WormBase WS298

A byte-faithful mirror of the parts of WormBase release WS298 the Liu lab depends on: the five ontologies, the seven association files, and two classes of the AceDB dump. Files are exactly as WormBase served them — still gzipped, original filenames, nothing decompressed, reorganised or re-encoded.

WS298 is WormBase's final production release. Ongoing curation moved to the Alliance of Genome Resources, so this is a terminal snapshot rather than one that will be superseded — which is the reason to pin it rather than track a moving current-production-release/ alias.

Upstream: wormbase.org · downloads.wormbase.org · ONTOLOGY/ directory for this release · WormBase 2024 paper

Every file here is traceable to a single upstream URL; see Provenance.

Layout

WS298/
├── ontology/     five ontologies + seven association files (12 files, 22 MB)
└── acedb/        Paper and LongText from the AceDB dump (2 files, 120 MB)

The WS298/ontology/ path is not arbitrary. It is exactly the cache layout eutely.wormbase.Release expects, so a snapshot of this repo can be read directly as a staged release with no copying or renaming — see Usage.

Ontologies

anatomy, development and phenotype are worm-specific and authored by WormBase. disease and gene are the full Disease and Gene Ontologies, which WormBase mirrors rather than authors.

File	Terms	IDs	Size
anatomy_ontology.WS298.obo.gz	7,192	WBbt:	160 KB
development_ontology.WS298.obo.gz	777	WBls:	29 KB
phenotype_ontology.WS298.obo.gz	2,712	WBPhenotype:	176 KB
disease_ontology.WS298.obo.gz	14,430	DOID:	1.3 MB
gene_ontology.WS298.obo.gz	48,165	GO:	4.5 MB

All five declare format-version: 1.2.

Associations

An association is one statement that some entity stands in a named relation to one ontology term, backed by evidence. Six sources in four wire formats, 1,323,659 statements between them.

File	Source	Format	Rows	Terms	Size
anatomy_association.WS298.wb.gz	anatomy	GAF 2.0	461,223	WBbt:	3.7 MB
development_association.WS298.wb.gz	development	GAF 2.0	74,571	WBls:	382 KB
phenotype_association.WS298.wb.gz	phenotype	GAF 2.0	439,924	WBPhenotype:	3.1 MB
gene_association.WS298.wb.gz	gene	GAF 2.2	312,203	GO:	4.4 MB
disease_association.WS298.daf.txt.gz	disease	DAF 1.0	2,364	DOID:	37 KB
disease_association.by_orthology.WS298.tsv.txt.gz	disease_by_orthology	TSV	33,036	DOID:	222 KB
gene_association_nonnoctua.WS298.wb.gz	—	GAF 2.2	294,407	GO:	4.1 MB

Notes on the columns that differ between sources: in anatomy, column 4 is an expression certainty, not a relation; in gene it is a real GAF 2.2 relation (enables, involved_in, …). disease is curated from worm experiments and its subject is often an allele or strain rather than a gene, while disease_by_orthology is inferred from a human ortholog and so carries neither evidence code nor reference. The two disease files answer the same question with incomparable evidence, which is why they stay separate rather than being concatenated.

gene_association_nonnoctua is not a seventh source: every one of its rows appears verbatim in gene_association. It is the GO set with the Noctua/GO-CAM rows removed, included here only so the mirror is complete.

Rows are not records. A GAF row naming two comma-separated terms is two statements. Parsing the seven files yields slightly more records than they have rows — 461,422 records from anatomy's 461,223 rows, 2,503 from disease's 2,364. The table above counts rows, because that is what is in the file.

AceDB dump

Two classes from the WS298 AceDB dump, kept under their published names.

File	Contents	Records	Size (gz)	Size (raw)
Paper.xml.gz	Bibliography: title, journal, authors, abstract pointer	64,863 <Paper>	23 MB	302 MB
LongText.xml.gz	Free-text bodies — paper abstracts, EMBL records	671,404 stanzas	97 MB	973 MB

⚠️ LongText.xml.gz is not XML. Despite the .xml.gz name it is AceDB .ace format — 671,404 LongText : "<id>" stanzas of free text, and zero XML tags in the entire file. Feeding it to an XML parser fails immediately. Paper.xml.gz is genuine XML. The misnomer is upstream's; the name is preserved here so the file still matches anyone else's copy of the same dump, but do not select a parser by suffix.

The two connect through the abstract pointer: a <Paper> carries <Abstract><LongText>WBPaper00000003</LongText></Abstract>, and the matching LongText : "WBPaper00000003" stanza holds the abstract text.

Neither file records its release internally. They are placed under WS298/ because that is the release they were dumped from, not because anything in the bytes says so.

Usage

With eutely

The layout is the one eutely.wormbase caches into, so a snapshot is readable as-is:

from pathlib import Path

from huggingface_hub import snapshot_download
from eutely.wormbase import Filter, Release, load_associations, load_ontology

root = Path(snapshot_download("liuhlab/wormbase", repo_type="dataset"))
ws298 = Release("WS298", root=root)

anatomy = load_ontology("anatomy", release=ws298)
anatomy["WBbt:0005672"].name                                     # 'AWC'
len(anatomy.descendants("WBbt:0003681", ("is_a", "part_of")))    # 215 parts of the pharynx

assoc = load_associations("anatomy", release=ws298)
assoc.by_term("WBbt:0005672")                                    # genes expressed in AWC

Pass root= and nothing downloads from WormBase — which is the point on a compute node with no outbound network.

Without eutely

Everything is gzipped text; no special reader is required.

import gzip

with gzip.open("WS298/ontology/gene_association.WS298.wb.gz", "rt") as fh:
    rows = [line.rstrip("\n").split("\t") for line in fh if not line.startswith("!")]

The dataset viewer does not render these files, and no configs block claims it can: OBO, GAF, DAF and .ace are not tabular formats the Hub can infer, and the tab-separated ones carry ! comment headers rather than a column row. Download and parse them directly.

Three things that will bite you

Most phenotype records are negative. 318,218 of 439,924 assert that a gene does not produce a phenotype. "The genes for this phenotype" is the wrong question unless you read column 4 — a NOT qualifier — or filter on it.

Most GO records are not C. elegans. Only 134,390 of gene_association's 312,203 rows carry taxon:6239; the rest are nine other nematodes — C. briggsae, C. remanei, P. pacificus, B. malayi and five more.

Watch the arithmetic here. A grep for the bare column value returns 134,137, but 253 further worm rows name a second, interacting taxon and so read taxon:6239|taxon:287 — always a pathogen (P. aeruginosa, E. coli, B. thuringiensis …), never another host. Those are C. elegans rows. No row carries taxon:6239 in the interacting position alone, so 134,390 is the count of rows about the worm and 134,137 is only the count of rows about the worm and nothing else.

Anatomy containment is part_of, not is_a. Walking is_a alone answers nothing about what lies inside the pharynx. Widen the relation set when traversing the anatomy ontology; in the development ontology, note that preceded_by is a temporal ordering rather than a hierarchy.

Provenance

Downloaded from downloads.wormbase.org on 2026-07-26.

The twelve files in WS298/ontology/ each came from exactly one URL, formed by appending the filename to the release's ONTOLOGY directory:

https://downloads.wormbase.org/releases/current-production-release/ONTOLOGY/<filename>

So anatomy_ontology.WS298.obo.gz is …/ONTOLOGY/anatomy_ontology.WS298.obo.gz, and so on for the other eleven. Note the path goes through the current-production-release/ alias: that is the only path WormBase serves, and the concrete releases/WS298/ directory the filenames imply answers 403. Because WS298 is the final release, the alias and the pin name the same bytes — but if WormBase ever advances the alias, these files remain WS298 and upstream would not.

The two files in WS298/acedb/ come from the same release's AceDB per-class dump tree. That directory is reachable from a browser but Cloudflare-gated to non-interactive clients, so it cannot be re-fetched by script — which is part of why they are mirrored here at all.

Every file was verified as intact gzip and parsed end to end before upload, and re-verified SHA-256-identical to the source after a round trip through this repo. The counts in the tables above are measured from these exact bytes, not copied from upstream documentation — where the two disagreed, the bytes won.

Licensing

This is a redistribution of third-party data with mixed terms, labelled cc-by-4.0 because that is the strictest condition in the bundle. Per component:

Component	Licence
WormBase-authored data (anatomy, development, phenotype; AceDB dumps)	CC0 1.0
Gene Ontology and its annotations (gene_ontology, gene_association*)	CC BY 4.0 — GO citation policy
Human Disease Ontology (disease_ontology)	CC0 1.0

Attribution is therefore required for the GO-derived files and not for the rest. Complying with CC BY 4.0 across the whole set satisfies every component. No file here has been modified, so attribution to the original creators is the only obligation.

Citation

Cite the upstream resources, not this mirror:

@article{wormbase2024,
  title   = {WormBase 2024: status and transitioning to Alliance infrastructure},
  journal = {Genetics},
  volume  = {227},
  number  = {1},
  year    = {2024},
  doi     = {10.1093/genetics/iyae050}
}

@article{geneontology2023,
  title   = {The Gene Ontology knowledgebase in 2023},
  journal = {Genetics},
  volume  = {224},
  number  = {1},
  year    = {2023},
  doi     = {10.1093/genetics/iyad031}
}

Maintenance

Mirrored by the Liu lab for eutely. WS298 is terminal, so this repo is a fixed snapshot: it will not be re-cut for new releases.