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Files & Filesets (files_fileset)

The Catalog files_fileset collection connects knowledge-graph edges to the underlying source files on the IGVF Data Portal or ENCODE Portal.

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Accession patterns

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Portal metadata

Each file record on the portal includes:
  • file_format — e.g. tsv, bed, bigBed
  • output_type — processed data category
  • file_format_specification — link to the document defining column names and types in the file (critical for tracing fields through adapters)
  • Assay, lab, biosample, and release status
The Catalog loading pipeline reads these portal objects in file_fileset_adapter.py when building files_filesets nodes.

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Querying by fileset

Use files_fileset=<accession> on many endpoints to restrict results to a single dataset, for example:

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Field lineage

Column names in the raw portal file are transformed by KG loading adapters before appearing in API responses. See Field lineage for portal → adapter → Arango → API mappings.

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Browse all indexed files

See the Data Sources index for a table of file accessions referenced in this documentation with portal and format-spec links.