| --- |
| license: other |
| license_name: cc-by-nc-sa-3.0-annotations-pubmed-texts |
| license_link: https://creativecommons.org/licenses/by-nc-sa/3.0/ |
| features: |
| - name: input |
| dtype: string |
| - name: output |
| dtype: json |
| - name: schema |
| list: |
| - name: label |
| dtype: string |
| - name: description |
| dtype: string |
| configs: |
| - config_name: default |
| data_files: |
| - split: train |
| path: data/mlee_train.jsonl |
| - split: validation |
| path: data/mlee_validation.jsonl |
| - split: test |
| path: data/mlee_test.jsonl |
| --- |
| |
| # MLEE (mneb format) — nested event extraction, **span-linked** |
|
|
| The Multi-Level Event Extraction corpus (Pyysalo et al., Bioinformatics 2012) converted into |
| the mneb `json_structures` event-extraction format. MLEE annotates biomedical events across |
| multiple levels of biological organisation — from molecular through cellular and tissue to |
| organism level — over PubMed abstracts on angiogenesis. |
|
|
| **This dataset keeps event-as-argument nesting.** A third of MLEE's argument links point at |
| another *event* rather than an entity, 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 MLEE document. |
|
|
| ## Splits |
|
|
| The **official** MLEE partition is preserved. |
|
|
| | Split | Records | With events | Events | |
| |---|---:|---:|---:| |
| | train | 131 | 131 | 3,206 | |
| | validation | 44 | 44 | 1,102 | |
| | test | 87 | 87 | 2,132 | |
| | **Total** | **262** | **262** | **6,440** | |
|
|
| TextEE instead discards the official boundary and makes five random re-splits, so no number |
| reported on a TextEE split is directly comparable to this one. |
|
|
| ## Record format |
|
|
| ```jsonc |
| { |
| "input": "<document text>", |
| "output": {"json_structures": {"<event_type>": [<event>, ...]}}, |
| "schema": [] |
| } |
| ``` |
|
|
| 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": "Cause", "text": "anti-VEGF neutralizing antibody", "start": 1705, "end": 1736} |
| {"role": "Theme", "text": "stimulated", "start": 1611, "end": 1621} |
| ``` |
|
|
| The first is an entity mention. The second is an **event link**: `(1611, 1621)` is the trigger |
| span of a `Positive_regulation` 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 from `PMID-10586954` — *"The insulin-conditioned RPE cell media stimulated |
| capillary endothelial cell proliferation, an effect that was completely blocked by anti-VEGF |
| neutralizing antibody"*. Three top-level events; the `Theme` chain |
| `blocked → stimulated → proliferation` is the nesting: |
|
|
| ```jsonc |
| "Negative_regulation": [{ |
| "trigger": {"text": "blocked", "start": 1694, "end": 1701}, |
| "arguments": [{"role": "Theme", "text": "stimulated", "start": 1611, "end": 1621}, |
| {"role": "Cause", "text": "anti-VEGF neutralizing antibody", |
| "start": 1705, "end": 1736}]}], |
| "Positive_regulation": [{ |
| "trigger": {"text": "stimulated", "start": 1611, "end": 1621}, |
| "arguments": [{"role": "Theme", "text": "proliferation", "start": 1649, "end": 1662}]}], |
| "Cell_proliferation": [{ |
| "trigger": {"text": "proliferation", "start": 1649, "end": 1662}, |
| "arguments": [{"role": "Theme", "text": "capillary endothelial cell", |
| "start": 1622, "end": 1648}]}] |
| ``` |
|
|
| A conversion that simply *dropped* event-valued arguments would say only that something was |
| blocked by an antibody, losing that what was blocked is the stimulation of proliferation. |
|
|
| ### How faithful the span links are |
|
|
| - **Telling a link from an entity mention:** on MLEE, **0** of the 5,767 entity-valued |
| arguments sit on a span that is also a trigger. The test "this argument's span matches a |
| trigger span" therefore has no false positives here. |
| - **Telling *which* event a link points at:** 2,417 of the 2,832 links (**85.3%**) match |
| exactly one event of the right type. The other 415 (14.7%) land on a trigger span shared by |
| several same-type events, and the span cannot disambiguate them. |
| - Consequently 238 of the 6,678 raw `E` lines (3.6%) come out byte-identical to another entry |
| of the same type and are **collapsed**, leaving 6,440 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 |
|
|
| - **29 event types**, **14 role types** (role strings kept verbatim, so `Theme2`, |
| `Participant2..4` and `Instrument2` are *not* collapsed into their base role). |
| - **8,599 raw argument links** = 5,767 entity-valued + 2,832 event-valued (**32.9%** of all |
| argument links are event-to-event). After the collapse above the files hold **8,155 argument |
| instances** = 5,660 entity spans + 2,495 span links. |
| - **2,260 events (33.9%)** take at least one event argument. |
| - Raw nesting depth histogram `{1: 4416, 2: 1981, 3: 269, 4: 10}` — **max depth 4**. |
| - Nesting is almost entirely driven by the three regulation types; the sole exception is |
| `Planned_process`, which takes an event argument 9 times. Only `Theme` and `Cause` are ever |
| event-linked. |
|
|
| **Note on event counts.** Two of the 6,678 raw `E` lines are byte-identical duplicate |
| annotations (`PMID-16076702` E28/E29 and `PMID-19540587` E11/E25 — same type, same trigger, |
| same arguments); they collapse under the same rule as everything else. |
|
|
| Full type/role inventory and nesting patterns: `mlee_label_summary.md`. |
| Browsable rendering: `mlee_vis.html` (open directly; data embedded, no server needed). |
|
|
| ## How this was derived |
|
|
| Built from the `MLEE-1.0.2-rev1` standoff release (`standoff/full/*.{txt,ann}`), with the |
| official split membership taken from the filenames in |
| `standoff/{development/train, development/test, test/test}`: |
|
|
| 1. Each document's `.ann` (a1 + a2 merged: entity mentions, event triggers and `E` event |
| lines) is parsed into a single text-bound annotation map. |
| 2. 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. |
| 3. 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. |
| 4. Relation (`R`), equivalence (`*`) and attribute (`A`/`M`: Negation, Speculation) lines are |
| **not** carried over. Event-type and role strings are kept verbatim. |
|
|
| 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 |
|
|
| - **Annotations** are licensed under **Creative Commons BY-NC-SA 3.0**. This is a |
| **non-commercial, share-alike** licence: derivative works must carry the same terms, and |
| commercial use is not permitted. Please attribute by citing the paper below and linking to |
| <http://www.nactem.ac.uk/MLEE/>. |
| - **Abstracts** are from PubMed, a database of the U.S. National Library of Medicine; see the |
| [NLM copyright information](http://www.nlm.nih.gov/databases/download.html). |
|
|
| ## Citation |
|
|
| ```bibtex |
| @article{Pyysalo12mlee, |
| author = {Sampo Pyysalo and Tomoko Ohta and Makoto Miwa and Han-Cheol Cho and |
| Jun'ichi Tsujii and Sophia Ananiadou}, |
| title = {Event extraction across multiple levels of biological organization}, |
| journal = {Bioinformatics}, |
| volume = {28}, |
| number = {18}, |
| pages = {i575--i581}, |
| year = {2012} |
| } |
| ``` |
|
|
