Host data file

README.md

@@ -6,7 +6,7 @@ language_creators:
 language:
 - en
 license:
-- unknown
+- cc-by-4.0
 multilinguality:
 - monolingual
 size_categories:
@@ -76,14 +76,30 @@ dataset_info:
 ## Dataset Description
 
 - **Homepage:** [linnaeus](http://linnaeus.sourceforge.net/)
-- **Repository:**
+- **Repository:** https://github.com/cambridgeltl/MTL-Bioinformatics-2016/tree/master/data/linnaeus-IOB
 - **Paper:** [BMC Bioinformatics](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-85)
 - **Leaderboard:**
 - **Point of Contact:**
 
 ### Dataset Summary
 
-LINNAEUS is a general-purpose dictionary matching software, capable of processing multiple types of document formats in the biomedical domain (MEDLINE, PMC, BMC, OTMI, text, etc.). It can produce multiple types of output (XML, HTML, tab-separated-value file, or save to a database). It also contains methods for acting as a server (including load balancing across several servers), allowing clients to request matching over a network. A package with files for recognizing and identifying species names is available for LINNAEUS, showing 94% recall and 97% precision compared to LINNAEUS-species-corpus.
+The LINNAEUS corpus consists of 100 full-text documents from the PMCOA
+document set which were randomly selected.  All mentions of species terms were manually
+annotated and normalized to the NCBI taxonomy IDs of the intended species.
+
+The original LINNAEUS corpus is available in a TAB-separated standoff format.  The resource does not define training,
+development or test subsets.
+
+We converted the corpus into BioNLP shared task standoff format using a custom script, split it into 50-, 17-, and 33-
+document training, development and test sets, and then converted these into the CoNLL format using standoff2conll.
+
+As  a  full-text  corpus,  LINNAEUS  contains  comparatively  frequent
+non-ASCII characters, which were mapped to ASCII using the
+standoff2conll -a option.
+The conversion was highly accurate, but due to sentence-splitting errors within entity mentions,
+the number of annotations in the converted data was larger by four (100.09%) than that
+in the source data.  99.77% of names in the original annotation matched names in the converted
+data.
 
 ### Supported Tasks and Leaderboards
 
@@ -170,23 +186,35 @@ An example from the dataset is:
 
 ### Licensing Information
 
-[More Information Needed]
+This version of the dataset is licensed under [Creative Commons Attribution 4.0 International](https://github.com/cambridgeltl/MTL-Bioinformatics-2016/blob/master/LICENSE.md).
 
 ### Citation Information
 
 ```bibtex
+@article{crichton2017neural,
+  title={A neural network multi-task learning approach to biomedical named entity recognition},
+  author={Crichton, Gamal and Pyysalo, Sampo and Chiu, Billy and Korhonen, Anna},
+  journal={BMC Bioinformatics},
+  volume={18},
+  number={1},
+  pages={368},
+  year={2017},
+  publisher={BioMed Central}
+  doi = {10.1186/s12859-017-1776-8},
+  issn = {1471-2105},
+  url = {https://doi.org/10.1186/s12859-017-1776-8},
+}
 @article{Gerner2010,
-abstract = {The task of recognizing and identifying species names in biomedical literature has recently been regarded as critical for a number of applications in text and data mining, including gene name recognition, species-specific document retrieval, and semantic enrichment of biomedical articles.},
-author = {Gerner, Martin and Nenadic, Goran and Bergman, Casey M},
-doi = {10.1186/1471-2105-11-85},
-issn = {1471-2105},
-journal = {BMC Bioinformatics},
-number = {1},
-pages = {85},
-title = {{LINNAEUS: A species name identification system for biomedical literature}},
-url = {https://doi.org/10.1186/1471-2105-11-85},
-volume = {11},
-year = {2010}
+  author = {Gerner, Martin and Nenadic, Goran and Bergman, Casey M},
+  doi = {10.1186/1471-2105-11-85},
+  issn = {1471-2105},
+  journal = {BMC Bioinformatics},
+  number = {1},
+  pages = {85},
+  title = {{LINNAEUS: A species name identification system for biomedical literature}},
+  url = {https://doi.org/10.1186/1471-2105-11-85},
+  volume = {11},
+  year = {2010}
 }
 ```
 

data/linnaeus.zip

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:d3a232d89f02508c30c92e1ad011d953d2739ddaeb33de8ac370165ddbb3826f
+size 972920

dataset_infos.json

@@ -1 +0,0 @@
-{"linnaeus": {"description": "A novel corpus of full-text documents manually annotated for species mentions.\n", "citation": "@article{gerner2010linnaeus,\n         title={LINNAEUS: a species name identification system for biomedical literature},\n         author={Gerner, Martin and Nenadic, Goran and Bergman, Casey M},\n         journal={BMC bioinformatics},\n         volume={11},\n         number={1},\n         pages={85},\n         year={2010},\n         publisher={Springer}\n}\n", "homepage": "http://linnaeus.sourceforge.net/", "license": "", "features": {"id": {"dtype": "string", "id": null, "_type": "Value"}, "tokens": {"feature": {"dtype": "string", "id": null, "_type": "Value"}, "length": -1, "id": null, "_type": "Sequence"}, "ner_tags": {"feature": {"num_classes": 3, "names": ["O", "B", "I"], "names_file": null, "id": null, "_type": "ClassLabel"}, "length": -1, "id": null, "_type": "Sequence"}}, "post_processed": null, "supervised_keys": null, "builder_name": "linnaeus", "config_name": "linnaeus", "version": {"version_str": "1.0.0", "description": null, "major": 1, "minor": 0, "patch": 0}, "splits": {"train": {"name": "train", "num_bytes": 4772417, "num_examples": 11936, "dataset_name": "linnaeus"}, "validation": {"name": "validation", "num_bytes": 1592823, "num_examples": 4079, "dataset_name": "linnaeus"}, "test": {"name": "test", "num_bytes": 2802877, "num_examples": 7143, "dataset_name": "linnaeus"}}, "download_checksums": {"https://drive.google.com/u/0/uc?id=1OletxmPYNkz2ltOr9pyT0b0iBtUWxslh&export=download": {"num_bytes": 18204624, "checksum": "30522c752fd90e6da05f117a52da13174b246e4980e46840e6e1737dc67e1d27"}}, "download_size": 18204624, "post_processing_size": null, "dataset_size": 9168117, "size_in_bytes": 27372741}}

linnaeus.py

@@ -42,7 +42,8 @@ A novel corpus of full-text documents manually annotated for species mentions.
 """
 
 _HOMEPAGE = "http://linnaeus.sourceforge.net/"
-_URL = "https://drive.google.com/u/0/uc?id=1OletxmPYNkz2ltOr9pyT0b0iBtUWxslh&export=download"
+# Source data: https://github.com/cambridgeltl/MTL-Bioinformatics-2016/tree/master/data/linnaeus-IOB
+_URL = "data/linnaeus.zip"
 _BIOBERT_NER_DATASET_DIRECTORY = "linnaeus"
 _TRAINING_FILE = "train.tsv"
 _DEV_FILE = "devel.tsv"
@@ -130,7 +131,7 @@ class Linnaeus(datasets.GeneratorBasedBuilder):
                     # tokens are tab separated
                     splits = line.split("\t")
                     tokens.append(splits[0])
-                    ner_tags.append(splits[1].rstrip())
+                    ner_tags.append(splits[1].split("-")[0])
             # last example
             yield guid, {
                 "id": str(guid),