Filter Documentation

For non-genomic parameters, the Progenetix resource uses a query syntax based around the Beacon v2 “filters” concept.

List of filters recognized by different query endpoints

Generally, a CURIE syntax is used whenever available.

Ontology with CURIE-based syntax

CURIE prefix Code/Ontology Examples
NCIT NCIt Neoplasm 1 NCIT:C27676
HP HPO2 HP:0012209
PMID NCBI Pubmed ID PMID:28966033
geo NCBI Gene Expression Omnibus3 geo:GPL6504, geo:GSE19331, geo:GSM253289
arrayexpress EBI ArrayExpress 4 arrayexpress:E-MEXP-1008
cellosaurus Cellosaurus - a knowledge resource on cell lines 5 cellosaurus:CVCL_1650
Uberon Uberon Anatomical Ontology 6 UBERON:0000992

Private filters

Since some classifications cannot directly be referenced, and in accordance with the upcoming Beacon v2 concept of “private filters”, Progenetix uses additionally a set of structured non-CURIE identifiers.

Filter prefix Code/Ontology Example
icdom ICD-O 37 Morphologies (Progenetix) icdom-81703
icdot ICD-O 37 Topographies(Progenetix) icdot-C04.9
TCGA The Cancer Genome Atlas (Progenetix)8 TCGA-000002fc-53a0-420e-b2aa-a40a358bba37
cBP cBioPortal9 cBP-MSK_IMPACT_2017
pgxcohort Progenetix cohorts 10 pgxcohort-arraymap

Handling of hierarchical terminologies

Hierarchical terminologies allow queries at different levels, to include all its children terms. The Progenetix query filter system adopts this inclusion logic if the classification / code type is hierarchy-based.

Examples for codes with hierarchical treatment within the filter space are:


  1. National Cancer Institute Thesaurus Neoplasm NCIt Neoplasm 

  2. Human phenotype ontology HPO 

  3. Supported identifiers include platforms(GPL), series(GSE) and samples(GSM).GEO Overview 

  4. Supports ArrayExpress Accession ID. ArrayExpress browse 

  5. Cellosaurus accession ID. 

  6. Uberon ID 

  7. International Classification of Diseases for Oncology, 3rd Edition ICD-O-3  2

  8. Supports TCGA Sample UUID. 

  9. Supports cBioPortal Study ID. 

  10. Cohorts defined in Progenetix involving a collection of related samples. Currently includes (add pgxcohort-): arraymap, 2021progenetix, DIPG, TCGA, TCGAcancers, gao2021signatures

@qingyao 2021-04-14
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