Draft Xenopus laevis (African clawed frog) and Xenopus tropicalis (tropical clawed frog)

[brianraymor]

Context

To reduce Q1 scope, Xenopus laevis and Xenopus tropicalis will move to Q2.

Changelog

Appendix A. Changelog

• Required Ontologies
  • Added Xenopus Anatomy Ontology (XAO) release 2024-09-03 XAO 11.1
• Required Gene Annotations
  • Added Xenopus laevis Xenopus_laevis_v10.1 (GCA_017654675.1) Ensembl Beta
  • Added Xenopus tropicalis UCB_Xtro_10.0 (GCA_000004195.4) Ensembl 113
• obs (Cell metadata)
  • Updated the ontology requirements for cell_type_ontology_term_id to include:
    • XAO for Xenopus laevis and Xenopus tropicalis
  • Updated the ontology requirements for development_stage_ontology_term_id to include:
    • XAO for Xenopus laevis and Xenopus tropicalis
  • Updated the ontology requirements for tissue_ontology_term_id to include:
    • XAO for Xenopus laevis and Xenopus tropicalis
• var and raw.var (Gene Metadata)
  • Updated feature_reference to include:
    • Xenopus laevis
    • Xenopus tropicalis

Design

Required Ontologies

Ontology	OBO Prefix	Releases	OLS
Xenopus Anatomy Ontology	XAO	2024-09-03 XAO 11.1	xenopus_anatomy.owl

Editorial Notes

This ontology is under active development. CELLxGENE pins ontology releases in each version of the schema. A specific release of the ontology above must be selected in the future.

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Required Gene Annotations

Organism	Source	Required version	Download
NCBITaxon:8355 for Xenopus laevis	ENSEMBL	Xenopus_laevis_v10.1 (GCA_017654675.1) Ensembl Beta	genes.gtf
NCBITaxon:8364 for Xenopus tropicalis	ENSEMBL	UCB_Xtro_10.0 (GCA_000004195.4) Ensembl 113	Xenopus_tropicalis.UCB_Xtro_10.0.113.gtf

Editorial Notes

There is no available Ensembl reference except for Xenopus laevis , except as a Beta release.

BGEE references a suppressed RefSeq version.

The alternatives for selecting a non-Ensembl genome reference are:

See the current NCBI reference

See Xenbase Genome Downloads

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obs (Cell Metadata)

cell_type_ontology_term_id

Key	cell_type_ontology_term_id
Annotator	Curator MUST annotate.
Value	categorical with str categories. This MUST be "unknown" when: no appropriate term can be found (e.g. the cell type is unknown) assay_ontology_term_id is "EFO:0010961" for Visium Spatial Gene Expression, uns['spatial']['is_single'] is True, and the corresponding value of in_tissue is 0 The following CL terms MUST NOT be used: "CL:0000255" for eukaryotic cell "CL:0000257" for Eumycetozoan cell "CL:0000548" for animal cell For organism_ontolology_term_id Value "NCBITaxon:8355" for Xenopus laevis or "NCBITaxon:8364" for Xenopus tropicalis MUST be either a CL term or the most accurate descendant of XAO:0003012 for cell excluding XAO:0004290 for cell part and its descendants

development_stage_ontology_term_id

Key	development_stage_ontology_term_id
Annotator	Curator MUST annotate.
Value	categorical with str categories. If unavailable, this MUST be "unknown". For organism_ontolology_term_id Value "NCBITaxon:8355" for Xenopus laevis or "NCBITaxon:8364" for Xenopus tropicalis MUST be the most accurate descendant of XAO:1000000 for Xenopus developmental stage excluding XAO:0000437 for death, XAO:10000817 for unspecified stage, and XAO:1000094 for NF stage and its descendants

organism_ontology_term_id

Key	organism_ontology_term_id
Annotator	Curator MUST annotate.
Value	str. One of the following terms MUST be used: For Organism MUST Use Xenopus laevis "NCBITaxon:8355" Xenopus tropicalis "NCBITaxon:8364"

tissue_ontology_term_id

Key	tissue_ontology_term_id
Annotator	Curator MUST annotate.
Value	categorical with str categories. If tissue_type is "cell culture" this MUST follow the requirements for cell_type_ontology_term_id. If tissue_type is "tissue" or "organoid" then: For organism_ontolology_term_id Value "NCBITaxon:8355" for Xenopus laevis or "NCBITaxon:8364" for Xenopus tropicalis MUST be either an UBERON term or the most accurate descendant of XAO:0000000 for Xenopus anatomical entity excluding XAO:0003003 for unspecified, XAO:0003005 for female organism, XAO:0003006 for male organism, and XAO:0003012 for cell and its descendants

var

feature_reference

Key	feature_reference
Annotator	CELLxGENE Discover MUST annotate.
Value	str. This MUST be the reference organism for a feature: Reference Organism MUST Use Xenopus laevis "NCBITaxon:8355" Xenopus tropicalis "NCBITaxon:8364"

References

Xenbase - The Xenopus model organism knowledgebase

BGEE - Xenopus laevis
BGEE - Xenopus tropicalis

[SESDNA]

@bnelson-czi is curating this dataset [XCL | Xenopus Cell Landscape] https://bis.zju.edu.cn/XCL/
It uses this reference genome: https://www.xenbase.org/xenbase/doNewsRead.do?id=198

[brianraymor]

I'd note that there is a more recent (2021) release - https://www.xenbase.org/xenbase/doNewsRead.do?id=827 - which is the version available in Ensembl rapid release.

[SESDNA]

@brianraymor I recommend using the Ensembl rapid release genome for X. laevis because as you pointed out it is the same as the one on Xenbase and it has Ensembl IDs. This satisfies our needs. (https://rapid.ensembl.org/Xenopus_laevis_GCA_017654675.1/Info/Index)

[brianraymor]

Added to schema 5.3.0.

[jahilton]

Main Qs I have right now...

• Feature standards - need to confirm the following:
  • The most appropriate gene annotation references will be GCF_000004195.4 (X. tropicalis) & GCF_017654675.1 (X. laevis).
  • The stable identifiers to require in the var.index will be the db_xref attributes in those gtf files (e.g. GeneID:101731805, GeneID:2642076)
  • The feature_name values should be the corresponding gene_id attributes from the gtf files (e.g. pi16 for GeneID:101731805, ND4L for GeneID:2642076)
• cell/obs metadata
  • are the cell_type_ontology_term_id, development_stage_ontology_term_id, tissue_ontology_term_id XAO branches/restrictions appropriate - any additional terms to block or allow?
  • donor_id - how are single cell data typically sampled? is it 1 individual == 1 sample, are multiple individuals pooled into 1 sample?
  • is there additional information not captured that should be required to make the submissions more reusable?
• species/subspecies
  • NCBITaxon lists X. l. laevis & X. l. sudanensis underneath X. laevis (NCBITaxon:8355). Do researchers know/track which they are using?
  • There are many taxonomic groups listed under Xenopus (NCBITaxon:8353). Is it common to study the species other than X. tropicalis/laevis?