Sex,,Sex of donor,FALSE,bil_donor_sex,ValueSet,Male,,,,categorical,, | ||
| donor genotype,bil:Specimen/Donor/Genotype,,"The genotype or transgenic line information (e.g. StrainName, CreDriverLine, ReporterName, etc.)",TRUE,,text,wt/wt,,,,categorical,, | ||
| organ local name,bil:Specimen/Donor/Organ local ID,,Local (lab) reference ID assigned to the organ/brain.,TRUE,,text,,,,,categorical,, |
There was a problem hiding this comment.
I understand that all fields above should belong to Donor class, but what about the fields about "organ"?
| species,bil:Specimen/Donor/Species,,"Common name for the donor species (e.g. Mouse, Human)",FALSE,[BICAN-Species/synonym],ValueSet,mouse,,,,categorical,, | ||
| species NCBI taxonomy,bil:Specimen/Donor/NCBITaxonomy,,NCBI Taxonomy ID for species; format ID with prefix 'NCBI:txid',FALSE,[NCBI Taxon],ValueSet,NCBI:txid10090,,,,categorical,, | ||
| donor age,bil:Specimen/Donor/Age,,Age of donor (if known),FALSE,,float,12,,,,continuous,, | ||
| donor age unit,bil:Specimen/Donor/Age unit,,Units for donor age,FALSE,bil_donor_age_units,ValueSet,Days,,,,categorical,, |
There was a problem hiding this comment.
I'm not sure if "nullable" should be False, since the description suggest otherwise
| @@ -0,0 +1,21 @@ | |||
| Proposed BICAN Field Name,Aliases,LinkML Class,Definition,Nullable,Permissible Values,Data Type,Data Examples,Min Value,Max Value,Unit,Statistical Variable Type,Subsets,Notes | |||
| histological stain name,bil:Image/Channel/Fluorophore,Anatomical Stain,Name of histological stain applied to tissue ,TRUE,histological_stain_name,ValueSet,GFAP,,,,categorical,, | |||
| nuclear stain name,bil:Image/Channel/Fluorophore,Nuclear Stain,Name of nuclear stain applied to tissue,FALSE,nuclear_stain_name,ValueSet,DAPI,,,,categorical,, | |||
There was a problem hiding this comment.
it has the same alias as "histological stain", is that ok?
| histological stain name,bil:Image/Channel/Fluorophore,Anatomical Stain,Name of histological stain applied to tissue ,TRUE,histological_stain_name,ValueSet,GFAP,,,,categorical,, | ||
| nuclear stain name,bil:Image/Channel/Fluorophore,Nuclear Stain,Name of nuclear stain applied to tissue,FALSE,nuclear_stain_name,ValueSet,DAPI,,,,categorical,, | ||
| probe set DOI,bil:Dataset/Methods,Bench Chemistry,"List of genes for which probes were made in imaging-based methods; protocols.io doi to a text file that contains the name of all target genes, the ensembl or NBCI id for the targeted id, and the barcode assigned to each targeted RNA if applicable.",FALSE,,text,,,,,continuous,Analysis, | ||
| probe sequences DOI,bil:Dataset/Methods,Bench Chemistry,List of probe sequences used to target genes for imaging-based methods,TRUE,,text,,,,,continuous,, |
There was a problem hiding this comment.
it has the same alias as "probe set DOI", is that ok?
| platform name,bil:Instrument/MicroscopeManufacturerAndModel,Probe Imaging,Name of platform that was used to acquire spatial transcriptomics,FALSE,platform_name,ValueSet,MERSCOPE,,,,categorical,Analysis, | ||
| machine name,,Probe Imaging,Name/ID of machine used to acquire data,TRUE,,text,Flounder10,,,,categorical,, | ||
| machine software version,,Probe Imaging,Version of software used for imaging (e.g. SoftwareVersion from experiment.json in MERSCOPE),TRUE,,text,232.221125.301,,,,categorical,, | ||
| number of z-sections,bil:Image/Channel/Slices,Probe Imaging,Slice number in z-axis,FALSE,,integer,,1,,,continuous,, |
There was a problem hiding this comment.
is this a total number of slices? or identifier for the specific slice?
| brain subdivision,brain_slab/brain_subdivision,Tissue Sample,The subdivision of the brain the tissue sample belongs to,TRUE,[brain_subdivision],ValueSet,cerebrum,,,,categorical,, | ||
| brain hemisphere,brain_slab/slab_hemisphere,Tissue Sample,The hemisphere of the brain the slab belongs to,TRUE,[hemisphere],ValueSet,right,,,,categorical,, | ||
| tissue sample type,,Tissue Sample,"Block, slab, etc.",FALSE,[tissue_sample_type],ValueSet,slab,,,,categorical,Tracking/Identification, | ||
| parent tissue sample name,,Tissue Sample,Upstream tissue sample from which tissue was derived (if addt�l specimen processsing after tissue received from portal),TRUE,,text,,,,,categorical,Tracking/Identification, |
There was a problem hiding this comment.
something wrong with the description, the same for the next line
| brain section local name,bil:Specimen/Sample/local ID,Tissue Cryosection,Local unique ID that represents the tissue cryosection to be processed,FALSE,,text,,,,,categorical,Identification, | ||
| brain section NIMP ID,,Tissue Cryosection,NIMP ID for the tissue cryosection,FALSE,,text,,,,,categorical,, | ||
| reference brain atlas,bil:Specimen/Sample/Atlas,Tissue Cryosection,Reference atlas used to pin locations,TRUE,"[DHBA, DMBA, HBA, MBA]",ValueSet,MBA,,,,categorical,, | ||
| atlas location,bil:Specimen/Sample/Location,Tissue Cryosection,"The (sub) location(s) or region where the tissue is found; structures from DHBA, MBA ontologies",TRUE,"[DHBA, DMBA, HBA, MBA]",ValueSet,MBA:315,,,,categorical,, |
There was a problem hiding this comment.
should this be "ValueSet"? seems like it has additional integer to specify the location
| @@ -0,0 +1,5 @@ | |||
| Proposed BICAN Field Name,Aliases,LinkML Class,Definition,Nullable,Permissible Values,Data Type,Data Examples,Min Value,Max Value,Unit,Statistical Variable Type,Subsets,Notes | |||
| gene name,,Bench Chemistry,The word or phrase that uniquely identifies the gene,FALSE,"[ENSEMBL, NCBI]",ValueSet,calbindin 2,,,,categorical,, | |||
There was a problem hiding this comment.
examples in this file don't match the permissible values
| tissue sample name,tissue_sample_local_name,Tissue Sample,Block of tissue that was used for further dissection and/or sectioning,FALSE,,text,,,,,categorical,Tracking/Identification, | ||
| brain subdivision,brain_slab/brain_subdivision,Tissue Sample,The subdivision of the brain the tissue sample belongs to,TRUE,[brain_subdivision],ValueSet,cerebrum,,,,categorical,, | ||
| brain hemisphere,brain_slab/slab_hemisphere,Tissue Sample,The hemisphere of the brain the slab belongs to,TRUE,[hemisphere],ValueSet,right,,,,categorical,, | ||
| tissue sample type,,Tissue Sample,"Block, slab, etc.",FALSE,[tissue_sample_type],ValueSet,slab,,,,categorical,Tracking/Identification, |
There was a problem hiding this comment.
i don't see "tissue_sample_type" in the `ValueSets"
| @@ -0,0 +1,13 @@ | |||
| Proposed BICAN Field Name,Aliases,LinkML Class,Definition,Nullable,Permissible Values,Data Type,Data Examples,Min Value,Max Value,Unit,Statistical Variable Type,Subsets,Notes | |||
| tissue sample name,tissue_sample_local_name,Tissue Sample,Block of tissue that was used for further dissection and/or sectioning,FALSE,,text,,,,,categorical,Tracking/Identification, | |||
| brain subdivision,brain_slab/brain_subdivision,Tissue Sample,The subdivision of the brain the tissue sample belongs to,TRUE,[brain_subdivision],ValueSet,cerebrum,,,,categorical,, | |||
There was a problem hiding this comment.
for consistency it should be probably "nimp_brain_subdivision", since that's the name of the file.
the same for the other elements in this file
Will attach to issue for review