nayib-jose-gloria
commented
1 week ago sex_ontology_term_id No schema changes are required. Editorial Notes There is ZFA:male organism and ZFA:female organism.
@brianraymor to clarify, we are currently choosing not to accept these ZFA terms for this first run at an experimental validator, correct? We could do so, but it would violate schema 5.2.0 as written, as I believe they are not descendants of PATO:0001894
brianraymor
Design
October 21 2024 Superseded by draft 5.2.1-experimental.md
This draft design reflects additions to corresponding sections in schema 5.2.0. Reviewers are expected to be familiar with the CELLxGENE schema.
Editorial Notes that are inlined in the design below will not be surfaced in the schema.
Required Ontologies
Editorial Notes
Reviewing:
Required Gene Annotations
Editorial Notes
Also see Lawson Lab zebrafish transcriptome annotation
obs(Cell Metadata)cell_type_ontology_term_id
No schema changes are required.
Editorial Notes
Also see Add CL bridge between species-specific and taxon-neutral ontology terms
development_stage_ontology_term_id
If
organism_ontolology_term_idis"NCBITaxon:7955"for Danio rerio this MUST be the most accurate ZFS term and MUST NOT beZFS:0000000for Unknown.Editorial Notes
Also see Development Stages
This may be outdated, but potential recommendations:
disease_ontology_term_id
No schema changes are required.
Editorial Notes
Propose to replace Disease Ontology with MONDO
organism_ontolology_term_id
organism_ontolology_term_idis"NCBITaxon:7955"for Danio reriosex_ontology_term_id
No schema changes are required.
Editorial Notes
There is ZFA:male organism and ZFA:female organism.
organism_cell_type_ontology_term_id
If
organism_ontolology_term_idis"NCBITaxon:7955"for Danio rerio this MUST be the most accurate descendant ofZFA:0009000for cell or"unknown"...Editorial Notes
Also see Add CL bridge between species-specific and taxon-neutral ontology terms
organism_tissue_ontology_term_id
If
organism_ontolology_term_idis"NCBITaxon:7955"for Danio rerio this MUST be the most accurate descendant ofZFA:0100000for zebrafish anatomical entity and MUST NOT beZFA:0009000for cell or any of its descendants.Editorial Notes
There is the potential to block other terms after review.
This allows the use of
ZFA:0001093for unspecifiedAlso see Add UBERON bridge between species-specific and taxon-neutral ontology terms
tissue_ontology_term_id
No schema changes are required.
Editorial Notes
Also see Add UBERON bridge between species-specific and taxon-neutral ontology terms
tissue_type
Editorial Notes
Pending discussion about the requirements for organoids and cell cultures.
var and raw.var (Gene Metadata)
feature_reference
str. This MUST be the reference organism for a feature:"NCBITaxon:7955"References
Zebrafish Information Network Zebrafish information network, the knowledgebase for Danio rerio research ZFIN Data Load Sheets Template
From multiallele fish to nonstandard environments, how ZFIN assigns phenotypes, human disease models, and gene expression annotations to genes
Alliance of Genome Resources
Zebrafish Book
Zebrahub and Zebrahub – Multimodal Zebrafish Developmental Atlas Reveals the State-Transition Dynamics of Late-Vertebrate Pluripotent Axial Progenitors
A single-cell transcriptome atlas for zebrafish development
ZSCAPE - Zebrafish Atlas of Perturbed Embryos
The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio
Line Designations and Wild-type Lines. Also Variants/Alleles.
A single cell transcriptome atlas of the developing zebrafish hindbrain
Demystifying Zebrafish
From Keir Balla: Tracing cell-type evolution by cross-species comparison of cell atlases An improved zebrafish transcriptome annotation for sensitive and comprehensive detection of cell type-specific genes
BGEE Reference