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Draft Xenopus laevis (African clawed frog) and Xenopus tropicalis (tropical clawed frog) #1019

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brianraymor opened this issue Sep 25, 2024 · 3 comments
Open

Draft Xenopus laevis (African clawed frog) and Xenopus tropicalis (tropical clawed frog) #1019

brianraymor opened this issue Sep 25, 2024 · 3 comments
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@brianraymor
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experimental approved schema as experimental multispecies discovery Adding new species to CELLxGENE schema CELLxGENE Discover dataset schema

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@brianraymor
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brianraymor commented Sep 25, 2024 •
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Pending Issues

Design

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

Ontology OBO Prefix Releases OLS
Xenopus Anatomy Ontology XAO Releases OLS

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.

See Xenopus Phenotype Ontology.

Required Gene Annotations

Organism Source Required version Download
organism_ontolology_term_id is "NCBITaxon:8355"
for Xenopus laevis		 ENSEMBL Beta (African clawed frog) GCA_017654675.1 genes.gtf
organism_ontolology_term_id is "NCBITaxon:8364"
for Xenopus tropicalis		 ENSEMBL (tropical clawed frog) UCB_Xtro_10.0 (GCA_000004195.4) 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

obs (Cell Metadata)

cell_type_ontology_term_id

No schema changes are required.

Editorial Notes

development_stage_ontology_term_id

If organism_ontolology_term_id is "NCBITaxon:8355" for Xenopus laevis or "NCBITaxon:8364" for Xenopus tropicalis this MUST be the most accurate descendant of XAO:1000000 for Xenopus developmental stage ...

Editorial Notes

This may be outdated, but potential recommendations:

UBERON:0000104 life cycle
    XAO:1000082 unfertilized egg stage (Xenopus)
        XAO:1000083 oocyte stage I (Xenopus)
        XAO:1000084 oocyte stage II (Xenopus)
        XAO:1000085 oocyte stage III (Xenopus)
        XAO:1000086 oocyte stage IV (Xenopus)
        XAO:1000087 oocyte stage V (Xenopus)
        XAO:1000088 oocyte stage VI (Xenopus)
        XAO:1000092 mature egg stage (Xenopus)
    UBERON:0000068 embryo stage
        UBERON:0000106 zygote stage
        UBERON:0000107 cleavage stage
            XAO:1000028 NF stage 2- (Xenopus)
            UBERON:0007232 2 cell stage
            UBERON:0007233 4 cell stage
            UBERON:0007236 8 cell stage
            XAO:1000015 NF stage 5 (16-cell) (Xenopus)
            XAO:1000016 NF stage 6 (32-cell) (Xenopus)
            XAO:1000029 NF stage 6.5 (Xenopus)
        UBERON:0000108 blastula stage
            XAO:1000017 NF stage 7 (Xenopus)
            XAO:1000018 NF stage 8 (Xenopus)
            XAO:1000019 NF stage 9 (Xenopus)
        UBERON:0000109 gastrula stage
            XAO:1000020 NF stage 10 (Xenopus)
            XAO:1000030 NF stage 10.25 (Xenopus)
            XAO:1000031 NF stage 10.5 (Xenopus)
            XAO:1000021 NF stage 11 (Xenopus)
            XAO:1000032 NF stage 11.5 (Xenopus)
            XAO:1000022 NF stage 12 (Xenopus)
            XAO:1000033 NF stage 12.5 (Xenopus)
        UBERON:0000110 neurula stage
            XAO:1000023 NF stage 13 (Xenopus)
            XAO:1000024 NF stage 14 (Xenopus)
            XAO:1000025 NF stage 15 (Xenopus)
            XAO:1000026 NF stage 16 (Xenopus)
            XAO:1000027 NF stage 17 (Xenopus)
            XAO:1000034 NF stage 18 (Xenopus)
            XAO:1000035 NF stage 19 (Xenopus)
            XAO:1000036 NF stage 20 (Xenopus)
            XAO:1000037 NF stage 21 (Xenopus)
        UBERON:0000111 organogenesis stage
            XAO:1000002 early tailbud stage (Xenopus)
                XAO:1000038 NF stage 22 (Xenopus)
                XAO:1000039 NF stage 23 (Xenopus)
                XAO:1000040 NF stage 24 (Xenopus)
                XAO:1000041 NF stage 25 (Xenopus)
                XAO:1000042 NF stage 26 (Xenopus)
                XAO:1000043 NF stage 27 (Xenopus)
                XAO:1000044 NF stage 28 (Xenopus)
            XAO:1000080 late tailbud stage (Xenopus)
                XAO:1000045 NF stage 29 and 30 (Xenopus)
                XAO:1000046 NF stage 31 (Xenopus)
                XAO:1000047 NF stage 32 (Xenopus)
                XAO:1000048 NF stage 33 and 34 (Xenopus)
                XAO:1000049 NF stage 35 and 36 (Xenopus)
                XAO:1000050 NF stage 37 and 38 (Xenopus)
                XAO:1000051 NF stage 39 (Xenopus)
                XAO:1000052 NF stage 40 (Xenopus)
                XAO:1000053 NF stage 41 (Xenopus)
                XAO:1000054 NF stage 42 (Xenopus)
                XAO:1000055 NF stage 43 (Xenopus)
                XAO:1000056 NF stage 44 (Xenopus)
    UBERON:0000092 post-embryonic stage
        UBERON:0000069 larval stage
            UBERON:0004728 amphibian larval stage
                UBERON:0009849 tadpole stage
                    XAO:1000089 premetamorphosis stage (Xenopus)
                        XAO:1000057 NF stage 45 (Xenopus)
                        XAO:1000058 NF stage 46 (Xenopus)
                        XAO:1000059 NF stage 47 (Xenopus)
                        XAO:1000060 NF stage 48 (Xenopus)
                        XAO:1000061 NF stage 49 (Xenopus)
                        XAO:1000062 NF stage 50 (Xenopus)
                        XAO:1000063 NF stage 51 (Xenopus)
                        XAO:1000064 NF stage 52 (Xenopus)
                        XAO:1000065 NF stage 53 (Xenopus)
                        XAO:1000066 NF stage 54 (Xenopus)
                    XAO:1000079 metamorphosing tadpole stage (Xenopus)
                        XAO:1000090 prometamorphosis stage (Xenopus)
                            XAO:1000067 NF stage 55 (Xenopus)
                            XAO:1000068 NF stage 56 (Xenopus)
                            XAO:1000069 NF stage 57 (Xenopus)
                        XAO:1000091 climax stage (Xenopus)
                            XAO:1000070 NF stage 58 (Xenopus)
                            XAO:1000071 NF stage 59 (Xenopus)
                            XAO:1000072 NF stage 60 (Xenopus)
                            XAO:1000073 NF stage 61 (Xenopus)
                            XAO:1000074 NF stage 62 (Xenopus)
                            XAO:1000075 NF stage 63 (Xenopus)
                            XAO:1000076 NF stage 64 (Xenopus)
                            XAO:1000077 NF stage 65 (Xenopus)
                            XAO:1000078 NF stage 66 (Xenopus)
        UBERON:0000066 fully formed stage
            UBERON:0000112 sexually immature stage
                UBERON:0034919 juvenile stage
            UBERON:0000113 post-juvenile
                UBERON:0018241 prime adult stage
                UBERON:0007222 late adult stage

disease_ontology_term_id

No schema changes are required.

Editorial Notes

ontology_cell_type_ontology_term_id

If organism_ontolology_term_id is "NCBITaxon:8355" for Xenopus laevis or "NCBITaxon:8364" for Xenopus tropicalis this MUST be the most accurate descendant of XAO:0003012 for cell or "unknown" ...

Editorial Notes

Also see Add CL bridge between species-specific and taxon-neutral ontology terms

organism_ontolology_term_id

organism_ontolology_term_id is "NCBITaxon:8355" for Xenopus laevis

organism_ontolology_term_id is "NCBITaxon:8364" for Xenopus tropicalis

organism_tissue_ontology_term_id

If organism_ontolology_term_id is "NCBITaxon:8355" for Xenopus laevis or "NCBITaxon:8364" for Xenopus tropicalis this MUST be the most accurate descendant of XAO:0000000 for Xenopus anatomical entity and MUST NOT be XAO:0003012 for cell or any of its descendants or XAO:1000000 for Xenopus developmental stage or any of its descendants.

Editorial Notes

There is the potential to block other terms after review.

This allows the use of XAO:0003003 for unspecified

sex_ontology_term_id

No schema changes are required.

Editorial Notes

tissue_ontology_term_id

No schema changes are required.

Editorial Notes

var and raw.var (Gene Metadata)

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
@brianraymor brianraymor added schema CELLxGENE Discover dataset schema multispecies discovery Adding new species to CELLxGENE labels Sep 25, 2024
@brianraymor brianraymor changed the title Draft Xenopus laevis and Xenopus tropicalis Draft Xenopus laevis (African clawed frog) and Xenopus tropicalis (tropical clawed frog) Sep 26, 2024
@brianraymor brianraymor self-assigned this Sep 30, 2024
@brianraymor brianraymor added the in review reviewing schema for species label Nov 5, 2024
@SESDNA
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SESDNA commented Nov 6, 2024

@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
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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
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SESDNA commented Nov 8, 2024

@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 brianraymor added experimental approved schema as experimental and removed in review reviewing schema for species labels Nov 20, 2024
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experimental approved schema as experimental multispecies discovery Adding new species to CELLxGENE schema CELLxGENE Discover dataset schema
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