Field Lineage

This page documents how fields flow from portal files (with file format specifications) through KG loading adapters into ArangoDB and the REST API. For automated deep traces, use the trace tool in igvf-catalog-dev-agents.

AFGR_caqtl_adapter.py

Arango / API field	Adapter expression	Notes
`name`	`_id`
`source`	`(computed)`
`method`	`(computed)`
`label`	`'caQTL'`
`p_value`	`pvalue`
`biosample_term`	`(computed)`
`biological_context`	`(computed)`
`class`	`(computed)`

AFGR_eqtl_adapter.py

Arango / API field	Adapter expression	Notes
`biological_context`	`(computed)`
`p_value`	`(computed)`
`effect_size`	`(computed)`
`class`	`(computed)`
`method`	`(computed)`
`label`	`'eQTL'`
`source`	`(computed)`
`name`	`'modulates expression of'`
`biosample_term`	`(computed)`

AFGR_sqtl_adapter.py

Arango / API field	Adapter expression	Notes
`biological_context`	`(computed)`
`p_value`	`pvalue`
`effect_size`	`(computed)`
`class`	`(computed)`
`method`	`(computed)`
`label`	`'spliceQTL'`
`source`	`(computed)`
`name`	`'modulates splicing of'`
`biosample_term`	`(computed)`

BlueSTARR_variants_biosamples_adapter.py

Referenced files: ENCFF420VPZ, IGVFFI0818FMCC, IGVFFI1663LKVQ, IGVFFI3351LASN, IGVFFI5288RAAV

Arango / API field	Adapter expression	Notes
`class`	`(computed)`
`label`	`(computed)`
`method`	`(computed)`
`biological_context`	`(computed)`
`biosample_term`	`(computed)`
`name`	`'modulates regulatory activity of'`
`source`	`(computed)`

DUAL_IPA_coding_variant_scores_adapter.py

Referenced files: IGVFFI6224HZMG

Arango / API field	Adapter expression	Notes
`source`	`(computed)`
`name`	`(computed)`
`method`	`(computed)`
`class`	`(computed)`
`label`	`(computed)`
`biological_context`	`(computed)`
`biosample_term`	`(computed)`

ESM_coding_variants_adapter.py

Referenced files: IGVFFI8105TNNO

Arango / API field	Adapter expression	Notes
`name`	`'codes for'`
`source`	`(computed)`
`label`	`(computed)`
`method`	`(computed)`
`class`	`(computed)`
`biosample_term`	`(computed)`
`biological_context`	`(computed)`

Mutpred2_coding_variants_adapter.py

Referenced files: IGVFFI6893ZOAA

Arango / API field	Adapter expression	Notes
`name`	`'codes for'`
`label`	`'codes for'`
`source`	`(computed)`
`method`	`(computed)`
`class`	`(computed)`
`biological_context`	`(computed)`
`biosample_term`	`(computed)`

SEM_motif_adapter.py

Referenced files: ENCFF001UVU, ENCFF242PUG, IGVFFI4892QCRR, IGVFFI8823UTCQ

Arango / API field	Adapter expression	Notes
`name`	`motif_key`
`source`	`'IGVF'`

SEM_prediction_adapter.py

Referenced files: ENCFF001UVU, ENCFF242PUG, IGVFFI4892QCRR, IGVFFI6807FCZT, IGVFFI6923RISY

Arango / API field	Adapter expression	Notes
`label`	`'predicted allele-specific binding'`
`method`	`(computed)`
`class`	`(computed)`
`biosample_term`	`(computed)`
`biological_context`	`(computed)`
`name`	`'modulates binding of'`
`source`	`'IGVF'`

SGE_variant_phenotype_adapter.py

Referenced files: IGVFFI9974PZRX

Arango / API field	Adapter expression	Notes
`source`	`(computed)`
`method`	`(computed)`
`class`	`(computed)`
`label`	`(computed)`
`biosample_term`	`(computed)`
`biological_context`	`(computed)`
`name`	`(computed)`

STARR_seq_adapter.py

Arango / API field	Adapter expression	Notes
`source`	`(computed)`
`name`	`'modulates expression in'`
`label`	`(computed)`
`method`	`(computed)`
`class`	`(computed)`
`biological_context`	`(computed)`
`biosample_term`	`(computed)`

VAMP_coding_variant_scores_adapter.py

Referenced files: IGVFFI0629IIQU, IGVFFI8987JRZH

Arango / API field	Adapter expression	Notes
`source`	`(computed)`
`name`	`(computed)`
`method`	`file_fileset_obj[...]`
`class`	`file_fileset_obj[...]`
`label`	`(computed)`
`biological_context`	`(computed)`
`biosample_term`	`(computed)`

Variant_EFFECTS_variant_gene_adapter.py

Referenced files: IGVFFI9602ILPC

Arango / API field	Adapter expression	Notes
`source`	`(computed)`
`effect_size`	`(computed)`
`class`	`'observed data'`
`label`	`'variant effect on gene expression'`
`name`	`'modulates expression of'`
`method`	`'Variant-EFFECTS'`
`biological_context`	`(computed)`
`biosample_term`	`(computed)`

adastra_asb_adapter.py

Arango / API field	Adapter expression	Notes
`biological_context`	`cell_gtrd_name`
`biosample_term`	`(computed)`
`source`	`(computed)`
`label`	`'allele-specific binding'`
`method`	`(computed)`
`class`	`(computed)`
`name`	`'modulates binding of'`

biogrid_gene_gene_adapter.py

Arango / API field	Adapter expression	Notes
`source`	`row[...]`
`name`	`'interacts with'`
`method`	`collection_method`
`label`	`(computed)`
`class`	`(computed)`

cV2F_variant_phenotype_adapter.py

Referenced files: IGVFFI1931RMNE, IGVFFI4594QVDO

Arango / API field	Adapter expression	Notes
`score`	`(computed)`
`source`	`(computed)`
`name`	`'associated with'`
`biological_context`	`(computed)`
`biosample_term`	`(computed)`
`method`	`(computed)`
`class`	`(computed)`
`label`	`(computed)`

ccre_adapter.py

Arango / API field	Adapter expression	Notes
`name`	`row[...]`
`method`	`(computed)`
`source`	`'ENCODE'`

cellosaurus_ontology_adapter.py

Arango / API field	Adapter expression	Notes
`name`	`(computed)`
`source`	`(computed)`

clingen_variant_disease_adapter.py

Arango / API field	Adapter expression	Notes
`gene_id`	`(computed)`
`name`	`'associated with'`
`source`	`(computed)`

coxpresdb_adapter.py

Referenced files: IGVFFI3321YNBP

Arango / API field	Adapter expression	Notes
`source`	`(computed)`
`name`	`'coexpressed with'`
`class`	`(computed)`
`method`	`(computed)`
`label`	`(computed)`

dbNSFP_adapter.py

Arango / API field	Adapter expression	Notes
`source`	`'dbNSFP 5.1a'`
`name`	`'codes for'`

depmap_adapter.py

Arango / API field	Adapter expression	Notes
`source`	`(computed)`
`name`	`'essential in'`

ebi_complex_adapter.py

Arango / API field	Adapter expression	Notes
`name`	`complex_row[...]`
`source`	`(computed)`

encode_E2G_CRISPR_adapter.py

Referenced files: ENCFF968BZL

Arango / API field	Adapter expression	Notes
`name`	`_id`
`method`	`(computed)`
`source`	`(computed)`
`score`	`(computed)`
`p_value`	`(computed)`
`class`	`(computed)`
`label`	`(computed)`
`biological_context`	`(computed)`
`biosample_term`	`(computed)`

encode_caqtl_adapter.py

Arango / API field	Adapter expression	Notes
`label`	`'caQTL'`
`method`	`(computed)`
`class`	`(computed)`
`source`	`'ENCODE'`
`biological_context`	`(computed)`
`biosample_term`	`(computed)`
`name`	`(computed)`

encode_element_gene_adapter.py

Referenced files: ENCFF006FTZ, ENCFF034GOH, ENCFF036LSB, ENCFF073KUI, ENCFF074MTS, ENCFF079SJR, ENCFF138UMI, ENCFF176YAF, ENCFF197HRR, ENCFF201SDO, ENCFF202FBA, ENCFF213WPV

Arango / API field	Adapter expression	Notes
`method`	`file_fileset[...]`
`label`	`(computed)`
`class`	`file_fileset[...]`
`score`	`(computed)`
`source`	`'ENCODE'`
`biological_context`	`(computed)`
`biosample_term`	`(computed)`
`name`	`'regulates'`

eqtl_catalog_adapter.py

Arango / API field	Adapter expression	Notes
`biosample_term`	`biosample_term`
`biological_context`	`biological_context`
`label`	`label`
`class`	`(computed)`
`method`	`(computed)`
`source`	`(computed)`
`name`	`name`
`gene_id`	`gene_id`
`p_value`	`p_value`
`effect_size`	`(computed)`

favor_adapter.py

Arango / API field	Adapter expression	Notes
`source`	`'FAVOR'`

file_fileset_adapter.py

Referenced files: ENCFF167FJQ, ENCFF420VPZ, ENCFF968BZL

Arango / API field	Adapter expression	Notes
`name`	`file_object[...]`
`method`	`method`
`class`	`class_type`
`source`	`(computed)`

gaf_adapter.py

Arango / API field	Adapter expression	Notes
`source`	`'Gene Ontology'`

gencc_diseases_genes_adapter.py

Arango / API field	Adapter expression	Notes
`name`	`'associated_with'`
`source`	`(computed)`

gencode_adapter.py

Arango / API field	Adapter expression	Notes
`name`	`info[...]`
`source`	`'GENCODE'`

gencode_gene_adapter.py

Arango / API field	Adapter expression	Notes
`gene_id`	`gene_id`
`name`	`info[...]`
`source`	`'GENCODE'`

gencode_gene_structure_adapter.py

Arango / API field	Adapter expression	Notes
`name`	`(computed)`
`gene_id`	`gene_id_no_version`
`source`	`(computed)`

gencode_protein_adapter.py

Arango / API field	Adapter expression	Notes
`name`	`(computed)`
`source`	`'GENCODE'`

gvatdb_asb_adapter.py

Arango / API field	Adapter expression	Notes
`p_value`	`pvalue`
`log10pvalue`	`log10pvalue`
`source`	`(computed)`
`label`	`'allele-specific binding'`
`method`	`(computed)`
`class`	`(computed)`
`name`	`'modulates binding of'`

gwas_adapter.py

Referenced files: IGVFFI1309WDQG

Arango / API field	Adapter expression	Notes
`name`	`study_id`
`source`	`(computed)`
`p_value`	`pvalue`
`class`	`(computed)`
`method`	`(computed)`
`label`	`(computed)`

human_mouse_element_adapter.py

Referenced files: ENCFF078OEX

Arango / API field	Adapter expression	Notes
`source`	`32`
`name`	`_id_human`
`method`	`'integrative'`

igvf_E2G_CRISPR_adapter.py

Arango / API field	Adapter expression	Notes
`source`	`(computed)`
`label`	`(computed)`
`class`	`file_fileset[...]`
`name`	`'modulates expression of'`
`method`	`method`
`biological_context`	`(computed)`
`biosample_term`	`(computed)`

mgi_human_mouse_ortholog_adapter.py

Arango / API field	Adapter expression	Notes
`name`	`'homologous to'`
`source`	`'MGI'`

motif_adapter.py

Arango / API field	Adapter expression	Notes
`name`	`_key`
`source`	`(computed)`

mouse_genomes_project_adapter.py

Arango / API field	Adapter expression	Notes
`name`	`spdi`
`source`	`'MOUSE GENOMES PROJECT'`

mpra_adapter.py

Referenced files: ENCFF802FUV, IGVFFI1323RCIE, IGVFFI1436TRIH, IGVFFI4914OUJH, IGVFFI8207IHFY

Arango / API field	Adapter expression	Notes
`name`	`element_name`
`method`	`(computed)`
`source`	`(computed)`
`class`	`(computed)`
`label`	`(computed)`
`biological_context`	`(computed)`
`biosample_term`	`(computed)`

oncotree_adapter.py

Arango / API field	Adapter expression	Notes
`name`	`node[...]`
`source`	`(computed)`

ontologies_adapter.py

Referenced files: IGVFFI0402TNDW, IGVFFI0719VRZV, IGVFFI1298JRGV, IGVFFI2369NSDT, IGVFFI4219OZTA, IGVFFI6182DQZM, IGVFFI7115PAJX, IGVFFI7985BGYI, IGVFFI8306RHIV, IGVFFI8953HXRQ, IGVFFI9789TIWM

Arango / API field	Adapter expression	Notes
`name`	`(computed)`
`source`	`(computed)`

orphanet_disease_adapter.py

Arango / API field	Adapter expression	Notes
`name`	`'associated_with'`
`source`	`(computed)`

pQTL_adapter.py

Arango / API field	Adapter expression	Notes
`label`	`'pQTL'`
`class`	`(computed)`
`method`	`(computed)`
`log10pvalue`	`(computed)`
`biological_context`	`(computed)`
`biosample_term`	`(computed)`
`source`	`(computed)`
`name`	`'associated with levels of'`

pharmgkb_drug_adapter.py

Arango / API field	Adapter expression	Notes
`name`	`drug_name`
`source`	`(computed)`

proteins_interaction_adapter.py

Referenced files: IGVFFI1165YVBA, IGVFFI4317VDGK

Arango / API field	Adapter expression	Notes
`source`	`source`
`name`	`'physically interacts with'`
`method`	`collection_method`
`label`	`detection_method`
`class`	`(computed)`

reactome_adapter.py

Arango / API field	Adapter expression	Notes
`source`	`'Reactome'`
`name`	`'belongs to'`

reactome_pathway_adapter.py

Arango / API field	Adapter expression	Notes
`name`	`name`
`source`	`'Reactome'`

scE2G_adapter.py

Referenced files: IGVFFI3412RLDF

Arango / API field	Adapter expression	Notes
`score`	`score`
`label`	`(computed)`
`method`	`method`
`class`	`collection_class`
`source`	`(computed)`
`name`	`'regulates'`

topld_adapter.py

Arango / API field	Adapter expression	Notes
`r2`	`(computed)`
`d_prime`	`(computed)`
`label`	`'linkage disequilibrum'`
`name`	`'correlated with'`
`source`	`'TopLD'`
`variant_id`	`(computed)`

​Field Lineage

​AFGR_caqtl_adapter.py

​AFGR_eqtl_adapter.py

​AFGR_sqtl_adapter.py

​BlueSTARR_variants_biosamples_adapter.py

​DUAL_IPA_coding_variant_scores_adapter.py

​ESM_coding_variants_adapter.py

​Mutpred2_coding_variants_adapter.py

​SEM_motif_adapter.py

​SEM_prediction_adapter.py

​SGE_variant_phenotype_adapter.py

​STARR_seq_adapter.py

​VAMP_coding_variant_scores_adapter.py

​Variant_EFFECTS_variant_gene_adapter.py

​adastra_asb_adapter.py

​biogrid_gene_gene_adapter.py

​cV2F_variant_phenotype_adapter.py

​ccre_adapter.py

​cellosaurus_ontology_adapter.py

​clingen_variant_disease_adapter.py

​coxpresdb_adapter.py

​dbNSFP_adapter.py

​depmap_adapter.py

​ebi_complex_adapter.py

​encode_E2G_CRISPR_adapter.py

​encode_caqtl_adapter.py

​encode_element_gene_adapter.py

​eqtl_catalog_adapter.py

​favor_adapter.py

​file_fileset_adapter.py

​gaf_adapter.py

​gencc_diseases_genes_adapter.py

​gencode_adapter.py

​gencode_gene_adapter.py

​gencode_gene_structure_adapter.py

​gencode_protein_adapter.py

​gvatdb_asb_adapter.py

​gwas_adapter.py

​human_mouse_element_adapter.py

​igvf_E2G_CRISPR_adapter.py

​mgi_human_mouse_ortholog_adapter.py

​motif_adapter.py

​mouse_genomes_project_adapter.py

​mpra_adapter.py

​oncotree_adapter.py

​ontologies_adapter.py

​orphanet_disease_adapter.py

​pQTL_adapter.py

​pharmgkb_drug_adapter.py

​proteins_interaction_adapter.py

​reactome_adapter.py

​reactome_pathway_adapter.py

​scE2G_adapter.py

​topld_adapter.py