README.md

---
pretty_name: WormBase WS298 — ontologies, associations, and AceDB dumps
license: cc-by-4.0
language:
  - en
tags:
  - biology
  - genomics
  - c-elegans
  - caenorhabditis-elegans
  - wormbase
  - ontology
  - gene-ontology
  - obo
  - gaf
size_categories:
  - 1M<n<10M
---

# 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](https://www.alliancegenome.org/), 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rather than one that will be superseded — which is the reason to pin it rather than track a moving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](https://wormbase.org/) · [downloads.wormbase.org](https://downloads.wormbase.org/)
· [ONTOLOGY/ directory for this release](https://downloads.wormbase.org/releases/current-production-release/ONTOLOGY/)
· [WormBase 2024 paper](https://doi.org/10.1093/genetics/iyae050)

Every file here is traceable to a single upstream URL; see [Provenance](#provenance).

## Layout

```text
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`](https://github.com/liuhlab/eutely) expects, so a snapshot of this repo
can be read directly as a staged release with no copying or renaming — see [Usage](#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`](https://github.com/liuhlab/eutely) caches into, so a
snapshot is readable as-is:

```python
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.

```python
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](https://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:

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

So `anatomy_ontology.WS298.obo.gz` is
[…/ONTOLOGY/anatomy_ontology.WS298.obo.gz](https://downloads.wormbase.org/releases/current-production-release/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](https://creativecommons.org/publicdomain/zero/1.0/) |
| Gene Ontology and its annotations (`gene_ontology`, `gene_association*`) | [CC BY 4.0](https://creativecommons.org/licenses/by/4.0/) — [GO citation policy](https://geneontology.org/docs/go-citation-policy/) |
| Human Disease Ontology (`disease_ontology`) | [CC0 1.0](https://disease-ontology.org/about/) |

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:

```bibtex
@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](https://github.com/liuhlab) for [`eutely`](https://github.com/liuhlab/eutely).
WS298 is terminal, so this repo is a fixed snapshot: it will not be re-cut for new releases.