ingenix/mapping_benchmark

Mapping benchmark

A collection of harmonized gene-expression datasets, somatic mutation tables and a MONDO disease hierarchy for benchmarking the matching of biological models to patient tumour profiles.

The collection brings together patient samples, patient-derived xenografts (PDXs) and cancer cell lines. Expression datasets share a 19,260-gene reference panel, and disease descriptions were mapped to MONDO by our team using metadata supplied by the original authors.

Component	Contents	Format
Expression	Five datasets with TPM values, sample metadata and MONDO labels	AnnData / H5AD
Mutations	Nine source tables for variant calls, clinical annotations, copy number and ontology evidence	Parquet
Disease hierarchy	15,481 MONDO terms and 25,555 parent relations	Parquet

Expression datasets

Each H5AD contains a sample-by-gene matrix. All five datasets use the same ordered gene panel.

Dataset	Biological material	Samples	Genes	Zero-padded genes	File
PDXE	Patient-derived xenografts	357	19,260	315	pdxe_tpm.h5ad
META-PRISM	Metastatic patient tumours	932	19,260	79	metaprism_tpm.h5ad
TCGA	Patient tissue samples	11,425	19,260	29	tcga_tpm.h5ad
DepMap 24Q4	Cancer cell lines	1,508	19,260	285	depmap_tpm.h5ad
GSE317901	Head-and-neck cancer patient/PDX samples	114	19,260	106	gse317901_tpm.h5ad

What is stored in each H5AD?

Field	Description
X	Gene-expression values in TPM, stored as a sparse matrix
obs_names	Sample identifiers used to join expression and mutation data
obs["ontology_disease_matched_id"]	MONDO disease identifiers added by our team
obs["ontology_disease_matched_name"]	Corresponding disease names added by our team
obs	Selected source-derived tissue, histology and disease descriptors; available fields vary by dataset
var_names	Harmonized Ensembl gene identifiers
var["artificial_gene"]	Boolean flag identifying genes appended to complete the common panel

Zero padding: genes missing from a dataset's standardized gene set were added with all-zero expression and artificial_gene=True. A value of False means that the gene was already present; it does not guarantee nonzero expression.

Preparation

Gene harmonization. Gene identifiers were standardized. Genes were filtered against a common reference panel of 19,260 genes. Genes outside the reference panel were excluded. Missing panel genes were appended with zeros, and the final columns were sorted by Ensembl identifier.

Expression processing. For PDXE, human transcript TPM values were aggregated to genes and rescaled to one million per sample over the selected panel. META-PRISM TPM measurements were matched to clinical records. TCGA used GDC unstranded gene TPM values. DepMap 24Q4 log2(TPM+1) values were converted back to TPM. GSE317901 TPM measurements were associated with patient/PDX sample metadata.

Disease annotation. MONDO labels were added by our team based on the authors' metadata columns. Samples without a validly formatted MONDO identifier were excluded. Expression values in the final export were preserved from the corresponding standardized matrices.

Mutation data

OncoTree version: all 897 exported codes and levels match the official release oncotree_2025_10_03 (3 October 2025).

Nine tables support the mutation axis. Values and identifiers were preserved from the processed sources.

File	Contents	Retained columns	Rows
tcga_mutations.parquet	TCGA somatic variant calls	sample_id, gene_id_ensembl, variant_classification, aa_change	2,845,982
tcga_clinical.parquet	TCGA OncoTree and MSI annotations	sample_id, cancer_type_oncotree, msi_score_mantis, msi_score_sensor	10,953
depmap_mutations.parquet	DepMap 25Q3 somatic variant calls	Consensus_model_id, is_default_entry_for_model, gene_id_ensembl, protein_change, variant_info, ref, alt, gt, ps	750,004
depmap_subtypes.parquet	DepMap 25Q3 OncoTree and MSI subtype tags	Consensus_model_id, Subtype	5,828
depmap_copy_number.parquet	DepMap 25Q3 copy-number vectors	Consensus_model_id, omics_features	1,095
depmap_features.parquet	DepMap 25Q3 copy-number feature identifiers	copy_number_features	1
oncotree.parquet	OncoTree cancer codes and levels	oncotree_code, oncotree_level	897
cell_lines.parquet	Cellosaurus MSI and mutation annotations for DepMap lines	cvcl_id, msi_status, mutations	1,507
metaprism_clinical.parquet	META-PRISM patient, sample and OncoTree annotations	patient_id, sample_id, cancer_type_oncotree	1,031

Copy number. Each omics_features vector is indexed by the ordered copy_number_features list in depmap_features.parquet. Read the files together.

Sample matching. TCGA uses sample_id, DepMap uses Consensus_model_id, Cellosaurus uses cvcl_id, and META-PRISM supplies patient_id and sample_id. Apply the benchmark's cohort-specific matching rules.

Missing evidence. Missing calls or annotations alone do not imply a negative biomarker label. Coverage and eligibility are determined by the mutation-axis code.

External META-PRISM mutations. The full MAF remains on the authors' public server. The benchmark downloads it and checks the SHA-256 recorded in mutation_sources.yaml; it is not duplicated here.

MONDO disease hierarchy

mondo_ontology/train-00000-of-00001.parquet contains 15,481 terms, 25,555 parent relations and ten columns.

Columns	Description
mondo_id, name	Disease identifier and name
mondo_level	Minimum distance from the root
parent_mondo_id	One selected direct parent, provided for convenience
direct_ancestors_ids, direct_ancestors_names, len_direct_ancestors	All direct parents and their count
all_ancestors_ids, all_ancestors_names, len_all_ancestors	Ancestors and their count

Use direct_ancestors_ids when reconstructing the graph, because terms may have more than one parent.

The non-human animal disease branch (MONDO:0005583 and 62 exclusive descendants) was removed. The resulting graph is acyclic and has one root, MONDO:0000001.

Sources and attribution

Component	Original source
PDXE expression	NIBR; Gao et al., Nature Medicine (2015), doi:10.1038/nm.3954; PDXE data deposit
META-PRISM expression	Gustave Roussy; META-PRISM processed data
TCGA expression	NCI/NHGRI; Genomic Data Commons
DepMap expression	Broad Institute; DepMap 24Q4 Public
GSE317901 expression	Queen's University Belfast and collaborators; GEO GSE317901
TCGA mutations and clinical annotations	cBioPortal Datahub, *tcga_pan_can_atlas_2018*/data_mutations.txt
META-PRISM clinical annotations	Publication supplementary material, Table S1
DepMap mutation-axis inputs	Broad Institute; DepMap Public 25Q3; somatic calls, subtype tags, copy-number measurements and feature identifiers
MONDO	Monarch Initiative; Mondo Disease Ontology; official OBO reference
Cellosaurus	SIB Swiss Institute of Bioinformatics; Cellosaurus; doi:10.7171/jbt.18-2902-002.
OncoTree	Memorial Sloan Kettering Cancer Center; OncoTree, release oncotree_2025_10_03

Licence and reuse

Source-specific licences and attribution requirements apply. The collection does not assign a single licence to all components.

The PDXE deposit, DepMap 24Q4 expression release and MONDO ontology identify CC BY 4.0. META-PRISM processed expression tables were made publicly available by the authors. TCGA expression was obtained through GDC open-access resources. GEO data are subject to NCBI's data-use notice.

Mutation-axis files	Licence and reuse
tcga_mutations.parquet, tcga_clinical.parquet	Adapted tables offered under ODbL 1.0 with cBioPortal attribution. The datahub also includes a TCGA-specific GDAC notice; applicable study terms require release review.
Four depmap_* tables	CC BY 4.0
cell_lines.parquet	CC BY 4.0, as stated by Cellosaurus. Rows and columns were selected for this export.
oncotree.parquet	CC BY 4.0.
metaprism_clinical.parquet	The publication states CC BY-NC-ND 4.0.

Contains information from the cBioPortal datahub, which is made available under the Open Database License (ODbL) 1.0.

The ODbL designation above applies to the two identified TCGA tables; other components retain their source-specific terms.