STellaris API

STellaris API is a RESTful Application Program Interface to STellaris database resource.

General form

1. URL from

https://spatial.rhesusbase.com/api/[resource]/[argument]/([argument]...)

[resource] = datasets-info | gene | gene/transcript | spatially-variable-gene | expression-rank-score | job-info

Information of datasets or genes

1. datasets-info

This resource returns the basic information about some or a given dataset.

URL form: https://spatial.rhesusbase.com/api/datasets-info/[ST ID/"all"]

Need one argument:

(1) ST ID
    • A unique id for a spatial transcriptome dataset
    • Example: STW-H-Bone-ST-1
(2) "all"
    • all datasets
    • Example: https://spatial.rhesusbase.com/api/datasets-info/all

Example:

  • https://spatial.rhesusbase.com/api/datasets-info/STW-H-Bone-ST-1
  • Result:
    {"id":"STW-H-Bone-ST-1","method":"ST","species":"Homo sapiens","strain":null,"organ":"Bone","tissue":"\"RA,SPA\"","pathological":"TRUE","developmental_stage":"Adult","section":"9","section_id":"\"RA_A_1,RA_A_2,RA_A_3,RA_B_1,RA_B_2,RA_B_3,RA_C_1,RA_C_2,RA_C_3,SPA_A_1,SPA_A_2,SPA_A_3,SPA_B_1,SPA_B_2,SPA_B_3,SPA_C_1,SPA_C_2,SPA_C_3\"","date_published":"2019-12-11T16:00:00.000Z","title":"Exploring inflammatory signatures in arthritic joint biopsies with Spatial Transcriptomics","journal":"Scientific Reports","pmid":"31831833","url":"https://doi.org/10.1038/s41598-019-55441-y\r"}

2. gene

This resource returns basic information of a gene.

URL form: https://spatial.rhesusbase.com/api/gene/[Ensembl ID]

Need one argument:

    Ensembl ID
    • identifier for a gene from the Ensembl database
    • Example: ENSG00000154856

Example:

  • https://spatial.rhesusbase.com/api/gene/ENSG00000000003
  • Result:
    [{"ensembl_id":"ENSG00000000003","symbol":"TSPAN6","entrez_id":"7105","descriptive_name":"tetraspanin 6 [Source:HGNC Symbol;Acc:HGNC:11858]","other_designations":"tetraspanin-6|A15 homolog|putative NF-kappa-B-activating protein 321|tetraspan TM4SF|tetraspanin TM4-D|transmembrane 4 superfamily member 6","name_synonyms":"T245|TM4SF6|TSPAN-6","dbXrefs":"MIM:300091|HGNC:HGNC:11858|Ensembl:ENSG00000000003|AllianceGenome:HGNC:11858","version":15,"gene_source":"ensembl_havana","name_source":"HGNC Symbol","biotype":"protein_coding","chrom_scaf":"X","start":100627108,"end":100639991,"strand":"-1","map_location":"Xq22.1","organism":"Homo sapiens"}]

3. gene/transcript

This resource returns some basic information of transcript from a gene.

URL form: https://spatial.rhesusbase.com/api/gene/transcript/[Ensembl ID]

Need one argument:

    Ensembl ID
    • identifier for a gene from the Ensembl database
    • Example: ENSG00000154856

Example:

  • https://spatial.rhesusbase.com/api/gene/transcript/ENSG00000000003
  • Result:
    [{"ensembl_id":"ENSG00000000003","ensembl_transcript_id":"ENST00000373020","name":"TSPAN6-201","version":9,"source":"ensembl_havana","type":"protein_coding","count":5,"length":3768,"start":100627108,"end":100636806,"tss":100636806,"refseq_mrna":"NM_003270","refseq_ncrna":"-","tsl":"tsl1 (assigned to previous version 8)"},{"ensembl_id":"ENSG00000000003","ensembl_transcript_id":"ENST00000494424","name":"TSPAN6-202","version":1,"source":"havana","type":"processed_transcript","count":5,"length":820,"start":100633442,"end":100639991,"tss":100639991,"refseq_mrna":"-","refseq_ncrna":"-","tsl":"tsl2"},{"ensembl_id":"ENSG00000000003","ensembl_transcript_id":"ENST00000496771","name":"TSPAN6-203","version":5,"source":"havana","type":"processed_transcript","count":5,"length":1025,"start":100632541,"end":100636689,"tss":100636689,"refseq_mrna":"-","refseq_ncrna":"-","tsl":"tsl3"}]...

4. spatially-variable-gene

This resource returns spatially variable genes.

URL form: https://spatial.rhesusbase.com/api/spatially-variable-gene/[geneOrSection]/[identifier]

Need two argument:

    geneOrSection
    • either retrive spatially variable genes by gene symbol or by section id
    • Example: gene,section
    identifier
    • gene symbol or section id
    • Example: IGF1,ETOH

Example:

  • https://spatial.rhesusbase.com/api/spatially-variable-gene/section/ETOH
  • Result:
    [{"gene_symbol":"TAC1","section_id":"ETOH","span":59.8264,"p_value":0.0000162133,"q_value":0.00171553,"ensembl_id":"ENSG00000006128"},{"gene_symbol":"SELE","section_id":"ETOH","span":59.8264,"p_value":0.0000131115,"q_value":0.00143688,"ensembl_id":"ENSG00000007908"},{"gene_symbol":"POMT2","section_id":"ETOH","span":182.803,"p_value":0.0000100238,"q_value":0.00114983,"ensembl_id":"ENSG00000009830"},{"gene_symbol":"CD9","section_id":"ETOH","span":104.577,"p_value":0.000974796,"q_value":0.0472911,"ensembl_id":"ENSG00000010278"},{"gene_symbol":"DCN","section_id":"ETOH","span":59.8264,"p_value":0.000446288,"q_value":0.0254779,"ensembl_id":"ENSG00000011465"},{"gene_symbol":"LTF","section_id":"ETOH","span":59.8264,"p_value":0.0000185734,"q_value":0.00191571,"ensembl_id":"ENSG00000012223"},{"gene_symbol":"ACP3","section_id":"ETOH","span":182.803,"p_value":5.24025e-14,"q_value":2.2971e-11,"ensembl_id":"ENSG00000014257"},{"gene_symbol":"CHDH","section_id":"ETOH","span":19.5795,"p_value":0.000545153,"q_value":0.0301406,"ensembl_id":"ENSG00000016391"},{"gene_symbol":"IGF1","section_id":"ETOH","span":104.577,"p_value":2.51839e-8,"q_value":0.00000551976,"ensembl_id":"ENSG00000017427"},{"gene_symbol":"APBA2","section_id":"ETOH","span":34.2253,"p_value":1.01252e-13,"q_value":4.28542e-11,"ensembl_id":"ENSG00000034053"}]...
  • https://spatial.rhesusbase.com/api/spatially-variable-gene/gene/ID2
  • Result:
    [{"gene_symbol":"ID2","section_id":"A1","span":41.4276,"p_value":0.00223874,"q_value":0.011349,"id":"STW-H-Colon-Visium-3","organ_tissue":"Colon"},{"gene_symbol":"ID2","section_id":"A4","span":41.4276,"p_value":0.000525282,"q_value":0.0042025,"id":"STW-H-Colon-Visium-2","organ_tissue":"Colon"},{"gene_symbol":"ID2","section_id":"A8","span":60,"p_value":0.00188399,"q_value":0.0276741,"id":"STW-H-Colon-Visium-1","organ_tissue":"Colon"},{"gene_symbol":"ID2","section_id":"GSM5764428","span":113.001,"p_value":0.000173087,"q_value":0.00561641,"id":"STW-H-Liver-Visium-4","organ_tissue":"Liver"},{"gene_symbol":"ID2","section_id":"ST_Sample_6.5PCW_3","span":1017.73,"p_value":0.0000977554,"q_value":0.0099832,"id":"STW-H-Heart-ST-2","organ_tissue":"Heart"},{"gene_symbol":"ID2","section_id":"ST_Sample_6.5PCW_4","span":1072.97,"p_value":0.00904449,"q_value":0.0428436,"id":"STW-H-Heart-ST-2","organ_tissue":"Heart"},{"gene_symbol":"ID2","section_id":"ST_Sample_9PCW_3","span":1215.74,"p_value":0.00208705,"q_value":0.0214011,"id":"STW-H-Heart-ST-3","organ_tissue":"Heart"},{"gene_symbol":"ID2","section_id":"ST_Sample_9PCW_6","span":1098.58,"p_value":0.0034152,"q_value":0.0171635,"id":"STW-H-Heart-ST-3","organ_tissue":"Heart"}]...

5. expression-rank-score

This resource returns Expression Expression Rank Score of a gene.

URL form: https://spatial.rhesusbase.com/api/expression-rank-score/[gene symbol name]

Need one argument:

    gene symbol name
    • Example: IGF1

Example:

  • https://spatial.rhesusbase.com/api/expression-rank-score/IGF1
  • Result:
    [{"gene_symbol":"IGF1","counts":104,"CPM":9.4928,"CPM_log":2.35069,"rank":2220,"rank_score":"0.04476969436074041","section_id":"151507","organ_tissue":"Dorsolateral prefrontal cortex"},{"gene_symbol":"IGF1","counts":108,"CPM":11.5815,"CPM_log":2.53223,"rank":2030,"rank_score":"0.0505381375760412","section_id":"151508","organ_tissue":"Dorsolateral prefrontal cortex"}]...

Spatial Mapping Result

1. job-info

This resource returns some information about your job.

Need one argument:

    Job ID
    • a job id assigned after running a spatial mapping ( A universally unique identifier (UUID) )
    • Example: 8dd3efa0-1884-11ed-8536-0d8688eaef3a

Example:

  • https://spatial.rhesusbase.com/api/job-info/8dd3efa0-1884-11ed-8536-0d8688eaef3a
  • Result:
    {"rid":"8dd3efa0-1884-11ed-8536-0d8688eaef3a","title":"An important job!","email":"someone@mail.com","organ":"Spinal Cord","tissue":"Lumbar Spinal Cord Tissue Sections","matrixfilepath":"public/uploads/2022810/8dd3efa0-1884-11ed-8536-0d8688eaef3a/28fb5e40-1886-11ed-8536-0d8688eaef3a.matrix.mtx.gz","barcodesfilepath":"public/uploads/2022810/8dd3efa0-1884-11ed-8536-0d8688eaef3a/290681d0-1886-11ed-8536-0d8688eaef3a.barcodes.tsv.gz","featuresfilepath":"public/uploads/2022810/8dd3efa0-1884-11ed-8536-0d8688eaef3a/2906a8e0-1886-11ed-8536-0d8688eaef3a.features.tsv.gz","resultpath":"public/results/8dd3efa0-1884-11ed-8536-0d8688eaef3a","uploadtime":"2022-08-10T08:26:41.139Z","finishtime":"2022-08-10T08:26:41.146Z","status":"error"}

2. Registered scRNA-seq Data (h5ad)

This resource returns the mapped scRNA-seq data in h5ad format.

Need one argument:

    Job ID
    • a job id assigned after running a spatial mapping ( A universally unique identifier (UUID) )
    • Example: 8dd3efa0-1884-11ed-8536-0d8688eaef3a

Example:

  • https://spatial.rhesusbase.com/api/mapping-result/h5ad/sc/8dd3efa0-1884-11ed-8536-0d8688eaef3a
  • Result: sc_rigistered.h5ad

3. Table Results (csv)

This resource returns all table result files in csv format.

Need one argument:

    Job ID
    • a job id assigned after run a spatial mapping ( A universally unique identifier (UUID) )
    • Example: 8dd3efa0-1884-11ed-8536-0d8688eaef3a

Example:

  • https://spatial.rhesusbase.com/api/mapping-result/table/8dd3efa0-1884-11ed-8536-0d8688eaef3a
  • Result: table.tar.gz

4. PDF Graph Results (pdf)

This resource returns all graph result file in pdf format.

Need one argument:

    Job ID
    • a job id assigned after running a spatial mapping ( A universally unique identifier (UUID) )
    • Example: 8dd3efa0-1884-11ed-8536-0d8688eaef3a

Example:

  • https://spatial.rhesusbase.com/api/mapping-result/pdf/8dd3efa0-1884-11ed-8536-0d8688eaef3a
  • Result: pdf.tar.gz