| --- |
| license: other |
| license_name: bionlp-st-2011-terms |
| license_link: https://bionlp-st.dbcls.jp/GE/2011/downloads/ |
| dataset_info: |
| config_name: default |
| features: |
| - name: input |
| dtype: string |
| - name: output |
| dtype: json |
| - name: schema |
| dtype: json |
| configs: |
| - config_name: default |
| data_files: |
| - split: train |
| path: data/train.jsonl |
| - split: validation |
| path: data/validation.jsonl |
| --- |
| |
| # GENIA 2011 (mneb format) — joint NER + nested event extraction |
|
|
| The BioNLP Shared Task 2011 GE corpus (Kim et al., 2011) converted into the mneb |
| joint `entities` + `json_structures` format. GENIA is a biomedical entity and end-to-end |
| event extraction dataset over PubMed abstracts and PMC full texts. |
|
|
| **This dataset keeps event-as-argument nesting.** Roughly a third of GENIA's argument links |
| point at another *event* rather than an entity — regulation events take other events as their |
| `Theme` or `Cause` — and prior conversions (including TextEE's) drop them. Here they are kept |
| **without leaving the flat mneb record shape**: every argument is a plain |
| `{role,text,start,end}` span, and an argument that points at an event carries that event's |
| *trigger* span. See [Event arguments](#event-arguments). |
|
|
| Char offsets are character-based and end-exclusive (`input[start:end] == text`). |
| One record = one source `.txt` file (PMC full-text sections are **not** merged into papers). |
|
|
| ## Splits |
|
|
| | Split | Records | With events | Events | |
| |---|---:|---:|---:| |
| | train | 908 | 765 | 9,560 | |
| | validation | 259 | 225 | 2,988 | |
| | **Total** | **1,167** | **990** | **12,548** | |
|
|
| There is **no labelled test split.** The official blind-test archive contains 347 `.txt`/`.a1` |
| inputs, but BioNLP-ST did not publicly release their `.a2` event gold. This release therefore |
| contains the official train/devel partition only; treating the blind inputs as empty output |
| would create false negatives. Note that this differs from TextEE, which discards the official |
| boundary and makes five random re-splits instead — no number reported on a TextEE split is |
| directly comparable to this one. |
|
|
| ## Supported tasks and retained layers |
|
|
| - **NER:** `protein` and generic `entity` mentions in `output.entities`. |
| - **Event detection (ED):** event triggers in `output.json_structures`. |
| - **Event argument extraction (EAE)** and **end-to-end event extraction (E2E):** trigger and |
| argument spans, including span-linked event arguments. |
| - **Joint NER + EE:** both layers occur in the same record and use the same character offsets. |
|
|
| Equivalence, event attributes and normalisations are not exposed, so this release does not |
| claim relation extraction, coreference, negation or speculation as supported tasks. |
|
|
| ## Entity layer — 2 types, 16,976 mentions |
|
|
| | Entity type | Train | Validation | Total | |
| |---|---:|---:|---:| |
| | entity | 480 | 181 | 661 | |
| | protein | 11,625 | 4,690 | 16,315 | |
| | **Total** | **12,105** | **4,871** | **16,976** | |
|
|
| `protein` is the public form of `.a1` label `Protein`; `entity` is the public form of the |
| generic `.a2` label `Entity` used for non-protein physical participants, sites and locations. |
| The names are uniformly lower-case with spaces, matching mneb's public entity-label policy. |
|
|
| ## Record format |
|
|
| ```jsonc |
| { |
| "input": "<document text>", |
| "output": { |
| "entities": {"protein": [<span>, ...], "entity": [<span>, ...]}, |
| "json_structures": {"<event type>": [<event>, ...]} |
| }, |
| "schema": {"entities": [<entity definition>, ...], |
| "json_structures": [<event definition>, ...]} |
| } |
| ``` |
|
|
| The active `data/train.jsonl` and `data/validation.jsonl` use lower-case, space-separated |
| event labels (for example `gene expression`), preserving the convention introduced by |
| yangwang825. Compatibility files prefixed `genia2011_` retain the official event strings |
| (for example `Gene_expression`). NER labels are normalized in both views. |
|
|
| An event is `{"trigger": {"text","start","end"}, "arguments": [<arg>, ...]}`. There is |
| nothing else: no `type` field on the event (its type is the `json_structures` key), and no |
| object nested inside an argument. |
|
|
| ### Event arguments |
|
|
| Every argument has the same four keys, whether it points at an entity or at another event: |
|
|
| ```jsonc |
| {"role": "Theme", "text": "interferon regulatory factor 4", "start": 19, "end": 49} |
| {"role": "Theme", "text": "expression", "start": 55, "end": 65} |
| ``` |
|
|
| The first is an entity mention. The second is an **event link**: `(55, 65)` is the trigger span |
| of a `gene expression` event, which is listed at the top level of the same record. This is how |
| mneb expresses links generally — repeat the span, no ids (cf. `mneb/bc5cdr`, whose relation |
| `head`/`tail` repeat the entity spans). |
|
|
| Because a linked child must be reachable, **every** event appears at the top level, not only |
| the roots. To resolve links: |
|
|
| ```python |
| def resolve(js): |
| """Index every event by its trigger span, then read arguments as links where they match.""" |
| by_span = {} |
| for etype, evs in js.items(): |
| for ev in evs: |
| by_span.setdefault((ev["trigger"]["start"], ev["trigger"]["end"]), []).append((etype, ev)) |
| for etype, evs in js.items(): |
| for ev in evs: |
| for a in ev["arguments"]: |
| target = by_span.get((a["start"], a["end"])) # None => entity mention |
| yield etype, ev, a, target |
| ``` |
|
|
| A real example — *"Down-regulation of interferon regulatory factor 4 gene expression…"*. Two |
| top-level events; the `Theme` link `Down-regulation → expression` is the nesting: |
|
|
| ```jsonc |
| "negative regulation": [{ |
| "trigger": {"text": "Down-regulation", "start": 0, "end": 15}, |
| "arguments": [{"role": "Theme", "text": "expression", "start": 55, "end": 65}]}], |
| "gene expression": [{ |
| "trigger": {"text": "expression", "start": 55, "end": 65}, |
| "arguments": [{"role": "Theme", "text": "interferon regulatory factor 4", |
| "start": 19, "end": 49}]}] |
| ``` |
|
|
| ### How faithful the span links are |
|
|
| - **Telling a link from an entity mention:** just **1** of the 11,590 entity-valued arguments |
| sits on a span that is also a trigger, so the test "this argument's span matches a trigger |
| span" has a single false positive corpus-wide. |
| - **Telling *which* event a link points at:** 3,860 of the 5,502 links (**70.2%**) match |
| exactly one event of the right type. The other 1,642 (29.8%) land on a trigger span shared by |
| several same-type events, and the span cannot disambiguate them — GENIA 2011 is the worst of |
| the three BioNLP corpora here, because one regulation trigger routinely heads several events. |
| - Consequently 1,012 of the 13,560 raw `E` lines (7.5%) come out byte-identical to another entry |
| of the same type and are **collapsed**, leaving 12,548 events. Those are exactly the parents |
| that differed only in an unresolvable choice of child; keeping both copies would double-count |
| in any set-based metric. |
|
|
| Everything else round-trips: the offset invariant holds on every span, and the set of emitted |
| `(type, trigger, role/span)` signatures equals the same set computed straight off the raw |
| standoff, for every document. |
|
|
| ## Statistics |
|
|
| - **9 event types**, **10 role types** (role strings kept verbatim, so `Theme2`/`Theme3`/ |
| `Theme4`/`Site2` are *not* collapsed into their base role). |
| - **17,092 raw argument links** = 11,590 entity-valued + 5,502 event-valued (**32.2%** of all |
| argument links are event-to-event). After the collapse above the files hold **15,652 argument |
| instances** = 11,354 entity spans + 4,298 span links. |
| - **4,964 events (36.6%)** take at least one event argument. |
| - Raw nesting depth histogram `{1: 8596, 2: 4209, 3: 710, 4: 44, 5: 1}` — **max depth 5**. |
| - Nesting is driven entirely by the three regulation types; no other event type ever takes an |
| event argument, and only `Theme` and `Cause` are ever event-linked. |
|
|
| Full type/role inventory and nesting patterns: `genia2011_label_summary.md`. |
| Browsable rendering: `genia2011_vis.html` (open directly; data embedded, no server needed). |
|
|
| ## How this was derived |
|
|
| Required by clause 5 of the source licence. Built from the official |
| `BioNLP-ST_2011_genia_train_data_rev1` and `..._devel_data_rev1` archives: |
|
|
| 1. Each document's `.a1` (Protein entities) and `.a2` (event triggers, `Entity` spans and |
| `E` event lines) are parsed into a single text-bound annotation map; their id spaces do |
| not collide. |
| 2. `Protein` and `Entity` annotations become NER mentions under normalized public labels. |
| 3. Each `E` line becomes an event grouped under its own type; `Role:T…` arguments become the |
| entity's span and `Role:E…` arguments become the child event's **trigger** span. Both come |
| out in the same `{role,text,start,end}` shape. |
| 4. Every event is listed at the top level, so a linked child is always resolvable. Entries that |
| are byte-identical under one event type are then collapsed. |
| 5. Equivalence (`*`), attribute (`A`/`M`: Negation, Speculation) and normalisation (`N`) |
| lines are **not** carried over. The converter and compatibility files preserve official |
| event-type strings; the active files normalize only event-type labels. Roles remain verbatim |
| in both views. |
|
|
| The raw standoff gives labels but no prose label descriptions. The descriptions embedded in |
| the full schema and published in `schema.json` are concise mneb-authored paraphrases based on |
| the official task definition and paper; they are not source annotations or quotations. |
|
|
| Verification built into the converter: every emitted span is re-checked against the source |
| text (`input[start:end] == text`, 0 failures); the set of emitted `(type, trigger, role/span)` |
| signatures is compared against the same set computed straight off the raw standoff and is equal |
| for every document; and a link audit reports, for every event-valued argument, whether its |
| child is uniquely identifiable from the span (the numbers quoted above). |
|
|
| ## Licence and terms of use |
|
|
| Distributed under the **BioNLP Shared Task 2011 licence terms**, which permit redistribution |
| with these conditions: |
|
|
| - **Research use.** The annotations are to be used primarily for scholarly research in NLP, |
| IE and related disciplines. Derived data may be produced only for bona fide research of a |
| **non-profit** nature. |
| - **Commercial or non-academic public use requires permission** from the BioNLP-ST'11 |
| organisers. |
| - **Abstracts** come from PubMed® (U.S. National Library of Medicine) and are subject to the |
| PubMed licence terms. **Full texts** come from the PMC Open Access Subset; each article |
| carries its own Creative Commons or similar licence. |
| - Copyright in the annotations belongs to the BioNLP-ST'11 organisers. |
|
|
| Please read the full terms at the source link above before redistributing or building on |
| this data. |
|
|
| ## Citation |
|
|
| ```bibtex |
| @inproceedings{Kim11genia2011, |
| author = {Jin-Dong Kim and Yue Wang and Toshihisa Takagi and Akinori Yonezawa}, |
| title = {Overview of Genia Event Task in BioNLP Shared Task 2011}, |
| booktitle = {Proceedings of BioNLP Shared Task 2011 Workshop}, |
| year = {2011} |
| } |
| ``` |
|
|
