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Draft Ambystoma mexicanum (axolotl) #1014

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

Draft Ambystoma mexicanum (axolotl) #1014

brianraymor opened this issue Sep 25, 2024 · 3 comments
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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 commented Sep 25, 2024 •
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Pending Issues

  1. There is no Ensembl gene reference which is a CELLxGENE requirement for the moment.
  2. tissue_ontology_term_id There are +750 deprecated AAO terms cross-referenced in the UBERON ontology. The schema could require a term from that set, assuming that it's the correct subset of UBERON terms for this species or "no changes are required to the schema".

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 Release Download
? ? ? ?

Editorial Notes

No species specific ontologies were discovered.

See Utility of the Amphibian Anatomical Ontology for Interdisciplinary Research:

AmphibAnat (www.amphibanat.org) and the associated Amphibian Anatomical Ontology (AAO) provide a means to assemble and formalize the vocabularies for amphibian anatomy, embryology, and taxonomy.

but the website no longer exists. The Amphibian Gross Anatomy Ontology was deprecated and recommends UBERON. Also see Inventory of current bridges between Uberon/CL and foreign resources for references to the deprecated AAO bridges.

Required Gene Annotations

Organism Source Required version Download
"NCBITaxon:8296"
for Axolotol		 Axolotl-omics AmexG_v6.0-DD AmexT_v47-AmexG_v6.0-DD.gtf

Editorial Notes

There is no available Ensembl reference.

NCBI Genomes

@SESDNA selected:

Axolotl-omics.org assemblies

obs (Cell Metadata)

cell_type_ontology_term_id

No schema change is required.

Editorial Notes

There is one deprecated AAO term cross-referenced in the CL ontology:

CL:0000247 Rohon-Beard neuron semapv:crossSpeciesExactMatch AAO:0010316

development_stage_ontology_term_id

If organism_ontolology_term_id is "NCBITaxon:8296" for Ambystoma mexicanum this MUST be ...

Editorial Notes

Pending. See Axolotl Embryo Staging Series derived ffom Table of stages of the normal development of axolotl embryos by N.P. Bordzilovskaya and T.A. Dettlaff.

Mapping these stages to UBERON:

Stage Series Description UBERON label UBERON term UBERON parent label UBERON parent term
1 Preblastula egg zygote stage UBERON:0000106 embryo stage UBERON:0000068
2 Preblastula 2 cells 2 cell stage UBERON:0007232 cleavage stage UBERON:0000107
3 Preblastula 4 cells 4 cell stage UBERON:0007233 cleavage stage UBERON:0000107
4 Preblastula 8 cells 8 cell stage [UBERON:0007236] cleavage stage UBERON:0000107
5 Preblastula 16 cells cleavage stage UBERON:0000107
6 Preblastula 32 cells cleavage stage UBERON:0000107
7 Preblastula 64 cells cleavage stage UBERON:0000107
8 Blastula & Gastrula Early blastula blastula stage UBERON:0000108
9 Blastula & Gastrula Late blastula blastula stage UBERON:0000108
10 Blastula & Gastrula Early gastrula I gastrula stage UBERON:0000109
10.5 Blastula & Gastrula Early gastrula II gastrula stage UBERON:0000109
10.75 Blastula & Gastrula Middle gastrula I gastrula stage UBERON:0000109
11 Blastula & Gastrula Middle gastrula II gastrula stage UBERON:0000109
11.5 Blastula & Gastrula Late gastrula I gastrula stage UBERON:0000109
12 Blastula & Gastrula Late gastrula II gastrula stage UBERON:0000109
12.5 Blastula & Gastrula Late gastrula III gastrula stage UBERON:0000109
13 Neurula Early neurula I neurula stage UBERON:0000110
14 Neurula Early neurula II neurula stage UBERON:0000110
15 Neurula Early neurula III neurula stage UBERON:0000110
16 Neurula Middle neurula II neurula stage UBERON:0000110
17 Neurula Late neurula I neurula stage UBERON:0000110
18 Neurula Late neurula II neurula stage UBERON:0000110
19 Neurula Late neurula III neurula stage UBERON:0000110
20 Neurula Late neurula IV neurula stage UBERON:0000110
21-25 Early Tailbud organogenesis stage UBERON:0000111
26-30 Middle Tailbud organogenesis stage UBERON:0000111
31-35 Late Tailbud organogenesis stage UBERON:0000111
36-43 Prehatched to Hatched late embryonic stage UBERON:0007220
44 Prehatched to Hatched just hatched post-embryonic stage UBERON:0007221

There are a similar set of development stages for Xenopus laevis from BGEE modeling that include Tailbud stages:

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

organism_ontolology_term_id

organism_ontolology_term_id is "NCBITaxon:8296" for Ambystoma mexicanum

sex_ontology_term_id

No schema changes are required.

Editorial Notes

See What determines whether an axolotl will grow up to be male or female?

See Miniscule differences between sex chromosomes in the giant genome of a salamander

tissue_ontology_term_id

If organism_ontolology_term_id is "NCBITaxon:8296" for Ambystoma mexicanum this MUST be ...

Editorial Notes

There are two alternatives for the design:

  1. There are +750 deprecated AAO terms cross-referenced in the UBERON ontology. The schema could require a term from that set, assuming that it's the correct subset of UBERON terms for this species.
  2. No changes are required to the schema.

References

Axobase

Gene and transgenics nomenclature for the laboratory axolotl – Ambystoma mexicanum

Axolotl-omics

Sal-Site

Axolotl Cell Atlas

The Axolotl’s journey to the modern molecular era

Decoding the Axolotl genome

Advancements to the axolotl model for regeneration and aging

Initial characterization of the large genome of the salamander Ambystoma mexicanum using shotgun and laser capture chromosome sequencing
The giant axolotl genome uncovers the evolution, scaling, and transcriptional control of complex gene loci
@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 Ambystoma mexicanum Draft Ambystoma mexicanum (axolotl) Sep 26, 2024
@brianraymor brianraymor self-assigned this Sep 30, 2024
@brianraymor brianraymor mentioned this issue Oct 10, 2024
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@brianraymor brianraymor added the in review reviewing schema for species label Nov 4, 2024
@brianraymor
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@jahilton @BAevermann - would you check my math for the development_stage_ontology_term_id ? You're also welcome to comment on other pending issues per the top-level summary comment.

@jahilton
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jahilton commented Nov 7, 2024

  • UBERON:0007234 is obsolete 4-8 cell stage. 8 cell stage is UBERON:0007236
  • Preblastula x3 have the wrong parent term ID - UBERON:0007232 UBERON:0000107
  • Stage 44 is "just hatched" which seems like it should be soon after hatching (and thus neotate/UBERON:0007221 is appropriate). post-embryonic stage covers everything after hatching, so is extremely broad.

@SESDNA
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SESDNA commented Nov 8, 2024

@brianraymor I recommend using the Axolotl-Omics ref genome AmexG_v6.0-DD GTF

@brianraymor brianraymor added experimental approved schema as experimental and removed in review reviewing schema for species labels Dec 3, 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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