Rebuild from the original release with character offsets

README.md

@@ -1,32 +1,94 @@
 ---
+pretty_name: BioRED
+license: other
+language:
+- en
 dataset_info:
-  config_name: default
+- config_name: ner
   features:
-    - name: input
-      dtype: string
-    - name: output
-      dtype: json
-    - name: schema
-      struct:
-        - name: entities
-          list:
-            - name: label
-              dtype: string
-            - name: description
-              dtype: string
-        - name: relations
-          list:
-            - name: label
-              dtype: string
-            - name: description
-              dtype: string
+  - name: input
+    dtype: string
+  - name: output
+    dtype: json
+  - name: schema
+    dtype: json
+- config_name: re
+  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
-      - split: test
-        path: data/test.jsonl
+- config_name: ner
+  data_files:
+  - split: train
+    path: data/ner/train.jsonl
+  - split: validation
+    path: data/ner/validation.jsonl
+  - split: test
+    path: data/ner/test.jsonl
+- config_name: re
+  data_files:
+  - split: train
+    path: data/re/train.jsonl
+  - split: validation
+    path: data/re/validation.jsonl
+  - split: test
+    path: data/re/test.jsonl
 ---
+
+# BioRED
+
+BioRED (named entity recognition and relation extraction), rebuilt for MNEB from the original release with character-level offsets.
+
+**Source:** https://ftp.ncbi.nlm.nih.gov/pub/lu/BioRED/BIORED.zip (PubTator files)
+
+| config | split | records |
+| --- | --- | --- |
+| ner | train | 751 |
+| ner | validation | 191 |
+| ner | test | 190 |
+| re | train | 751 |
+| re | validation | 191 |
+| re | test | 190 |
+
+## Labels
+
+**entities:** `gene or gene product`, `chemical entity`, `disease or phenotypic feature`, `sequence variant`, `organism taxon`, `cell line`
+
+## Format
+
+Each record has `input` (the text), `output` (gold annotations grouped by label) and `schema` (the label set with descriptions). Offsets are character offsets into `input`, half-open `[start, end)`.
+
+```
+"output": {
+  "entities":  {"<label>": [{"text", "start", "end"}]},
+  "relations": {"<label>": [{"head": {"text", "start", "end"},
+                             "tail": {"text", "start", "end"}}]},
+  "events":    {"<label>": [{"trigger": {"text", "start", "end"},
+                             "arguments": [{"role", "text", "start", "end"}]}]}
+}
+```
+
+Each schema item has a `description` and a `description_source`: `official` when adapted from the dataset's paper or guideline, `mneb` when written for MNEB. Relation datasets also give `setting` (`end_to_end` or `gold_entity`) and `negative_label`; relation items give `symmetric`. Event items list the `roles` valid for that event type.
+
+Within a record, identical annotations are kept once and outer whitespace is trimmed from spans; source annotations are otherwise kept as annotated.
+
+## Notes
+
+- Licence: public domain (US Government work, NCBI).
+- Config `ner`: every mention. Config `re`: relations between given mentions, one representative mention per concept and piece (as in CalOn).
+- Documents longer than 1,200 characters are cut at whitespace outside every annotated span (CalOn, arXiv:2610.17113); annotations whose parts fall in different pieces are dropped and counted.
+- All relation types are non-directional (symmetric). Novelty labels are not kept.
+
+## Build
+
+Built by `scripts/datasets/biored.py` in the MNEB repository.
+
+## Citation
+
+Luo et al. (2022), BioRED: a rich biomedical relation extraction dataset. Briefings in Bioinformatics.
+
+License: other

data/train.jsonl

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:34de47b2869d84a5befa344fd09cba30ca1053852eeecdf1e70f3dff8de36d79
-size 11587950

schema.json

@@ -1,62 +0,0 @@
-{
-  "entities": [
-    {
-      "label": "gene or gene product",
-      "description": "A gene, protein, mRNA, or other gene product mentioned in biomedical text."
-    },
-    {
-      "label": "disease or phenotypic feature",
-      "description": "A disease, symptom, syndrome, or disease-related phenotypic feature."
-    },
-    {
-      "label": "chemical entity",
-      "description": "A chemical substance, drug, or other chemical compound."
-    },
-    {
-      "label": "organism taxon",
-      "description": "An organism or taxonomic species."
-    },
-    {
-      "label": "sequence variant",
-      "description": "A genomic or protein sequence variant, including substitutions, insertions, deletions, and other mutations."
-    },
-    {
-      "label": "cell line",
-      "description": "An established cell line used in biomedical research."
-    }
-  ],
-  "relations": [
-    {
-      "label": "association",
-      "description": "A general biological association that cannot be classified into a more specific relation type."
-    },
-    {
-      "label": "positive correlation",
-      "description": "A positive association in which one entity promotes, induces, increases, or is positively correlated with the other."
-    },
-    {
-      "label": "negative correlation",
-      "description": "A negative association in which one entity inhibits, suppresses, treats, decreases, or protects against the other."
-    },
-    {
-      "label": "bind",
-      "description": "A direct physical binding or molecular interaction between two entities."
-    },
-    {
-      "label": "comparison",
-      "description": "An explicit comparison between two entities without asserting another specific relation."
-    },
-    {
-      "label": "cotreatment",
-      "description": "A relation indicating that two chemicals or drugs are administered together as part of the same treatment."
-    },
-    {
-      "label": "drug interaction",
-      "description": "A pharmacodynamic interaction between two chemicals or drugs."
-    },
-    {
-      "label": "conversion",
-      "description": "A relation indicating that one chemical is converted or transformed into another chemical."
-    }
-  ]
-}